FisMat2017 - Submission - View

Abstract's title: Is Funneled Landscape of Proteins really explicitly sequence-dependent?
Submitting author: Tatjana Skrbic
Affiliation: Universita' Ca' Foscari Venezia
Affiliation Address: Dipartimento di Scienze Molecolari e Nanosistemi, Universita` Ca’ Foscari di Venezia, Campus Scientifico, Edificio Alfa, Via Torino 155, 30170 Venezia Mestre, Italy
Country: Italy
Oral presentation/Poster (Author's request): Oral presentation
Other authors and affiliations: Achille Giacometti (Dipartimento di Scienze Molecolari e Nanosistemi, Universita` Ca’ Foscari di Venezia Campus Scientifico, Edificio Alfa, Via Torino 155,30170 Venezia Mestre, Italy), Trinh X. Hoang (Center for Computational Physics, Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi, Vietnam), Jayanth R. Banavar (Department of Physics, University of Maryland, College Park, Maryland 20742, USA), Amos Maritan (Dipartimento di Fisica, Universita` di Padova, via Marzolo 8, I-35131 Padova, Italy; CNISM, Unita` di Padova, Via Marzolo 8, I-35131 Padova, Italy; and Sezione INFN, Universita` di Padova, I-35131 Padova, Italy)
Abstract

Using two independent Monte Carlo simulation methods, we analize the (zero temperature) ground state of a simple physical model for a protein with a two beads representation for each amino acid. One bead is centered at the Cα atom representing the backbone and one representing the side chain, both considered as hard spheres. Consecutive backbone beads are, however, allowed for a partial interpenetration to account for the fact that the Cα-Cα′ distance in real proteins is usually smaller than the diameter of the van der Waals sphere associated with each backbone amino acid. In addition to excluded volumes, each backbone bead interact with other non-consecutive beads along the chain, mimicking the non-specific hydrophobic interactions promoting the folding of the protein. A detailed study of the resulting phase diagram displays a very rich polymorphism, including morphology of all prototypical 4 classes of native states in real proteins: all-α, all-β, α + β and α/β. Remarkably, the last two are included in a relatively small coexistence region that connect the first two and the collapsed phase. Comparison of the obtained topologies within this region with the native states of real proteins shows a that in all cases the expected topology is correctly reproduced, with root-mean-square deviations from the corresponding native states are always within 8 A, when the atomistic details are re-insterted, with no additional time evolution. The results of the present study shed new lights on the energy landscape theory, where non-specific interactions are forming the secondary structures at the early stage of the folding process, followed by specific sequence-depedent interactions driving the final folding to the native state.