Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.
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Terry P Lybrand | David S Cerutti | T. Lybrand | D. Cerutti | R. Stenkamp | I. Le Trong | Isolde Le Trong | Ronald E Stenkamp
[1] Early mechanistic events in biotin dissociation from streptavidin , 2002, Nature Structural Biology.
[2] J. Tainer,et al. Structural Basis for Isozyme-specific Regulation of Electron Transfer in Nitric-oxide Synthase*[boxs] , 2004, Journal of Biological Chemistry.
[3] Jenn-Huei Lii,et al. Systematic Comparison of Experimental, Quantum Mechanical, and Molecular Mechanical Bond Lengths for Organic Molecules , 1996 .
[4] R. Stenkamp,et al. The high-resolution structure of (+)-epi-biotin bound to streptavidin. , 2006, Acta crystallographica. Section D, Biological crystallography.
[5] R. Stenkamp,et al. Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin‐biotin system , 1998, Protein science : a publication of the Protein Society.
[6] P. Kollman,et al. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .
[7] G. Voth,et al. Flexible simple point-charge water model with improved liquid-state properties. , 2006, The Journal of chemical physics.
[8] Sebastian Doniach,et al. Protein flexibility in solution and in crystals , 1999 .
[9] B. Halle. Biomolecular cryocrystallography: structural changes during flash-cooling. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[10] T. Lybrand,et al. Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex. , 2008, Biochemistry.
[11] J. Martí,et al. A molecular dynamics simulation study of hydrogen bonding in aqueous ionic solutions , 2005 .
[12] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[13] P. Kollman,et al. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .
[14] T. Straatsma,et al. THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .
[15] D. Baker,et al. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. , 2003, Journal of molecular biology.
[16] J Andrew McCammon,et al. Discovery of a novel binding trench in HIV integrase. , 2004, Journal of medicinal chemistry.
[17] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[18] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[19] Jung-Hsin Lin,et al. Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. , 2007, Journal of the American Chemical Society.
[20] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .
[21] T. Lybrand,et al. A structural snapshot of an intermediate on the streptavidin-biotin dissociation pathway. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[22] J A McCammon,et al. Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. , 2001, Biophysical journal.
[23] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[24] B. Katz,et al. Binding to protein targets of peptidic leads discovered by phage display: crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence. , 1995, Biochemistry.
[25] K N Houk,et al. The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site. , 2007, Journal of the American Chemical Society.
[26] P. Stayton,et al. Structural studies of the streptavidin binding loop , 1997, Protein science : a publication of the Protein Society.
[27] Gianni Cardini,et al. Glycerol condensed phases Part I. A molecular dynamics study , 1999 .
[28] Sheng-Xiang Lin,et al. Mapping of steroids binding to 17 beta-hydroxysteroid dehydrogenase type 1 using Monte Carlo energy minimization reveals alternative binding modes. , 2005, Biochemistry.
[29] M. Wilchek,et al. Ligand Exchange between Proteins , 2002, The Journal of Biological Chemistry.
[30] K. Schulten,et al. Molecular dynamics study of unbinding of the avidin-biotin complex. , 1997, Biophysical journal.
[31] A. Chilkoti,et al. Structural studies of binding site tryptophan mutants in the high-affinity streptavidin-biotin complex. , 1998, Journal of molecular biology.
[32] N. Greenfield. Using circular dichroism spectra to estimate protein secondary structure , 2007, Nature Protocols.
[33] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[34] J. Åqvist,et al. Ion-water interaction potentials derived from free energy perturbation simulations , 1990 .
[35] S. Weerasinghe,et al. A Kirkwood−Buff Derived Force Field for Mixtures of Urea and Water , 2003 .
[36] P. Vekilov,et al. Entropy and surface engineering in protein crystallization. , 2006, Acta crystallographica. Section D, Biological crystallography.
[37] D. Hyre,et al. Ser45 plays an important role in managing both the equilibrium and transition state energetics of the streptavidin—biotin system , 2000, Protein science : a publication of the Protein Society.
[38] R. Sousa. Use of glycerol, polyols and other protein structure stabilizing agents in protein crystallization. , 1995, Acta crystallographica. Section D, Biological crystallography.
[39] D. Logothetis,et al. Hydrogen-bonding dynamics between adjacent blades in G-protein beta-subunit regulates GIRK channel activation. , 2006, Biophysical journal.