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Published online before print September 8, 2006
Protein Science, DOI: 10.1110/ps.062145106
 Copyright © 2006 The Protein Society
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Theoretical investigation of the photoinitiated folding of HP-36

Soonmin Jang1, Narasimha Sreerama2, Vivian H.-C. Liao3, S. Hsiu-Feng Lu4, Feng-Yin Li5, Seokmin Shin1, Robert W. Woody2 and Sheng Hsien Lin4

1 School of Chemistry, Seoul National University, Seoul 151-747, Korea
2 Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
3 Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 106, Taiwan, Republic of China
4 Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei and 106, Taiwan, Republic of China
5 Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan, Republic of China

(RECEIVED February 9, 2006; FINAL REVISION June 22, 2006; ACCEPTED June 24, 2006)

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.

Keywords: protein structure/folding; computational analysis of protein structure; phototriggering; uncaged protein; circular dichroism

Reprint requests to: Feng-Yin Li, Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan, Republic of China; e-mail: feng64{at}nchu.edu.tw; fax: 886-4-22862547; or Robert W. Woody, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; e-mail: rww{at}lamar.colostate.edu; fax: 1-970-4910494.

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.062145106.


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