Proteopedia - User contributions [en]

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-06T07:43:44Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对该酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性。整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确提供这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在PDB库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200、His440和Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成阳离子-ψ相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，<scene name='1vot/1vot_440/1'>特殊的氢键C-H→O相互作用</scene>在石杉碱甲的亚乙基甲基和残基His440主链氧原子之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
PBD编码[[1vot]]包含单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自加利福尼亚电鳐（[http://en.wikipedia.org/wiki/Torpedo_californica Torpedo_californica]）的乙酰胆碱酯酶
）。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

See [[1vot]] in English.

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T16:37:00Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成像阳离子ψ相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，<scene name='1vot/1vot_440/1'>特殊的氢键C-H→O相互作用</scene>在石杉碱甲的亚乙基甲基和残基His440主链氧原子之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
PBD编码[[1vot]]包含单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自加利福尼亚电鳐（[http://en.wikipedia.org/wiki/Torpedo_californica Torpedo_californica]）的乙酰胆碱酯酶
）。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

See [[1vot]] in English.

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:38:29Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成像阳离子ψ相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，<scene name='1vot/1vot_440/1'>特殊的氢键C-H→O相互作用</scene>在石杉碱甲的亚乙基甲基和残基His440主链氧原子之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
PBD编码[[1vot]]包含单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自加利福尼亚电鳐（[http://en.wikipedia.org/wiki/Torpedo_californica Torpedo_californica]）的乙酰胆碱酯酶
]）。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

See [[1vot]] in English.

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:33:08Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成像阳离子pi相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，<scene name='1vot/1vot_440/1'>特殊的氢键C-H→O相互作用</scene>在石杉碱甲的亚乙基甲基和残基His440主链氧原子之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
PBD编码[[1vot]]包含单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自加利福尼亚电鳐（[http://en.wikipedia.org/wiki/Torpedo_californica Torpedo_californica]）的乙酰胆碱酯酶
]）。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:27:16Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成像阳离子pi相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，<scene name='1vot/1vot_440/1'>特殊的氢键C-H→O相互作用</scene>在石杉碱甲的乙基和残基His440主链氧原子之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
PBD编码[[1vot]]包含单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自加利福尼亚电鳐（[http://en.wikipedia.org/wiki/Torpedo_californica Torpedo_californica]）的乙酰胆碱酯酶
]）。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:26:00Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成像阳离子pi相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，特殊的氢键C-H→O相互作用在<scene name='1vot/1vot_440/1'>石杉碱甲的乙基和残基His440主链氧原子</scene>之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
PBD编码[[1vot]]包含单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自加利福尼亚电鳐（[http://en.wikipedia.org/wiki/Torpedo_californica Torpedo_californica]）的乙酰胆碱酯酶
]）。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:25:26Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成像阳离子pi相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，特殊的氢键C-H→O相互作用在<scene name='1vot/1vot_440/1'>石杉碱甲的乙基和残基His440主链氧原子</scene>之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
PBD编码[[1vot]]包含单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自加利福尼亚电鳐[http://en.wikipedia.org/wiki/Torpedo_californica Torpedo_californica]）的乙酰胆碱酯酶
]）。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Aricept Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:24:31Z

Yechun Xu:

[[Image:E2020_interactins_in_AChE_gorge.jpg|left|250px]] 

{{STRUCTURE_1eve| PDB=1eve | SCENE=Main_Page/E2020_in_ache_spinning/1 }}

'''抗老年痴呆药物安理申（Aricept）与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
部分乙酰胆碱酯酶的抑制剂已用于老年痴呆疾病的治疗或正处于临床研究阶段。 '''E2020''', 商品名为'''安理申''', 属于1-苄基-4-哌啶类乙酰胆碱酯酶（[[acetylcholinesterase]]）抑制剂。该抑制剂由日本的Eisai公司研发成功。此类抑制剂是在加利福尼亚电鳐乙酰胆碱酯酶三维结构([[1ea5]])的解析之前，基于定量构效关系研究而设计改造获得的。动物模型研究表明E2020能有效改善胆碱能功能减退。E2020与乙酰胆碱酯酶的结合力非常强，其与电鳐和老鼠乙酰胆碱酯酶的结合常数在纳摩尔级。

==结果==
E2020与乙酰胆碱酯酶复合物的晶体结构表明E2020采用了<scene name='1eve/E2020_close_up_with_84_279/10'>非常独特的取向</scene>结合于乙酰胆碱酯酶，其结合部位从乙酰胆碱酯酶活性口袋底部的阴离子结合位点的<scene name='1eve/E2020_close_up_with_84lbld/5'>残基W84</scene>一直延伸口袋顶部外周阴离子结合位点的<scene name='1eve/E2020_close_up_with_84_279lbld/4'>残基W279</scene>附近。但是，E2020并不直接与酶的催化三联体或者氧离子空穴相互作用，而是通过<scene name='1eve/E20_interactionshown/7'>溶剂水分子</scene>与其间接作用。

==结论==
晶体结构表明E2020的设计充分考虑了乙酰胆碱酯酶狭长活性口袋的多个重要特征，从而使该药物与乙酰胆碱酯酶的结合力非常强，同时对乙酰胆碱酯酶的选择性结合远远高于丁酰胆碱酯酶。此外，该复合物的晶体结构还提供了进一步改造E2020的信息，如从三维结构中看到活性口袋中仍有空隙，可以通过改造E2020从而使小分子与乙酰胆碱酯酶的结合更加充分。

==关于这个结构==
PBD编码1EVE是单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自加利福尼亚电鳐（[http://en.wikipedia.org/wiki/Torpedo_californica Torpedo_californica]）的乙酰胆碱酯酶）
与多糖和[http://en.wikipedia.org/wiki/ligands 配体]E20的复合物结构。乙酰胆碱酯酶（[[Acetylcholinesterase]]），其酶学命名号为[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.7 EC 3.1.1.7]。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with E2020 (Aricept): implications for the design of new anti-Alzheimer drugs., Kryger G, Silman I, Sussman JL, Structure. 1999 Mar 15;7(3):297-307. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10368299 10368299]
[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Kryger, G.]]
[[Category: Silman, I.]]
[[Category: Sussman, J.L.]]
[[Category: E20]]
[[Category: NAG]]
[[Category: alpha/beta hydrolase]]
[[Category: alzheimer's disease]]
[[Category: catalytic triad]]
[[Category: drug]]
[[Category: glycosylated protein]]
[[Category: neurotransmitter cleavage]]
[[Category: serine hydrolase]]

''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov 8 12:39:55 2007''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:19:58Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成像阳离子pi相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，特殊的氢键C-H→O相互作用在<scene name='1vot/1vot_440/1'>石杉碱甲的乙基和残基His440主链氧原子</scene>之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
PBD编码[[1vot]]包含单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自[http://en.wikipedia.org/wiki/Torpedo_californica 加利福尼亚电鳐的乙酰胆碱酯酶
]）。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Aricept Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:17:22Z

Yechun Xu:

[[Image:E2020_interactins_in_AChE_gorge.jpg|left|250px]] 

{{STRUCTURE_1eve| PDB=1eve | SCENE=Main_Page/E2020_in_ache_spinning/1 }}

'''抗老年痴呆药物安理申（Aricept）与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
部分乙酰胆碱酯酶的抑制剂已用于老年痴呆疾病的治疗或正处于临床研究阶段。 '''E2020''', 商品名为'''安理申''', 属于1-苄基-4-哌啶类乙酰胆碱酯酶（[[acetylcholinesterase]]）抑制剂。该抑制剂由日本的Eisai公司研发成功。此类抑制剂是在加利福尼亚电鳐乙酰胆碱酯酶三维结构([[1ea5]])的解析之前，基于定量构效关系研究而设计改造获得的。动物模型研究表明E2020能有效改善胆碱能功能减退。E2020与乙酰胆碱酯酶的结合力非常强，其与电鳐和老鼠乙酰胆碱酯酶的结合常数在纳摩尔级。

==结果==
E2020与乙酰胆碱酯酶复合物的晶体结构表明E2020采用了<scene name='1eve/E2020_close_up_with_84_279/10'>非常独特的取向</scene>结合于乙酰胆碱酯酶，其结合部位从乙酰胆碱酯酶活性口袋底部的阴离子结合位点的<scene name='1eve/E2020_close_up_with_84lbld/5'>残基W84</scene>一直延伸口袋顶部外周阴离子结合位点的<scene name='1eve/E2020_close_up_with_84_279lbld/4'>残基W279</scene>附近。但是，E2020并不直接与酶的催化三联体或者氧离子空穴相互作用，而是通过<scene name='1eve/E20_interactionshown/7'>溶剂水分子</scene>与其间接作用。

==结论==
晶体结构表明E2020的设计充分考虑了乙酰胆碱酯酶狭长活性口袋的多个重要特征，从而使该药物与乙酰胆碱酯酶的结合力非常强，同时对乙酰胆碱酯酶的选择性结合远远高于丁酰胆碱酯酶。此外，该复合物的晶体结构还提供了进一步改造E2020的信息，如从三维结构中看到活性口袋中仍有空隙，可以通过改造E2020从而使小分子与乙酰胆碱酯酶的结合更加充分。

==关于这个结构==
PBD编码1EVE是单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自[http://en.wikipedia.org/wiki/Torpedo_californica 加利福尼亚电鳐的乙酰胆碱酯酶
]）与多糖和[http://en.wikipedia.org/wiki/ligands 配体]E20的复合物结构。乙酰胆碱酯酶（[[Acetylcholinesterase]]），其酶学命名号为[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.7 EC 3.1.1.7]。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with E2020 (Aricept): implications for the design of new anti-Alzheimer drugs., Kryger G, Silman I, Sussman JL, Structure. 1999 Mar 15;7(3):297-307. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10368299 10368299]
[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Kryger, G.]]
[[Category: Silman, I.]]
[[Category: Sussman, J.L.]]
[[Category: E20]]
[[Category: NAG]]
[[Category: alpha/beta hydrolase]]
[[Category: alzheimer's disease]]
[[Category: catalytic triad]]
[[Category: drug]]
[[Category: glycosylated protein]]
[[Category: neurotransmitter cleavage]]
[[Category: serine hydrolase]]

''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov 8 12:39:55 2007''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:15:41Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成像阳离子pi相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，特殊的氢键C-H→O相互作用在<scene name='1vot/1vot_440/1'>石杉碱甲的乙基和残基His440主链氧原子</scene>之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
[[1vot]] is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Torpedo_californica Torpedo californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOT OCA].

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T12:13:53Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。<scene name='1vot/1vot_ache_interactions/1'>石杉碱甲与乙酰胆碱酯酶形成的主要相互作用</scene>包括：在口袋底部与<scene name='1vot/1vot_199_130_117/1'>残基Tyr130</scene>形成的直接氢键以及与<scene name='1vot/1vot_199_130_117/1'>残基Glu199和Gly117</scene>通过水分子作中介的氢键；与<scene name='1vot/1vot_84_330/1'>残基Trp84和Phe330</scene>形成像阳离子pi相互作用，其氨基氮原子与两残基芳香环的中心距离分别为4.8和4.7埃；在狭长口袋顶部，石杉碱甲通过两个水分子作中介分别与<scene name='1vot/1vot_70_72_81_85_121/2'>残基Tyr70，Asp72，Ser81，Asn85和Tyr121</scene>形成氢键相互作用。此外，特殊的氢键C-H→O相互作用在石杉碱甲的乙基和残基His440主链氧原子之间形成，其距离非常短，仅为3埃。

{{Clear}}

==关于此结构==
[[1vot]] is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Torpedo_californica Torpedo californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOT OCA].

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T11:53:45Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外， <scene name='1vot/Active_site/6'>残基Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。

The principal interactions of <scene name='1vot/1vot_ache_interactions/1'>HupA with TcAChE</scene> are including: a direct <scene name='1vot/1vot_199_130_117/1'>hydrogen bond (HB) with Tyr130 and HBs with Glu199 and Gly117 </scene>through a water molecule as a linker at the bottom of the gorge; cation-pi interactions between the amino group of <scene name='1vot/1vot_84_330/1'>HupA and Trp84 and Phe330</scene> with the distance between the nitrogen and the centroid of the aromatic rings of 4.8 and 4.7 Å, respectively; at the top of the gorge, HBs through two water molecules as linkers formed between the amino group of <scene name='1vot/1vot_70_72_81_85_121/2'>HupA and Tyr70, Asp72, Ser81, Asn85 and Tyr121</scene>. An unusually short (~3.0 Å) C-H→O HB has been seen between the ethylidene methyl group of <scene name='1vot/1vot_440/1'>HupA and the main chain oxygen of His440</scene>.

{{Clear}}

==关于此结构==
[[1vot]] is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Torpedo_californica Torpedo californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOT OCA].

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T11:38:45Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
分辨率为2.5埃的石杉碱甲与从加利福尼亚电鳐中提取的乙酰胆碱酯酶复合物的晶体结构于1997年测定（其在蛋白质库中的编码为'''1vot'''）。晶体结构表明石杉碱甲以非常出乎意料的取向与乙酰胆碱酯酶结合，与其对乙酰胆碱酯酶高亲合力性质相对应的是石杉碱甲与关键蛋白质残基形成了较强的相互作用。乙酰胆碱酯酶的催化活性位点位于其<scene name='1vot/Active_site/1'>狭长口袋</scene>的底部，<scene name='1vot/Active_site/2'>十四个芳香性残基</scene>坐落在整个口袋的内壁。乙酰胆碱酯酶的天然底物<scene name='1vot/Active_site/3'>乙酰胆碱</scene>与<scene name='1vot/Active_site/5'>催化三联体</scene>（Ser200, His440, and Glu327）之一的残基<scene name='1vot/Active_site/4'>Ser200</scene>直接键连。此外，残基<scene name='1vot/Active_site/6'>Trp84和Phe330</scene>对配体识别结合也非常重要。与乙酰胆碱相似，石杉碱甲也结合于乙酰胆碱酯酶的催化活性位点，其取向基本上与乙酰胆碱的取向<scene name='1vot/Active_site/8'>垂直</scene>。

The principal interactions of <scene name='1vot/1vot_ache_interactions/1'>HupA with TcAChE</scene> are including: a direct <scene name='1vot/1vot_199_130_117/1'>hydrogen bond (HB) with Tyr130 and HBs with Glu199 and Gly117 </scene>through a water molecule as a linker at the bottom of the gorge; cation-pi interactions between the amino group of <scene name='1vot/1vot_84_330/1'>HupA and Trp84 and Phe330</scene> with the distance between the nitrogen and the centroid of the aromatic rings of 4.8 and 4.7 Å, respectively; at the top of the gorge, HBs through two water molecules as linkers formed between the amino group of <scene name='1vot/1vot_70_72_81_85_121/2'>HupA and Tyr70, Asp72, Ser81, Asn85 and Tyr121</scene>. An unusually short (~3.0 Å) C-H→O HB has been seen between the ethylidene methyl group of <scene name='1vot/1vot_440/1'>HupA and the main chain oxygen of His440</scene>.

{{Clear}}

==关于此结构==
[[1vot]] is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Torpedo_californica Torpedo californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOT OCA].

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T10:22:43Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局（FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

<scene name='1vot/Huperzinea/2'>石杉碱甲</scene> 的结构同其他[[乙酰胆碱酯酶抑制剂和底物]]具有一定的相似性.整个分子结构比较刚性，包括芳香坏和在生理pH下可能质子化的氨基。在石杉碱甲和乙酰胆碱酯酶复合物的三维结构测定之前，有很多关于石杉碱甲与乙酰胆碱酯酶的作用模式以及其药效团如何与蛋白质残基相互作用等的猜测。因此，该复合物晶体结构的解析可以准确的提供了这些疑问的答案，同时为进一步基于复合物结构而设计出更加有效的石杉碱甲类似物（或衍生物）等乙酰胆碱酯酶抑制剂提供帮助。
<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
The crystal structure of the complex of ''Torpedo californica'' AChE (''Tc''AChE) with HupA at 2.5 Å resolution (pdb code '''1vot''') was determined in 1997 and it shows an unexpected orientation for the inhibitor with surprisingly few strong direct interactions with protein residues to explain its high affinity. The active site of ''Tc''AChE was found to be buried at the bottom of a <scene name='1vot/Active_site/1'>deep and narrow gorge</scene>, lined by <scene name='1vot/Active_site/2'>14 aromatic residues</scene> (colored darkmagenta). The ''Tc''AChE natural substrate <scene name='1vot/Active_site/3'>acetylcholine</scene> (ACh) directly binds <scene name='1vot/Active_site/4'>Ser200</scene> within the <scene name='1vot/Active_site/5'>catalytic triad</scene> (Ser200, His440, and Glu327). The residues <scene name='1vot/Active_site/6'>Trp84 and Phe330</scene> are also important in the ligand recognition. HupA also binds to ''Tc''AChE at this active site, but its <scene name='1vot/Active_site/8'>observed orientation is almost orthogonal</scene> in comparison to ACh. The principal interactions of <scene name='1vot/1vot_ache_interactions/1'>HupA with TcAChE</scene> are including: a direct <scene name='1vot/1vot_199_130_117/1'>hydrogen bond (HB) with Tyr130 and HBs with Glu199 and Gly117 </scene>through a water molecule as a linker at the bottom of the gorge; cation-pi interactions between the amino group of <scene name='1vot/1vot_84_330/1'>HupA and Trp84 and Phe330</scene> with the distance between the nitrogen and the centroid of the aromatic rings of 4.8 and 4.7 Å, respectively; at the top of the gorge, HBs through two water molecules as linkers formed between the amino group of <scene name='1vot/1vot_70_72_81_85_121/2'>HupA and Tyr70, Asp72, Ser81, Asn85 and Tyr121</scene>. An unusually short (~3.0 Å) C-H→O HB has been seen between the ethylidene methyl group of <scene name='1vot/1vot_440/1'>HupA and the main chain oxygen of His440</scene>.

{{Clear}}

==关于此结构==
[[1vot]] is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Torpedo_californica Torpedo californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOT OCA].

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T09:59:18Z

Yechun Xu:

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局(FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。

The structure of <scene name='1vot/Huperzinea/2'>HupA</scene> shows some similarity to other known [[AChE inhibitors and substrates]]. The molecule is fairly rigid and contains an aromatic system as well as a primary amino group that is probably protonated at physiological pH. Various suggestions have been made with respect to its orientation within the active site of AChE, and with respect to the amino acid residue with which its putative pharmacophoric groups might interact. Solution of the 3D structure of a complex of HupA with AChE would permit unequivocal resolution of this issue and it would also provide a rational basis for structure-related drug design aimed at developing synthetic analogues of HupA with improved therapeutic properties.

<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
The crystal structure of the complex of ''Torpedo californica'' AChE (''Tc''AChE) with HupA at 2.5 Å resolution (pdb code '''1vot''') was determined in 1997 and it shows an unexpected orientation for the inhibitor with surprisingly few strong direct interactions with protein residues to explain its high affinity. The active site of ''Tc''AChE was found to be buried at the bottom of a <scene name='1vot/Active_site/1'>deep and narrow gorge</scene>, lined by <scene name='1vot/Active_site/2'>14 aromatic residues</scene> (colored darkmagenta). The ''Tc''AChE natural substrate <scene name='1vot/Active_site/3'>acetylcholine</scene> (ACh) directly binds <scene name='1vot/Active_site/4'>Ser200</scene> within the <scene name='1vot/Active_site/5'>catalytic triad</scene> (Ser200, His440, and Glu327). The residues <scene name='1vot/Active_site/6'>Trp84 and Phe330</scene> are also important in the ligand recognition. HupA also binds to ''Tc''AChE at this active site, but its <scene name='1vot/Active_site/8'>observed orientation is almost orthogonal</scene> in comparison to ACh. The principal interactions of <scene name='1vot/1vot_ache_interactions/1'>HupA with TcAChE</scene> are including: a direct <scene name='1vot/1vot_199_130_117/1'>hydrogen bond (HB) with Tyr130 and HBs with Glu199 and Gly117 </scene>through a water molecule as a linker at the bottom of the gorge; cation-pi interactions between the amino group of <scene name='1vot/1vot_84_330/1'>HupA and Trp84 and Phe330</scene> with the distance between the nitrogen and the centroid of the aromatic rings of 4.8 and 4.7 Å, respectively; at the top of the gorge, HBs through two water molecules as linkers formed between the amino group of <scene name='1vot/1vot_70_72_81_85_121/2'>HupA and Tyr70, Asp72, Ser81, Asn85 and Tyr121</scene>. An unusually short (~3.0 Å) C-H→O HB has been seen between the ethylidene methyl group of <scene name='1vot/1vot_440/1'>HupA and the main chain oxygen of His440</scene>.

{{Clear}}

==关于此结构==
[[1vot]] is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Torpedo_californica Torpedo californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOT OCA].

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

Huperzine A Complexed with Acetylcholinesterase (Chinese)

2009-08-05T09:58:14Z

Yechun Xu: New page: 250px {{STRUCTURE_1vot| PDB=1vot | SCENE= }} '''石杉碱甲与乙酰胆碱酯酶复合物的三维结构''' ==背景介绍== [[Image:HuperzineA3.jpg|left|25...

[[Image:1vot.jpg|left|250px]]

{{STRUCTURE_1vot| PDB=1vot | SCENE= }}

'''石杉碱甲与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
[[Image:HuperzineA3.jpg|left|250px]]
中国科研工作者在20世纪80年代从'''中药'''[http://zh.wikipedia.org/wiki/%E4%B8%AD%E8%8D%AF]千层塔中分离得到天然产物<scene name='1vot/Huperzinea/2'>石杉碱甲</scene>被证实是[[乙酰胆碱酯酶]]的可逆抑制剂，对乙酰胆碱酯酶具有特定、高效的抑制活性。早在1000多年前，中国人已将千层塔用于擦伤、疲惫、肿胀、精神分裂症以及重症肌无力等疾病的治疗。从1996年开始，药品名为双益平[http://www.54md.com/drugstore/pic/gpic_25fd25197010a0fb4a680516735e613c.jpg]的石杉碱甲已在中国广泛用于早老年痴呆症的治疗。与美国食品药品管理局(FDA）批准的目前用于老年痴呆症治疗的多奈哌齐（Donepezil，商品名Aricept）、利伐司替明（Rivastigmine，商品名Exelon）和加兰他敏（Galanthamine，商品名Reminyl）三个药相比，石杉碱甲具有能更好渗透血脑屏障、生物口服利用度更高和对乙酰胆碱酯酶抑制时效更长的特点。
The structure of <scene name='1vot/Huperzinea/2'>HupA</scene> shows some similarity to other known [[AChE inhibitors and substrates]]. The molecule is fairly rigid and contains an aromatic system as well as a primary amino group that is probably protonated at physiological pH. Various suggestions have been made with respect to its orientation within the active site of AChE, and with respect to the amino acid residue with which its putative pharmacophoric groups might interact. Solution of the 3D structure of a complex of HupA with AChE would permit unequivocal resolution of this issue and it would also provide a rational basis for structure-related drug design aimed at developing synthetic analogues of HupA with improved therapeutic properties.

<applet load='1vot' size='500' frame='true' align='right'
scene='1vot/Com_view/1' />

==三维结构==
The crystal structure of the complex of ''Torpedo californica'' AChE (''Tc''AChE) with HupA at 2.5 Å resolution (pdb code '''1vot''') was determined in 1997 and it shows an unexpected orientation for the inhibitor with surprisingly few strong direct interactions with protein residues to explain its high affinity. The active site of ''Tc''AChE was found to be buried at the bottom of a <scene name='1vot/Active_site/1'>deep and narrow gorge</scene>, lined by <scene name='1vot/Active_site/2'>14 aromatic residues</scene> (colored darkmagenta). The ''Tc''AChE natural substrate <scene name='1vot/Active_site/3'>acetylcholine</scene> (ACh) directly binds <scene name='1vot/Active_site/4'>Ser200</scene> within the <scene name='1vot/Active_site/5'>catalytic triad</scene> (Ser200, His440, and Glu327). The residues <scene name='1vot/Active_site/6'>Trp84 and Phe330</scene> are also important in the ligand recognition. HupA also binds to ''Tc''AChE at this active site, but its <scene name='1vot/Active_site/8'>observed orientation is almost orthogonal</scene> in comparison to ACh. The principal interactions of <scene name='1vot/1vot_ache_interactions/1'>HupA with TcAChE</scene> are including: a direct <scene name='1vot/1vot_199_130_117/1'>hydrogen bond (HB) with Tyr130 and HBs with Glu199 and Gly117 </scene>through a water molecule as a linker at the bottom of the gorge; cation-pi interactions between the amino group of <scene name='1vot/1vot_84_330/1'>HupA and Trp84 and Phe330</scene> with the distance between the nitrogen and the centroid of the aromatic rings of 4.8 and 4.7 Å, respectively; at the top of the gorge, HBs through two water molecules as linkers formed between the amino group of <scene name='1vot/1vot_70_72_81_85_121/2'>HupA and Tyr70, Asp72, Ser81, Asn85 and Tyr121</scene>. An unusually short (~3.0 Å) C-H→O HB has been seen between the ethylidene methyl group of <scene name='1vot/1vot_440/1'>HupA and the main chain oxygen of His440</scene>.

{{Clear}}

==关于此结构==
[[1vot]] is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Torpedo_californica Torpedo californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOT OCA].

==参考文献==
Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat. Struct. Biol. 1997 Jan;4(1):57-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8989325 8989325]

Huperzine A from ''Huperzia'' species-An ethnopharmacolgical review., Ma X, Tan C, Zhu D, Gang D, Xiao P, J. Ethnopharmacol. 2007 Aug;113(1):15-34.
PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17644292 17644292]

[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Harel, M.]]
[[Category: Raves, M L.]]
[[Category: Silman, I.]]
[[Category: Sussman, J L.]]
[[Category: hydrolase]]
[[Category: neurotransmitter cleavage]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:26:42 2008''

File:HuperzineA3.jpg

2009-08-04T06:51:15Z

Yechun Xu:

File:HuperzineA.jpg

2009-08-03T13:43:35Z

Yechun Xu:

Aricept Complexed with Acetylcholinesterase (Chinese)

2009-08-03T10:02:10Z

Yechun Xu: New page: 250px {{STRUCTURE_1eve| PDB=1eve | SCENE=Main_Page/E2020_in_ache_spinning/1 }} '''抗老年痴呆药物安理申（Aricept）...

[[Image:E2020_interactins_in_AChE_gorge.jpg|left|250px]] 

{{STRUCTURE_1eve| PDB=1eve | SCENE=Main_Page/E2020_in_ache_spinning/1 }}

'''抗老年痴呆药物安理申（Aricept）与乙酰胆碱酯酶复合物的三维结构'''

==背景介绍==
部分乙酰胆碱酯酶的抑制剂已用于老年痴呆疾病的治疗或正处于临床研究阶段。 '''E2020''', 商品名为'''安理申''', 属于1-苄基-4-哌啶类乙酰胆碱酯酶（[[acetylcholinesterase]]）抑制剂。该抑制剂由日本的Eisai公司研发成功。此类抑制剂是在加利福尼亚电鳐乙酰胆碱酯酶三维结构([[1ea5]])的解析之前，基于定量构效关系研究而设计改造获得的。动物模型研究表明E2020能有效改善胆碱能功能减退。E2020与乙酰胆碱酯酶的结合力非常强，其与电鳐和老鼠乙酰胆碱酯酶的结合常数在纳摩尔级。

==结果==
E2020与乙酰胆碱酯酶复合物的晶体结构表明E2020采用了<scene name='1eve/E2020_close_up_with_84_279/10'>非常独特的取向</scene>结合于乙酰胆碱酯酶，其结合部位从乙酰胆碱酯酶活性口袋底部的阴离子结合位点的<scene name='1eve/E2020_close_up_with_84lbld/5'>残基W84</scene>一直延伸口袋顶部外周阴离子结合位点的<scene name='1eve/E2020_close_up_with_84_279lbld/4'>残基W279</scene>附近。但是，E2020并不直接与酶的催化三联体或者氧离子空穴相互作用，而是通过<scene name='1eve/E20_interactionshown/7'>溶剂水分子</scene>与其间接作用。

==结论==
晶体结构表明E2020的设计充分考虑了乙酰胆碱酯酶狭长活性口袋的多个重要特征，从而使该药物与乙酰胆碱酯酶的结合力非常强，同时对乙酰胆碱酯酶的选择性结合远远高于丁酰胆碱酯酶。此外，该复合物的晶体结构还提供了进一步改造E2020的信息，如从三维结构中看到活性口袋中仍有空隙，可以通过改造E2020从而使小分子与乙酰胆碱酯酶的结合更加充分。

==关于这个结构==
PBD编码1EVE是单个[http://en.wikipedia.org/wiki/Protein 蛋白质]（其序列来自[http://en.wikipedia.org/wiki/Torpedo_californica 加利福尼亚电鳐]）与多糖和[http://en.wikipedia.org/wiki/ligands 配体]E20的复合物结构。乙酰胆碱酯酶（[[Acetylcholinesterase]]），其酶学命名号为[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.7 EC 3.1.1.7]。所有关于这个结构的信息可以从[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EVE OCA]获得。

==参考文献==
Structure of acetylcholinesterase complexed with E2020 (Aricept): implications for the design of new anti-Alzheimer drugs., Kryger G, Silman I, Sussman JL, Structure. 1999 Mar 15;7(3):297-307. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10368299 10368299]
[[Category: Acetylcholinesterase]]
[[Category: Single protein]]
[[Category: Torpedo californica]]
[[Category: Kryger, G.]]
[[Category: Silman, I.]]
[[Category: Sussman, J.L.]]
[[Category: E20]]
[[Category: NAG]]
[[Category: alpha/beta hydrolase]]
[[Category: alzheimer's disease]]
[[Category: catalytic triad]]
[[Category: drug]]
[[Category: glycosylated protein]]
[[Category: neurotransmitter cleavage]]
[[Category: serine hydrolase]]

''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov 8 12:39:55 2007''

Flexibility of aromatic residues in acetylcholinesterase

2009-07-28T09:46:07Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/2' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/11'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/3'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/4'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/3'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/6'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. 2008, 95, 2500-2511.
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2009-07-28T09:42:58Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/2' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/11'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/3'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/4'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/3'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/5'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. 2008, 95, 2500-2511.
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2009-07-28T09:29:06Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/2' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/9'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/2'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/4'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. 2008, 95, 2500-2511.
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2009-07-28T09:20:50Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/8'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/2'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/4'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. 2008, 95, 2500-2511.
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2009-07-28T05:36:24Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/2'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/4'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. 2008, 95, 2500-2511.
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-31T03:52:27Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/2'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/4'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-31T03:40:43Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/2'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/4'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-31T03:37:52Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/2'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/4'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load='Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T09:06:38Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/2'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/4'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T08:53:33Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/4'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T08:47:32Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/3'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T08:45:13Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T08:42:53Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Omega_loop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/1'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T08:38:56Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/3'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupiii/1'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T08:33:14Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Groupii/2'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T08:18:08Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/2'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T08:00:05Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/6'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T07:47:34Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/5'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_f330/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T07:31:22Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/5'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
F120 as well as W233, W432, Y70, Y121, F331, F288, and F290 fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T07:29:08Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/5'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), F120, F288, F290, F330, F331, W84, W233, W279, W432, Y70, Y121, Y130, Y334, and Y442. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T07:14:10Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Flexibility_of_aromatic_residues_in_acetylcholinesterase/14_residues/5'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), <scene name='Aromatic_residues/14_residues_f120/1'>F120</scene>, <scene name='Aromatic_residues/14_residues_f288/1'>F288</scene>, <scene name='Aromatic_residues/14_residues_f290/1'>F290</scene>, <scene name='Aromatic_residues/14_residues_f330/3'>F330</scene>, <scene name='Aromatic_residues/14_residues_f331/1'>F331</scene>, <scene name='Aromatic_residues/14_residues_w84/1'>W84</scene>, <scene name='Aromatic_residues/14_residues_w233/1'>W233</scene>, <scene name='Aromatic_residues/14_residues_w279/1'>W279</scene>, <scene name='Aromatic_residues/14_residues_w432/1'>W432</scene>, <scene name='Aromatic_residues/14_residues_y70/1'>Y70</scene>, <scene name='Aromatic_residues/14_residues_y121/1'>Y121</scene>, <scene name='Aromatic_residues/14_residues_y130/1'>Y130</scene>, <scene name='Aromatic_residues/14_residues_y334/1'>Y334</scene>, and <scene name='Aromatic_residues/14_residues_y442/2'>Y442</scene>. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T07:00:03Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Aromatic_residues/14_residues/2'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), <scene name='Aromatic_residues/14_residues_f120/1'>F120</scene>, <scene name='Aromatic_residues/14_residues_f288/1'>F288</scene>, <scene name='Aromatic_residues/14_residues_f290/1'>F290</scene>, <scene name='Aromatic_residues/14_residues_f330/3'>F330</scene>, <scene name='Aromatic_residues/14_residues_f331/1'>F331</scene>, <scene name='Aromatic_residues/14_residues_w84/1'>W84</scene>, <scene name='Aromatic_residues/14_residues_w233/1'>W233</scene>, <scene name='Aromatic_residues/14_residues_w279/1'>W279</scene>, <scene name='Aromatic_residues/14_residues_w432/1'>W432</scene>, <scene name='Aromatic_residues/14_residues_y70/1'>Y70</scene>, <scene name='Aromatic_residues/14_residues_y121/1'>Y121</scene>, <scene name='Aromatic_residues/14_residues_y130/1'>Y130</scene>, <scene name='Aromatic_residues/14_residues_y334/1'>Y334</scene>, and <scene name='Aromatic_residues/14_residues_y442/2'>Y442</scene>. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T06:57:14Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Aromatic_residues/Ache_apo_14aromaticresidues/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Aromatic_residues/14_residues/2'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), <scene name='Aromatic_residues/14_residues_f120/1'>F120</scene>, <scene name='Aromatic_residues/14_residues_f288/1'>F288</scene>, <scene name='Aromatic_residues/14_residues_f290/1'>F290</scene>, <scene name='Aromatic_residues/14_residues_f330/3'>F330</scene>, <scene name='Aromatic_residues/14_residues_f331/1'>F331</scene>, <scene name='Aromatic_residues/14_residues_w84/1'>W84</scene>, <scene name='Aromatic_residues/14_residues_w233/1'>W233</scene>, <scene name='Aromatic_residues/14_residues_w279/1'>W279</scene>, <scene name='Aromatic_residues/14_residues_w432/1'>W432</scene>, <scene name='Aromatic_residues/14_residues_y70/1'>Y70</scene>, <scene name='Aromatic_residues/14_residues_y121/1'>Y121</scene>, <scene name='Aromatic_residues/14_residues_y130/1'>Y130</scene>, <scene name='Aromatic_residues/14_residues_y334/1'>Y334</scene>, and <scene name='Aromatic_residues/14_residues_y442/2'>Y442</scene>. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).
Ache_apo_14aromaticresidues

Flexibility of aromatic residues in acetylcholinesterase

2008-07-30T06:19:30Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Aromatic_residues/Ache_apo/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Aromatic_residues/14_residues/2'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), <scene name='Aromatic_residues/14_residues_f120/1'>F120</scene>, <scene name='Aromatic_residues/14_residues_f288/1'>F288</scene>, <scene name='Aromatic_residues/14_residues_f290/1'>F290</scene>, <scene name='Aromatic_residues/14_residues_f330/3'>F330</scene>, <scene name='Aromatic_residues/14_residues_f331/1'>F331</scene>, <scene name='Aromatic_residues/14_residues_w84/1'>W84</scene>, <scene name='Aromatic_residues/14_residues_w233/1'>W233</scene>, <scene name='Aromatic_residues/14_residues_w279/1'>W279</scene>, <scene name='Aromatic_residues/14_residues_w432/1'>W432</scene>, <scene name='Aromatic_residues/14_residues_y70/1'>Y70</scene>, <scene name='Aromatic_residues/14_residues_y121/1'>Y121</scene>, <scene name='Aromatic_residues/14_residues_y130/1'>Y130</scene>, <scene name='Aromatic_residues/14_residues_y334/1'>Y334</scene>, and <scene name='Aromatic_residues/14_residues_y442/2'>Y442</scene>. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== Group I: residues with fixed side-chain conformation ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== Group II: residues with flexible side chains ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}

[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).

Flexibility of aromatic residues in acetylcholinesterase

2008-06-30T16:02:42Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Aromatic_residues/Ache_apo/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Aromatic_residues/14_residues/2'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), <scene name='Aromatic_residues/14_residues_f120/1'>F120</scene>, <scene name='Aromatic_residues/14_residues_f288/1'>F288</scene>, <scene name='Aromatic_residues/14_residues_f290/1'>F290</scene>, <scene name='Aromatic_residues/14_residues_f330/3'>F330</scene>, <scene name='Aromatic_residues/14_residues_f331/1'>F331</scene>, <scene name='Aromatic_residues/14_residues_w84/1'>W84</scene>, <scene name='Aromatic_residues/14_residues_w233/1'>W233</scene>, <scene name='Aromatic_residues/14_residues_w279/1'>W279</scene>, <scene name='Aromatic_residues/14_residues_w432/1'>W432</scene>, <scene name='Aromatic_residues/14_residues_y70/1'>Y70</scene>, <scene name='Aromatic_residues/14_residues_y121/1'>Y121</scene>, <scene name='Aromatic_residues/14_residues_y130/1'>Y130</scene>, <scene name='Aromatic_residues/14_residues_y334/1'>Y334</scene>, and <scene name='Aromatic_residues/14_residues_y442/2'>Y442</scene>. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== F120 ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== W279 ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chains of W279 were colored in red and the ligands were green." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}
=== F330 ===
[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== W84 ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).

Flexibility of aromatic residues in acetylcholinesterase

2008-06-30T16:00:35Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Aromatic_residues/Ache_apo/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Aromatic_residues/14_residues/2'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), <scene name='Aromatic_residues/14_residues_f120/1'>F120</scene>, <scene name='Aromatic_residues/14_residues_f288/1'>F288</scene>, <scene name='Aromatic_residues/14_residues_f290/1'>F290</scene>, <scene name='Aromatic_residues/14_residues_f330/3'>F330</scene>, <scene name='Aromatic_residues/14_residues_f331/1'>F331</scene>, <scene name='Aromatic_residues/14_residues_w84/1'>W84</scene>, <scene name='Aromatic_residues/14_residues_w233/1'>W233</scene>, <scene name='Aromatic_residues/14_residues_w279/1'>W279</scene>, <scene name='Aromatic_residues/14_residues_w432/1'>W432</scene>, <scene name='Aromatic_residues/14_residues_y70/1'>Y70</scene>, <scene name='Aromatic_residues/14_residues_y121/1'>Y121</scene>, <scene name='Aromatic_residues/14_residues_y130/1'>Y130</scene>, <scene name='Aromatic_residues/14_residues_y334/1'>Y334</scene>, and <scene name='Aromatic_residues/14_residues_y442/2'>Y442</scene>. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== F120 ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== W279 ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}
=== F330 ===
[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== W84 ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).

File:Pp W279 abcde m3.pdb

2008-06-30T15:57:18Z

Yechun Xu:

Flexibility of aromatic residues in acetylcholinesterase

2008-06-30T15:42:34Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Aromatic_residues/Ache_apo/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Aromatic_residues/14_residues/2'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), <scene name='Aromatic_residues/14_residues_f120/1'>F120</scene>, <scene name='Aromatic_residues/14_residues_f288/1'>F288</scene>, <scene name='Aromatic_residues/14_residues_f290/1'>F290</scene>, <scene name='Aromatic_residues/14_residues_f330/3'>F330</scene>, <scene name='Aromatic_residues/14_residues_f331/1'>F331</scene>, <scene name='Aromatic_residues/14_residues_w84/1'>W84</scene>, <scene name='Aromatic_residues/14_residues_w233/1'>W233</scene>, <scene name='Aromatic_residues/14_residues_w279/1'>W279</scene>, <scene name='Aromatic_residues/14_residues_w432/1'>W432</scene>, <scene name='Aromatic_residues/14_residues_y70/1'>Y70</scene>, <scene name='Aromatic_residues/14_residues_y121/1'>Y121</scene>, <scene name='Aromatic_residues/14_residues_y130/1'>Y130</scene>, <scene name='Aromatic_residues/14_residues_y334/1'>Y334</scene>, and <scene name='Aromatic_residues/14_residues_y442/2'>Y442</scene>. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== F120 ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== W279 ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m2.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation2/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}
=== F330 ===
[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== W84 ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

{{Clear}}

== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

{{Clear}}

== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).

File:Pp W279 abcde m2.pdb

2008-06-30T15:38:42Z

Yechun Xu:

Flexibility of aromatic residues in acetylcholinesterase

2008-06-30T15:09:32Z

Yechun Xu:

<applet load='1ea5.pdb' size='350' frame='true' scene='Aromatic_residues/Ache_apo/1' align='right' caption="3D structure of TcAChE based on pdb code 1ea5" />

== Flexibility of aromatic residues in the active-gorge of AChE ==
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme.There are <scene name='Aromatic_residues/14_residues/2'>14 conserved aromatic amino acids</scene> lined along the gorge of ''Torpedo californica'' AChE (TcAChE), <scene name='Aromatic_residues/14_residues_f120/1'>F120</scene>, <scene name='Aromatic_residues/14_residues_f288/1'>F288</scene>, <scene name='Aromatic_residues/14_residues_f290/1'>F290</scene>, <scene name='Aromatic_residues/14_residues_f330/3'>F330</scene>, <scene name='Aromatic_residues/14_residues_f331/1'>F331</scene>, <scene name='Aromatic_residues/14_residues_w84/1'>W84</scene>, <scene name='Aromatic_residues/14_residues_w233/1'>W233</scene>, <scene name='Aromatic_residues/14_residues_w279/1'>W279</scene>, <scene name='Aromatic_residues/14_residues_w432/1'>W432</scene>, <scene name='Aromatic_residues/14_residues_y70/1'>Y70</scene>, <scene name='Aromatic_residues/14_residues_y121/1'>Y121</scene>, <scene name='Aromatic_residues/14_residues_y130/1'>Y130</scene>, <scene name='Aromatic_residues/14_residues_y334/1'>Y334</scene>, and <scene name='Aromatic_residues/14_residues_y442/2'>Y442</scene>. The side-chain conformational analyses based on the multuple available crystal structures and molecular dyanmics (MD) simulation trajectories show that the degree of flexibility of these 14 aromatic side chains is diverse. While those of <scene name='Aromatic_residues/14_residues_f330_w279/1'>F330 and W279 </scene>are both very flexible, the side-chain conformations of <scene name='Aromatic_residues/14_residues_group2/1'>F120, W233, W432, Y70, Y121, F288, F290 and F331</scene> appear to be fixed. Residues located on, or adjacent to the <scene name='Aromatic_residues/14_residues_omegaloop/1'>omega-loop (C67-C94)</scene>, viz. <scene name='Aromatic_residues/14_residues_group3/2'>W84, Y130, Y442, and Y334</scene>, display different flexibilities in the MD simulations and in the crystal structures.

{{Clear}}

=== F120 ===
[[Image:F120.png|thumb|Fig. 1. The χ1/χ2 plot of F120.|300px|left]]
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ1 and χ2 angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB.

{{Clear}}

=== W279 ===
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ1/χ2 plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]]
<applet load=Pp_W279_abcde_m1.pdb' size='300' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation1/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2." />

{{Clear}}
The side-chain flexibility of W279 is quite high in both data sets. The MD simulation of the native enzyme could produce most of side-chain conformations revealed by the crystal structures of complexes, suggesting that not the induced-fit but rather the preexisting equilibrium dynamics are involved in the conformational changes of W279 with regard to binding of these ligands. Moreover, it is striking that a standard χ1/χ2 rotomer plot of tryptophan would miss several of these regions both explored in MD simulation and crystal structures, such as group f (Figure 2).Rational drug design, based on structural information, might profit by taking into account conformational heterogeneity observed in MD simulations.

{{Clear}}
=== F330 ===
[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ1/χ2 plot of F330. Details are as in Fig. 1. b)The χ1/χ2 of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]]

F330 is known for to have high side-chain flexibility as revealed by earlier experimental and simulation studies. The same conclusion was obtained in the current study. The only puzzle is that in some native structures F330 adopts an unfavored side-chain orientation according to PROCHECK. The re-examination of the electron density of these ‘strange’ native structures indicated that there may be a PEG bound in the active-site gorge of the structures in which the side-chain conformation of F330 is unfavorable.

{{Clear}}

=== W84 ===
[[Image:W84.jpg|thumb|Fig. 4. The χ1/χ2 plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]]

W84 as well as Y130, Y442, and Y334 behave differently in crystal structures and in MD trajectories. Comparison of the two data sets revealed that not only the side-chains of the four residues but also the main-chain of the omega-loop (C67-C94) on which the four residues are located or are adjacent to are different. In all the crystal structures, the conformation of the omega-loop is quite fixed because of the crystal packing. In contrast, this loop is very flexible in the MD simulation. A 2nd MD simulation, with main-chain fixed, which mimics the effect of the crystal packing, however, produced side-chain conformations similar to those in the crystal structures (Fig. 4b).

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== Conclusions ==

The side-chain flexibility analyses of the 14 aromatic residues based on the multiple crystal structures, together with the MD simulation trajectories, could benefit structure-based drug design for AChE, and understanding of the dynamic properties of the active-site gorge as well as ligand trafficking within it. The good agreement between conformational sampling of the crystal structures and the MD simulations suggests that the latter is a valid method to explore the conformational landscape of the residues as well as of the whole protein.

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== References ==

*[http://www.proteinscience.org/cgi/content/abstract/17/4/601] Yechun Xu, Jacques Philippe Colletier, Hualiang Jiang, Israel Silman, Joel L. Sussman, Martin Weik. Induced-fit of preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Prot. Sci. 2008, 17, 601-605.
*[http://www.biophysj.org/cgi/content/abstract/biophysj.108.129601v1] Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, Joel L. Sussman. Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray vs MD. Biophys. J. (in press).