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Theoretical investigation of the photoinitiated folding of HP-36

¹ Department of Applied Chemistry, Sejong University, Seoul 143-747, 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 106, Taiwan, Republic of China
⁵ Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan, Republic of China
⁶ School of Chemistry, Seoul National University, Seoul 151-747, Korea

(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

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