%0 Journal Article %1 ISI:000236946200014 %A Imamura, H %A Chen, JZY %C DIV JOHN WILEY & SONS INC, 111 RIVER ST, HOBOKEN, NJ 07030 USA %D 2006 %I WILEY-LISS %J PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS %K beta hairpin in middle out reptation zipping %N 3 %P 555-570 %R 10.1002/prot.20846 %T Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in beta-hairpins %V 63 %X We study the dependence of folding time, nucleation site, and stability of a model beta-hairpin on the location of a cross-strand hydrophobic pair, using a coarse-grained off-lattice model with the aid of Monte Carlo simulations. Our simulations have produced 6500 independent folding trajectories dynamically, forming the basis for extensive statistical analysis. Four folding pathways, zipping-out, middle-out, zipping-in, and reptation, have been closely monitored and discussed in all seven sequences studied. A hydrophobic pair placed near the beta-turn or in the middle section effectively speed up folding; a hydrophobic pair placed close to the terminal ends or next to the beta-turn encourages stability of the entire chain.

@article{ISI:000236946200014, abstract = {{We study the dependence of folding time, nucleation site, and stability of a model beta-hairpin on the location of a cross-strand hydrophobic pair, using a coarse-grained off-lattice model with the aid of Monte Carlo simulations. Our simulations have produced 6500 independent folding trajectories dynamically, forming the basis for extensive statistical analysis. Four folding pathways, zipping-out, middle-out, zipping-in, and reptation, have been closely monitored and discussed in all seven sequences studied. A hydrophobic pair placed near the beta-turn or in the middle section effectively speed up folding; a hydrophobic pair placed close to the terminal ends or next to the beta-turn encourages stability of the entire chain.}}, added-at = {2009-01-13T22:49:17.000+0100}, address = {{DIV JOHN WILEY \& SONS INC, 111 RIVER ST, HOBOKEN, NJ 07030 USA}}, affiliation = {{Chen, JZY (Reprint Author), Univ Waterloo, Dept Phys, Waterloo, ON N2L 3G1, Canada. Univ Waterloo, Dept Phys, Waterloo, ON N2L 3G1, Canada. Fudan Univ, Dept Macromol Sci, Key Lab Mol Engn Polymers, Shanghai, Peoples R China.}}, author = {Imamura, H and Chen, JZY}, author-email = {{jeffchen@uwaterloo.ca}}, biburl = {https://www.bibsonomy.org/bibtex/27fd8011956d5ce686d909cee443e69c0/huiyangsfsu}, cited-references = {{AURORA R, 1997, J BIOL CHEM, V272, P1413. AWASTHI SK, 2001, BIOPOLYMERS, V58, P465. BARKEMA GT, 1998, PHYS REV LETT, V81, P1865. BINDER K, 1988, MONTE CARLO SIMULATI, P127. BINDER K, 1997, REP PROG PHYS, V60, P487. 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ZHOU YQ, 2002, PROTEINS, V47, P154.}}, doc-delivery-number = {{034QR}}, doi = {{10.1002/prot.20846}}, interhash = {03a7c05678ee7ff126811a9001d69a9e}, intrahash = {7fd8011956d5ce686d909cee443e69c0}, issn = {{0887-3585}}, journal = {{PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}}, journal-iso = {{Proteins}}, keywords = {beta hairpin in middle out reptation zipping}, keywords-plus = {{ACTIVATION-RELAXATION TECHNIQUE; MONTE-CARLO SIMULATIONS; FREE-ENERGY LANDSCAPE; MOLECULAR-DYNAMICS; PROTEIN-G; WEAK-INTERACTIONS; DESIGNED PEPTIDE; SHEET STRUCTURES; SOLVENT MODEL; MINIMAL MODEL}}, language = {{English}}, month = {{MAY 15}}, number = {{3}}, number-of-cited-references = {{86}}, pages = {{555-570}}, publisher = {{WILEY-LISS}}, subject-category = {{Biochemistry \& Molecular Biology; Biophysics}}, times-cited = {{10}}, timestamp = {2009-01-13T22:49:17.000+0100}, title = {{Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in beta-hairpins}}, type = {{Article}}, unique-id = {{ISI:000236946200014}}, volume = {{63}}, year = {{2006}} }