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Articles

Temperature adaptation analysis of a psychrophilic mannanase through structural, functional and molecular dynamics simulation

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Pages 1270-1277 | Received 21 Apr 2018, Accepted 20 Jun 2018, Published online: 12 Jul 2018

References

  • Cavicchioli R, Siddiqui KS, Andrews D, et al. Low-temperature extremophiles and their applications. Curr Opin Biotechnol. 2002;13:253–261. doi: 10.1016/S0958-1669(02)00317-8
  • Singh P, Hamid B, Lone MA, et al. Evaluation of pectinase activity from the psychrophilic fungal strain Truncatella angustata-BPF5 for use in wine industry. Endocytobio Cell Res. 2012;22:57–61.
  • Sahay S, Hamid B, Singh P, et al. Evaluation of pectinolytic activities for oenological uses from psychrotrophic yeasts. Lett Appl Microbiol. 2013;57:115–121. doi: 10.1111/lam.12081
  • Collins T, Hoyoux A, Dutron A, et al. Use of glycoside hydrolase family 8 xylanases in baking. J Cereal Sci. 2006;43:79–84. doi: 10.1016/j.jcs.2005.08.002
  • Do TT, Quyen DT, Nguyen TN, et al. Molecular characterization of a glycosyl hydrolase family 10 xylanase from Aspergillus Niger. Protein Expr Purif. 2013;92(2):196–202. doi: 10.1016/j.pep.2013.09.011
  • Feller G. Psychrophilic enzymes: from folding to function and biotechnology. Scientifica. 2013;2013:1–28. Available at: http://www.hindawi.com/journals/scientifica/2013/512840/. doi: 10.1155/2013/512840
  • Chauhan PS, Puri N, Sharma P, et al. Mannanases: microbial sources, production, properties and potential biotechnological applications. Appl Microbiol Biotechnol. 2012;93(5):1817–1830. doi: 10.1007/s00253-012-3887-5
  • Kourkoutas Y, Koutinas AA, Kanellaki M, et al. Continuous wine fermentation using psychrophilic yeast immobilized on apple cuts at different temperatures. Food Microbiol. 2002;19(2–3):127–134. doi: 10.1006/fmic.2001.0468
  • Burhan H, Ravinder SR, Deepak C, et al. Psychrophilic yeasts and their biotechnological applications – A review. African J Biotechnol. 2014;13(22):2188–2197. doi: 10.5897/AJB2014.13644
  • Laitila A, Wilhelmson A, Kotaviita E, et al. Yeasts in an industrial malting ecosystem. J Indust Microbiol Biotechnol. 2006;33:953–966. doi: 10.1007/s10295-006-0150-z
  • Kudanga T, Mwenje E, Mandivenga F, et al. Esterases and putative lipases from tropical isolates of Aureobasidium pullulans. J. Basic Microbiol. 2007;47:138–147. doi: 10.1002/jobm.200610207
  • Alias N, Mazian MA, Salleh AB, et al. Molecular cloning and optimization for high level expression of cold-adapted serine protease from antarctic yeast Glaciozyma antarctica PI12. Enzyme Res. 2014;2014:1–20. doi: 10.1155/2014/197938
  • Ramli ANM, Mahadi NM, Shamsir MS, et al. Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function. J Comput Aided Mol Des. 2012;26(8):947–961. doi: 10.1007/s10822-012-9585-7
  • Ramli ANM, Azhar MA, Shamsir MS, et al. Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis. J Mol Model. 2013;19(8):3369–3383. doi: 10.1007/s00894-013-1861-5
  • Parvizpour S, Razmara J, Ramli ANM, et al. Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12. J Comput Aided Mol Des. 2014;28:685–698. doi: 10.1007/s10822-014-9751-1
  • Parvizpour S, Razmara J, Jomah AF, et al. Structural prediction of a novel laminarinase from the psychrophilic Glaciozyma antarctica PI12 and its temperature adaptation analysis. J Mol Model. 2015;21(3):63. doi: 10.1007/s00894-015-2617-1
  • Liu Z, Qi W, He Z. Optimization of beta-mannanase production from Bacillus licheniformis TJ-101 using response surface methodology. Chem Biochem Eng. 2008;22:355–362.
  • Tailford LE, Ducros VMA, Flint JE, et al. Understanding how diverse beta-mannanases recognize heterogeneous substrates. Biochemistry. 2009;48(29):7009–7018. doi: 10.1021/bi900515d
  • Akita M, Takeda N, Hirasawa K, et al. Crystallization and preliminary X-ray study of alkaline man- nanase from an alkaliphilic Bacillus isolate. Acta Crystallogr D Biol Crystallogr. 2004;60:1490–1492. doi: 10.1107/S0907444904014313
  • Bourgault R, Oakley AJ, Bewley JD, et al. Three-dimensional structure of (1,4)- β -D-mannan mannanohydrolase from tomato fruit. Protein Sci. 2005;14:1233–1241. doi: 10.1110/ps.041260905
  • Larsson AM, Anderson L, Xu B, et al. Three-dimensional crystal structure and enzymic characterization of b-mannanase Man5A from blue mussel Mytilus edulis. J Mol Biol. 2006;357:1500–1510. doi: 10.1016/j.jmb.2006.01.044
  • Zakaria MM, Yamamoto S, Yagi T. Purification and characterization of an endo-1,4-b-mannanase from Bacillus sub- tilis KU-1. FEMS Microbiol Lett. 1998;158:25–31.
  • Chauhan PS, Tripathi SP, Sangamwar AT, et al. Cloning, molecular modeling and docking analysis of alkali-thermostable β-mannanase from Bacillus nealsonii PN-11. Appl Microbiol Biotechnol. 2015;99(21):8917–8925. doi: 10.1007/s00253-015-6613-2
  • Chauhan PS, Jaiswar S. Molecular dynamic simulation studies of bacterial thermostable mannanase unwinding the enzymatic catalysis. Biocatal Agric Biotechnol. 2017;9:41–47.
  • Chandra MRS, Lee YS, Park IH, et al. Isolation, purification and characterization of a thermostable b-Mannanase from Paenibacillus sp. DZ3. J Korean Soc Appl Biol Chem. 2011;54(3):325–331. doi: 10.3839/jksabc.2011.052
  • Altschul SF, Gish W, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res. 1997;215(17):3389–3402. doi: 10.1093/nar/25.17.3389
  • Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. doi: 10.1016/S0022-2836(05)80360-2
  • Gough J, Karplus K, Hughey R, et al. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 2001;313(4):903–919. doi: 10.1006/jmbi.2001.5080
  • Eisenberg D, Lüthy R, Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Meth Enzymol. 1997;277:396–404. doi: 10.1016/S0076-6879(97)77022-8
  • Laskowski RA, MacArthur MW, Moss DS, et al. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993;26(2):283–291. doi: 10.1107/S0021889892009944
  • Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 1993;2(9):1511–1519. doi: 10.1002/pro.5560020916
  • Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acid Res. 2007;35(2):W407–W410. doi: 10.1093/nar/gkm290
  • Papaleo E, Pasi M, Riccardi L, et al. Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases. FEBS Lett. 2008;582(6):1008–1018. doi: 10.1016/j.febslet.2008.02.048
  • Yang LW, Eyal E, Bahar I, et al. Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics. 2009;25:606–614. doi: 10.1093/bioinformatics/btp023
  • Barrett CP, Hall BA, Noble ME. Dynamite: a simple way to gain insight into protein motions. Acta Crystallogr D Biol Crystallogr. 2004;60:2280–2287. doi: 10.1107/S0907444904019171
  • Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612. doi: 10.1002/jcc.20084
  • Razmara J, Deris S, Parvizpour S. A rapid protein structure alignment algorithm based on a text modeling technique. Bioinformation. 2011;6(9):344. doi: 10.6026/97320630006344
  • Parvizpour S, Razmara J, Shamsir MS, et al. The role of alternative salt bridges in cold adaptation of a novel psychrophilic laminarinase. J Biomol Str Dynam. 2016;1102:1–18.
  • Tronelli D, Maugini E, Bossa F, et al. Structural adaptation to low temperatures—analysis of the subunit interface of oligomeric psychrophilic enzymes. FEBS J. 2007;274(17):4595–4608. doi: 10.1111/j.1742-4658.2007.05988.x

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