1
|
Guo W, Sun S, Sanchez JE, Lopez-Hernandez AE, Ale TA, Chen J, Afrin T, Qiu W, Xie Y, Li L. Using a comprehensive approach to investigate the interaction between Kinesin-5/Eg5 and the microtubule. Comput Struct Biotechnol J 2022; 20:4305-4314. [PMID: 36051882 PMCID: PMC9396395 DOI: 10.1016/j.csbj.2022.08.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 01/02/2023] Open
Abstract
Kinesins are microtubule-based motor proteins that play important roles ranging from intracellular transport to cell division. Human Kinesin-5 (Eg5) is essential for mitotic spindle assembly during cell division. By combining molecular dynamics (MD) simulations with other multi-scale computational approaches, we systematically studied the interaction between Eg5 and the microtubule. We find the electrostatic feature on the motor domains of Eg5 provides attractive interactions to the microtubule. Additionally, the folding and binding energy analysis reveals that the Eg5 motor domain performs its functions best when in a weak acidic environment. Molecular dynamics analyses of hydrogen bonds and salt bridges demonstrate that, on the binding interfaces of Eg5 and the tubulin heterodimer, salt bridges play the most significant role in holding the complex. The salt bridge residues on the binding interface of Eg5 are mostly positive, while salt bridge residues on the binding interface of tubulin heterodimer are mostly negative. Such salt bridge residue distribution is consistent with electrostatic potential calculations. In contrast, the interface between α and β-tubulins is dominated by hydrogen bonds rather than salt bridges. Compared to the Eg5/α-tubulin interface, the Eg5/β-tubulin interface has a greater number of salt bridges and higher occupancy for salt bridges. This asymmetric salt bridge distribution may play a significant role in Eg5′s directionality. The residues involved in hydrogen bonds and salt bridges are identified in this work and may be helpful for anticancer drug design.
Collapse
Affiliation(s)
- Wenhan Guo
- Computational Science Program, University of Texas at El Paso, El Paso, TX, USA
| | - Shengjie Sun
- Computational Science Program, University of Texas at El Paso, El Paso, TX, USA
| | - Jason E. Sanchez
- Computational Science Program, University of Texas at El Paso, El Paso, TX, USA
| | | | - Tolulope A. Ale
- Computational Science Program, University of Texas at El Paso, El Paso, TX, USA
| | - Jiawei Chen
- Department of Physics, University of Texas at El Paso, El Paso, TX, USA
| | - Tanjina Afrin
- Department of Physics, University of Texas at El Paso, El Paso, TX, USA
- Department of Physics, Oregon State University, Corvallis, OR, USA
| | - Weihong Qiu
- Department of Physics, Oregon State University, Corvallis, OR, USA
| | - Yixin Xie
- Department of Information Technology, Kennesaw State University, Kennesaw, GA, USA
| | - Lin Li
- Computational Science Program, University of Texas at El Paso, El Paso, TX, USA
- Department of Physics, University of Texas at El Paso, El Paso, TX, USA
- Corresponding author.
| |
Collapse
|