255
Views
23
CrossRef citations to date
0
Altmetric
Research Articles

Spectroscopic and MD simulation studies on unfolding processes of mitochondrial carbonic anhydrase VA induced by urea

, , , , &
Pages 1987-1997 | Received 25 Aug 2015, Accepted 23 Sep 2015, Published online: 27 Jan 2016

References

  • Anwer, K., Sonani, R., Madamwar, D., Singh, P., Khan, F., Bisetty, K., … Hassan, M. I. (2015). Role of N-terminal residues on folding and stability of C-phycoerythrin: Simulation and urea-induced denaturation studies. Journal of Biomolecular Structure and Dynamics, 33, 121–133. doi:10.1080/07391102.2013.855144
  • Beck, D. A., & Daggett, V. (2004). Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods, 34, 112–120. doi:10.1016/j.ymeth.2004.03.008S1046202304000568[pii]
  • Bennion, B. J., & Daggett, V. (2003). The molecular basis for the chemical denaturation of proteins by urea. Proceedings of the National Academy of Sciences, 100, 5142–5147. doi:10.1073/pnas.09301221000930122100[pii]
  • Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81, 3684–3690. doi:10.1063/1.448118
  • Boriack-Sjodin, P. A., Heck, R. W., Laipis, P. J., Silverman, D. N., & Christianson, D. W. (1995). Structure determination of murine mitochondrial carbonic anhydrase V at 2.45-A resolution: Implications for catalytic proton transfer and inhibitor design. Proceedings of the National Academy of Sciences, 92, 10949–10953.10.1073/pnas.92.24.10949
  • Bywater, R. P. (2013). Protein folding: A problem with multiple solutions. Journal of Biomolecular Structure and Dynamics, 31, 351–362. doi:10.1080/07391102.2012.703062
  • Camilloni, C., Guerini Rocco, A. G., Eberini, I., Gianazza, E., Broglia, R. A., & Tiana, G. (2008). Urea and guanidinium chloride denature protein L in different ways in molecular dynamics simulations. Biophysical Journal, 94, 4654–4661. doi:10.1529/biophysj.107.125799biophysj.107.125799[pii]
  • Corbett, R. J., & Roche, R. S. (1984). Use of high-speed size-exclusion chromatography for the study of protein folding and stability. Biochemistry, 23, 1888–1894. doi:10.1021/bi00303a047
  • De Simone, G., & Supuran, C. T. (2007). Antiobesity carbonic anhydrase inhibitors. Current Topics in Medicinal Chemistry, 7, 879–884. doi:10.2174/156802607780636762
  • Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133–7155. doi:10.1021/bi00483a001
  • Dill, K. A., & MacCallum, J. L. (2012). The protein-folding problem, 50 years on. Science, 338, 1042–1046. doi:10.1126/science.1219021338/6110/1042[pii]
  • Gillet, J. N., & Ghosh, I. (2013). Concepts on the protein folding problem. Journal of Biomolecular Structure and Dynamics, 31, 1020–1023. doi:10.1080/07391102.2012.748546
  • Hamidur Rahaman, M. K. A. K., Imtaiyaz Hassan, Md, Islam, A., & Ali Akbar Moosavi-Movahedi, F. A. (2013). Evidence of non-coincidence of normalized sigmoidal curves of two different structural properties for two-state protein folding/unfolding. The Journal of Chemical Thermodynamics, 58, 351–358. doi:10.1016/j.jct.2012.11.024
  • Haque, M. A., Zaidi, S., Ubaid-Ullah, S., Prakash, A., Hassan, M. I., Islam, A., … Ahmad, F. (2015). In vitro and in silico studies of urea-induced denaturation of yeast iso-1-cytochrome c and its deletants at pH 6.0 and 25 degrees C. Journal of Biomolecular Structure Dynamics, 33, 1493–1502. doi: 10.1080/07391102.2014.958760
  • Hubert, H. B., Feinleib, M., McNamara, P. M., & Castelli, W. P. (1983). Obesity as an independent risk factor for cardiovascular disease: A 26-year follow-up of participants in the Framingham Heart Study. Circulation, 67, 968–977. doi:10.1161/01.CIR.67.5.968
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 27–38. doi:10.1016/0263-7855(96)00018-5
  • Idrees, D., Kumar, S., Rehman, S. A., Gourinath, S., Islam, A., Ahmad, F., & Hassan, M. I. (2016). Cloning, expression, purification and characterization of human mitochondrial carbonic anhydrase VA. Biotech. ( In press).
  • Imtaiyaz Hassan, M., Shajee, B., Waheed, A., Ahmad, F., & Sly, W. S. (2013). Structure, function and applications of carbonic anhydrase isozymes. Bioorganic & Medicinal Chemistry, 21, 1570–1582. doi:10.1016/j.bmc.2012.04.044S0968-0896(12)00328-8[pii]
  • Joshi, R. R. (2013). Protein folding: interplay of hydrophobic-hydrophilic forces? Journal of Biomolecular Structure and Dynamics, 31, 965–966. doi:10.1080/07391102.2012.748530
  • Konerding, D. E., Cheatham, T. E., 3rd, Kollman, P. A., & James, T. L. (1999). Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method. Journal of Biomolecular NMR, 13, 119–131. doi:10.1023/A:1008353423074
  • Naganathan, A. N., Doshi, U., & Munoz, V. (2007). Protein folding kinetics: Barrier effects in chemical and thermal denaturation experiments. Journal of the American Chemical Society, 129, 5673–5682. doi:10.1021/ja0689740
  • Nagao, Y., Batanian, J. R., Clemente, M. F., & Sly, W. S. (1995). Genomic organization of the human gene (CAS) and pseudogene for mitochondrial carbonic anhydrase V and their localization to chromosomes 16q and 16p. Genomics, 28, 477–484. doi:S0888754385711779[pii]
  • Nagao, Y., Platero, J. S., Waheed, A., & Sly, W. S. (1993). Human mitochondrial carbonic anhydrase: cDNA cloning, expression, subcellular localization, and mapping to chromosome 16. Proceedings of the National Academy of Sciences, 90, 7623–7627.10.1073/pnas.90.16.7623
  • Naiyer, A., Hassan, M. I., Islam, A., Sundd, M., & Ahmad, F. (2015). Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques. Journal of Biomolecular Structure and Dynamics, 33, 2267–2284. doi:10.1080/07391102.2014.999354
  • Naz, F., Singh, P., Islam, A., Ahmad, F., & Imtaiyaz Hassan, M. (2015). Human microtubule affinity-regulating kinase 4 is stable at extremes of pH. Journal of Biomolecular Structure and Dynamics. 1–11. doi: 10.1080/07391102.2015.1074942
  • Oshima, H., & Kinoshita, M. (2015). Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water. The Journal of Chemical Physics, 142, 145103–145115. doi:10.1063/1.4917075
  • Pace, C. N. (1986). Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods in Enzymology, 131, 266–280. doi:10.1016/0076-6879(86)31045-0
  • Pinard, M. A., Mahon, B., & McKenna, R. (2015). Probing the surface of human carbonic anhydrase for clues towards the design of isoform specific inhibitors. Biomed Research International, 2015, 453543. doi:10.1155/2015/453543
  • Poulsen, S. A., Wilkinson, B. L., Innocenti, A., Vullo, D., & Supuran, C. T. (2008). Inhibition of human mitochondrial carbonic anhydrases VA and VB with para-(4-phenyltriazole-1-yl)-benzenesulfonamide derivatives. Bioorganic & Medicinal Chemistry Letters, 18, 4624–4627. doi:10.1016/j.bmcl.2008.07.010S0960-894X(08)00778-6[pii]
  • Privalov, P. L. (1979). Stability of proteins: Small globular proteins. Advance Protein Chemistry, 33, 167–241. doi:10.1016/S0065-3233(08)60460-X
  • Pronk, S., Pall, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29, 845–854. doi:10.1093/bioinformatics/btt055btt055[pii]
  • Rahaman, H., Alam Khan, M. K., Hassan, M. I., Islam, A., Moosavi-Movahedi, A. A., & Ahmad, F. (2015). Heterogeneity of equilibrium molten globule state of cytochrome c induced by weak salt denaturants under physiological condition. PLoS One, 10, e0120465. doi:10.1371/journal.pone.0120465PONE-D-14-42826[pii]
  • Santoro, M. M., & Bolen, D. W. (1988). Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry, 27, 8063–8068. doi:10.1021/bi00421a014
  • Shah, G. N., Morofuji, Y., Banks, W. A., & Price, T. O. (2013). High glucose-induced mitochondrial respiration and reactive oxygen species in mouse cerebral pericytes is reversed by pharmacological inhibition of mitochondrial carbonic anhydrases: Implications for cerebral microvascular disease in diabetes. Biochemical and Biophysical Research Communications, 440, 354–358. doi:10.1016/j.bbrc.2013.09.086S0006-291X(13)01579-9[pii]
  • Shah, G. N., Rubbelke, T. S., Hendin, J., Nguyen, H., Waheed, A., Shoemaker, J. D., & Sly, W. S. (2013). Targeted mutagenesis of mitochondrial carbonic anhydrases VA and VB implicates both enzymes in ammonia detoxification and glucose metabolism. Proceedings of the National Academy of Sciences, 110, 7423–7428. doi:10.1073/pnas.1305805110
  • Singh, R., Hassan, M. I., Islam, A., & Ahmad, F. (2015). Cooperative unfolding of residual structure in heat denatured proteins by urea and guanidinium chloride. PLoS One, 10, e0128740. doi:10.1371/journal.pone.0128740PONE-D-15-06397[pii]
  • Smith, L. J., Jones, R. M., & van Gunsteren, W. F. (2005). Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulations. Proteins, 58, 439–449. doi:10.1002/prot.20287
  • Supuran, C. T. (2008). Carbonic anhydrases: Novel therapeutic applications for inhibitors and activators. Nature Reviews Drug Discovery, 7, 168–181. doi:10.1038/nrd2467nrd2467[pii]
  • Tanford, C. (1968). Protein denaturation. Advances in Protein Chemistry, 23, 121–282. doi:10.1016/S0065-3233(08)60401-5
  • Ubaid-ullah, S., Haque, M. A., Zaidi, S., Hassan, M. I., Islam, A., Batra, J. K., … Ahmad, F. (2014). Effect of sequential deletion of extra N-terminal residues on the structure and stability of yeast iso-1-cytochrome-c. Journal of Biomolecular Structure and Dynamics, 32, 2005–2016. doi:10.1080/07391102.2013.848826
  • van Karnebeek, C. D., Sly, W. S., Ross, C. J., Salvarinova, R., Yaplito-Lee, J., Santra, S., … Stockler-Ipsiroglu, S. (2014). Mitochondrial carbonic anhydrase VA deficiency resulting from CA5A alterations presents with hyperammonemia in early childhood. The American Journal of Human Genetics, 94, 453–461. doi:10.1016/j.ajhg.2014.01.006S0002-9297(14)00007-X[pii]
  • Zaidi, S., Hassan, M. I., Islam, A., & Ahmad, F. (2014). The role of key residues in structure, function, and stability of cytochrome-c. Cellular and Molecular Life Sciences, 71, 229–255. doi:10.1007/s00018-013-1341-1
  • Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32, 2359–2368. doi:10.1002/jcc.21816

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.