Abstract
Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique.
Highlights
Molecular dynamics simulation in virus researchHirotaka Ode 1,2*, Masaaki Nakashima, Shingo Kitamura 1,3, Wataru Sugiura 1,4 and Hironori Sato 2
Proteins fluctuate spontaneously in solution (Ishima and Torchia, 2000)
Molecular dynamics (MD) IN STRUCTURAL BIOLOGY MD simulation currently allows us to investigate the structural dynamics of proteins on timescales of nanoseconds to microseconds, and will probably allow investigation to milliseconds in the future (Figure 1) (Henzler-Wildman and Kern, 2007; Dror et al, 2010)
Summary
Hirotaka Ode 1,2*, Masaaki Nakashima, Shingo Kitamura 1,3, Wataru Sugiura 1,4 and Hironori Sato 2. Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. We summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
