Downhill Binding Energy Surface of the Barnase-Barstar Complex

作者：Wang Ling; Siu Shirley W I; Gu Wei; Helms Volkhard^*

来源：Biopolymers, 2010, 93(11): 977-985.

DOI：10.1002/bip.21507

• potential energy surface
• binding funnel
• molecular dynamics
• umbrella sampling
• weighted histogram analysis method (WHAM)
• potential of mean force (PMF)

We have employed biased molecular dynamics simulations in explicit solvent to characterize the one-dimensional potential of mean force for the dissociation process of the barnase-barstar protein-protein complex. Unbinding of barstar from wild-type barnase was compared with dissociation from four charge-deletion mutants of barnase. Interestingly, we find in all cases that unbinding of barnase and barstar is an uphill process on a smooth, tilted energy landscape. The total free energy difference between the dissociated and bound state was similar for wild-type barnase-barstar and for the R87A mutant of barnase. The values for the three other mutant barnase mutants K27A, R59A, and R83Q were only about half as much. Besides, we have analyzed the conformational dynamics of important residues at the barnase-barstar interface. In the bound state, their conformational fluctuations are reduced relatively to the free state because of the formation of intermolecular contacts. Interestingly, we find that some residues also show decreased mobility at intermediate stages of the unbinding process suggesting that these residues may be involved in the first contacts being formed on binding.

• 出版日期2010-11
• 单位上海生物信息技术研究中心