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Investigating Protein Unfolding and Stability Using Chaotropic Agents and Molecular Dynamics Simulation

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Protein Folding Dynamics and Stability

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Abstract

Protein folding and unfolding processes follow a thermodynamically favourable transitional path. The folding process occurs on a timescale in the order of milliseconds; therefore, observing the correct transitional pathway is challenging. However, with the advancement of computer science, it is now possible to decipher the structural level changes in the folding pathway of the protein using the molecular dynamics (MD) simulation. The MD simulation can provide detailed information about various energetic terms, structural parameters, etc. One can calculate the secondary structure changes with respect to time using MD simulation and correlate them with the CD spectra results. It can also generate thousands of snapshots that can be used to determine accurate unfolding pathways through structure visualization. In this chapter, we describe how chaotropic agents and MD simulation can be used in combination to study the stability and unfolding process of a protein. We also discuss the software used in the MD simulation with a detailed methodology of the GROMACS tool. Lastly, we take two case studies to show the process of urea and GdnHCl-induced denaturation of proteins analysed through MD simulation.

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Authors and Affiliations

  1. Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India

    Rohit Shukla & Timir Tripathi

  2. Regional Director’s Office, Indira Gandhi National Open University, Regional Centre Kohima, Kohima, India

    Timir Tripathi

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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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Shukla, R., Tripathi, T. (2023). Investigating Protein Unfolding and Stability Using Chaotropic Agents and Molecular Dynamics Simulation. In: Saudagar, P., Tripathi, T. (eds) Protein Folding Dynamics and Stability. Springer, Singapore. https://doi.org/10.1007/978-981-99-2079-2_10

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