Sandbox Reserved 321: Difference between revisions

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==Substructure 2 of InhA==

<scene name='Sandbox_Reserved_321/Substructure_2/1'>Substructure 2</scene> contains the c-terminal region of the molecule and consists of a small β strand <scene name='Sandbox_Reserved_321/B-7/1'>(B-7)</scene>, and two α helices <scene name='Sandbox_Reserved_321/A-6_and_a-7/1'>(A-6 and A-7)</scene> which are connected by a short five residue loop<ref name ="making drugs for inhA"/>. The C-terminal domain consits of two other α helices <scene name='Sandbox_Reserved_321/A-8_and_a-9/1'>(A-8 and A-9)</scene><ref name ="making drugs for inhA"/>.

<scene name='Sandbox_Reserved_321/Substructure_2/1'>Substructure 2</scene> contains the c-terminal region of the molecule and consists of a small β strand <scene name='Sandbox_Reserved_321/B-7/1'>(B-7)</scene>, and two α helices <scene name='Sandbox_Reserved_321/A-6_and_a-7/1'>(A-6 and A-7)</scene> which are connected by a short five residue loop<ref name ="making drugs for inhA"/>. The C-terminal domain consits of two other α helices <scene name='Sandbox_Reserved_321/A-8_and_a-9/2'>(A-8 and A-9)</scene><ref name ="making drugs for inhA"/>.

==Hydrophobic Binding Pocket==

InhA contains a <scene name='Sandbox_Reserved_321/Binding/2'>hydrophobic pocket</scene>where ligands bind to a higly conserved binding site<ref name ="mech of thioamide drug action"/>. The site is lined with the hydrophobic residues tyrosine 158 (Y158), phenylalanine 149 (F149) methionine 199 (M199, trypotophan 222 (W222), leucine 218 (K218), methionine 161 (M161), and proline 193 (P193)<ref name ="mech of thioamide drug action"/>. The fatty acyl binding site is also located in the hydrophobic pocket of InhA and consists primairly of the substrate binding loop <scene name='Sandbox_Reserved_321/Substrate_binding_lopp/2'>(residues 196-219)</scene><ref name ="Fatty acyl in InhA">PMID:10336454</ref>.

InhA contains a <scene name='Sandbox_Reserved_321/Binding/2'>hydrophobic pocket</scene> where ligands bind to a higly conserved binding site<ref name ="mech of thioamide drug action"/>. The site is lined with the hydrophobic residues tyrosine 158 (Y158), phenylalanine 149 (F149) methionine 199 (M199), trypotophan 222 (W222), leucine 218 (K218), methionine 161 (M161), and proline 193 (P193)<ref name ="mech of thioamide drug action"/>. The fatty acyl binding site is also located in the hydrophobic pocket of InhA and consists primairly of the substrate binding loop <scene name='Sandbox_Reserved_321/Substrate_binding_lopp/2'>(residues 196-219)</scene><ref name ="Fatty acyl in InhA">PMID:10336454</ref>.

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InhA plays a key role in the synthesis of fatty acids, particularly in ''M. tuberculosis'' which has type one fatty acid synthesis (FASI) and type two fatty acid synthesis (FASII) which together function in the synthesis of mycolic acids<ref name ="Function of M Tb">PMID:18552191</ref>. FASI synthesizes C16-18 and C24-26 fatty acids ~~these~~ are then sent to FASII promotes chain extension, forming long-chain meromycolic acids that are 56-64 carbons in length<ref name ="Fatty Acid Synthesis">PMID:18804030</ref>. The final step in FASII is completed by InhA which reduces 2-trans-enoyl-ACP's with chain lengths over twelve carbons in a NADP dependent manner where the hydride transfer precedes protonation<ref name ="Function of M Tb"/><ref name ="Roles of T158">PMID:10521269</ref>.

InhA plays a key role in the synthesis of fatty acids, particularly in ''M. tuberculosis'' which, has type one fatty acid synthesis (FASI) and type two fatty acid synthesis (FASII) which together function in the synthesis of mycolic acids<ref name ="Function of M Tb">PMID:18552191</ref>. FASI synthesizes C16-18 and C24-26 fatty acids. The fatty acids from FASI are then sent to FASII which promotes chain extension, forming long-chain meromycolic acids that are 56-64 carbons in length<ref name ="Fatty Acid Synthesis">PMID:18804030</ref>. The final step in FASII is completed by InhA which reduces 2-trans-enoyl-ACP's with chain lengths over twelve carbons in a NADP dependent manner where the hydride transfer precedes protonation<ref name ="Function of M Tb"/><ref name ="Roles of T158">PMID:10521269</ref>.

The reaction takes place as follows. Initially NADH binds to the active site mediated by [http://en.wikipedia.org/wiki/Van_der_Waals_force van der Waal] interactions with phenylalanine 41 (F41) and ~~interactions~~ with lysine 165 <scene name='Sandbox_Reserved_321/Lys165/1'>(K165)</scene><ref name ="Roles of T158"/><ref name ="crystallographic studies"/>. Binding of NADH is mediated through van der Waal ineractions with the side chains of leucine 218 and methionine 155 <scene name='Sandbox_Reserved_321/K218_and_m_155/1'>(K218 and M155)</scene>to the phosphate group and causes a conformational change in the Aspartate 42 and Arginine 43 <scene name='Sandbox_Reserved_321/Asp_42_and_arg_43/1'>(E42 and R43)</scene> side chains and an over all conformational change in InhA<ref name ="crystallographic studies"/><ref name ="mech of thioamide drug action"/>. In addition tyrosine 158 <scene name='Sandbox_Reserved_321/Tyr_158/1'>(Y158)</scene> plays an important role in aligning the carbonyl substrate, in fact; rotation about its Cα-Cβ bond by 60° brings it into a position where it can hydrogen bond to the carbonyl of the 2-trans enoyl-ACP and provide it with electrophilic stabilization<ref name ="Roles of T158"/>. The substrate binds in a U-shaped conformation with its trans double bond adjacent to the nicotinamide ring of NAD+<ref name ="Fatty acyl in InhA"/>. Inha then reduces the 2-trans double bond of the substrate by forming a enoyl intermediate through the transfer of a hydride ion from NADH to the third carbon of the substrate, followed by protonation of the second carbon<ref name ="crystallographic studies"/>. The binding of both the substrate and the cofactor induces another conformational change in InhA that allows for the release of the meromycolic acid product<ref name ="crystallographic studies"/>. The meromycolic acids undergo [http://en.wikipedia.org/wiki/Claisen_condensation claisen condensation] with a C26 fatty acid followed by reduction to a mature mycolic acid<ref name ="Fatty Acid Synthesis"/><ref name ="crystallographic studies"/>.

The reaction takes place as follows. Initially NADH binds to the active site mediated by [http://en.wikipedia.org/wiki/Van_der_Waals_force van der Waal] interactions with the side chains of phenylalanine 41 (F41), leucine 218 and methionine 155 <scene name='Sandbox_Reserved_321/K218_and_m_155/1'>(K218 and M155)</scene> to the phosphate group of NADH There are additional interaction with lysine 165 <scene name='Sandbox_Reserved_321/Lys165/1'>(K165)</scene>that also mediates binding<ref name ="Roles of T158"/><ref name ="crystallographic studies"/>. Binding og NADH causes a conformational change in the Aspartate 42 and Arginine 43 <scene name='Sandbox_Reserved_321/Asp_42_and_arg_43/1'>(E42 and R43)</scene> side chains and an over all conformational change in InhA<ref name ="crystallographic studies"/><ref name ="mech of thioamide drug action"/>. In addition tyrosine 158 <scene name='Sandbox_Reserved_321/Tyr_158/1'>(Y158)</scene> plays an important role in aligning the carbonyl substrate, in fact; rotation about its Cα-Cβ bond by 60° brings it into a position where it can hydrogen bond to the carbonyl of the 2-trans enoyl-ACP and provide it with electrophilic stabilization<ref name ="Roles of T158"/>. The substrate binds in a U-shaped conformation with its trans double bond adjacent to the nicotinamide ring of NAD+<ref name ="Fatty acyl in InhA"/>. Inha then reduces the 2-trans double bond of the substrate by forming a enoyl intermediate through the transfer of a hydride ion from NADH to the third carbon of the substrate, followed by protonation of the second carbon<ref name ="crystallographic studies"/>. The binding of both the substrate and the cofactor induces another conformational change in InhA that allows for the release of the meromycolic acid product<ref name ="crystallographic studies"/>. The meromycolic acids undergo [http://en.wikipedia.org/wiki/Claisen_condensation claisen condensation] with a C26 fatty acid followed by reduction to a mature mycolic acid<ref name ="Fatty Acid Synthesis"/><ref name ="crystallographic studies"/>.

Sandbox Reserved 321: Difference between revisions

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@@ Line 29: / Line 29: @@
 ==Substructure 2 of InhA==
-<scene name='Sandbox_Reserved_321/Substructure_2/1'>Substructure 2</scene> contains the c-terminal region of the molecule and consists of a small β strand <scene name='Sandbox_Reserved_321/B-7/1'>(B-7)</scene>, and two α helices <scene name='Sandbox_Reserved_321/A-6_and_a-7/1'>(A-6 and A-7)</scene> which are connected by a short five residue loop<ref name ="making drugs for inhA"/>.  The C-terminal domain consits of two other α helices <scene name='Sandbox_Reserved_321/A-8_and_a-9/1'>(A-8 and A-9)</scene><ref name ="making drugs for inhA"/>.
+<scene name='Sandbox_Reserved_321/Substructure_2/1'>Substructure 2</scene> contains the c-terminal region of the molecule and consists of a small β strand <scene name='Sandbox_Reserved_321/B-7/1'>(B-7)</scene>, and two α helices <scene name='Sandbox_Reserved_321/A-6_and_a-7/1'>(A-6 and A-7)</scene> which are connected by a short five residue loop<ref name ="making drugs for inhA"/>.  The C-terminal domain consits of two other α helices <scene name='Sandbox_Reserved_321/A-8_and_a-9/2'>(A-8 and A-9)</scene><ref name ="making drugs for inhA"/>.
 ==Hydrophobic Binding Pocket==
-InhA contains a <scene name='Sandbox_Reserved_321/Binding/2'>hydrophobic pocket</scene>where ligands bind to a higly conserved binding site<ref name ="mech of thioamide drug action"/>. The site is lined with the hydrophobic residues tyrosine 158 (Y158), phenylalanine 149 (F149) methionine 199 (M199, trypotophan 222 (W222), leucine 218 (K218), methionine 161 (M161), and proline 193 (P193)<ref name ="mech of thioamide drug action"/>.  The fatty acyl binding site is also located in the hydrophobic pocket of InhA and consists primairly of the substrate binding loop <scene name='Sandbox_Reserved_321/Substrate_binding_lopp/2'>(residues 196-219)</scene><ref name ="Fatty acyl in InhA">PMID:10336454</ref>.
+InhA contains a <scene name='Sandbox_Reserved_321/Binding/2'>hydrophobic pocket</scene> where ligands bind to a higly conserved binding site<ref name ="mech of thioamide drug action"/>. The site is lined with the hydrophobic residues tyrosine 158 (Y158), phenylalanine 149 (F149) methionine 199 (M199), trypotophan 222 (W222), leucine 218 (K218), methionine 161 (M161), and proline 193 (P193)<ref name ="mech of thioamide drug action"/>.  The fatty acyl binding site is also located in the hydrophobic pocket of InhA and consists primairly of the substrate binding loop <scene name='Sandbox_Reserved_321/Substrate_binding_lopp/2'>(residues 196-219)</scene><ref name ="Fatty acyl in InhA">PMID:10336454</ref>.
@@ Line 40: / Line 40: @@
 [[Image:Pathway2.png|thumb|right|upright=2|alt=Proposed mechanism.|Formulated mechanism of Mycolic acid synthesis as proposed by  Wilson et al.<ref name ="Drug Induced Alterations">PMID:10536008</ref>.]]
-InhA plays a key role in the synthesis of fatty acids, particularly in ''M. tuberculosis'' which has type one fatty acid synthesis (FASI) and type two fatty acid synthesis (FASII) which together function in the synthesis of mycolic acids<ref name ="Function of M Tb">PMID:18552191</ref>.  FASI synthesizes C16-18 and C24-26 fatty acids these are then sent to FASII promotes chain extension, forming long-chain meromycolic acids that are 56-64 carbons in length<ref name ="Fatty Acid Synthesis">PMID:18804030</ref>.  The final step in FASII is completed by InhA which reduces 2-trans-enoyl-ACP's with chain lengths over twelve carbons in a NADP dependent manner where the hydride transfer precedes protonation<ref name ="Function of M Tb"/><ref name ="Roles of T158">PMID:10521269</ref>.
+InhA plays a key role in the synthesis of fatty acids, particularly in ''M. tuberculosis'' which, has type one fatty acid synthesis (FASI) and type two fatty acid synthesis (FASII) which together function in the synthesis of mycolic acids<ref name ="Function of M Tb">PMID:18552191</ref>.  FASI synthesizes C16-18 and C24-26 fatty acids.  The fatty acids from FASI are then sent to FASII which promotes chain extension, forming long-chain meromycolic acids that are 56-64 carbons in length<ref name ="Fatty Acid Synthesis">PMID:18804030</ref>.  The final step in FASII is completed by InhA which reduces 2-trans-enoyl-ACP's with chain lengths over twelve carbons in a NADP dependent manner where the hydride transfer precedes protonation<ref name ="Function of M Tb"/><ref name ="Roles of T158">PMID:10521269</ref>.
-The reaction takes place as follows.  Initially NADH binds to the active site mediated by [http://en.wikipedia.org/wiki/Van_der_Waals_force van der Waal] interactions with phenylalanine 41 (F41) and interactions with lysine 165 <scene name='Sandbox_Reserved_321/Lys165/1'>(K165)</scene><ref name ="Roles of T158"/><ref name ="crystallographic studies"/>.  Binding of NADH is mediated through van der Waal ineractions with the side chains of leucine 218 and methionine 155 <scene name='Sandbox_Reserved_321/K218_and_m_155/1'>(K218 and M155)</scene>to the phosphate group and causes a conformational change in the Aspartate 42 and Arginine 43 <scene name='Sandbox_Reserved_321/Asp_42_and_arg_43/1'>(E42 and R43)</scene> side chains and an over all conformational change in InhA<ref name ="crystallographic studies"/><ref name ="mech of thioamide drug action"/>.  In addition tyrosine 158 <scene name='Sandbox_Reserved_321/Tyr_158/1'>(Y158)</scene> plays an important role in aligning the carbonyl substrate, in fact; rotation about its Cα-Cβ bond by 60° brings it into a position where it can hydrogen bond to the carbonyl of the 2-trans enoyl-ACP and provide it with electrophilic stabilization<ref name ="Roles of T158"/>.  The substrate binds in a U-shaped conformation with its trans double bond adjacent to the nicotinamide ring of NAD+<ref name ="Fatty acyl in InhA"/>.  Inha then reduces the 2-trans double bond of the substrate by forming a enoyl intermediate through the transfer of a hydride ion from NADH to the third carbon of the substrate, followed by protonation of the second carbon<ref name ="crystallographic studies"/>.  The binding of both the substrate and the cofactor induces another conformational change in InhA that allows for the release of the meromycolic acid product<ref name ="crystallographic studies"/>.  The meromycolic acids undergo [http://en.wikipedia.org/wiki/Claisen_condensation claisen condensation] with a C26 fatty acid followed by reduction to a mature mycolic acid<ref name ="Fatty Acid Synthesis"/><ref name ="crystallographic studies"/>.
+The reaction takes place as follows.  Initially NADH binds to the active site mediated by [http://en.wikipedia.org/wiki/Van_der_Waals_force van der Waal] interactions with the side chains of phenylalanine 41 (F41), leucine 218 and methionine 155 <scene name='Sandbox_Reserved_321/K218_and_m_155/1'>(K218 and M155)</scene> to the phosphate group of NADH There are additional interaction with lysine 165 <scene name='Sandbox_Reserved_321/Lys165/1'>(K165)</scene>that also mediates binding<ref name ="Roles of T158"/><ref name ="crystallographic studies"/>.   Binding og NADH causes a conformational change in the Aspartate 42 and Arginine 43 <scene name='Sandbox_Reserved_321/Asp_42_and_arg_43/1'>(E42 and R43)</scene> side chains and an over all conformational change in InhA<ref name ="crystallographic studies"/><ref name ="mech of thioamide drug action"/>.  In addition tyrosine 158 <scene name='Sandbox_Reserved_321/Tyr_158/1'>(Y158)</scene> plays an important role in aligning the carbonyl substrate, in fact; rotation about its Cα-Cβ bond by 60° brings it into a position where it can hydrogen bond to the carbonyl of the 2-trans enoyl-ACP and provide it with electrophilic stabilization<ref name ="Roles of T158"/>.  The substrate binds in a U-shaped conformation with its trans double bond adjacent to the nicotinamide ring of NAD+<ref name ="Fatty acyl in InhA"/>.  Inha then reduces the 2-trans double bond of the substrate by forming a enoyl intermediate through the transfer of a hydride ion from NADH to the third carbon of the substrate, followed by protonation of the second carbon<ref name ="crystallographic studies"/>.  The binding of both the substrate and the cofactor induces another conformational change in InhA that allows for the release of the meromycolic acid product<ref name ="crystallographic studies"/>.  The meromycolic acids undergo [http://en.wikipedia.org/wiki/Claisen_condensation claisen condensation] with a C26 fatty acid followed by reduction to a mature mycolic acid<ref name ="Fatty Acid Synthesis"/><ref name ="crystallographic studies"/>.