2007/03/24 by F. Marty Ytreberg, Svetlana Aroutiounian, Ytreberg, F. Marty +4
Biochemistry, Genetics and Molecular Biology · Materials Science · Physics and Astronomy · #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #Computational Physics (physics.comp-ph) #Enzyme Structure and Function #FOS: Biological sciences #FOS: Physical sciences #Protein Structure and Dynamics #Protein purification and stability #physics.bio-ph #physics.comp-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.physics/0703222
7 pages, 3 figures
arxiv created 2007/03/24 · openalex publication_date 2007/03/24 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can accelerate canonical all-atom sampling, but require properly distributed coarse ensembles. We therefore demonstrate that full sampling can indeed be achieved in a sufficiently simplified protein model, as verified by a recently developed convergence analysis. The model accounts for protein backbone geometry in that rigid peptide planes rotate according to atomistically defined dihedral angles, but there are only two degrees of freedom (phi and psi dihedrals) per residue. Our convergence analysis indicates that small proteins (up to 89 residues in our tests) can be simulated for more than 50 "structural decorrelation times" in less than a week on a single processor. We show that the fluctuation behavior is reasonable, as well as discussing applications, limitations, and extensions of the model.