%0 Journal Article %1 ISI:000225951500018 %A Ota, M %A Ikeguchi, M %A Kidera, A %C 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA %D 2004 %I NATL ACAD SCIENCES %J PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA %K dynamic pathway programming %N 51 %P 17658-17663 %R 10.1073/pnas.0407015102 %T Phylogeny of protein-folding trajectories reveals a unique pathway to native structure %V 101 %X To scrutinize how a protein folds at atomic resolution, we performed 200 molecular dynamics simulations (each of 50 ns) of the miniprotein Trp-cage on the computational grid. Within the trajectories, 58 folding and 31 unfolding events were identified and subjected to extensive comparison and classification. Based on an analogy with biological sequences, the folding and unfolding trajectories (arrays of sequential snapshots of structures) were aligned by dynamic programming allowing gaps. A phylogenetic tree derived from the alignments revealed four distinct groups of the trajectories, characterized by the Trp side-chain motions and the main-chain motions. It was found that only one group attained the native structure and that the other three led to pseudonative structures having the correct main-chain trace but different nonnative Trp side-chain rotamers, indicating that those four folded structures were each attained through a unique folding pathway.

@article{ISI:000225951500018, abstract = {{To scrutinize how a protein folds at atomic resolution, we performed 200 molecular dynamics simulations (each of 50 ns) of the miniprotein Trp-cage on the computational grid. Within the trajectories, 58 folding and 31 unfolding events were identified and subjected to extensive comparison and classification. Based on an analogy with biological sequences, the folding and unfolding trajectories (arrays of sequential snapshots of structures) were aligned by dynamic programming allowing gaps. A phylogenetic tree derived from the alignments revealed four distinct groups of the trajectories, characterized by the Trp side-chain motions and the main-chain motions. It was found that only one group attained the native structure and that the other three led to pseudonative structures having the correct main-chain trace but different nonnative Trp side-chain rotamers, indicating that those four folded structures were each attained through a unique folding pathway.}}, added-at = {2009-01-14T03:20:57.000+0100}, address = {{2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA}}, affiliation = {{Ota, M (Reprint Author), Tokyo Inst Technol, Global Sci Informat \& Comp Ctr, Meguro Ku, Tokyo 1528550, Japan. Tokyo Inst Technol, Global Sci Informat \& Comp Ctr, Meguro Ku, Tokyo 1528550, Japan. Yokohama City Univ, Grad Sch Integrated Sci, Yokohama, Kanagawa 2300045, Japan.}}, author = {Ota, M and Ikeguchi, M and Kidera, A}, author-email = {{mota@gsic.titech.ac.jp}}, biburl = {https://www.bibsonomy.org/bibtex/2b2f727babfc320e8dbcb60b3a608bf9c/huiyangsfsu}, cited-references = {{BALDWIN RL, 1995, J BIOMOL NMR, V5, P103. BROOKS CL, 2002, ACCOUNTS CHEM RES, V35, P447. CHAN CK, 1997, P NATL ACAD SCI USA, V94, P1779. CHOWDHURY S, 2003, J MOL BIOL, V327, P711, DOI 10.1016/S0022-2836(03)00177-3. DEGROOT BL, 2001, J MOL BIOL, V309, P299. DILL KA, 1995, PROTEIN SCI, V4, P561. DUAN Y, 1998, SCIENCE, V282, P740. DUNBRACK RL, 1993, J MOL BIOL, V230, P543. ENGLANDER SW, 2000, ANNU REV BIOPH BIOM, V29, P213. FERSHT AR, 1995, CURR OPIN STRUC BIOL, V5, P79. FERSHT AR, 2002, CELL, V108, P573. FOSTER I, 2004, GRID 2 BLUEPRINT NEW. GNANAKARAN S, 2003, CURR OPIN STRUC BIOL, V13, P168, DOI 10.1016/S0959-440X(03)00040-X. GOTOH O, 1982, J MOL BIOL, V162, P705. HENIKOFF S, 1991, NUCLEIC ACIDS RES, V19, P6565. KAMIYA N, 2002, PROTEIN SCI, V11, P2297, DOI 10.1110/ps.0213102. KARPLUS M, 2002, NAT STRUCT BIOL, V9, P646. KOIKE R, 2003, FEBS LETT, V533, P9. KUWAJIMA K, 1996, J MOL BIOL, V264, P806. LEVINTHAL C, 1968, J CHIM PHYS PCB, V65, P44. LITZKOW M, 1988, P 8 INT C DISTR COMP. NEEDLEMAN SB, 1970, J MOL BIOL, V48, P443. NEIDIGH JW, 2002, NAT STRUCT BIOL, V9, P425. NOLTING B, 1999, PROTEIN FOLDING KINE. PAIN RH, 2000, MECH PROTEIN FOLDING. PARK SH, 1999, NAT STRUCT BIOL, V6, P943. PITERA JW, 2003, P NATL ACAD SCI USA, V100, P7587, DOI 10.1073/pnas.1330954100. QIU LL, 2002, J AM CHEM SOC, V124, P12952, DOI 10.1021/ja0279141. RIPOLL DR, 2004, J MOL BIOL, V339, P915, DOI 10.1016/j.jmb.2004.04.002. SAITOU N, 1987, MOL BIOL EVOL, V4, P406. SIMMERLING C, 2002, J AM CHEM SOC, V124, P11258, DOI 10.1021/ja0273851. SNOW CD, 2002, J AM CHEM SOC, V124, P14548, DOI 10.1021/ja0286041. SNOW CD, 2002, NATURE, V420, P102, DOI 10.1038/nature01160. TSUI V, 2000, BIOPOLYMERS, V56, P275. UZAWA T, 2004, P NATL ACAD SCI USA, V101, P1171, DOI 10.1073/pnas.0305376101. VILA JA, 2003, P NATL ACAD SCI USA, V100, P14812, DOI 10.1073/pnas.2436463100. WANG JM, 2000, J COMPUT CHEM, V21, P1049. WOLYNES PG, 1995, SCIENCE, V267, P1619. ZAGROVIC B, 2003, J COMPUT CHEM, V24, P1432, DOI 10.1002/jcc.10297. ZHOU RH, 2003, P NATL ACAD SCI USA, V100, P13280, DOI 10.1073/pnas.2233312100.}}, doc-delivery-number = {{882PT}}, doi = {{10.1073/pnas.0407015102}}, interhash = {bfc1b9b7d61acdf74dd7680dbcf70129}, intrahash = {b2f727babfc320e8dbcb60b3a608bf9c}, issn = {{0027-8424}}, journal = {{PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}}, journal-iso = {{Proc. Natl. Acad. Sci. U. S. A.}}, keywords = {dynamic pathway programming}, keywords-plus = {{MOLECULAR-DYNAMICS SIMULATIONS; TRP-CAGE; TRANSITION-STATES; EXPLICIT WATER; PEPTIDE; INTERMEDIATE; PREDICTION; RESOLUTION; KINETICS; EXCHANGE}}, language = {{English}}, month = {{DEC 21}}, number = {{51}}, number-of-cited-references = {{40}}, pages = {{17658-17663}}, publisher = {{NATL ACAD SCIENCES}}, subject-category = {{Multidisciplinary Sciences}}, times-cited = {{21}}, timestamp = {2009-01-14T03:20:57.000+0100}, title = {{Phylogeny of protein-folding trajectories reveals a unique pathway to native structure}}, type = {{Article}}, unique-id = {{ISI:000225951500018}}, volume = {{101}}, year = {{2004}} }