Monte Carlo simulations of protein-like heteropolymers

• Autorzy: Sikorski A. , Romiszowski P.
• Języki publikacji: EN

Abstrakty

EN

Properties of a simple model of polypeptide chains were studied by the means of the Monte Carlo method. The chains were built on the (310) hybrid lattice. The residues inter­acted with long-range potential. There were two kinds of residues: hydrophobic and hy- drophilic forming a typical helical pattern -HHPPHPP-. Short range potential was used to prefer helical conformations of the chain. It was found that at low temperatures the model chain formes dense and partially ordered structures (non-unique). The presence of the lo­cal potential led to an increase of helicity. The effect of the interplay between the two po­tentials was studied. After the collapse of the chain further annealing caused rearrange­ment of helical structures. Dynamic properties of the chain at low temperature depended strongly on the local chain ordering.

Słowa kluczowe

EN

lattice model; protein folding; protein-like heteropolymer; polypeptide chain; protein structure; Monte Carlo method; protein dynamics

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2001
• Tom: 48
• Numer: 1
• Opis fizyczny: p.77-81,fig.

Twórcy

autor

Sikorski A.

• University of Warsaw, L.Pasteura 1, 02-093 Warsaw, Poland

autor

Romiszowski P.

Bibliografia

• 1.Anfinsen, C.B. (1973) Principles that govern the folding of protein chains. Science 181, 223-230.
• 2.Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Yee, D.P., Thomas, P.D. & Chan, H.S. (1995) Principles of protein folding A perspective from simple exact models. Protein Sci. 4, 561-602.
• 3.Sikorski, A. & Skolnick, J. (1989) Monte Carlo studies on equilibrium globular protein folding. III. The four helix bundle. Biopolymers 28, 1097-1113.
• 4.Sikorski, A. & Skolnick, J. (1989) Monte Carlo simulation of equilibrium globular folding. alpha-Helical bundles with long loops. Proc. Natl. Acad. Sci. U.S.A. 86, 2668-2672.
• 5.Sikorski, A. & Skolnick, J. (1990) Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. II. alpha-Helical motifs. J. Mol. Biol. 212, 819-836.
• 6.Kolinski, A. & Madziar, P. (1997) Collapse transition in protein-like lattice polymers: The effect of sequence patterns. Biopolymers 42, 537-548.
• 7.Romiszowski, P. & Sikorski, A. (1999) A Monte Carlo study of properties of protein-like heteropolymers. Physica A. 273, 190-197.
• 8.Romiszowski, P. & Sikorski, A. (2000) The influence of sequence patterns and local conformational preferences on the structure of collapsed polypeptide. Biopolymers 54, 262-272.
• 9.Kolinski, A. & Skolnick, J. (1993) Monte Carlo simulation of protein folding. I. Lattice model and interaction scheme. Proteins 18, 338-352.
• 10.Kolinski, A. & Skolnick, J. (1997) High coordination lattice models of protein structure, dynamics and thermodynamics. Acta Biochim. Polon. 44, 389-422.
• 11.Nishikawa, K., Momany, F.A. & Scheraga, H.A. (1974) Low-energy structures of two dipeptides and their relation to bend conformations. Macromolecules 7, 797-805.
• 12.Kolinski, A., Milik, M., Rycombel, J. & Skolnick, J. (1995) A reduced model of short range interactions in polypeptide chain. J. Chem. Phys. 103, 4312- 4323.