%0 Journal Article %1 ISI:000252450100043 %A Suzuki, Yoko %A Noel, Jeff K. %A Onuchic, Jose N. %C CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA %D 2008 %I AMER INST PHYSICS %J JOURNAL OF CHEMICAL PHYSICS %K and effects engergetic geometric %N 2 %R 10.1063/1.2812956 %T An analytical study of the interplay between geometrical and energetic effects in protein folding %V 128 %X Analytical studies have several advantages for an understanding of the mechanisms of protein folding such as the interplay between geometrical and energetic effects. In this paper, we introduce a Gaussian filament with a C-alpha structure-based (G (o) over bar) potential as a new theoretical scheme based on a Hamiltonian approach. This model takes into account geometrical information in a realistic fashion without the need of phenomenological descriptions. In order to make this model more appropriate for comparison with protein folding simulations and experiments, we introduce a many-body interaction into the potential term to enhance cooperativity. We apply our new analytical model to a beta-hairpin-type peptide and compare our results with a molecular dynamics simulation of a structure-based model. (c) 2008 American Institute of Physics.

@article{ISI:000252450100043, abstract = {{Analytical studies have several advantages for an understanding of the mechanisms of protein folding such as the interplay between geometrical and energetic effects. In this paper, we introduce a Gaussian filament with a C-alpha structure-based (G (o) over bar) potential as a new theoretical scheme based on a Hamiltonian approach. This model takes into account geometrical information in a realistic fashion without the need of phenomenological descriptions. In order to make this model more appropriate for comparison with protein folding simulations and experiments, we introduce a many-body interaction into the potential term to enhance cooperativity. We apply our new analytical model to a beta-hairpin-type peptide and compare our results with a molecular dynamics simulation of a structure-based model. (c) 2008 American Institute of Physics.}}, added-at = {2009-01-10T06:43:01.000+0100}, address = {{CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}}, affiliation = {{Onuchic, JN (Reprint Author), Univ Calif San Diego, Ctr Theoret Biol Phys, La Jolla, CA 92093 USA. {[}Noel, Jeff K.; Onuchic, Jose N.] Univ Calif San Diego, Ctr Theoret Biol Phys, La Jolla, CA 92093 USA. {[}Suzuki, Yoko] Meisei Univ, Sch Sci \& Engn, Dept Phys, Tokyo 1918506, Japan.}}, article-number = {{025101}}, author = {Suzuki, Yoko and Noel, Jeff K. and Onuchic, Jose N.}, author-email = {{youko@phys.meisei-u.ac.jp jonuchic@ucsd.edu}}, biburl = {https://www.bibsonomy.org/bibtex/200e19ec289d83eb9f8db5372a5886377/huiyangsfsu}, cited-references = {{BOCZKO EM, 1995, SCIENCE, V269, P393. BRYNGELSON JD, 1987, P NATL ACAD SCI USA, V84, P7524. BRYNGELSON JD, 1989, J PHYS CHEM-US, V93, P6902. CLEMENTI C, 2000, J MOL BIOL, V298, P937. 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Phys.}}, keywords = {and effects engergetic geometric}, keywords-plus = {{ASSOCIATIVE MEMORY HAMILTONIANS; TERTIARY STRUCTURE RECOGNITION; TRANSITION-STATE ENSEMBLE; STATISTICAL-MECHANICS; LANDSCAPE THEORY; RANDOM HETEROPOLYMERS; STRUCTURE PREDICTION; COMPUTER-SIMULATION; GLASS TRANSITIONS; ATOMIC-RESOLUTION}}, language = {{English}}, month = {{JAN 14}}, number = {{2}}, number-of-cited-references = {{55}}, publisher = {{AMER INST PHYSICS}}, subject-category = {{Physics, Atomic, Molecular \& Chemical}}, times-cited = {{0}}, timestamp = {2009-01-10T06:43:01.000+0100}, title = {{An analytical study of the interplay between geometrical and energetic effects in protein folding}}, type = {{Article}}, unique-id = {{ISI:000252450100043}}, volume = {{128}}, year = {{2008}} }