A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models

[1]  Gregory C Rutledge,et al.  A novel algorithm for creating coarse-grained, density dependent implicit solvent models. , 2008, The Journal of chemical physics.

[2]  Gregory A Voth,et al.  The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures. , 2009, The Journal of chemical physics.

[3]  D Thirumalai,et al.  The nature of folded states of globular proteins , 1992, Biopolymers.

[4]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[5]  Y. Levi-Kalisman,et al.  Matrices of Acidic β‐Sheet Peptides as Templates for Calcium Phosphate Mineralization , 2008 .

[6]  Alessandra Villa,et al.  Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation. , 2009, Physical chemistry chemical physics : PCCP.

[7]  Alessandra Villa,et al.  Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model. , 2009, Physical chemistry chemical physics : PCCP.

[8]  Lanyuan Lu,et al.  Multiscale Coarse-Graining of the Protein Energy Landscape , 2010, PLoS Comput. Biol..

[9]  Cecilia Clementi,et al.  Coarse-grained models of protein folding: toy models or predictive tools? , 2008, Current opinion in structural biology.

[10]  H. Matsui,et al.  Peptide‐Based Nanotubes and Their Applications in Bionanotechnology , 2005, Advanced materials.

[11]  Tristan Bereau,et al.  Generic coarse-grained model for protein folding and aggregation. , 2009, The Journal of chemical physics.

[12]  Siewert J Marrink,et al.  Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. , 2011, Physical chemistry chemical physics : PCCP.

[13]  Ehud Gazit,et al.  Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology. , 2007, Trends in biotechnology.

[14]  Kurt Kremer,et al.  Tunable generic model for fluid bilayer membranes. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[15]  Scott Brown,et al.  Coarse-grained sequences for protein folding and design , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[16]  A. Liwo,et al.  A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[17]  William George Noid,et al.  Extended ensemble approach for deriving transferable coarse-grained potentials , 2009 .

[18]  Ruth Nussinov,et al.  Coarse-grained representation of β-helical protein building blocks , 2007 .

[19]  Joan-Emma Shea,et al.  Self-assembly of β-sheet forming peptides into chiral fibrillar aggregates , 2007 .

[20]  Florian Müller-Plathe,et al.  Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. , 2002, Chemphyschem : a European journal of chemical physics and physical chemistry.

[21]  Gregory A Voth,et al.  A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.

[22]  R. Jernigan,et al.  Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .

[23]  Michael L Klein,et al.  Understanding nature's design for a nanosyringe. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Kurt Kremer,et al.  Simulation of polymer melts. I. Coarse‐graining procedure for polycarbonates , 1998 .

[25]  Wilfred F van Gunsteren,et al.  Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. , 2007, Chemphyschem : a European journal of chemical physics and physical chemistry.

[26]  Normand Mousseau,et al.  Coarse-grained protein molecular dynamics simulations. , 2007, The Journal of chemical physics.

[27]  Berk Hess,et al.  Modeling multibody effects in ionic solutions with a concentration dependent dielectric permittivity. , 2006, Physical review letters.

[28]  Gregory A Voth,et al.  Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.

[29]  Kurt Kremer,et al.  Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back , 2009 .

[30]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[31]  Kurt Kremer,et al.  Comparison between coarse-graining models for polymer systems: Two mapping schemes for polystyrene , 2007 .

[32]  Peter J Bond,et al.  Insertion and assembly of membrane proteins via simulation. , 2006, Journal of the American Chemical Society.

[33]  Wataru Shinoda,et al.  Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants , 2007 .

[34]  John G. Curro,et al.  Mapping of Explicit Atom onto United Atom Potentials , 1998 .

[35]  Florian Müller-Plathe,et al.  Multicentered Gaussian‐based potentials for coarse‐grained polymer simulations: Linking atomistic and mesoscopic scales , 2005 .

[36]  Ilpo Vattulainen,et al.  Multiscale modeling of emergent materials: biological and soft matter. , 2009, Physical chemistry chemical physics : PCCP.

[37]  E. Gazit.  Mechanisms of amyloid fibril self‐assembly and inhibition , 2005, The FEBS journal.

[38]  Yundong Wu,et al.  Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model:  Molecular Dynamics Study of Polyalanine-Based Peptides. , 2007, Journal of chemical theory and computation.

[39]  S. Stupp,et al.  Branched peptide-amphiphiles as self-assembling coatings for tissue engineering scaffolds. , 2006, Journal of Biomedical Materials Research. Part A.

[40]  C. Hall,et al.  Phase diagrams describing fibrillization by polyalanine peptides. , 2004, Biophysical journal.

[41]  Michele Cascella,et al.  A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements. , 2010, Journal of chemical theory and computation.

[42]  A. Irbäck,et al.  Three-helix-bundle protein in a Ramachandran model. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Wataru Shinoda,et al.  A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. , 2009, Journal of chemical theory and computation.

[44]  G. Schatz,et al.  Modeling self-assembly processes driven by nonbonded interactions in soft materials. , 2008, The journal of physical chemistry. B.

[45]  Attila Szolnoki,et al.  Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions , 2010, PLoS Comput. Biol..

[46]  Gregory A. Voth,et al.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. , 2008, The Journal of chemical physics.

[47]  R. Larson,et al.  The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.

[48]  George M. Whitesides,et al.  Beyond molecules: Self-assembly of mesoscopic and macroscopic components , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[49]  Kurt Kremer,et al.  Coarse-Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities , 2009 .

[50]  R. C. Reeder,et al.  A Coarse Grain Model for Phospholipid Simulations , 2001 .

[51]  J Andrew McCammon,et al.  Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model. , 2006, Journal of chemical theory and computation.

[52]  Carl Henrik Görbitz,et al.  Microporous organic materials from hydrophobic dipeptides. , 2007, Chemistry.

[53]  Gregory C Rutledge,et al.  Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains. , 2009, The Journal of chemical physics.

[54]  Daniel Borgis,et al.  A coarse-grained protein-protein potential derived from an all-atom force field. , 2007, The journal of physical chemistry. B.

[55]  Jan Fischer,et al.  Modeling of aqueous poly(oxyethylene) solutions. 2. Mesoscale simulations. , 2008, The journal of physical chemistry. B.

[56]  Margaret E. Johnson,et al.  Representability problems for coarse-grained water potentials. , 2007, The Journal of chemical physics.

[57]  A. Lyubartsev,et al.  Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[58]  Jim Pfaendtner,et al.  A systematic methodology for defining coarse-grained sites in large biomolecules. , 2008, Biophysical journal.

[59]  M. Ghadiri,et al.  Peptide Nanotubes and Beyond , 1998 .

[60]  Kurt Kremer,et al.  Combined Coarse-Grained and Atomistic Simulation of Liquid Bisphenol A-Polycarbonate: Liquid Packing and Intramolecular Structure , 2003 .

[61]  Kurt Kremer,et al.  Effects of excluded volume and bond length on the dynamics of dense bead-spring polymer melts , 2002 .

[62]  Kurt Kremer,et al.  Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations , 2006 .

[63]  Michael L. Klein,et al.  A coarse grain model for n-alkanes parameterized from surface tension data , 2003 .

[64]  Gregory A Voth,et al.  Multiscale coarse-graining and structural correlations: connections to liquid-state theory. , 2007, The journal of physical chemistry. B.

[65]  P. Derreumaux,et al.  A coarse‐grained protein force field for folding and structure prediction , 2007, Proteins.

[66]  T. Holmes,et al.  Novel peptide-based biomaterial scaffolds for tissue engineering. , 2002, Trends in biotechnology.

[67]  Tap Ha-Duong,et al.  Protein Backbone Dynamics Simulations Using Coarse-Grained Bonded Potentials and Simplified Hydrogen Bonds. , 2010, Journal of chemical theory and computation.

[68]  R. Weissleder,et al.  Peptide-based biomaterials for protease-enhanced drug delivery. , 2006, Biomacromolecules.

[69]  Wataru Shinoda,et al.  Coarse-grained potential models for phenyl-based molecules: I. Parametrization using experimental data. , 2010, The journal of physical chemistry. B.

[70]  D. Altschuh,et al.  A peptide-based, ratiometric biosensor construct for direct fluorescence detection of a protein analyte. , 2008, Bioconjugate chemistry.

[71]  Alessandra Villa,et al.  Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water. , 2010, Journal of chemical theory and computation.

[72]  R. Jernigan,et al.  Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. , 1996, Journal of molecular biology.

[73]  Alexander J. Marchut,et al.  Solvent effects on the conformational transition of a model polyalanine peptide , 2004, Protein science : a publication of the Protein Society.

[74]  C. Hall,et al.  Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[75]  Henry Bock,et al.  Mesoscale modeling of complex binary fluid mixtures: towards an atomistic foundation of effective potentials. , 2006, The Journal of chemical physics.

[76]  Cecilia Clementi,et al.  Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[77]  Gregory A Voth,et al.  Coarse-grained peptide modeling using a systematic multiscale approach. , 2007, Biophysical journal.

[78]  Berk Hess,et al.  Osmotic coefficients of atomistic NaCl (aq) force fields. , 2006, The Journal of chemical physics.

[79]  Sang-Jin Suh,et al.  Recent advances in peptide probe-based biosensors for detection of infectious agents. , 2009, Journal of microbiological methods.

[80]  Thomas M Truskett,et al.  Coarse-grained strategy for modeling protein stability in concentrated solutions. , 2005, Biophysical journal.

[81]  B. Maigret,et al.  Self assembly of peptides near or within membranes using coarse grained MD simulations , 2009 .

[82]  A. Liwo,et al.  A united‐residue force field for off‐lattice protein‐structure simulations. I. Functional forms and parameters of long‐range side‐chain interaction potentials from protein crystal data , 1997 .

[83]  P. Wolynes,et al.  Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer , 1999 .

[84]  Kurt Kremer,et al.  Classical simulations from the atomistic to the mesoscale and back: coarse graining an liquid crystal. , 2008, Soft matter.

[85]  K. Binder,et al.  Coarse-grained models for fluids and their mixtures: Comparison of Monte Carlo studies of their phase behavior with perturbation theory and experiment. , 2008, The Journal of chemical physics.

[86]  Alexander Lukyanov,et al.  Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.

[87]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[88]  Julien Michel,et al.  Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations. , 2008, The journal of physical chemistry. B.

[89]  A. Mark,et al.  Coarse grained model for semiquantitative lipid simulations , 2004 .

[90]  Ilpo Vattulainen,et al.  Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer. , 2009, The Journal of chemical physics.