Helix–coil transitions in a simple polypeptide model

A simplified model of a polypeptide chain is described. Each residue is represented by a single interaction center. The energy of the chain and the force acting on each residue are given as a function of the residue coordinates. Terms to approximate the effect of solvent and the stabilization energy of helix formation are included. The model is used to study equilibrium and dynamical aspects of the helix–coil transition. The equilibrium properties examined include helix–coil equilibrium constants and their dependence on chain position. Dynamical properties are examined by a stochastic simulation of the Brownian motion of the chain in its solvent surroundings. Correlations in the motions of the residues are found to have an important influence on the helix–coil transition rates.

[1]  J. Andrew McCammon,et al.  Diffusive langevin dynamics of model alkanes , 1979 .

[2]  E. Helfand,et al.  Brownian Dynamics Study of Polymer Conformational Transitions , 1979 .

[3]  C. Tanford,et al.  The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. , 1971, The Journal of biological chemistry.

[4]  M. Levitt.  A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.

[5]  J. Hermans.  Experimental free energy and enthalpy of formation of the alpha-helix. , 1966, The Journal of physical chemistry.

[6]  H. Scheraga,et al.  Helix-Coil Stability for the Naturally Occurring Amino Acids in Water. VIII. Valine Parameters from Random Poly(hydroxypropylglutamine-co-L-valine) and Poly(hydroxybutylglutamine-co-L-valine) , 1973 .

[7]  W. Jencks,et al.  Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[8]  J. H. Weiner,et al.  Brownian dynamics study of a polymer chain of linked rigid bodies. II. Results for longer chains , 1980 .

[9]  H. Kramers.  Brownian motion in a field of force and the diffusion model of chemical reactions , 1940 .

[10]  R. Zana.  On the rate‐determining step for helix propagation in the helix–coil transition of polypeptides in solution , 1975 .

[11]  H. Ushio,et al.  Kinetic studies of the helix–coil transition in aqueous solutions of poly(L‐lysine) , 1979 .

[12]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

[13]  G. Schwarz,et al.  Cooperative conformational transitions of linear biopolymers. , 1970, Angewandte Chemie.

[14]  M. Karplus,et al.  Protein-folding dynamics , 1976, Nature.

[15]  S. Swaminathan,et al.  Monte Carlo computer simulation of hydrophobic bonding , 1979 .

[16]  M. Levitt,et al.  Computer simulation of protein folding , 1975, Nature.

[17]  H. C. Andersen,et al.  Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids , 1971 .

[18]  Ian J. Tickle,et al.  X-ray analysis of glucagon and its relationship to receptor binding , 1975, Nature.

[19]  Bruce J. Berne,et al.  A Monte Carlo simulation of the hydrophobic interaction , 1979 .

[20]  J. Engel,et al.  Kinetic studies on the helix-coil transition of fluorescent labeled poly(-L-lysine) by the temperature-jump technique. , 1979, Biophysical chemistry.

[21]  T. Sano,et al.  Kinetic studies of the helix-coil transition in aqueous solutions of poly(alpha-L-glutamic acid) using the electric field pulse method. , 1976, Journal of the American Chemical Society.

[22]  J. Mccammon,et al.  Efficient trajectory simulation methods for diffusional barrier crossing processes , 1980 .

[23]  S. Lifson,et al.  Neighbor Interactions and Internal Rotations in Polymer Molecules. IV. Solvent Effect on Internal Rotations , 1960 .

[24]  M. Volkenstein,et al.  Statistical mechanics of chain molecules , 1969 .

[25]  Frederic M. Richards,et al.  Packing of α-helices: Geometrical constraints and contact areas☆ , 1978 .

[26]  C Boesch,et al.  1H nuclear-magnetic-resonance studies of the molecular conformation of monomeric glucagon in aqueous solution. , 1978, European journal of biochemistry.

[27]  T. Creighton,et al.  Experimental studies of protein folding and unfolding. , 1978, Progress in biophysics and molecular biology.

[28]  L. Pauling,et al.  The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. , 1951, Proceedings of the National Academy of Sciences of the United States of America.

[29]  D. Ermak,et al.  Brownian dynamics with hydrodynamic interactions , 1978 .

[30]  G. Schwarz,et al.  Kinetics of cooperative conformational transitions of lineal biopolymers. , 1972, Angewandte Chemie.

[31]  J. Hermans,et al.  Calorimetric heat of the helix-coil transition of poly-L-glutamic acid. , 1966, Journal of the American Chemical Society.

[32]  V. Lim.  Polypeptide chain folding through a highly helical intermediate as a general principle of globular protein structure formation , 1978, FEBS letters.

[33]  M. Fixman,et al.  Simulation of polymer dynamics. I. General theory , 1978 .

[34]  S. Rackovsky,et al.  Influence of ordered backbone structure on protein folding. A study of some simple models. , 1978, Macromolecules.

[35]  G. Schwarz,et al.  Kinetics of the helix-coil transition of a polypeptide with non-ionic side groups, derived from ultrasonic relaxation measurements. , 1979, Biophysical chemistry.

[36]  J. Hynes,et al.  Reactive dynamics for diffusive barrier crossing , 1978 .

[37]  H. Fujita,et al.  Statistical Thermodynamic Analysis of Helix-Coil Transitions in Polypeptides , 1976 .

[38]  G. T. Evans,et al.  Liquid state rotational dynamics of nonrigid molecules. III. Four, five, and six bond chains , 1979 .

[39]  M. Fixman.  Simulation of polymer dynamics. II. Relaxation rates and dynamic viscosity , 1978 .

[40]  D. Chandler,et al.  Theory of the hydrophobic effect , 1977 .