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Molecular Dynamics Simulation to Study Thermal Unfolding in Proteins

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Protein Folding Dynamics and Stability

Abstract

The proper folding of a protein is essential for its biological functions. Thermal denaturation of protein structure has been used as an essential tool to understand the unfolding mechanism and measure thermodynamic stability. New technologies have made it feasible to heat proteins using femtosecond laser technology and nanoparticle-targeting methods locally. It is crucial to comprehend how quickly proteins can unfold or lose their function at high temperatures. Protein folding and unfolding have been widely modelled using molecular dynamics (MD) simulations. MD simulations provide information about protein folding that is otherwise impractical through experimental approaches. Techniques like targeted molecular dynamics (TMD) simulations and acid-thermal denaturation correspond to varying degrees of success with experimental observations. These simulations, utilized in tandem with experiments, provide crucial information on the protein folding mechanism. Because of recent computer hardware and software improvements, it is now possible to include a broad range of temperature factors in thermal denaturation studies. In this chapter, we dwell on these details and discuss the thermal unfolding of proteins and their applications. Various computational methods and tools and their uses in protein folding/unfolding studies are described. We also cover an overview of limitations, significant contributions, and recent advancements in MD simulation approaches to study protein folding.

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Acknowledgement

M.I.H. thanks the Council of Scientific and Industrial Research for financial support [Project No. 27(0368)/20/EMR-II].

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Authors and Affiliations

  1. Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India

    Md Imtaiyaz Hassan, Taj Mohammad, Afreen Khan, Md Nayab Sulaimani & Asimul Islam

  2. Department Computer Science, Jamia Millia Islamia, New Delhi, India

    Mohd. Umair, Yash Mathur & Afsar Alam

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  1. Md Imtaiyaz Hassan
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  2. Mohd. Umair
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Correspondence to Md Imtaiyaz Hassan .

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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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Hassan, M.I. et al. (2023). Molecular Dynamics Simulation to Study Thermal Unfolding in Proteins. In: Saudagar, P., Tripathi, T. (eds) Protein Folding Dynamics and Stability. Springer, Singapore. https://doi.org/10.1007/978-981-99-2079-2_12

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