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Results: 1 to 20 of 38

1.

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites.

Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL Jr, Karplus PA.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):449-53. doi: 10.1073/pnas.1107115108. Epub 2011 Dec 23.

PMID:
22198840
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Unfolding simulations reveal the mechanism of extreme unfolding cooperativity in the kinetically stable alpha-lytic protease.

Salimi NL, Ho B, Agard DA.

PLoS Comput Biol. 2010 Feb 26;6(2):e1000689. doi: 10.1371/journal.pcbi.1000689.

PMID:
20195497
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Probing the function of heme distortion in the H-NOX family.

Olea C, Boon EM, Pellicena P, Kuriyan J, Marletta MA.

ACS Chem Biol. 2008 Nov 21;3(11):703-10. doi: 10.1021/cb800185h.

PMID:
19032091
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB).

Lee TW, James MN.

Biochim Biophys Acta. 2008 Feb;1784(2):319-34. Epub 2007 Nov 29.

PMID:
18157955
[PubMed - indexed for MEDLINE]
5.

Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase.

Lyubimov AY, Heard K, Tang H, Sampson NS, Vrielink A.

Protein Sci. 2007 Dec;16(12):2647-56.

PMID:
18029419
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Mesophile versus thermophile: insights into the structural mechanisms of kinetic stability.

Kelch BA, Agard DA.

J Mol Biol. 2007 Jul 20;370(4):784-95. Epub 2007 May 10.

PMID:
17543987
[PubMed - indexed for MEDLINE]
7.

Structural and mechanistic exploration of acid resistance: kinetic stability facilitates evolution of extremophilic behavior.

Kelch BA, Eagen KP, Erciyas FP, Humphris EL, Thomason AR, Mitsuiki S, Agard DA.

J Mol Biol. 2007 May 4;368(3):870-83. Epub 2007 Feb 22.

PMID:
17382344
[PubMed - indexed for MEDLINE]
8.

Denatured state effects and the origin of nonclassical phi values in protein folding.

Cho JH, Raleigh DP.

J Am Chem Soc. 2006 Dec 27;128(51):16492-3.

PMID:
17177385
[PubMed - indexed for MEDLINE]
9.

On the precision of experimentally determined protein folding rates and phi-values.

de los Rios MA, Muralidhara BK, Wildes D, Sosnick TR, Marqusee S, Wittung-Stafshede P, Plaxco KW, Ruczinski I.

Protein Sci. 2006 Mar;15(3):553-63.

PMID:
16501226
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Ultrahigh resolution structures of nitrophorin 4: heme distortion in ferrous CO and NO complexes.

Maes EM, Roberts SA, Weichsel A, Montfort WR.

Biochemistry. 2005 Sep 27;44(38):12690-9.

PMID:
16171383
[PubMed - indexed for MEDLINE]
11.
12.

Pulse proteolysis: a simple method for quantitative determination of protein stability and ligand binding.

Park C, Marqusee S.

Nat Methods. 2005 Mar;2(3):207-12. Epub 2005 Feb 17.

PMID:
15782190
[PubMed - indexed for MEDLINE]
13.

Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases.

Jaswal SS, Truhlar SM, Dill KA, Agard DA.

J Mol Biol. 2005 Mar 25;347(2):355-66. Epub 2005 Jan 28.

PMID:
15740746
[PubMed - indexed for MEDLINE]
14.

Probing the high energy states in proteins by proteolysis.

Park C, Marqusee S.

J Mol Biol. 2004 Nov 5;343(5):1467-76.

PMID:
15491624
[PubMed - indexed for MEDLINE]
15.

Refinement of macromolecular structures by the maximum-likelihood method.

Murshudov GN, Vagin AA, Dodson EJ.

Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55.

PMID:
15299926
[PubMed]
16.

The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain.

Fuhrmann CN, Kelch BA, Ota N, Agard DA.

J Mol Biol. 2004 May 14;338(5):999-1013.

PMID:
15111063
[PubMed - indexed for MEDLINE]
17.

The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography.

Kang BS, Devedjiev Y, Derewenda U, Derewenda ZS.

J Mol Biol. 2004 Apr 30;338(3):483-93. Erratum in: J Mol Biol. 2004 Jun 25;340(1):191.

PMID:
15081807
[PubMed - indexed for MEDLINE]
18.

Heme distortion modulated by ligand-protein interactions in inducible nitric-oxide synthase.

Li D, Stuehr DJ, Yeh SR, Rousseau DL.

J Biol Chem. 2004 Jun 18;279(25):26489-99. Epub 2004 Apr 2.

PMID:
15066989
[PubMed - indexed for MEDLINE]
Free Article
19.

Disabling the folding catalyst is the last critical step in alpha-lytic protease folding.

Cunningham EL, Agard DA.

Protein Sci. 2004 Feb;13(2):325-31.

PMID:
14739318
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

The folding landscape of Streptomyces griseus protease B reveals the energetic costs and benefits associated with evolving kinetic stability.

Truhlar SM, Cunningham EL, Agard DA.

Protein Sci. 2004 Feb;13(2):381-90. Epub 2004 Jan 10.

PMID:
14718653
[PubMed - indexed for MEDLINE]
Free PMC Article

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