1m8d: Difference between revisions

Revision as of 14:52, 21 February 2008

inducible nitric oxide synthase with Chlorzoxazone bound

OverviewOverview

Nitric oxide is a key signaling molecule in many biological processes, making regulation of nitric oxide levels highly desirable for human medicine and for advancing our understanding of basic physiology. Designing inhibitors to specifically target one of the three nitric oxide synthase (NOS) isozymes that form nitric oxide from the L-Arg substrate poses a significant challenge due to the overwhelmingly conserved active sites. We report here 10 new X-ray crystallographic structures of inducible and endothelial NOS oxygenase domains cocrystallized with chlorzoxazone and four nitroindazoles: 5-nitroindazole, 6-nitroindazole, 7-nitroindazole, and 3-bromo-7-nitroindazole. Each of these bicyclic aromatic inhibitors has only one hydrogen bond donor and therefore cannot form the bidentate hydrogen bonds that the L-Arg substrate makes with Glu371. Instead, all of these inhibitors induce a conformational change in Glu371, creating an active site with altered molecular recognition properties. The cost of this conformational change is approximately 1-2 kcal, based on our measured constants for inhibitor binding to the wild-type and E371A mutant proteins. These inhibitors derive affinity by pi-stacking above the heme and replacing both intramolecular (Glu371-Met368) and intermolecular (substrate-Trp366) hydrogen bonds to the beta-sheet architecture underlying the active site. When bound to NOS, high-affinity inhibitors in this class are planar, whereas weaker inhibitors are nonplanar. Isozyme differences were observed in the pterin cofactor site, the heme propionate, and inhibitor positions. Computational docking predictions match the crystallographic results, including the Glu371 conformational change and inhibitor-binding orientations, and support a combined crystallographic and computational approach to isozyme-specific NOS inhibitor analysis and design.

About this StructureAbout this Structure

1M8D is a Single protein structure of sequence from Mus musculus with , , , , and as ligands. Active as Nitric-oxide synthase, with EC number 1.14.13.39 Full crystallographic information is available from OCA.

ReferenceReference

Conformational changes in nitric oxide synthases induced by chlorzoxazone and nitroindazoles: crystallographic and computational analyses of inhibitor potency., Rosenfeld RJ, Garcin ED, Panda K, Andersson G, Aberg A, Wallace AV, Morris GM, Olson AJ, Stuehr DJ, Tainer JA, Getzoff ED, Biochemistry. 2002 Nov 26;41(47):13915-25. PMID:12437348

Page seeded by OCA on Thu Feb 21 13:52:39 2008

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OCA

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-[[Image:1m8d.jpg|left|200px]]<br /><applet load="1m8d" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1m8d.jpg|left|200px]]<br /><applet load="1m8d" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1m8d, resolution 2.35&Aring;" />
 '''inducible nitric oxide synthase with Chlorzoxazone bound'''<br />
 ==Overview==
-Nitric oxide is a key signaling molecule in many biological processes, making regulation of nitric oxide levels highly desirable for human, medicine and for advancing our understanding of basic physiology., Designing inhibitors to specifically target one of the three nitric oxide, synthase (NOS) isozymes that form nitric oxide from the L-Arg substrate, poses a significant challenge due to the overwhelmingly conserved active, sites. We report here 10 new X-ray crystallographic structures of, inducible and endothelial NOS oxygenase domains cocrystallized with, chlorzoxazone and four nitroindazoles: 5-nitroindazole, 6-nitroindazole, 7-nitroindazole, and 3-bromo-7-nitroindazole. Each of these bicyclic, aromatic inhibitors has only one hydrogen bond donor and therefore cannot, form the bidentate hydrogen bonds that the L-Arg substrate makes with, Glu371. Instead, all of these inhibitors induce a conformational change in, Glu371, creating an active site with altered molecular recognition, properties. The cost of this conformational change is approximately 1-2, kcal, based on our measured constants for inhibitor binding to the, wild-type and E371A mutant proteins. These inhibitors derive affinity by, pi-stacking above the heme and replacing both intramolecular, (Glu371-Met368) and intermolecular (substrate-Trp366) hydrogen bonds to, the beta-sheet architecture underlying the active site. When bound to NOS, high-affinity inhibitors in this class are planar, whereas weaker, inhibitors are nonplanar. Isozyme differences were observed in the pterin, cofactor site, the heme propionate, and inhibitor positions. Computational, docking predictions match the crystallographic results, including the, Glu371 conformational change and inhibitor-binding orientations, and, support a combined crystallographic and computational approach to, isozyme-specific NOS inhibitor analysis and design.
+Nitric oxide is a key signaling molecule in many biological processes, making regulation of nitric oxide levels highly desirable for human medicine and for advancing our understanding of basic physiology. Designing inhibitors to specifically target one of the three nitric oxide synthase (NOS) isozymes that form nitric oxide from the L-Arg substrate poses a significant challenge due to the overwhelmingly conserved active sites. We report here 10 new X-ray crystallographic structures of inducible and endothelial NOS oxygenase domains cocrystallized with chlorzoxazone and four nitroindazoles: 5-nitroindazole, 6-nitroindazole, 7-nitroindazole, and 3-bromo-7-nitroindazole. Each of these bicyclic aromatic inhibitors has only one hydrogen bond donor and therefore cannot form the bidentate hydrogen bonds that the L-Arg substrate makes with Glu371. Instead, all of these inhibitors induce a conformational change in Glu371, creating an active site with altered molecular recognition properties. The cost of this conformational change is approximately 1-2 kcal, based on our measured constants for inhibitor binding to the wild-type and E371A mutant proteins. These inhibitors derive affinity by pi-stacking above the heme and replacing both intramolecular (Glu371-Met368) and intermolecular (substrate-Trp366) hydrogen bonds to the beta-sheet architecture underlying the active site. When bound to NOS, high-affinity inhibitors in this class are planar, whereas weaker inhibitors are nonplanar. Isozyme differences were observed in the pterin cofactor site, the heme propionate, and inhibitor positions. Computational docking predictions match the crystallographic results, including the Glu371 conformational change and inhibitor-binding orientations, and support a combined crystallographic and computational approach to isozyme-specific NOS inhibitor analysis and design.
 ==About this Structure==
-M8D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with BOG, SO4, HEM, H4B, CLW and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nitric-oxide_synthase Nitric-oxide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M8D OCA].
+M8D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=BOG:'>BOG</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=HEM:'>HEM</scene>, <scene name='pdbligand=H4B:'>H4B</scene>, <scene name='pdbligand=CLW:'>CLW</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nitric-oxide_synthase Nitric-oxide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M8D OCA].
 ==Reference==
@@ Line 16: / Line 16: @@
 [[Category: Aberg, A.]]
 [[Category: Andersson, G.]]
-[[Category: Garcin, E.D.]]
+[[Category: Garcin, E D.]]
-[[Category: Getzoff, E.D.]]
+[[Category: Getzoff, E D.]]
 [[Category: Panda, K.]]
-[[Category: Rosenfeld, R.J.]]
+[[Category: Rosenfeld, R J.]]
-[[Category: Stuehr, D.J.]]
+[[Category: Stuehr, D J.]]
-[[Category: Tainer, J.A.]]
+[[Category: Tainer, J A.]]
-[[Category: Wallace, A.V.]]
+[[Category: Wallace, A V.]]
 [[Category: BOG]]
 [[Category: CLW]]
@@ Line 31: / Line 31: @@
 [[Category: inhibitor-induced conformational change]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:13:27 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:52:39 2008''