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Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design

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Abstract

Inter-residue interactions in protein structures provide valuable insights into protein folding and stability. Understanding these interactions can be helpful in many crucial applications, including rational design of therapeutic small molecules and biologics, locating functional protein sites, and predicting protein–protein and protein–ligand interactions. The process of developing machine learning models incorporating inter-residue interactions has been improved recently. This review highlights the theoretical models incorporating inter-residue interactions in predicting folding and unfolding rates of proteins. Utilizing contact maps to depict inter-residue interactions aids researchers in developing computer models for detecting remote homologs and interface residues within protein–protein complexes which, in turn, enhances our knowledge of the relationship between sequence and structure of proteins. Further, the application of contact maps derived from inter-residue interactions is highlighted in the field of drug discovery. Overall, this review presents an extensive assessment of the significant models that use inter-residue interactions to investigate folding rates, unfolding rates, remote homology, and drug development, providing potential future advancements in constructing efficient computational models in structural biology.

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Data Availability

All the data and materials are available to the corresponding author upon reasonable request.

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Funding

Funding was provided by Science and Engineering Research Board (YSS/2015/002124) Balasubramanian Harihar.

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  1. Balasubramanian Harihar and Konda Mani Saravanan have contributed equally to this work.

Authors and Affiliations

  1. Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India

    Balasubramanian Harihar, Konda Mani Saravanan & Samuel Selvaraj

  2. Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India

    Balasubramanian Harihar & Michael M. Gromiha

  3. Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, 600073, India

    Konda Mani Saravanan

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Harihar, B., Saravanan, K.M., Gromiha, M.M. et al. Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design. Mol Biotechnol (2024). https://doi.org/10.1007/s12033-024-01119-4

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