Sandbox207: Difference between revisions

Line 68:

:[http://www.ncbi.nlm.nih.gov/pubmed/11532280 <6>]

:On the recognition face, there are two binding sites of equal affinity to calcium, consisting of residues <scene name='Sandbox207/Phosphocholine/4'>Asp60, Asn61, Glu138, Asp140, and the main chain carbonyl of Gln139 -in red-</scene> for the first calcium ion and residues<scene name='Sandbox207/Phosphocholine/5'>Glu138, Asp140, Gln150, and Glu147 green- ~~-in~~</scene> for the second calcium ion. An interaction appears between the two calcium ions and the oxygens of the phosphate group and the choline group, which stays in a hydrophobic pocket formed by residues <scene name='Sandbox207/Phosphocholine/7'>Phe66, Leu64, Thr76, and Glu81</scene>. The face of Phe66 (in light blue) is exposed, allowing it to have '''hydrophobic interactions''' with the methyl groups of the choline. Glu81 (in magenta) interacts with the positively charged nitrogen on choline.

:On the recognition face, there are two binding sites of equal affinity to calcium, consisting of residues <scene name='Sandbox207/Phosphocholine/4'>Asp60, Asn61, Glu138, Asp140, and the main chain carbonyl of Gln139 -in red-</scene> for the first calcium ion and residues<scene name='Sandbox207/Phosphocholine/5'>Glu138, Asp140, Gln150, and Glu147 -in green-</scene> for the second calcium ion. An interaction appears between the two calcium ions and the oxygens of the phosphate group and the choline group, which stays in a hydrophobic pocket formed by residues <scene name='Sandbox207/Phosphocholine/7'>Phe66, Leu64, Thr76, and Glu81</scene>. The face of Phe66 (in light blue) is exposed, allowing it to have '''hydrophobic interactions''' with the methyl groups of the choline. Glu81 (in magenta) interacts with the positively charged nitrogen on choline.

:'''The binding site for Clq''' is found of the '''effector face''', or opposite to the phosphocholine binding site. This site is located at the open shallow end of a cleft, where a depression is formed. The pocket is limited by the '''loops 86-92 and 112-114''' on the protomer's C-terminus, and Tyr175 on the other. Residues Asp112 and Tyr75 are the contact residues for the Clq. The substitution of these residues with Ala results in '''significantly reduced affinity for CRP'''. Glu88 causes a conformational changed in CRP which is needed before complementation activation can occur, whereas Asn158 and His38 are needed for the proper geometry at the binding site. Substitution of Ala for Lys114 resulted in more '''Clq-binding''' and '''increased complement activation'''.

:[http://biology.kenyon.edu/BMB/Chime2/2005/Jenny/FRAMES/ <2>]

Line 78:

==References==

1

1- R & D Systems, ''Technical information''

[http://www.rndsystems.com/cb_detail_objectname_SU05_CReactiveProtein.aspx <1>]

2

2- ''C-reactive Protein'', Jennifer Kao and Melissa Martin, 2007.

[http://biology.kenyon.edu/BMB/Chime2/2005/Jenny/FRAMES/ <2>]

3

3- ''C-reactive protein: a critical update'', Mark B. Pepys and Gideon M. Hirschfield, June 15, 2003.

[http://www.jci.org/articles/view/18921 <3>]

4

4-

[http://en.wikipedia.org/wiki/C-reactive_protein <4>]

5

~~[http://www.rndsystems.com/cb_detail_objectname_SU05_CReactiveProtein.aspx <5>]~~

6

5- ''Human C-reactive protein: expression, structure, and function'', Volanakis JE., August 2001.

[http://www.ncbi.nlm.nih.gov/pubmed/11532280 <6>]

[http://www.ncbi.nlm.nih.gov/pubmed/11532280 <5>]

7

6- ''Study Refutes Protein's Role in Heart Attacks'', Jennifer Couzin-Frankel, June 30, 2009.

[http://news.sciencemag.org/sciencenow/2009/06/30-02.html <7>]

[http://news.sciencemag.org/sciencenow/2009/06/30-02.html <6>]

7- ''C-reactive Protein at the Interface Between Innate Immunity, Inflammation: CRP Structure & Expression'', Andres Peisajovich,1 Lorraine Marnell,2 Carolyn Mold,3 Terry W Du Clos 4.

[http://www.medscape.com/viewarticle/575924_3 <7>]

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@@ Line 68: / Line 68: @@
 :[http://www.ncbi.nlm.nih.gov/pubmed/11532280 <6>]
-:On the recognition face, there are two binding sites of equal affinity to calcium, consisting of residues <scene name='Sandbox207/Phosphocholine/4'>Asp60, Asn61, Glu138, Asp140, and the main chain carbonyl of Gln139 -in red-</scene> for the first calcium ion and residues<scene name='Sandbox207/Phosphocholine/5'>Glu138, Asp140, Gln150, and Glu147 green- -in</scene> for the second calcium ion. An interaction appears between the two calcium ions and the oxygens of the phosphate group and the choline group, which stays in a hydrophobic pocket formed by residues <scene name='Sandbox207/Phosphocholine/7'>Phe66, Leu64, Thr76, and Glu81</scene>. The face of Phe66 (in light blue) is exposed, allowing it to have '''hydrophobic interactions''' with the methyl groups of the choline. Glu81 (in magenta) interacts with the positively charged nitrogen on choline.
+:On the recognition face, there are two binding sites of equal affinity to calcium, consisting of residues <scene name='Sandbox207/Phosphocholine/4'>Asp60, Asn61, Glu138, Asp140, and the main chain carbonyl of Gln139 -in red-</scene> for the first calcium ion and residues<scene name='Sandbox207/Phosphocholine/5'>Glu138, Asp140, Gln150, and Glu147 -in green-</scene> for the second calcium ion. An interaction appears between the two calcium ions and the oxygens of the phosphate group and the choline group, which stays in a hydrophobic pocket formed by residues <scene name='Sandbox207/Phosphocholine/7'>Phe66, Leu64, Thr76, and Glu81</scene>. The face of Phe66 (in light blue) is exposed, allowing it to have '''hydrophobic interactions''' with the methyl groups of the choline. Glu81 (in magenta) interacts with the positively charged nitrogen on choline.
 :'''The binding site for Clq''' is found of the '''effector face''', or opposite to the phosphocholine binding site. This site is located at the open shallow end of a cleft, where a depression is formed. The pocket is limited by the '''loops 86-92 and 112-114''' on the protomer's C-terminus, and Tyr175 on the other. Residues Asp112 and Tyr75 are the contact residues for the Clq. The substitution of these residues with Ala results in '''significantly reduced affinity for CRP'''. Glu88 causes a conformational changed in CRP which is needed before complementation activation can occur, whereas Asn158 and His38 are needed for the proper geometry at the binding site. Substitution of Ala for Lys114 resulted in more '''Clq-binding''' and '''increased complement activation'''.
 :[http://biology.kenyon.edu/BMB/Chime2/2005/Jenny/FRAMES/ <2>]
@@ Line 78: / Line 78: @@
 ==References==
+- R & D Systems, ''Technical information''
 [http://www.rndsystems.com/cb_detail_objectname_SU05_CReactiveProtein.aspx <1>]
+- ''C-reactive Protein'', Jennifer Kao and Melissa Martin, 2007.
 [http://biology.kenyon.edu/BMB/Chime2/2005/Jenny/FRAMES/ <2>]
+- ''C-reactive protein: a critical update'', Mark B. Pepys and Gideon M. Hirschfield, June 15, 2003.
 [http://www.jci.org/articles/view/18921 <3>]
+-
 [http://en.wikipedia.org/wiki/C-reactive_protein <4>]
-[http://www.rndsystems.com/cb_detail_objectname_SU05_CReactiveProtein.aspx <5>]
+- ''Human C-reactive protein: expression, structure, and function'', Volanakis JE., August 2001.
-[http://www.ncbi.nlm.nih.gov/pubmed/11532280 <6>]
+[http://www.ncbi.nlm.nih.gov/pubmed/11532280 <5>]
+- ''Study Refutes Protein's Role in Heart Attacks'', Jennifer Couzin-Frankel, June 30, 2009.
-[http://news.sciencemag.org/sciencenow/2009/06/30-02.html <7>]
+[http://news.sciencemag.org/sciencenow/2009/06/30-02.html <6>]
+- ''C-reactive Protein at the Interface Between Innate Immunity, Inflammation: CRP Structure & Expression'', Andres Peisajovich,1 Lorraine Marnell,2 Carolyn Mold,3 Terry W Du Clos 4.
+[http://www.medscape.com/viewarticle/575924_3 <7>]