%0 Journal Article %J Journal of Chemical Physics %D 1992 %T Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides %A Andrzej Koliński %A Jeffrey Skolnick %K Conformational Changes %K Coupling %K Globular Clusters %K Lattice Gas %K Molecular Models %K Monte Carlo Method %K Polypeptides %K Proteins %K Randomness %K Resolution %X A discretized model of globular proteins is employed in a Monte Carlo study of the helix–coil transition of polyalanine and the collapse transition of polyvaline. The present lattice realization permits real protein crystal structures to be represented at the level of 1 Å resolution. Furthermore, the Monte Carlo dynamic scheme is capable of moving elements of assembled secondary and supersecondary structure. The potentials of mean force for the interactions are constructed from the statistics of a set of high resolution x‐ray structures of nonhomologous proteins. The cooperativity of formation of ordered structures is found to be larger when the major contributions to the conformational energy of the low temperature states come from hydrogen bonds and short range conformational propensities. The secondary structure seen in the folded state is the result of an interplay between the short and long range interactions. Compactness itself, driven by long range, nonspecific interactions, seems to be insufficient to generate any appreciable secondary structure. A detailed examination of the dynamics of highly helical model proteins demonstrates that all elements of secondary structure are mobile in the present algorithm, and thus the folding pathways do not depend on the use of a lattice approximation. Possible applications of the present model to the prediction of protein 3D structures are briefly discussed. %B Journal of Chemical Physics %V 97 %P 9412–9426 %G eng %U http://link.aip.org/link/doi/10.1063/1.463317 %R 10.1063/1.463317 %0 Journal Article %J The Journal of Chemical Physics %D 1991 %T Static and dynamic properties of a new lattice model of polypeptide chains %A Andrzej Koliński %A Mariusz Milik %A Jeffrey Skolnick %K Alanines %K Chains %K Glycine %K Lattice Dynamics %K Polypeptides %K Proteins %K Relaxation Time %K Self−Diffusion %X The equilibrium and dynamic properties of a new lattice model of proteins are explored in the athermal limit. In this model, consecutive α‐carbons of the model polypeptide are connected by vectors of the type (±2,±1,0). In all cases, the chains have a finite backbone thickness which is close to that present in real proteins. Three different polypeptides are examined: polyglycine, polyalanine, and polyleucine. In the latter two cases, the side chains (whose conformations are extracted from known protein crystal structures) are included. For the equilibrium chain dimensions, with increasing side chain bulkiness, the effective chain length is smaller. The calculations suggest that these model polypeptides are in the same universality class as other polymer models. One surprising result is that although polyalanine and polyleucine have chiral sidechains, they do not induce a corresponding handedness of the main chain. For both polyleucine and polyalanine, the scaling of the self‐diffusion constant and the terminal relaxation time are consistent with Rouse dynamics of excluded volume chains. Polyglycine exhibits a slightly stronger chain length dependence for these properties. This results from a finite length effect due to moderately long lived, local self‐entanglements arising from the thin effective cross section of the chain backbone. %B The Journal of Chemical Physics %V 94 %P 3978 %G eng %U http://link.aip.org/link/JCPSA6/v94/i5/p3978/s1&Agg=doi %R 10.1063/1.460675