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Molecular Dynamics Simulation Methods to Study Structural Dynamics of Proteins

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Protein Folding Dynamics and Stability

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Abstract

Molecular dynamics (MD) simulation is a computational technique for understanding the physical motions of atomic and molecular particles. In this approach, atoms and molecules interact for a defined time period, revealing information on the dynamic evolution of the system. Newton’s equations of motion are used to determine the trajectories of atoms and molecules. The forces and potential energy between atoms and molecules are calculated using molecular mechanics force fields or interatomic potentials. The approach was originally created for applications in the field of theoretical physics; however, it is now used in other areas, including materials science, theoretical chemistry, computational biology, etc. This technique determines the time-dependent behaviour of a molecular system. MD simulation has been widely used to study the conformational changes of biomacromolecules to explore the structure and dynamics of proteins, nucleic acids, and their complexes. It has also been used to study the protein–ligand interactions, which are essential for various processes inside the cell, such as signal transduction, immune reaction, and gene regulation. The data help explore the regulatory mechanisms of various biological processes. MD studies also provide a theoretical background for drug design and discovery. Therefore, MD simulation has been extensively used by researchers in combination with biochemical and biophysical methods to obtain a dynamic understanding of biomolecular behaviour. This chapter discusses various MD simulation methods and how they are used to study the structural dynamics of proteins.

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  1. Department of Bioinformatics, Central University of South Bihar, Gaya, India

    Anil Kumar & Krishna Kumar Ojha

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  1. Department of Biotechnology, National Institute of Technology, Warangal, Telangana, India

    Prakash Saudagar

  2. Department of Biochemistry, North-Eastern Hill University, Shillong, Meghalaya, India

    Timir Tripathi

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Kumar, A., Ojha, K.K. (2023). Molecular Dynamics Simulation Methods to Study Structural Dynamics of Proteins. In: Saudagar, P., Tripathi, T. (eds) Protein Folding Dynamics and Stability. Springer, Singapore. https://doi.org/10.1007/978-981-99-2079-2_5

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