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Protein Folding with a Reduced Model and Inaccurate Short‐Range Restraints
Author(s) -
Plewczynska Dorota,
Kolinski Andrzej
Publication year - 2005
Publication title -
macromolecular theory and simulations
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.37
H-Index - 56
eISSN - 1521-3919
pISSN - 1022-1344
DOI - 10.1002/mats.200500020
Subject(s) - dihedral angle , force field (fiction) , monte carlo method , replica , protein folding , statistical physics , protein secondary structure , lattice protein , torsion (gastropod) , molecular dynamics , protein data bank , folding (dsp implementation) , protein structure , biological system , algorithm , chemistry , physics , computer science , computational chemistry , mathematics , molecule , nuclear magnetic resonance , engineering , statistics , biology , structural engineering , art , hydrogen bond , visual arts , organic chemistry , quantum mechanics , zoology
Summary: A reduced high‐coordination lattice protein model and the Replica Exchange Monte Carlo sampling were employed in de novo folding simulations of a set of representative small proteins. Three distinct situations were analyzed. In the first series of simulations, the folding was controlled purely by the generic force field of the model. In the second, a bias was introduced towards the theoretically predicted secondary structure. Finally, we superimposed soft restraints towards the native‐like local conformation of the backbone. The short‐range restraints used in these simulations are based on approximate values of ϕ and ψ dihedral angles, which may simulate restraints derived from inaccurate experimental measurements. Incorporating such data into the reduced model required developing a procedure, which transforms the ϕ and ψ coordinates into coordinates of the protein alpha carbon trace. It has been shown that such limited data are sufficient for de novo determination of three‐dimensional structures of small and topologically not too complex proteins.Protein folding based on secondary structure prediction and simulated torsion angles data.