title: Serine protease identification (in vitro) and molecular structure predictions (in silico) from a phytopathogenic fungus, Alternaria solani.
abstract: Serine proteases are involved in an enormous number of biological processes. The present study aims at characterizing three-dimensional (3D) molecular architecture of serine proteases from early blight pathogen, Alternaria solani that are hypothesized to be markers of phytopathogenicity. A serine protease was purified to homogeneity and MALDI-TOF-MS/MS analysis revealed that protease produced by A. solani belongs to alkaline serine proteases (AsP). AsP is made up of 403 amino acid residues with molecular weight of 42.1 kDa (Isoelectric point - 6.51) and its molecular formula was C1859 H2930 N516 O595 S4 . AsP structure model was built based on its comparative homology with serine protease using the program, MODELER. AsP had 16 β-sheets and 10 α-helices, with Ser(350) (G347-G357), Asp(158) (D158-H169), and His(193) (H193-G203) in separate turn/coil structures. Biological metal binding region situated near 6th-helix and His(193) residue is responsible for metal binding site. Also, calcium ion (Ca(2+)) is coordinated by the carboxyl groups of Lys(84), Ile(85), Lys(86), Asp(87), Phe(88), Ala(89), Ala(90) (K84-A90) for first Ca(2+) binding site and carbonyl oxygen atom of Lys(244), Gly(245), Arg(246), Thr(247), Lys(248), Lys(249), and Ala(250) (K244-A250), for second Ca(2+) binding site. Moreover, Ramachandran plot analysis of protein residues falling into most favored secondary structures were determined (83.3%). The predicted molecular 3D structural model was further verified using PROCHECK, ERRAT, and VADAR servers to confirm the geometry and stereo-chemical parameters of the molecular structural design. The functional analysis of AsP 3D molecular structure predictions familiar in the current study may provide a new perspective in the understanding and identification of antifungal protease inhibitor designing.
authors.affiliation: Department of Plant Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India; Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
authors.forename: Murugesan
authors.initials: M
authors.lastname: Chandrasekaran
authors.forename: Raman
authors.initials: R
authors.lastname: Chandrasekar
authors.forename: Tongmin
authors.initials: T
authors.lastname: Sa
authors.forename: Muthukrishnan
authors.initials: M
authors.lastname: Sathiyabama
mesh_terms: D000528:Alternaria / Q000201:enzymology*; D000595:Amino Acid Sequence; D003198:Computer Simulation; D007526:Isoelectric Point; D008958:Models, Molecular; D008969:Molecular Sequence Data; D008970:Molecular Weight; D010802:Phylogeny; D011487:Protein Conformation; D017385:Sequence Homology; D057057:Serine Proteases / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D057057:Serine Proteases
keywords: 3D Molecular structural design, Ramachandran plot; Alternaria solani; ERRAT; MALDI-TOF-MS/MS; MODELER; PROCHECK; Serine protease