Structure prediction and functional characterization of secondary metabolite proteins of Ocimum

被引:53
作者
Roy, Sudeep [1 ]
Maheshwari, Nidhi [1 ]
Chauhan, Rashi [1 ]
Sen, Naresh Kumar [1 ]
Sharma, Ashok [1 ]
机构
[1] CSIR, Cent Inst Med & Aromat Plants, Biotechnol Div, Kukrail Picnik Spot Rd,PO CIMAP, Lucknow 226015, Uttar Pradesh, India
关键词
Ocimum; Homology modeling; CLC protein work bench; Secondary structure prediction; Swiss-PDB Viewer;
D O I
10.6026/97320630006315
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Various species of Ocimum have acquired special attention due to their medicinal properties. Different parts of the plant (root, stem, flower, leaves) are used in the treatment of a wide range of disorders from centuries. Experimental structures (X-ray and NMR) of proteins from different Ocimum species, are not yet available in the Protein Databank (PDB). These proteins play a key role in various metabolic pathways in Ocimum. 3D structures of the proteins are essential to determine most of their functions. Homology modeling approach was employed in order to derive structures for these proteins. A program meant for comparative modeling-Modeller 9v7 was utilized for the purpose. The modeled proteins were further validated by Prochek and Verify-3d and Errat servers. Amino acid composition and polarity of these proteins was determined by CLC-Protein Workbench tool. Expasy's Prot-param server and Cys_rec tool were used for physico-chemical and functional characterization of these proteins. Studies of secondary structure of these proteins were carried out by computational program, Profunc. Swiss-pdb viewer was used to visualize and analyze these homology derived structures. The structures are finally submitted in Protein Model Database, PMDB so that they become accessible to other users for further studies.
引用
收藏
页码:315 / 319
页数:5
相关论文
共 19 条
[1]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[2]   The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 [J].
Bairoch, A ;
Apweiler, R .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :45-48
[3]   The PMDB Protein Model Database [J].
Castrignano, Tiziana ;
De Meo, Paolo D'Onorio ;
Cozzetto, Domenico ;
Talamo, Ivano Giuseppe ;
Tramontano, Anna .
NUCLEIC ACIDS RESEARCH, 2006, 34 :D306-D309
[4]   VERIFICATION OF PROTEIN STRUCTURES - PATTERNS OF NONBONDED ATOMIC INTERACTIONS [J].
COLOVOS, C ;
YEATES, TO .
PROTEIN SCIENCE, 1993, 2 (09) :1511-1519
[5]   VERIFY3D: Assessment of protein models with three-dimensional profiles [J].
Eisenberg, D ;
Luthy, R ;
Bowie, JU .
MACROMOLECULAR CRYSTALLOGRAPHY, PT B, 1997, 277 :396-404
[6]   CALCULATION OF PROTEIN EXTINCTION COEFFICIENTS FROM AMINO-ACID SEQUENCE DATA [J].
GILL, SC ;
VONHIPPEL, PH .
ANALYTICAL BIOCHEMISTRY, 1989, 182 (02) :319-326
[7]   CORRELATION BETWEEN STABILITY OF A PROTEIN AND ITS DIPEPTIDE COMPOSITION - A NOVEL-APPROACH FOR PREDICTING INVIVO STABILITY OF A PROTEIN FROM ITS PRIMARY SEQUENCE [J].
GURUPRASAD, K ;
REDDY, BVB ;
PANDIT, MW .
PROTEIN ENGINEERING, 1990, 4 (02) :155-161
[8]  
IKAI A, 1980, J BIOCHEM-TOKYO, V88, P1895
[9]  
Kaplan W, 2001, Brief Bioinform, V2, P195, DOI 10.1093/bib/2.2.195
[10]   Biosynthesis of t-Anethole in Anise: Characterization of t-Anol/Isoeugenol Synthase and an O-Methyltransferase Specific for a C7-C8 Propenyl Side Chain [J].
Koeduka, Takao ;
Baiga, Thomas J. ;
Noel, Joseph P. ;
Pichersky, Eran .
PLANT PHYSIOLOGY, 2009, 149 (01) :384-394