Structural and functional role of invariant water molecules in matrix metalloproteinases: a data-mining approach
- 14 June 2021
- journal article
- research article
- Published by Taylor & Francis Ltd in Journal of Biomolecular Structure and Dynamics
- Vol. 40 (20), 10074-10085
- https://doi.org/10.1080/07391102.2021.1938683
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. SarmaKeywords
This publication has 51 references indexed in Scilit:
- Conserved Water Molecules in Family 1 Glycosidases: A DXMS and Molecular Dynamics StudyBiochemistry, 2013
- Biological role of matrix metalloproteinases: a critical balanceEuropean Respiratory Journal, 2010
- Features and development of CootActa crystallographica. Section D, Structural biology, 2010
- Progress in matrix metalloproteinase researchMolecular Aspects of Medicine, 2008
- Conserved Water Molecules Stabilize the Ω-Loop in Class A β-LactamasesAntimicrobial Agents and Chemotherapy, 2008
- Control of matrix metalloproteinase catalytic activityMatrix Biology, 2007
- X-ray Structure of Human proMMP-1Online Journal of Public Health Informatics, 2005
- The Protein Data BankNucleic Acids Research, 2000
- Astacins, serralysins, snake venom and matrix metalloproteinases exhibit identical zinc‐binding environments (HEXXHXXGXXH and Met‐turn) and topologies and should be grouped into a common family, the ‘metzincins’FEBS Letters, 1993
- Basic local alignment search toolJournal of Molecular Biology, 1990