Probing the Structural and Energetic Basis of Kinesin鈥揗icrotubule Binding Using Computational Alanine-Scanning Mutagenesis

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• 作者：Minghui Li ; Wenjun Zheng
• 刊名：Biochemistry
• 出版年：2011
• 出版时间：October 11, 2011
• 年：2011
• 卷：50
• 期：40
• 页码：8645-8655
• 全文大小：393K
• 年卷期：v.50,no.40(October 11, 2011)
• ISSN：1520-4995

文摘

Kinesin鈥搈icrotubule (MT) binding plays a critical role in facilitating and regulating the motor function of kinesins. To obtain a detailed structural and energetic picture of kinesin鈥揗T binding, we performed large-scale computational alanine-scanning mutagenesis based on long-time molecular dynamics (MD) simulations of the kinesin鈥揗T complex in both ADP and ATP states. First, we built three all-atom kinesin鈥揗T models: human conventional kinesin bound to ADP and mouse KIF1A bound to ADP and ATP. Then, we performed 30 ns MD simulations followed by kinesin鈥揗T binding free energy calculations for both the wild type and mutants obtained after substitution of each charged residue of kinesin with alanine. We found that the kinesin鈥揗T binding free energy is dominated by van der Waals interactions and further enhanced by electrostatic interactions. The calculated mutational changes in kinesin鈥揗T binding free energy are in excellent agreement with results of an experimental alanine-scanning study with a root-mean-square error of 0.32 kcal/mol [Woehlke, G., et al. (1997) Cell 90, 207鈥?16]. We identified a set of important charged residues involved in the tuning of kinesin鈥揗T binding, which are clustered on several secondary structural elements of kinesin (including well-studied loops L7, L8, L11, and L12, helices 伪4, 伪5, and 伪6, and less-explored loop L2). In particular, we found several key residues that make different contributions to kinesin鈥揗T binding in ADP and ATP states. The mutations of these residues are predicted to fine-tune the motility of kinesin by modulating the conformational transition between the ADP state and the ATP state of kinesin.