Comparison of Transition States Obtained upon Modeling of Unfolding of Immunoglobulin-Binding Domains of Proteins L and G Caused by External Action with Transition States Obtained in the Absence of Force Probed by Experiments

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A. V. Glyakina¹, N. K. Balabaev¹, and O. V. Galzitskaya^2*

¹Institute of Mathematical Problems of Biology, Russian Academy of Sciences, ul. Institutskaya 4, 142290 Pushchino, Moscow Region, Russia

²Institute of Protein Research, Russian Academy of Sciences, ul. Institutskaya 4, 142290 Pushchino, Moscow Region, Russia; fax: (495) 632-7871; E-mail: ogalzit@vega.protres.ru

^* To whom correspondence should be addressed.

Received March 31, 2008; Revision received June 2, 2008

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We have studied the extent of coincidence of the pathway of unfolding of protein globules upon experimental modeling of protein unfolding caused by external actions and denaturants. To this end, we compared experimental Φ-values reported in the literature and Φ-values obtained by us upon modeling of unfolding of immunoglobulin-binding domains of proteins L and G caused by external actions at a constant rate. A comparison of the results of calculation with the experimental data shows that the folding pathways for protein L coincide, while those for protein G do not coincide despite structural similarity of these proteins.

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KEY WORDS: protein structure, molecular dynamics, folding pathway, mechanical unfolding, atom–atomic contacts, folding nucleus, transition state

DOI: 10.1134/S0006297909030110

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