Protein dynamics and molecular motions study in relation to molecular interaction between proteins from sulfur oxidizing proteobacteria Allochromatium vinosum

References

• Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins, 17(4), 412–425. doi:10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Amadei, A., Linssen, A. B., de Groot, B. L., van Aalten, D. M., & Berendsen, H. J. (1996). An efficient method for sampling the essential subspace of proteins. Journal of Biomolecular Structure & Dynamics, 13(4), 615–625. doi:10.1080/07391102.1996.10508874
   PubMed Web of Science ®Google Scholar
• Bahar, I., Atilgan, A. R., Demirel, M. C., & Erman, B. (1998). Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function andstability. Physical Review Letters, 80(12), 2733–2736. doi:10.1103/PhysRevLett.80.2733
   Web of Science ®Google Scholar
• 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. Journal of Chemical Physics., 81(8), 3684–3690. doi:10.1063/1.448118
   Web of Science ®Google Scholar
• Berendsen, H. J. C., Grigera, J. R., & Straatsma, T. P. (1987). The missing term in effective pair potentials. The Journal of Physical Chemistry, 91(24), 6269–6271. doi:10.1021/j100308a038
   Web of Science ®Google Scholar
• Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983). CHARMM: A program for macromolecular energy minimization and dynamics calculations. Journal of Computational Chemistry, 4(2), 187–217. doi:10.1002/jcc.540040211
   Web of Science ®Google Scholar
• Chen, R., & Weng, Z. (2002). Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins: Structure, Function, and Genetics, 47(3), 281–294. doi:10.1002/prot.10092
   PubMed Web of Science ®Google Scholar
• Chen, R., & Weng, Z. (2003). A novel shape complementarity scoring function for protein-protein docking. Proteins: Structure, Function, and Genetics, 51(3), 397–408. doi:10.1002/prot.10334
   PubMed Web of Science ®Google Scholar
• Cort, J. R., Mariappan, S. V., Kim, C. Y., Park, M. S., Peat, T. S., Waldo, G. S., Terwilliger, T. C., & Kennedy, M. A. (2001). Solution structure of Pyrobaculum aerophilum DsrC, an archaeal homologue of the gamma subunit of dissimilatory sulfite reductase. European Journal of Biochemistry, 268(22), 5842–5850. doi:10.1046/j.0014-2956.2001.02529.x
   PubMedGoogle Scholar
• Cort, J. R., Selan, U., Schulte, A., Grimm, F., Kennedy, M. A., & Dahl, C. (2008). Allochromatium vinosum DsrC: Solution-state NMR structure, redox properties and interaction with DsrEFH, a protein essential for purple sulfur bacterial sulfur oxidation. Journal of Molecular Biology., 382(3), 692–707. doi:10.1016/j.jmb.2008.07.022
   PubMed Web of Science ®Google Scholar
• Dahl, C., Engels, S., Pott-Sperling, A. S., Schulte, A., Sander, J., LüBbe, Y., Deuster, O., & Brune, D. C. (2005). Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum. Journal of Bacteriology, 187(4), 1392–1404. doi:10.1128/JB.187.4.1392-1404.2005
   PubMed Web of Science ®Google Scholar
• Dahl, C., Franz, B., Hensen, D., Kesselheim, A., & Zigann, R. (2013). Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: Identification of SoeABC as a major player and relevance of SoxYZ in the process. Microbiology, 159(Pt_12), 2626–2638. doi:10.1099/mic.0.071019-0
   PubMed Web of Science ®Google Scholar
• de Vries, S. J., van Dijk, M., & Bonvin, A. M. J. J. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883–897. doi:10.1038/nprot.2010.32
   PubMed Web of Science ®Google Scholar
• Dominguez, C., Boelens, R., & Bonvin, A. (2003). HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society, 125(7), 1731–1737. doi:10.1021/ja026939x
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., Pedersen, L. G., et. al. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics., 103(19), 8577–8593. doi:10.1063/1.470117
   Web of Science ®Google Scholar
• Frauenfelder, H., Sligar, S. G., & Wolynes, P. G. (1991). The energy landscapes and motions of proteins. Science (New York, N.Y.).), 254(5038), 1598–1603. doi:10.1126/science.1749933
   PubMed Web of Science ®Google Scholar
• Frigaard, N., & Dahl, C. (2009). Sulfur metabolism in phototrophic sulfur bacteria. In: Robert Poole K. (Ed.), Advances in microbial physiology (Vol. 54, pp. 103–200). Academic Press.
   Google Scholar
• Ghosh, S., & Bagchi, A. (2018). Insight into the molecular mechanism of the sulfur oxidation process by reverse sulfite reductase (rSiR) from sulfur oxidizer Allochromatium vinosum. J. of Mol. Modeling, 24, 117. doi:10.1007/s00894-018-3652-5
   PubMed Web of Science ®Google Scholar
• Ghosh, S., & Bagchi, A. (2019). Structural study to analyze the DNA-binding properties of DsrC protein from the dsr operon of sulfur-oxidizing bacterium Allochromatium vinosum. J. of Mol. Modeling, 25, 74. doi:10.1007/s00894-019-3945-3
   PubMed Web of Science ®Google Scholar
• Ghosh, S., & Bagchi, A. (2015). Comparative analysis of the mechanisms of sulfur anion oxidation and reduction by dsr operon to maintain environmental sulfur balance. Computational Biology and Chemistry., 59, 177–184. doi:10.1016/j.compbiolchem.2015.07.001
   PubMed Web of Science ®Google Scholar
• Grein, F. (2010). Biochemical, biophysical and functional analysis of the DsrMKJOP transmembrane complex from Allochromatium vinosum [PhD thesis]. Rhenish Friedrich Wilhelm University.
   Google Scholar
• Grein, F., Pereira, I. A. C., & Dahl, C. (2010a). Biochemical characterization of individual components of the Allochromatium vinosum DsrMKJOP transmembrane complex aids understanding of complex function in vivo. Journal of Bacteriology, 192(24), 6369–6377. doi:10.1128/JB.00849-10
   PubMed Web of Science ®Google Scholar
• Hess, B. (2008). P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory and Computation, 4(1), 116–122. doi:10.1021/ct700200b
   PubMed Web of Science ®Google Scholar
• Hess, B., Kutzner, C., Van Der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient load-balanced and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. doi:10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Hsieh, Y. C., Liu, M. Y., Wang, V. C., Chiang, Y. L., Liu, E. H., Wu, W. G., Chan, S. I., & Chen, C. J. (2010). Structural insights into the enzyme catalysis from comparison of three forms of dissimilatory sulphite reductase from Desulfovibrio gigas. Molecular Microbiology, 78(5), 1101–1116. doi:10.1111/j.1365-2958.2010.07390.x
   PubMed Web of Science ®Google Scholar
• Hünenberger, P. H., Mark, A. E., & van Gunsteren, W. F. (1995). Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. Journal of Molecular Biology., 252(4), 492–503. doi:10.1006/jmbi.1995.0514
   PubMed Web of Science ®Google Scholar
• Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12), 2577–2637. doi:10.1002/bip.360221211
   PubMed Web of Science ®Google Scholar
• Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017). The ClusPro web server for protein-protein docking. Nature Protocols, 12(2), 255–278. doi:10.1038/nprot.2016.169
   PubMed Web of Science ®Google Scholar
• Lübbe, Y. J., Youn, H.-S., Timkovich, R., & Dahl, C. (2006). Siro (haem) amide in Allochromatium vinosum and relevance of DsrL and DsrN, a homolog of cobyrinic acid a, c-diamide synthase, for sulphur oxidation. FEMS Microbiology Letters, 261(2), 194–202. doi:10.1111/j.1574-6968.2006.00343.x
   PubMed Web of Science ®Google Scholar
• Mander, G. J., Weiss, M. S., Hedderich, R., Kahnt, J., Ermler, U., & Warkentin, E. (2005). X-ray structure of the gamma-subunit of a dissimilatory sulfite reductase: Fixed and flexible C-terminal arms. FEBS Letters, 579(21), 4600–4604. doi:10.1016/j.febslet.2005.07.029
   PubMed Web of Science ®Google Scholar
• Manoharan, P., & Ghoshal, N. (2018). Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads. Journal of Biomolecular Structure and Dynamics., 36(7), 1878–1892. doi:10.1080/07391102.2017.1337590
   PubMed Web of Science ®Google Scholar
• Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298K. The Journal of Physical Chemistry A, 105(43), 9954–9960. doi:10.1021/jp003020w
   Web of Science ®Google Scholar
• Oliveira, T. F., Franklin, E., Afonso, J. P., Khan, A. R., Oldham, N. J., Pereira, I. A. C., & Archer, M. (2011). Structural insights into dissimilatory sulphite reductases: Structure of desulforubidin from Desulfomicrobium norvegicum. Frontiers in Microbiology, 2, 71. doi:10.3389/fmicb.2011.00071
   PubMed Web of Science ®Google Scholar
• Oliveira, T. F., Vonrhein, C., Matias, P. M., Venceslau, S. S., Pereira, I. A. C., & Archer, M. (2008). The Crystal Structure of Desulfovibrio vulgaris Dissimilatory Sulfite Reductase Bound to DsrC Provides Novel Insights Into the Mechanism of Sulfate Respiration. Journal of Biological Chemistry, 283(49), 34141–34149. doi:10.1074/jbc.M805643200
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics., 52(12), 7182–7190. doi:10.1063/1.328693
   Web of Science ®Google Scholar
• Paul, D. M., Chadah, T., Senthilkumar, B., Sethumadhavan, R., & Rajasekaran, R. (2018). Structural distortions due to missense mutations in human formylglycine generating enzyme leading to multiple sulfatase deficiency. Journal of Biomolecular Structure and Dynamics., 36(13), 3575–3585. doi:10.1080/07391102.2017.1394220
   PubMed Web of Science ®Google Scholar
• Pierce, B., & Weng, Z. (2007). ZRANK: Reranking protein docking predictions with an optimized energy function. Proteins: Structure, Function, and Bioinformatics, 67(4), 1078–1086. doi:10.1002/prot.21373
   PubMed Web of Science ®Google Scholar
• Sanchez, O., Ferrera, I., Dahl, C., & Mas, J. (2001). In vivo role of APS reductase in the purple sulfur bacterium Allochromatium vinosum. Archives of Microbiology., 176(4), 301–305. doi:10.1007/s002030100327
   PubMed Web of Science ®Google Scholar
• Sander, J., Engels-Schwarzlose, S., & Dahl, C. (2006). Importance of the DsrMKJOP complex for sulfur oxidation in Allochromatium vinosum and phylogenetic analysis of related complexes in other prokaryotes. Archives of Microbiology, 186(5), 357–366. doi:10.1007/s00203-006-0156-y
   PubMed Web of Science ®Google Scholar
• Schiffer, A., Parey, K., Warkentin, E., Diederichs, K., Huber, H., Stetter, K. O., Kroneck, P. M. H., & Ermler, U. (2008). Structure of the dissimilatory sulfite reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus. Journal of Molecular Biology., 379(5), 1063–1074. doi:10.1016/j.jmb.2008.04.027
   PubMed Web of Science ®Google Scholar
• Shen, H., Sun, H., & Li, G. (2012). What is the role of motif D in the nucleotide incorporation catalyzed by the RNA-dependent RNA polymerase from poliovirus? PLoS Computational Biology, 8(12), e1002851. doi:10.1371/journal.pcbi.1002851
   PubMed Web of Science ®Google Scholar
• Singh, A., Das, M., & Grover, A. (2020). Molecular mechanism of acetoacetyl-CoA enhanced kinetics for increased bioplastic production from Cupriavidus necator 428. Journal of Biomolecular Structure and Dynamics., 38(3), 827–840. doi:10.1080/07391102.2019.1590239.
   Web of Science ®Google Scholar
• Stockdreher, Y., Venceslau, S. S., Josten, M., Sahl, H.-G., Pereira, I. A. C., & Dahl, C. (2012). Cytoplasmic sulfur transferases in the purple sulfur bacterium Allochromatium vinosum: Evidence for sulfur transfer from DsrEFH to DsrC. PLoS One., 7(7), e40785. doi:10.1371/journal.pone.0040785
   PubMed Web of Science ®Google Scholar
• Tina, K. G., Bhadra, R., & Srinivasan, N. (2007). PIC: Protein interactions calculator. Nucleic Acids Research., 35(Web Server), W473–W476. doi:10.1093/nar/gkm423
   PubMed Web of Science ®Google Scholar
• Tournier, A. L., & Smith, J. C. (2003). Principal components of the protein dynamical transition. Physical Review Letters, 91(20), 208106. doi:10.1103/PhysRevLett.91.208106
   PubMed Web of Science ®Google Scholar
• Vajda, S., Yueh, C., Beglov, D., Bohnuud, T., Mottarella, S. E., Xia, B., Hall, D. R., & Kozakov, D. (2017). New additions to the ClusPro server motivated by CAPRI. Proteins: Structure, Function, and Bioinformatics, 85(3), 435–444. doi:10.1002/prot.25219
   PubMed Web of Science ®Google Scholar
• Vijayakumar, S., & Das, P. (2019). Structural, molecular motions and free-energy landscape of Leishmania sterol-14α-demethylase wild type and drug resistant mutant: A comparative molecular dynamics study. Journal of Biomolecular Structure and Dynamics., 37(6), 1477–1493. doi:10.1080/07391102.2018.1461135
   PubMed Web of Science ®Google Scholar
• Yang, L., Chen, G., Li, Y., Zhang, R., Liu, S., & Sang, P. (2019). Insight derived from molecular dynamics simulation into dynamics and molecular motions of cuticle-degrading serine protease Ver112. Journal of Biomolecular Structure and Dynamics., 37(8), 2004–2016. doi:10.1080/07391102.2018.1471418
   PubMed Web of Science ®Google Scholar