A minimal proteinlike lattice model: an alpha-helix motif.

A simple protein model of a four-helix bundle motif on a face-centered cubic lattice has been studied. Total energy of a conformation includes attractive interactions between hydrophobic residues, repulsive interactions between hydrophobic and polar residues, and a potential that favors helical turns. Using replica exchange Monte Carlo simulations we have estimated a set of parameters for which the native structure is a global minimum of conformational energy. Then we have shown that all the above types of interactions are necessary to guarantee the cooperativity of folding transition and to satisfy the thermodynamic hypothesis.

[1]  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.

[2]  M. Karplus,et al.  Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. , 1994, Journal of molecular biology.

[3]  J. Onuchic,et al.  The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. , 2000, Advances in protein chemistry.

[4]  Hue Sun Chan,et al.  History-dependent phenomena in the transverse Ising ferroglass: The free-energy landscape , 2000 .

[5]  M. Karplus,et al.  How does a protein fold? , 1994, Nature.

[6]  D. Thirumalai,et al.  Metastability of the folded states of globular proteins. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[7]  J. Skolnick,et al.  A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state. , 2003, Biophysical journal.

[8]  Harold A. Scheraga,et al.  Statistical Thermodynamics of Protein Folding: Comparison of a Mean-Field Theory with Monte Carlo Simulations , 1994 .

[9]  D. Thirumalai,et al.  Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. , 1996, Journal of molecular biology.

[10]  T. Head-Gordon,et al.  Minimalist models for protein folding and design. , 2003, Current opinion in structural biology.

[11]  J. Onuchic,et al.  Folding kinetics of proteinlike heteropolymers , 1994, cond-mat/9404001.

[12]  J. Sorenson,et al.  Redesigning the hydrophobic core of a model β‐sheet protein: Destabilizing traps through a threading approach , 1999, Proteins.

[13]  D. Thirumalai,et al.  Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. , 1999, Current opinion in structural biology.

[14]  Lorna J. Smith,et al.  Understanding protein folding via free-energy surfaces from theory and experiment. , 2000, Trends in biochemical sciences.

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

[16]  D. Raleigh,et al.  A de Novo Designed Protein Mimics the Native State of Natural Proteins , 1995 .

[17]  J. Skolnick,et al.  Reduced models of proteins and their applications , 2004 .

[18]  W. DeGrado,et al.  Design of a 4-helix bundle protein: synthesis of peptides which self-associate into a helical protein , 1987 .

[19]  H. Chan,et al.  Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling? , 2002, Journal of molecular biology.

[20]  U H Hansmann,et al.  New Monte Carlo algorithms for protein folding. , 1999, Current opinion in structural biology.

[21]  Gerard T. Barkema,et al.  Monte Carlo Methods in Statistical Physics , 1999 .

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

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

[24]  Seishi Shimizu,et al.  Cooperativity principles in protein folding. , 2004, Methods in enzymology.

[25]  J. Skolnick,et al.  Dynamic Monte Carlo study of the folding of a six-stranded Greek key globular protein. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[26]  A Kolinski,et al.  Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. , 1991, Journal of molecular biology.

[27]  A. Kolinski.  Protein modeling and structure prediction with a reduced representation. , 2004, Acta biochimica Polonica.

[28]  M. Hao,et al.  Molecular mechanisms for cooperative folding of proteins. , 1998, Journal of molecular biology.

[29]  M Karplus,et al.  The folding mechanism of larger model proteins: role of native structure. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Andrzej Kloczkowski,et al.  Inferring ideal amino acid interaction forms from statistical protein contact potentials , 2005, Proteins.

[31]  J Skolnick,et al.  Monte Carlo simulation of equilibrium globular protein folding: alpha-helical bundles with long loops. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Teresa Head-Gordon,et al.  Matching simulation and experiment (extended abstract): a new simplified model for simulating protein folding , 2000, RECOMB '00.