Structural and functional role of invariant water molecules in matrix metalloproteinases: a data-mining approach. Issue 20 (29th November 2022)

• Record Type: Journal Article
• Authors: Kumar, Hemant; Mandal, Suraj Kumar; Gogoi, Prerana; Kanaujia, Shankar Prasad
• Is Part Of: Journal of biomolecular structure & dynamics. Volume 40:Issue 20(2022)
• Page Start: 10074
• Page End: 10085
• Publication Date: 2022-11-29
• Subjects: Collagenases -- drug design -- extracellular matrix -- gelatinases -- molecular dynamics simulation -- in silico analysis; Biomolecules -- Periodicals; Molecular structure -- Periodicals; Molecular Biology -- Periodicals; Biomechanics -- Periodicals; 572
• DOI: 10.1080/07391102.2021.1938683
• Languages: English
• ISSNs: 0739-1102

Abstract

Abstract: Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases known to degrade extracellular matrix (ECM). Being involved in many biological and physiological processes of tissue remodeling, MMPs play a crucial role in many pathological conditions such as arthritis, cancer, cardiovascular diseases, etc. Typically, MMPs possess a propeptide, a zinc-containing catalytic domain, a hinge region and a hemopexin domain. Based on their structural domain organization and substrates, MMPs are classified into six different classes, viz. collagenases, stromelysins, gelatinases, matrilysins, membrane-type and other MMPs. As per previous studies, a set of invariant water (IW) molecules of MMP-1 (a collagenase) play a significant role in stabilizing their catalytic domain. However, a functional role of IW molecule in other classes of MMPs has not been reported yet. Thus, in this study, IW molecules of MMPs from different classes were located and their plausible role(s) have been assigned. The results suggest that IW molecules anchor the structurally and functionally essential metal ions present in the vicinity of the active site of MMPs. Further, they (in)directly interlink different structural features and bridge the active site metal ions of MMPs. This study provides the key IW molecules that are structurally and functionally relevant to MMPs and hence, in turn, might facilitate the development of potent generalized inhibitor(s) against different classes of MMPs. Communicated by Ramaswamy H. Sarma