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J Mol Graph Model. 2017 Aug;75:233-240. doi: 10.1016/j.jmgm.2017.05.018. Epub 2017 Jun 3.

Understanding the molecular basis of stability in Kunitz (STI) family of inhibitors in terms of a conserved core tryptophan residue: A theoretical investigation.

Author information

1
Amity Institute of Biotechnology (AIB), Amity University Haryana, India; Amity Institute of Intgerative Sciences and Health (AIISH), Amity University Haryana, NH-8, Panchgaon, Gurgaon, 122413, India.
2
Bioinformatics Infrastructure Facility (BIF), College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, 781022, India.
3
Amity Institute of Nanotechnology, Amity University Haryana, India.
4
Department of Chemistry, Amity School of Applied Sciences, Amity University Haryana, India. Electronic address: sudip22m@gmail.com.

Abstract

β-trefoil is one of the superfolds among proteins. Important classes of proteins like Interleukins (ILs), FibroblastGrowth Factors (FGFs), Kunitz (STI) family of inhibitors etc. belong to this fold. Kunitz (STI) family of inhibitors of proteins possess a highly conserved and structurally important Trytophan 91 (W91) residue, which stitches the top layer of the barrel with the lid. In this article we have investigated the molecular insights of the involvement of this W91 residue in the stability and folding pathway of Kunitz (STI) family. Winged bean Chymotrypsin inhibitor (WCI), a member of Kunitz (STI) family was chosen as a model system for carrying out the work. Molecular dynamics (MD) simulations were run with a set of total six proteins, including wild type WCI (WT) & five mutants namely W91F, W91M, W91A, W91H and W91I. Among all of them the coordinates of four proteins were taken from their crystal structures deposited in the Protein Data Bank (PDB), where as the coordinates for the rest two was generated using in-silico modelling. Our results suggest that truly this W91 residue plays a determining role in stability and folding pathway of Kunitz (STI) family. The mutants are less stable and more susceptible to quicker unfolding at higher temperatures compared to the wild type WCI. These effects are most pronounced for the smallest mutants namely W91H and W91A, indicating more is the cavity created by mutation at W91 position more the proteins becomes unstable.

KEYWORDS:

Core residue; Molecular Dynamics (MD) simulation; Protein stability; Winged-bean chymotrypsin Inhibitor (WCI); β-trefoil fold

PMID:
28600973
DOI:
10.1016/j.jmgm.2017.05.018
[Indexed for MEDLINE]

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