Conformational transitions of bio-molecular systems studied using adaptive bond bending elastic network model

摘要

Conformational transitions in proteins are essential for biological functions. Such transitions involve short-lived conformational states that are difficult to detect experimentally. Motivated by the utility and efficiency of elastic network models for describing the collective dynamics of proteins, in this study we present a new adaptive bond bending elastic network model for studying the conformational transition pathway of adenylate kinase and leucine transporter. Assuming that all the native contacts within these proteins are identical, we assigned a bond binding energy to the native contacts and computed the free energy of each image along the transition pathway. After plotting the free energy profiles, we found a few metastable intermediate states, separated by the free energy barriers. The observed intermediate states and the transition pathways for all proteins were in good agreement with those of the other methods and molecular dynamics simulations. Published under license by AIP Publishing.