Computational Fishing and Structural Analysis of MIPS Protein from Two Important Plant Groups

Hazra, Anjan

doi:10.18052/www.scipress.com/ILNS.42.18

ILNS > ILNS Volume 42 > Computational Fishing and Structural Analysis of...

< Back to Volume

Computational Fishing and Structural Analysis of MIPS Protein from Two Important Plant Groups

Full Text PDF

Abstract:

Myo Inositol 1-Phosphate Synthase (MIPS), which catalyzes the first step of inositol metabolism, has been reported from a diverse range of organism like bacteria to human including different groups of plants and animals. The present work is carried out to explore and analyze structural forms of the respective MIPS proteins from complete sequenced genome or proteome available on database of one representative from two important plant groups viz. bryophyte (Physcomitrella patens) and pteridophyte (Selaginella moellendorffii). Previously reported characteristic MIPS sequences was used to identify it’s homolog ones from those members under study. The explored sequences compared with a number of MIPS varieties from other plant members to study the conserveness or evolution of the protein/enzyme. ProtParam tool provided necessary theoretical physicochemical data of the predicted proteins, the three-dimensional structures were predicted through homology modelling with identified amino acid data. Structural evaluation and stereochemical analyses were performed using ProSA-webdisplaying Z-scores and Molprobityvisualising Ramachandran plot.

Info:

Periodical:

International Letters of Natural Sciences (Volume 42)

Pages:

18-27

DOI:

https://doi.org/10.18052/www.scipress.com/ILNS.42.18

Citation:

A. Hazra, "Computational Fishing and Structural Analysis of MIPS Protein from Two Important Plant Groups", International Letters of Natural Sciences, Vol. 42, pp. 18-27, 2015

Online since:

July 2015

Authors:

Anjan Hazra

Keywords:

Computational Protein Fishing (CPF), Homology Modeling, Myo Inositol 1-Phosphate Synthase, Phylogeny, Physicochemical Properties, Ramachandran Plot

Export:

RIS, BibTeX, Text

Distribution:

Open Access

This work is licensed under a
Creative Commons Attribution 4.0 International License

References:

[1] Basak A, Jha T. B. & Adhikari J., Biosynthesis of myo-inositol in lycopods: characteristics of the pteridophytic l-myo inositol 1-phosphate synthase and myoinositol- 1-phosphate phosphatase from the strobili of Lycopodium clavatum and Selaginella monospora, Acta Physiol Plant 34 (2012).

DOI: https://doi.org/10.1007/s11738-012-0924-z

[2] Basu P., Ganguli S., Gupta S., Datta A., Exploring Computational Protein Fishing (CPF) to identify Argonaute Proteins from Sequenced Crop Genomes International Letters of Natural Sciences Vol 33 (2015) pp.27-36.

DOI: https://doi.org/10.18052/www.scipress.com/ilns.33.27

[3] Balasubramanian J, Shahul Hammed MK, Tamilselvan R and Vijayakumar N., Artificial neural network: A forecast in pharmaceutical science. Nerve (2012) 1: 7-12.

[4] Castrignanò T, D'Onorio P, Meo D, Cozzetto1 D, Talamo1 I G, and Tramontano A., The PMDB Protein Model Database Nucleic Acids Research Volume 34, Issue suppl (2005) Pp. D306-D309.

DOI: https://doi.org/10.1093/nar/gkj105

[5] Chen et al., MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66 (2010) 12-21.

[6] Chhetri, D. R, Mukherjee A. K, Adhikari J., Partial purification and characterization of L-myo-inositol-1-phosphate synthase of pteridophytic origin. Acta Physiol. Plant., 28 (2006) 101-107.

DOI: https://doi.org/10.1007/s11738-006-0036-8

[7] Chhetri D. R, Choudhuri M, Mukherjee AK, Adhikari J., L-myo-inositol-1-phosphate synthase: partial purification and characterization from Gleichenia glauca. Biol. Plant. 49 (2005) 59-63.

DOI: https://doi.org/10.1007/s10535-005-0063-0

[8] Chhetri D. R, Yonzone S, Mukherjee A. K, Adhikari J., L-myo-inositol-1-phosphate synthase from Marchantia nepalensis: partial purification and properties, Gen. Appl. Plant physiology, (2006) 32(3-4), 153-164.

[9] Corpet F., 1988, Multiple sequence alignment with hierarchical clustering" Nucl. Acids Res., 16 (22), 10881-10890.

DOI: https://doi.org/10.1093/nar/16.22.10881

[10] Eswar N., Marti-Renom M. A., Webb B., Madhusudhan M. S., Eramian D., Shen M., Pieper U., Sali A., Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15 (2006).

DOI: https://doi.org/10.1002/0471250953.bi0506s15

[11] Felsenstein J., Confidence limits on phylogenies: An approach using the bootstrap Evolution 39 (1985) 783-791.

DOI: https://doi.org/10.2307/2408678

[12] Gasteiger E., Protein Identifi cation and Analysis Tools on the ExPASy Server. In: John M. Walker ed, The Proteomics Protocols Handbook, Humana Press, (2005) 571-607.

DOI: https://doi.org/10.1385/1-59259-890-0:571

[13] Gill SC., Von Hippel PH Extinction coefficient, Anal Biochem 182 (1989) 319- 328.

[14] Ikai A. J., Thermo stability and aliphatic index of globular proteins. J Biochem 88 (1980) 1895-1898..

[15] Jones D. T., Protein structure prediction in genomics. Brief Bioinform 2(2) (2001) 111-125.

[16] Kleiger G, and Eisenberg D., GXXXG and GXXXA Motifs Stabilize FAD and NAD (P)-binding Rossmann Folds Through C α–H⋯ O Hydrogen Bonds and van der Waals Interactions J. Mol. Biol. 323 (2002) 69-76.

DOI: https://doi.org/10.1016/s0022-2836(02)00885-9

[17] Kyte J, Doolottle RF, A simple method for displaying the hydropathic character of a protein, J Mol Biol 157 (1982) 105- 132.

[18] Majumder A.L., Chatterjee A., Ghosh D.K., Majee M., Diversification and evolution of L-myo-inositol 1-phosphate synthase. FEBS Lett. 553 (2003) 3–10.

DOI: https://doi.org/10.1016/s0014-5793(03)00974-8

[19] Majumder A.L., Johnson M.D., Henry S.A., 1L-myo-inositol 1-phosphate synthase. Acta Biochim. Biophys. 1348 (1997) 245–256.

[20] Matthew DG and Mark SH., Quaternary structure of rice non-symbiotic hemoglobin. J Biol Chem 276 (2001) 6834-6839.

[21] Norman R.A., McAlister M.S.B., Murray Rust J., Movahedzadeh F., Stoker N.G., & McDonald N.Q., Crystal structure of inositol 1 phosphate synthase from Mycobacterium tuberculosis, a key enzyme in phosphotidyl inositol synthesis. Structure , vol10 (2002).

DOI: https://doi.org/10.1016/s0969-2126(02)00718-9

[22] Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE., UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem. 25(13) (2004) 1605-12.

DOI: https://doi.org/10.1002/jcc.20084

[23] Ramachandran GN, Ramakrishnan C and Sasisek-haran V Stereochemistry of polypeptide chain configurations. J Mol Biol 7 (1963) 95-99.

[24] Banerjee R, Dhani R, Chhetri D, and Adhikari J, Occurrence of myo-inositol-1-phosphate phosphatase in pteridophytes: characteristics of the enzyme from the reproductive pinnules of Dryopteris filix-mas (L. ) Schott, Braz. J. Plant Physiol., 19(2) (2007).

DOI: https://doi.org/10.1590/s1677-04202007000200003

[25] Sneath P.H. A, and Sokal R.R., Numerical Taxonomy. Freeman, San Francisco. (1973).

[26] Stein A. J, & Geiger J.H., The crystal structure and mechanism of L myo inositol 1 phosphate synthase. Journal of Biological Chemistry 277 (2002) 9484-9491.

DOI: https://doi.org/10.1074/jbc.m109371200

[27] Tamura K., Stecher G., Peterson D., Filipski A., and Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6. 0. Molecular Biology and Evolution 30 (2013) 2725-2729.

DOI: https://doi.org/10.1093/molbev/mst197

[28] Vincentz M, Bandeira-Kobarg C, Gauer L, Schlogl P and Leite A., Evolutionary pattern of angiosperm bZIP factors homologous to the maize Opaque2 regulatory protein. J Mol Evol 56 (2003) 105-116.

DOI: https://doi.org/10.1007/s00239-002-2386-1

[29] Wiederstein M. & Sippl M. J, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research 35 (2007) W407-W410.

DOI: https://doi.org/10.1093/nar/gkm290

[30] Zuckerkandl E. and Pauling L, Evolutionary divergence and convergence in proteins. Edited in Evolving Genes and Proteins by V. Bryson and H.J. Vogel, pp Academic Press (1965) 97-166.

DOI: https://doi.org/10.1016/b978-1-4832-2734-4.50017-6

Show More Hide

Cited By:

This article has no citations.