Triggering loops and enzyme function: identification of loops that trigger and modulate movements.
暂无分享,去创建一个
[1] M Karplus,et al. Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. , 1990, Science.
[2] R. Nussinov,et al. Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: Thermal stability of protein domains and unfolding pathway , 2002, Proteins.
[3] R C Wade,et al. Electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[4] R. Nussinov,et al. Folding and binding cascades: Dynamic landscapes and population shifts , 2008, Protein science : a publication of the Protein Society.
[5] A. Fontana,et al. Limited Proteolysis in the Study of Protein Conformation , 1999 .
[6] G. Hammes. Multiple conformational changes in enzyme catalysis. , 2002, Biochemistry.
[7] M. Schotz,et al. The lipase gene family DOI 10.1194/jlr.R200007-JLR200 , 2002, Journal of Lipid Research.
[8] E. Goldsmith,et al. Changes in protein conformational mobility upon activation of extracellular regulated protein kinase-2 as detected by hydrogen exchange. , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[9] A. Joshua Wand,et al. Dynamic activation of protein function: A view emerging from NMR spectroscopy , 2001, Nature Structural Biology.
[10] Axel T. Brunger,et al. X-PLOR Version 3.1: A System for X-ray Crystallography and NMR , 1992 .
[11] L. A. Carreira,et al. Mechanism of enolase: the crystal structure of asymmetric dimer enolase-2-phospho-D-glycerate/enolase-phosphoenolpyruvate at 2.0 A resolution. , 1997, Biochemistry.
[12] B. Stoddard,et al. Combining Laue diffraction and molecular dynamics to study enzyme intermediates , 1996, Nature Structural Biology.
[13] Z. Derewenda,et al. Structure and function of lipases. , 1994, Advances in protein chemistry.
[14] A. Berry,et al. A functional role for a flexible loop containing Glu182 in the class II fructose-1,6-bisphosphate aldolase from Escherichia coli. , 2002, Journal of molecular biology.
[15] J. Berg,et al. Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.
[16] G J Williams,et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.
[17] J M Yon,et al. Conformational dynamics and enzyme activity. , 1998, Biochimie.
[18] B. Ramakrishnan,et al. Crystal structure of beta1,4-galactosyltransferase complex with UDP-Gal reveals an oligosaccharide acceptor binding site. , 2002, Journal of molecular biology.
[19] S. Kuhara,et al. Glycine-rich Region of Mitochondrial Processing Peptidase α-Subunit Is Essential for Binding and Cleavage of the Precursor Proteins* , 2000, The Journal of Biological Chemistry.
[20] R. Bywater,et al. Computational analysis of chain flexibility and fluctuations in Rhizomucor miehei lipase. , 1999, Protein engineering.
[21] M. Karplus,et al. Effective energy function for proteins in solution , 1999, Proteins.
[22] Ming‐Hong Hao,et al. Analyzing the normal mode dynamics of macromolecules by the component synthesis method: Residue clustering and multiple‐component approach , 1992, Biopolymers.
[23] G. Weber. Ligand binding and internal equilibria in proteins. , 1972, Biochemistry.
[24] C. Orengo,et al. Evolution of protein function, from a structural perspective. , 1999, Current opinion in chemical biology.
[25] S Doniach,et al. Protein dynamics simulations from nanoseconds to microseconds. , 1999, Current opinion in structural biology.
[26] Christian Cambillau,et al. Crystal structures of the bovine β4galactosyltransferase catalytic domain and its complex with uridine diphosphogalactose , 1999, The EMBO journal.
[27] J. Brewer,et al. The structure of yeast enolase at 2.25-A resolution. An 8-fold beta + alpha-barrel with a novel beta beta alpha alpha (beta alpha)6 topology. , 1989, The Journal of biological chemistry.
[28] T. Lazaridis,et al. On the unfolding of α‐lytic protease and the role of the pro region , 2000, Proteins.
[29] P. Kinnunen,et al. Active serine involved in the stabilization of the active site loop in the Humicola lanuginosa lipase. , 1998, Biochemistry.
[30] W. Bennett,et al. Structural and functional aspects of domain motions in proteins. , 1984, CRC critical reviews in biochemistry.
[31] M. Karplus,et al. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. , 1999, Journal of molecular biology.
[32] Ad Bax,et al. Flexibility and function in HIV-1 protease , 1995, Nature Structural Biology.
[33] D. Lawson,et al. Structural origins of the interfacial activation in Thermomyces (Humicola) lanuginosa lipase. , 2000, Biochemistry.
[34] B. Ramakrishnan,et al. Crystal structure of lactose synthase reveals a large conformational change in its catalytic component, the beta1,4-galactosyltransferase-I. , 2001, Journal of molecular biology.
[35] M. Haas,et al. Conformational lability of lipases observed in the absence of an oil-water interface: crystallographic studies of enzymes from the fungi Humicola lanuginosa and Rhizopus delemar. , 1995, Journal of lipid research.
[36] R. Nussinov,et al. Folding funnels, binding funnels, and protein function , 1999, Protein science : a publication of the Protein Society.
[37] Not just your average structures , 1996, Nature Structural Biology.
[38] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[39] B. Dijkstra,et al. Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. , 1999, Annual review of microbiology.
[40] J. Kuriyan,et al. The Conformational Plasticity of Protein Kinases , 2002, Cell.
[41] M Levitt,et al. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. , 1999, Journal of molecular biology.
[42] S. Hassan,et al. A critical analysis of continuum electrostatics: The screened Coulomb potential–implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins , 2002, Proteins.
[43] E. Sterchi,et al. Proteolytic enzymes : tools and targets , 1999 .
[44] D. V. van Aalten,et al. Essential dynamics of lipase binding sites: the effect of inhibitors of different chain length. , 1997, Protein engineering.
[45] D. Dryden,et al. Allostery without conformational change , 1984, European Biophysics Journal.
[46] W. Chazin,et al. Engineering and design of ligand-induced conformational change in proteins. , 2002, Current opinion in structural biology.
[47] D. Frenkel,et al. Molecular dynamics simulations. , 2002, Current opinion in structural biology.
[48] L. Lebioda,et al. Mechanism of enolase: the crystal structure of enolase-Mg2(+)-2-phosphoglycerate/phosphoenolpyruvate complex at 2.2-A resolution. , 1991, Biochemistry.
[49] R. Nussinov,et al. Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I. , 2003, Biochemistry.
[50] I. Rayment,et al. Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli. , 2001, Biochemistry.