Complex pathways in folding of protein G explored by simulation and experiment.
暂无分享,去创建一个
Diwakar Shukla | Vijay S Pande | Christian R Schwantes | Lisa J Lapidus | Lisa J. Lapidus | V. Pande | L. Lapidus | D. Shukla | C. Schwantes | Stephen J. DeCamp | Srabasti Acharya | Srabasti Acharya | Ling Wu | Michael King | Stephen J DeCamp | Ling Wu | Michael King | Christian Schwantes | S. Acharya
[1] Lisa J Lapidus,et al. How fast is protein hydrophobic collapse? , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[2] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[3] Shoji Takada,et al. Folding energy landscape and network dynamics of small globular proteins , 2009, Proceedings of the National Academy of Sciences.
[4] Vincent A. Voelz,et al. Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. , 2012, Journal of the American Chemical Society.
[5] Valerie Daggett,et al. GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate. , 2011, Biophysical journal.
[6] Thomas J Lane,et al. Probing the origins of two-state folding. , 2013, The Journal of chemical physics.
[7] Michael R. Shirts,et al. COMPUTING: Screen Savers of the World Unite! , 2000, Science.
[8] Athi N. Naganathan,et al. Direct observation of downhill folding of lambda-repressor in a microfluidic mixer. , 2009, Biophysical journal.
[9] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[10] D Baker,et al. Critical role of beta-hairpin formation in protein G folding. , 2000, Nature structural biology.
[11] Lisa J Lapidus,et al. Extremely slow intramolecular diffusion in unfolded protein L , 2010, Proceedings of the National Academy of Sciences.
[12] Eric J. Sorin,et al. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. , 2005, Biophysical journal.
[13] J. H. Ward. Hierarchical Grouping to Optimize an Objective Function , 1963 .
[14] P. Kollman. Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules , 1996 .
[15] Carlo Camilloni,et al. Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations. , 2011, The Journal of chemical physics.
[16] Eric Vanden-Eijnden,et al. Transition Path Theory for Markov Jump Processes , 2009, Multiscale Model. Simul..
[17] Vijay S Pande,et al. Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9. , 2013, Journal of chemical theory and computation.
[18] Soon-Ho Park,et al. Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing , 1999, Nature Structural Biology.
[19] Kyle A. Beauchamp,et al. Markov state model reveals folding and functional dynamics in ultra-long MD trajectories. , 2011, Journal of the American Chemical Society.
[20] Vijay S. Pande,et al. Screen Savers of the World Unite! , 2000, Science.
[21] Frank Noé,et al. Markov models of molecular kinetics: generation and validation. , 2011, The Journal of chemical physics.
[22] Shimon Weiss,et al. Femtomole mixer for microsecond kinetic studies of protein folding. , 2004, Analytical chemistry.
[23] Soon-Ho Park,et al. An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core. , 1997 .
[24] W. Wedemeyer,et al. Dynamic similarity of the unfolded states of proteins L and G. , 2007, Biochemistry.
[25] R. Austin,et al. Hydrodynamic Focusing on a Silicon Chip: Mixing Nanoliters in Microseconds , 1998 .
[26] Benjamin Schuler,et al. Microfluidic mixers for the investigation of rapid protein folding kinetics using synchrotron radiation circular dichroism spectroscopy. , 2008, Analytical chemistry.
[27] L. Lapidus,et al. Combining ultrarapid mixing with photochemical oxidation to probe protein folding. , 2013, Analytical chemistry.
[28] A. Gronenborn,et al. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. , 1993, Science.
[29] Guozhong Xu,et al. Radiolytic modification of basic amino acid residues in peptides: probes for examining protein-protein interactions. , 2003, Analytical chemistry.
[30] Thomas J Lane,et al. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. , 2011, Journal of chemical theory and computation.
[31] H. Roder,et al. An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core. , 1997, Biochemistry.
[32] D. Baker,et al. Critical role of β-hairpin formation in protein G folding , 2000, Nature Structural Biology.
[33] M. Gross,et al. Fast photochemical oxidation of protein footprints faster than protein unfolding. , 2009, Analytical chemistry.
[34] T. Sosnick,et al. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. , 2002, Journal of molecular biology.
[35] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[36] Berk Hess,et al. LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..
[37] Lisa J. Lapidus,et al. Protein hydrophobic collapse and early folding steps observed in a microfluidic mixer. , 2007, Biophysical journal.
[38] C. Schütte,et al. Supplementary Information for “ Constructing the Equilibrium Ensemble of Folding Pathways from Short Off-Equilibrium Simulations ” , 2009 .
[39] Lisa J. Lapidus,et al. Sub-millisecond chain collapse of the Escherichia coli globin ApoHmpH. , 2013, The journal of physical chemistry. B.
[40] Shimon Weiss,et al. Ruggedness in the folding landscape of protein L , 2008, HFSP journal.
[41] D. Case,et al. Exploring protein native states and large‐scale conformational changes with a modified generalized born model , 2004, Proteins.
[42] K. Ghosh,et al. Evidence of multiple folding pathways for the villin headpiece subdomain. , 2011, The journal of physical chemistry. B.