De Novo Protein Folding with Distributed Computational Resources

c 2009 by John von Neumann Institute for ComputingPermission to make digital or hard copies of portions of this work forpersonal or classroom use is granted provided that the copies are notmade or distributed for profit or commercial advantage and that copiesbear this notice and the full citation on the first page. To copy otherwiserequires prior specific permission by the publisher mentioned above.

[1]  A. Schug,et al.  Energy landscape paving simulations of the trp-cage protein. , 2005, The Journal of chemical physics.

[2]  J. Onuchic,et al.  Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.

[3]  K. Dill,et al.  A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .

[4]  C. Brooks,et al.  From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. , 2001, Annual review of physical chemistry.

[5]  Jeffrey C. Miller,et al.  Highly efficient endogenous human gene correction using designed zinc-finger nucleases , 2005, Nature.

[6]  P E Wright,et al.  DNA-induced alpha-helix capping in conserved linker sequences is a determinant of binding affinity in Cys(2)-His(2) zinc fingers. , 2000, Journal of molecular biology.

[7]  Karplus,et al.  Protein folding bottlenecks: A lattice Monte Carlo simulation. , 1991, Physical review letters.

[8]  P. Bolhuis,et al.  Sampling the multiple folding mechanisms of Trp-cage in explicit solvent , 2006, Proceedings of the National Academy of Sciences.

[9]  M J Sippl,et al.  Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.

[10]  Wolfgang Wenzel,et al.  De novo Folding of Two-Helix Potassium Channel Blockers with Free-Energy Models and Molecular Dynamics. , 2007, Journal of chemical theory and computation.

[11]  J. Doye,et al.  Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms , 1997, cond-mat/9803344.

[12]  J. W. Neidigh,et al.  Designing a 20-residue protein , 2002, Nature Structural Biology.

[13]  Wolfgang Wenzel,et al.  A stochastic tunneling approach for global minimization , 1999 .

[14]  A. Schug,et al.  Reproducible protein folding with the stochastic tunneling method. , 2003, Physical review letters.

[15]  G L Gilliland,et al.  Structural studies of the engrailed homeodomain , 1994, Protein science : a publication of the Protein Society.

[16]  S. Buldyrev,et al.  Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. , 2004, Biophysical journal.

[17]  Abhinav Verma,et al.  All‐atom de novo protein folding with a scalable evolutionary algorithm , 2007, J. Comput. Chem..

[18]  Richard Bonneau,et al.  Ab initio protein structure prediction: progress and prospects. , 2001, Annual review of biophysics and biomolecular structure.

[19]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[20]  A. Sali,et al.  Protein Structure Prediction and Structural Genomics , 2001, Science.

[21]  Michal Sharon,et al.  Alternative conformations of HIV-1 V3 loops mimic beta hairpins in chemokines, suggesting a mechanism for coreceptor selectivity. , 2003, Structure.

[22]  Chin-Kun Hu,et al.  Free energy landscape and folding mechanism of a β‐hairpin in explicit water: A replica exchange molecular dynamics study , 2005, Proteins.

[23]  Wolfgang Wenzel,et al.  Predictive in silico all-atom folding of a four-helix protein with a free-energy model. , 2004, Journal of the American Chemical Society.

[24]  P. Wright,et al.  Zinc finger proteins: new insights into structural and functional diversity. , 2001, Current opinion in structural biology.

[25]  H. Scheraga,et al.  Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations , 1984 .

[26]  C. Branden,et al.  Introduction to protein structure , 1991 .

[27]  A. Schug,et al.  All‐atom folding of the three‐helix HIV accessory protein with an adaptive parallel tempering method , 2004, Proteins.

[28]  Valerie Daggett,et al.  The complete folding pathway of a protein from nanoseconds to microseconds , 2003, Nature.

[29]  M J Sippl,et al.  Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. , 1992, Journal of molecular biology.

[30]  D. Warrell,et al.  Oxford textbook of medicine , 1983, The Ulster Medical Journal.

[31]  F. Rao,et al.  Replica exchange molecular dynamics simulations of reversible folding , 2003 .

[32]  T. Hubbard,et al.  Critical assessment of methods of protein structure prediction (CASP)‐round V , 2003, Proteins.

[33]  V. Pande,et al.  The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. , 2002, Journal of the American Chemical Society.

[34]  Wolfgang Wenzel,et al.  Investigation of the parallel tempering method for protein folding , 2005 .

[35]  Wolfgang Wenzel,et al.  Protein structure prediction by all-atom free-energy refinement , 2006, BMC Structural Biology.

[36]  S. Ishii,et al.  Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain. , 1999, Journal of molecular biology.

[37]  Akbar Nayeem,et al.  A comparative study of the simulated‐annealing and Monte Carlo‐with‐minimization approaches to the minimum‐energy structures of polypeptides: [Met]‐enkephalin , 1991 .

[38]  Carl Branden,et al.  The art of PS2 : the complete set of figures, panels and tables from introduction to protein structure , 1999 .

[39]  A. Linhananta,et al.  The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage. , 2005, The Journal of chemical physics.

[40]  L. Stryer,et al.  Implications of X-ray crystallographic studies of protein structure. , 1968, Annual review of biochemistry.

[41]  Wolfgang Wenzel,et al.  Biomolecular Structure Prediction Stochastic Optimization Methods , 2005 .

[42]  Wolfgang Wenzel,et al.  Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[43]  B. Rost Review: protein secondary structure prediction continues to rise. , 2001, Journal of structural biology.

[44]  A. Leach Molecular Modelling: Principles and Applications , 1996 .

[45]  W. Wenzel Predictive folding of a β-hairpin protein in an all-atom free-energy model , 2006 .

[46]  David J. Wales,et al.  Energy landscapes, global optimization and dynamics of the polyalanine Ac(ala)8NHMe , 2001 .

[47]  David J. Wales,et al.  Energy landscapes of model polyalanines , 2002 .

[48]  C. Anfinsen Principles that govern the folding of protein chains. , 1973, Science.

[49]  A. Schug,et al.  Basin hopping simulations for all-atom protein folding. , 2006, The Journal of chemical physics.

[50]  R. Abagyan,et al.  Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. , 1994, Journal of molecular biology.

[51]  Zaida Luthey-Schulten,et al.  Folding funnels: The key to robust protein structure prediction , 2002, J. Comput. Chem..

[52]  D. Yee,et al.  Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.

[53]  K. Dill,et al.  Protein folding in the landscape perspective: Chevron plots and non‐arrhenius kinetics , 1998, Proteins.

[54]  Ruben Abagyan,et al.  Ab InitioFolding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure , 1999 .

[55]  N. Pavletich,et al.  Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A , 1991, Science.

[56]  Wolfgang Wenzel,et al.  De novo folding of the DNA-binding ATF-2 zinc finger motif in an all-atom free-energy forcefield. , 2006, Angewandte Chemie.

[57]  David J Wales,et al.  Effect of salt bridges on the energy landscape of a model protein. , 2004, The Journal of chemical physics.

[58]  C. Pabo,et al.  DNA recognition by Cys2His2 zinc finger proteins. , 2000, Annual review of biophysics and biomolecular structure.

[59]  Harold A. Scheraga,et al.  Analysis of the Contribution of Internal Vibrations to the Statistical Weights of Equilibrium Conformations of Macromolecules , 1969 .

[60]  Giovanna Ghirlanda,et al.  Membrane Proteins , 2013, Methods in Molecular Biology.

[61]  W. Wenzel,et al.  Scaling behavior of stochastic minimization algorithms in a perfect funnel landscape , 1999 .

[62]  C. Dobson The structural basis of protein folding and its links with human disease. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[63]  Wolfgang Wenzel,et al.  Massively Parallel All Atom Protein Folding in a Single Day , 2007, PARCO.

[64]  V. Pande,et al.  Multiplexed-replica exchange molecular dynamics method for protein folding simulation. , 2003, Biophysical journal.

[65]  Julian Lee,et al.  Folding of small proteins using a single continuous potential. , 2004, The Journal of chemical physics.

[66]  J. M. Singer,et al.  Bouncing towards the optimum: Improving the results of Monte Carlo optimization algorithms , 1998 .

[67]  Valerie Daggett,et al.  The present view of the mechanism of protein folding , 2003, Nature Reviews Molecular Cell Biology.

[68]  Timothy F. Havel,et al.  NMR structure determination in solution: a critique and comparison with X-ray crystallography. , 1992, Annual review of biophysics and biomolecular structure.

[69]  N. Skelton,et al.  Tryptophan zippers: Stable, monomeric β-hairpins , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[70]  Stephen H White,et al.  Membrane proteins--pumping along. , 2005, Current opinion in structural biology.

[71]  P E Wright,et al.  Three-dimensional solution structure of a single zinc finger DNA-binding domain. , 1989, Science.

[72]  Wolfgang Wenzel,et al.  Predictive and reproducible de novo all-atom folding of a β-hairpin loop in an improved free-energy forcefield , 2007 .

[73]  F. Young Biochemistry , 1955, The Indian Medical Gazette.