- About this Journal
- Abstracting and Indexing
- Aims and Scope
- Annual Issues
- Article Processing Charges
- Articles in Press
- Author Guidelines
- Bibliographic Information
- Citations to this Journal
- Contact Information
- Editorial Board
- Editorial Workflow
- Free eTOC Alerts
- Publication Ethics
- Reviewers Acknowledgment
- Submit a Manuscript
- Subscription Information
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 925373, 9 pages
Structural Adaptation of Cold-Active RTX Lipase from Pseudomonas sp. Strain AMS8 Revealed via Homology and Molecular Dynamics Simulation Approaches
1Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
2Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
3Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
4Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
Received 8 January 2013; Revised 6 March 2013; Accepted 29 March 2013
Academic Editor: Yudong Cai
Copyright © 2013 Mohd. Shukuri Mohamad Ali et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- R. Gupta, N. Gupta, and P. Rathi, “Bacterial lipases: an overview of production, purification and biochemical properties,” Applied Microbiology and Biotechnology, vol. 64, no. 6, pp. 763–781, 2004.
- D. L. Ollis, E. Cheah, M. Cygler et al., “The alpha/beta hydrolase fold,” Protein Engineering, vol. 5, no. 3, pp. 197–211, 1992.
- T. Norin and F. Hæffner, “Molecular modelling of lipase catalysed reactions. Prediction of enantioselectivities,” Chemical and Pharmaceutical Bulletin, vol. 47, no. 5, pp. 591–600, 1999.
- K. E. Jaeger, S. Ransac, B. W. Dijkstra, C. Colson, M. Van Heuvel, and O. Misset, “Bacterial lipases,” FEMS Microbiology Reviews, vol. 15, no. 1, pp. 29–63, 1994.
- S. D'Amico, P. Claverie, T. Collins et al., “Molecular basis of cold adaptation,” Philosophical Transactions of the Royal Society B, vol. 357, no. 1423, pp. 917–925, 2002.
- H. Lilie, W. Haehnel, R. Rudolph, and U. Baumann, “Folding of a synthetic parallel β-roll protein,” FEBS Letters, vol. 470, no. 2, pp. 173–177, 2000.
- V. Spiwok, P. Lipovová, T. Skálová, et al., “Cold-active enzymes studied by comparative molecular dynamics simulation,” Journal of Molecular Modeling, vol. 13, no. 4, pp. 485–497, 2007.
- T. Collins, F. Roulling, F. Piette et al., “Fundamentals of cold-adapted enzymes,” in Psychrophiles: From Biodiversity to Biotechnology, R. Margesin, F. Schinner, J. C. Marx, and C. Gerday, Eds., pp. 211–227, Springer, Berlin, Germany, 2008.
- D. I. Paredes, K. Watters, D. J. Pitman, C. Bystroff, and J. S. Dordick, “Comparative void-volume analysis of psychrophilic and mesophilic enzymes: structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility,” BMC Structural Biology, vol. 11, no. 1, p. 42, 2011.
- E. Krieger, G. Vriend, and C. Spronk, “YASARA-Yet Another Scientific Artificial Reality Application”.
- S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990.
- S. Subramaniam, “The Biology Workbench—a seamless database and analysis environment for the biologist,” Proteins, vol. 32, no. 1, pp. 1–2, 1998.
- R. Meier, T. Drepper, V. Svensson, K. E. Jaeger, and U. Baumann, “A calcium-gated lid and a large β-roll sandwich are revealed by the crystal structure of extracellular lipase from Serratia marcescens,” Journal of Biological Chemistry, vol. 282, no. 43, pp. 31477–31483, 2007.
- C. Angkawidjaja, D. J. You, H. Matsumura et al., “Crystal structure of a family I.3 lipase from Pseudomonas sp. MIS38 in a closed conformation,” FEBS Letters, vol. 581, no. 26, pp. 5060–5064, 2007.
- D. Eisenberg, R. Lüthy, and J. U. Bowie, “VERIFY3D: assessment of protein models with three-dimensional profiles,” Macromolecular Crystallography B, vol. 277, pp. 396–404, 1997.
- G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, “Stereochemistry of polypeptide chain configurations,” Journal of molecular biology, vol. 7, pp. 95–99, 1963.
- D. C. Rapaport, The Art of Molecular Dynamics Simulation, Cambridge University Press, Cambridge, UK, 2004.
- Y. Duan, C. Wu, S. Chowdhury et al., “A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations,” Journal of Computational Chemistry, vol. 24, no. 16, pp. 1999–2012, 2003.
- T. Xu, B. Gao, L. Zhang, J. Lin, X. Wang, and D. Wei, “Template-based modeling of a psychrophilic lipase: conformational changes, novel structural features and its application in predicting the enantioselectivity of lipase catalyzed transesterification of secondary alcohols,” Biochimica et Biophysica Acta, vol. 1804, no. 12, pp. 2183–2190, 2010.
- D. Pascale, A. M. Cusano, F. Autore et al., “The cold-active Lip1 lipase from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 is a member of a new bacterial lipolytic enzyme family,” Extremophiles, vol. 12, no. 3, pp. 311–323, 2008.
- J. Pleiss, M. Fischer, and R. D. Schmid, “Anatomy of lipase binding sites: the scissile fatty acid binding site,” Chemistry and Physics of Lipids, vol. 93, no. 1-2, pp. 67–80, 1998.
- I. Linhartová, L. Bumba, J. Mašín et al., “RTX proteins: a highly diverse family secreted by a common mechanism,” FEMS Microbiology Reviews, vol. 34, no. 6, pp. 1076–1112, 2010.
- K. A. McCall, C. C. Huang, and C. A. Fierke, “Function and mechanism of zinc metalloenzymes,” Journal of Nutrition, vol. 130, no. 5, pp. 1437S–1446S, 2000.
- B. A. Tejo, A. B. Salleh, and J. Pleiss, “Structure and dynamics of Candida rugosa lipase: the role of organic solvent,” Journal of Molecular Modeling, vol. 10, no. 5-6, pp. 358–366, 2004.
- M. Giovanola, F. D'Antoni, M. Santacroce et al., “Role of a conserved glycine triplet in the NSS amino acid transporter KAAT1,” Biochimica Et Biophysica Acta, vol. 1818, no. 7, pp. 1737–1744, 2012.
- G. Colombo, G. Ottolina, and G. Carrea, “Modelling of enzyme properties in organic solvents,” Monatshefte fur Chemie, vol. 131, no. 6, pp. 527–547, 2000.
- W. C. Choi, H. K. Myung, H. S. Ro, R. R. Sang, T. K. Oh, and J. K. Lee, “Zinc in lipase L1 from Geobacillus stearothermophilus L1 and structural implications on thermal stability,” FEBS Letters, vol. 579, no. 16, pp. 3461–3466, 2005.
- M. El Khattabi, P. Van Gelder, W. Bitter, and J. Tommassen, “Role of the calcium ion and the disulfide bond in the Burkholderia glumae lipase,” Journal of Molecular Catalysis B, vol. 22, no. 5-6, pp. 329–338, 2003.
- A. B. Salleh, A. S. M. A. Rahim, R. N. Z. R. A. Rahman, T. C. Leow, and M. Basri, “The role of Arg157Ser in improving the compactness and stability of ARM lipase,” Journal of Computer Science Systems Biology, vol. 5, no. 2, pp. 039–046, 2012.
- H. Matsumura, T. Yamamoto, T. C. Leow et al., “Novel cation-π interaction revealed by crystal structure of thermoalkalophilic lipase,” Proteins, vol. 70, no. 2, pp. 592–598, 2008.
- T. C. Leow, R. N. Z. R. A. Rahman, M. Basri, and A. B. Salleh, “A thermoalkaliphilic lipase of Geobacillus sp. T1,” Extremophiles, vol. 11, no. 3, pp. 527–535, 2007.