Abstract
BackgroundThe M4 family of metalloproteases is comprised of a large number of zinc-containing metalloproteases. A large number of these enzymes are important virulence factors of pathogenic bacteria and therefore potential drug targets. Whereas some enzymes have potential for biotechnological applications, the M4 family of metalloproteases is known almost exclusively from bacteria. The aim of the study was to identify the structure and properties of M4 metalloprotease proteins. ResultsA total of 31 protein sequences of M4 metalloprotease retrieved from UniProt representing different species of bacteria have been characterized for various physiochemical properties. They were thermostable, hydrophillic protein of a molecular mass ranging from 38 to 66 KDa. Correlation on the basis of both enzymes and respective genes has also been studied by phylogenetic tree. B. cereus M4 metalloprotease (PDB ID: 1NPC) was selected as a representative species for secondary and tertiary structures among the M4 metalloprotease proteins. The secondary structure displaying 11 helices (H1-H11) is involved in 15 helix-helix interactions, while 4 β-sheet motifs composed of 15 β-strands in PDBsum. Possible disulfide bridges were absent in most of the cases. The tertiary structure of B. cereus M4 metalloprotease was validated by QMEAN4 and SAVES server (Ramachandran plot, verify 3D, and ERRAT) which proved the stability, reliability, and consistency of the tertiary structure of the protein. Functional analysis was done in terms of membrane protein topology, disease-causing region prediction, proteolytic cleavage sites prediction, and network generation. Transmembrane helix prediction showed absence of transmembrane helix in protein. Protein-protein interaction networks demonstrated that bacillolysin of B. cereus interacted with ten other proteins in a high confidence score. Five disorder regions were identified. Active sites analysis showed the zinc-binding residues—His-143, His-147, and Glu-167, with Glu-144 acting as the catalytic residues. ConclusionMoreover, this theoretical overview will help researchers to get a details idea about the protein structure and it may also help to design enzymes with desirable characteristics for exploiting them at industrial level or potential drug targets.
Highlights
The M4 family of metalloproteases is comprised of a large number of zinc-containing metalloproteases
The ProtParam includes the following computed parameters: molecular weight, isoelectric point, extinction coefficient (EC—quantitative study of protein-protein and protein-ligand interactions), instability index (II— stability of proteins), aliphatic index (AI—relative volume of protein occupied by aliphatic side chains), and Grand Average of Hydropathicities (GRAVY—sum of all hydropathicity values of all amino acids divided by number of residues in a sequence)
Twenty-two 100% conserved positions were found in aligned region comprising nonpolar amino acid, Ala, Leu, Gly, and Pro, Val; polar amino acid, Asn and Ser; aromatic amino acid, Tyr; acidic amino acid, Glutamic acid (Glu) and Aspartic acid (Asp); and basic amino acid, Arg and His
Summary
The M4 family of metalloproteases is comprised of a large number of zinc-containing metalloproteases. Metalloproteases are produced by all species of plants, animals, and microorganisms They are involved in many biological processes such as embryonic development, morphogenesis, processing of peptide hormones, release of cytokines and growth factors, cell-cell fusion, cell adhesion and migration, intestinal absorption of nutrients, viral polyprotein processing, bacterial cell wall biosynthesis, and metabolism of antibiotics [3]. Due to their active relation with many diseases, extracellular metalloproteases have been widely studied [4]
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