%0 Journal Article %1 ISI:000240851300007 %A Jang, Soonmin %A Sreerama, Narasimha %A Liao, Vivian H. C. %A Lu, S. Hsiu-Feng %A Li, Feng-Yin %A Shin, Seokmin %A Woody, Robert W. %A Lin, Sheng Hsien %C 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA %D 2006 %I COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT %J PROTEIN SCIENCE %K MD PCA RMSD circular dichroism %N 10 %P 2290-2299 %R 10.1110/ps.062145106 %T Theoretical investigation of the photoinitiated folding of HP-36 %V 15 %X A computational model was developed to examine the phototriggered folding of a caged protein, a protein modified with an organic photolabile cross-linker. Molecular dynamics simulations of the modified 36-residue fragment of subdomain B of chicken villin head piece with a photolabile linker were performed, starting from both the caged and the uncaged structures. Construction of a free-energy landscape, based on principal components as well as on radius of gyration versus root-mean-square deviation, and circular dichroism calculations were employed to characterize folding behavior and structures. The folded structures observed in the molecular dynamics trajectories were found to be similar to that of the wild-type protein, in agreement with the published experimental results. The free-energy landscapes of the modified and wild-type proteins have similar topology, suggesting common thermodynamic/kinetic behavior. The existence of small differences in the free-energy surface of the modified protein from that of the native protein, however, indicates subtle differences in the folding behavior.

@article{ISI:000240851300007, abstract = {{A computational model was developed to examine the phototriggered folding of a caged protein, a protein modified with an organic photolabile cross-linker. Molecular dynamics simulations of the modified 36-residue fragment of subdomain B of chicken villin head piece with a photolabile linker were performed, starting from both the caged and the uncaged structures. Construction of a free-energy landscape, based on principal components as well as on radius of gyration versus root-mean-square deviation, and circular dichroism calculations were employed to characterize folding behavior and structures. The folded structures observed in the molecular dynamics trajectories were found to be similar to that of the wild-type protein, in agreement with the published experimental results. The free-energy landscapes of the modified and wild-type proteins have similar topology, suggesting common thermodynamic/kinetic behavior. The existence of small differences in the free-energy surface of the modified protein from that of the native protein, however, indicates subtle differences in the folding behavior.}}, added-at = {2009-01-13T22:46:20.000+0100}, address = {{500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA}}, affiliation = {{Li, FY (Reprint Author), Natl Chung Hsing Univ, Dept Chem, Taichung 402, Taiwan. Natl Chung Hsing Univ, Dept Chem, Taichung 402, Taiwan. Seoul Natl Univ, Sch Chem, Seoul 151747, South Korea. Acad Sinica, Inst Atom \& Mol Sci, Taipei 106, Taiwan. Natl Taiwan Univ, Dept Bioenvironm Syst Engn, Taipei 106, Taiwan. Colorado State Univ, Dept Biochem \& Mol Biol, Ft Collins, CO 80523 USA. Sejong Univ, Dept Appl Chem, Seoul 143747, South Korea.}}, author = {Jang, Soonmin and Sreerama, Narasimha and Liao, Vivian H. C. and Lu, S. Hsiu-Feng and Li, Feng-Yin and Shin, Seokmin and Woody, Robert W. and Lin, Sheng Hsien}, author-email = {{feng64@nchu.edu.tw Robert.Woody@colostate.edu}}, biburl = {https://www.bibsonomy.org/bibtex/23c44330e3d9a9bd65f3132be1ee9a8ec/huiyangsfsu}, cited-references = {{AMADEI A, 1993, PROTEINS, V17, P412. BAUMKETNER A, 2003, PHYS REV E 1, V68, ARTN 051901. BAYLEY PM, 1969, J PHYS CHEM-US, V73, P228. BERENDSEN HJC, 1984, J CHEM PHYS, V81, P3684. BLAUER G, 1993, BIOCHEMISTRY-US, V32, P6674. BODE KA, 1998, J AM CHEM SOC, V120, P10938. BRETSCHER A, 1979, P NATL ACAD SCI USA, V76, P2321. BROCKWELL DJ, 2000, CURR OPIN STRUC BIOL, V10, P16. BURSULAYA BD, 1999, J AM CHEM SOC, V121, P9947. CHIU TK, 2005, P NATL ACAD SCI USA, V102, P7517, DOI 10.1073/pnas.0502495102. CLARK LB, 1995, J AM CHEM SOC, V117, P2375. DEMORI GMS, 2004, J PHYS CHEM B, V108, P12267, DOI 10.1021/jp0477699. DUAN Y, 1998, P NATL ACAD SCI USA, V95, P9897. DUAN Y, 1998, SCIENCE, V282, P740. 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ZHU Y, 2003, P NATL ACAD SCI USA, V100, P15486, DOI 10.1073/pnas.2136623100.}}, doc-delivery-number = {{089AD}}, doi = {{10.1110/ps.062145106}}, interhash = {1807d5a22c974dcd5364fbd76d9b0c4a}, intrahash = {3c44330e3d9a9bd65f3132be1ee9a8ec}, issn = {{0961-8368}}, journal = {{PROTEIN SCIENCE}}, journal-iso = {{Protein Sci.}}, keywords = {MD PCA RMSD circular dichroism}, keywords-plus = {{VILLIN HEADPIECE SUBDOMAIN; MOLECULAR-DYNAMICS SIMULATIONS; PROTEIN CIRCULAR-DICHROISM; CHARGE-TRANSFER TRANSITIONS; 3-HELIX BUNDLE PROTEIN; FREE-ENERGY SURFACE; SECONDARY STRUCTURE; BETA-HAIRPIN; ELECTRONIC SPECTROSCOPY; STRUCTURE PREDICTION}}, language = {{English}}, month = {{OCT}}, note = {Soonmin Jang, Narasimha Sreerama, Vivian H.-C. Liao, S. Hsiu-Feng Lu, Feng-Yin Li, Seokmin Shin, Robert W. Woody, and Sheng Hsien Lin Theoretical investigation of the photoinitiated folding of HP-36 Protein Sci 2006 15: 2290-2299. Published in Advance September 8, 2006, 10.1110/ps.062145106}, number = {{10}}, number-of-cited-references = {{81}}, pages = {{2290-2299}}, publisher = {{COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT}}, subject-category = {{Biochemistry \& Molecular Biology}}, times-cited = {{1}}, timestamp = {2009-01-13T22:46:21.000+0100}, title = {{Theoretical investigation of the photoinitiated folding of HP-36}}, type = {{Article}}, unique-id = {{ISI:000240851300007}}, volume = {{15}}, year = {{2006}} }