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Atomic molecular dynamics simulation advances of de novo-designed proteins

Published online by Cambridge University Press:  05 December 2024

Moye Wang Open the ORCID record for Moye Wang [Opens in a new window] ,
Anqi Ma ,
Hongjiang Wang  and
Xiaotong Lou
Moye Wang
Affiliation:
Research Department, PLA Strategic Support Force Medical Center, Beijing, China
Anqi Ma
Affiliation:
Research Department, PLA Strategic Support Force Medical Center, Beijing, China
Hongjiang Wang*
Affiliation:
Research Department, PLA Strategic Support Force Medical Center, Beijing, China
Xiaotong Lou*
Affiliation:
Research Department, PLA Strategic Support Force Medical Center, Beijing, China
*
Corresponding authors: Hongjiang Wang and Xiaotong Lou; Emails: wujiang_0706@163.com; louxt@sina.com
Corresponding authors: Hongjiang Wang and Xiaotong Lou; Emails: wujiang_0706@163.com; louxt@sina.com
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Abstract

Proteins are vital biological macromolecules that execute biological functions and form the core of synthetic biological systems. The history of de novo protein has evolved from initial successes in subordinate structural design to more intricate protein creation, challenging the complexities of natural proteins. Recent strides in protein design have leveraged computational methods to craft proteins for functions beyond their natural capabilities. Molecular dynamics (MD) simulations have emerged as a crucial tool for comprehending the structural and dynamic properties of de novo-designed proteins. In this study, we examined the pivotal role of MD simulations in elucidating the sampling methods, force field, water models, stability, and dynamics of de novo-designed proteins, highlighting their potential applications in diverse fields. The synergy between computational modeling and experimental validation continued to play a crucial role in the creation of novel proteins tailored for specific functions and applications.

Keywords

Advancesde novo design proteinsforce fieldmolecular dynamicssampling methodsstabilitywater models
Type
Review
Information
Quarterly Reviews of Biophysics , Volume 57 , 2024 , e14
Copyright
© The Author(s), 2024. Published by Cambridge University Press

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