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Experimental and Computational Methods to Determine Protein Structure and Stability

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Frontiers in Protein Structure, Function, and Dynamics

Abstract

Proteins are versatile biological macromolecules that are involved in many essential processes and basic functions of a cell, including catalytic activity, storage, transport, cell structure, metabolism, cell signaling, and immunity. The functions of proteins are dictated by their structures. For instance, the shape, catalytic activity, and specificity of enzymes depend on both the sequence of amino acids in their active site to which the substrate or drug binds and the nature of protein folding. The stability of protein will determine if a protein is in native folded conformation or the unfolded or denatured state. The key role of drug designing is to enhance protein stability since the marginal stability of a protein could cause loss of protein function, increased degradation, and difficulty in synthesizing protein-based drugs. The folded structure of a protein is stabilized by several atomic interactions such as electrostatic, hydrophobic, van der Waals, disulfide, and hydrogen bonds, while the entropic or non-entropic interactions dominate the unfolded protein conformations. This chapter provides an overview of the techniques to determine the structure and stability of proteins addressing the principles involved in structure prediction with specific highlights on widely used experimental methods and computational techniques, namely protein purification techniques, biophysical/biochemical characterization of proteins, protein structure determining methods, factors contributing to protein stability, and conformational analysis of protein folding. This combination of advanced experimental and computational approaches in predicting the protein structure and measuring its stability serves to an exciting future in drug designing and stability engineering.

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Acknowledgment

J.J. and his group thank the DST INDO-TAIWAN (GITA/DST/TWN/P-86/2019 dated: 04/03/2020), Board of Research in Nuclear Sciences (BRNS) (35/14/ 02/2018 BRNS/35009), Indian Council for Medical Research (ICMR) (No. BIC/12(07)/2015), DST-Science and Engineering Research Board (SERB) (No. EMR/2016/000498), UGC Research Award (No. F. 30-32/2016(SA-II) Dt.18.04.2016), DST-Fund for Improvement of S&T Infrastructure in Universities & Higher Educational Institutions (FIST) (SR/FST/LSI-667/2016) (C), DST-Promotion of University Research and Scientific Excellence (PURSE) (No. SR/PURSE Phase 2/38 (G), 2017 and MHRD-RUSA 2.0, New Delhi (F.24-51/2014-U, Policy (TNMulti-Gen), Dept. of Edn., Govt. of India, Dt.09.10.2018).

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Authors and Affiliations

  1. Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India

    Nachiappan Mutharasappan, Guru Ravi Rao, Richard Mariadasse, Saritha Poopandi, Amala Mathimaran, Prabhu Dhamodharan, Rajamanikandan Sundarraj & Jeyakanthan Jeyaraman

  2. Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Alagappa University, Karaikudi, Tamil Nadu, India

    Chitra Jeyaraj Pandian

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  1. Nachiappan Mutharasappan
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  2. Guru Ravi Rao
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Editors and Affiliations

  1. Institute of Biosciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, Uttar Pradesh, India

    Dev Bukhsh Singh

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

    Timir Tripathi

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Mutharasappan, N. et al. (2020). Experimental and Computational Methods to Determine Protein Structure and Stability. In: Singh, D., Tripathi, T. (eds) Frontiers in Protein Structure, Function, and Dynamics. Springer, Singapore. https://doi.org/10.1007/978-981-15-5530-5_2

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