Molecular mechanism of acetoacetyl-CoA enhanced kinetics for increased bioplastic production from Cupriavidus necator 428

References

• Abraham, M., Van Der Spoel, D., Lindahl, E., & Hess, B. (2014). The GROMACS development team. GROMACS User Manual Version, 5(2), 1–298.
   Google Scholar
• Aggarwal, M., Singh, A., Grover, S., Pandey, B., Kumari, A., & Grover, A. (2018). Role of pncA gene mutations W68R and W68G in pyrazinamide resistance. Journal of Cellular Biochemistry, 119(3), 2567–2578. doi:10.1002/jcb.26420
   PubMed Web of Science ®Google Scholar
• Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Bioinformatics, 17(4), 412–425. doi:10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1-3), 43–56. doi:10.1016/0010-4655(95)00042-E
   Web of Science ®Google Scholar
• Brooks, C. L., Onuchic, J. N., & Wales, D. J. (2001). Statistical thermodynamics. Taking a walk on a landscape. Science (New York, N.Y.), 293(5530), 612–613. doi:10.1126/science.1062559
   PubMed Web of Science ®Google Scholar
• Chenault, H. K., Simon, E. S., & Whitesides, G. M. (1988). Cofactor regeneration for enzyme-catalysed synthesis. Biotechnology and Genetic Engineering Reviews, 6(1), 221–270. doi:10.1080/02648725.1988.10647849
   PubMedGoogle Scholar
• Das, M., & Grover, A. (2018). Fermentation optimization and mathematical modeling of glycerol-based microbial poly (3-hydroxybutyrate) production. Process Biochemistry, 71, 1.
   Web of Science ®Google Scholar
• DeLano, W. L. (2002). PyMOLDeLano Scientific, Palo Alto, CA, USA. Retrieved from http://www.pymol.org.
   Google Scholar
• Delemotte, L., Kasimova, M. A., Klein, M. L., Tarek, M., & Carnevale, V. (2015). Free-energy landscape of ion-channel voltage-sensor–domain activation. Proceedings of the National Academy of Sciences United States of America, 112(1), 124–129. doi:10.1073/pnas.1416959112
   PubMed Web of Science ®Google Scholar
• Gosu, V., & Choi, S. (2014). Structural dynamic analysis of apo and ATP-bound IRAK4 kinase. Scientific Reports, 4, 5748. doi:10.1038/srep05748
   PubMed Web of Science ®Google Scholar
• Goyal, S., Jamal, S., Shanker, A., & Grover, A. (2017). Structural basis for drug resistance mechanisms against EGFR. Current Topics in Medicinal Chemistry, 17(22), 2509–2521.
   PubMed Web of Science ®Google Scholar
• Gulzar, M., Ali, S., Khan, F. I., Khan, P., Taneja, P., & Hassan, I. (2018). Binding mechanism of caffeic acid and simvastatin to the integrin linked kinase for therapeutic implications: A comparative docking and MD simulation studies. Journal of Biomolecular Structure and Dynamics, 1–37. doi:10.1080/07391102.2018.1546621
   PubMed Web of Science ®Google Scholar
• Hermann-Krauss, C., Koller, M., Muhr, A., Fasl, H., Stelzer, F., & Braunegg, G. (2013). Archaeal production of polyhydroxyalkanoate (PHA) co-and terpolyesters from biodiesel industry-derived by-products. Archaea. doi:10.1155/2013/129268
   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
• Hopewell, J., Dvorak, R., & Kosior, E. (2009). Plastics recycling: Challenges and opportunities. Philosophical Transactions of the Royal Society B: Biological Sciences, 364(1526), 2115–2126. doi:10.1098/rstb.2008.0311
   PubMed Web of Science ®Google Scholar
• Kim, J., Chang, J. H., Kim, E.-J., & Kim, K.-J. (2014). Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha. Biochemical and Biophysical Research Communications, 443(3), 783–788.
   PubMed Web of Science ®Google Scholar
• Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., … Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. doi:10.1021/ar000033j
   PubMed Web of Science ®Google Scholar
• Kumar, N., Singh, A., Grover, S., Kumari, A., Kumar Dhar, P., Chandra, R., & Grover, A. (2018). HHV-5 epitope: A potential vaccine candidate with high antigenicity and large coverage. Journal of Biomolecular Structure and Dynamics 1–37. doi:10.1080/07391102.2018.1477620
   Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations . Journal of Chemical Information and Modeling, 54(7), 1951–1962. doi:10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Lenz, R. W., & Marchessault, R. H. (2005). Bacterial polyesters: Biosynthesis, biodegradable plastics and biotechnology. Biomacromolecules, 6(1), 1–8. doi:10.1021/bm049700c
   PubMed Web of Science ®Google Scholar
• Marimuthu, P., & Singaravelu, K. (2018). Unraveling the molecular mechanism of benzothiophene and benzofuran scaffold merged compounds binding to anti-apoptotic myeloid cell leukemia 1. Journal of Biomolecular Structure and Dynamics 1–49. doi:10.1080/07391102.2018.1474805
   PubMed Web of Science ®Google Scholar
• Matsumoto, K. I., Tanaka, Y., Watanabe, T., Motohashi, R., Ikeda, K., Tobitani, K., … Taguchi, S. (2013). Directed evolution and structural analysis of NADPH-dependent acetoacetyl-CoA reductase from Ralstonia eutropha reveals two mutations responsible for enhanced kinetics. Applied and Environmental Microbiology, 79(19), 01713–01768.
   Web of Science ®Google Scholar
• Maximova, T., Zhang, Z., Carr, D. B., Plaku, E., & Shehu, A. (2018). Sample-based models of protein energy landscapes and slow structural rearrangements. Journal of Computational Biology, 25(1), 33–50. doi:10.1089/cmb.2017.0158
   PubMed Web of Science ®Google Scholar
• Mitsutake, A., Sugita, Y., & Okamoto, Y. (2001). Generalized‐ensemble algorithms for molecular simulations of. biopolymers. Peptide Science, 60(2), 96–123. doi:10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F
   Google Scholar
• Ozturk, S. B., & Kinzy, T. G. (2008). Guanine nucleotide exchange factor independence of the G-protein eEF1A through novel mutant forms and biochemical properties. Journal of Biological Chemistry, 283(34), 23244–23253. doi:10.1074/jbc.M801095200
   PubMed Web of Science ®Google Scholar
• Pandey, B., Grover, S., Goyal, S., Kumari, A., Singh, A., Jamal, S., … Grover, A. (2018). Alanine mutation of the catalytic sites of Pantothenate Synthetase causes distinct conformational changes in the ATP binding region. Scientific Reports, 8(1), 903.
   PubMedGoogle Scholar
• Pandey, B., Grover, S., Tyagi, C., Goyal, S., Jamal, S., Singh, A., … Grover, A. (2018). Dynamics of fluoroquinolones induced resistance in DNA gyrase of Mycobacterium tuberculosis. Journal of Biomolecular Structure and Dynamics, 36(2), 362–375. doi:10.1080/07391102.2016.1277784
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi:10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Sang, P., Du, X., Yang, L.-Q., Meng, Z.-H., & Liu, S.-Q. (2017). Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: A comparative molecular dynamics simulation study and the underlying mechanisms. RSC Advances, 7(46), 28580–28590. doi:10.1039/C6RA23230B
   Web of Science ®Google Scholar
• Schüttelkopf, A. W., & Van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. doi:10.1107/S0907444904011679
   PubMedGoogle Scholar
• Shukla, R., & Singh, T. R. (2019). Virtual screening, pharmacokinetics, molecular dynamics and binding free energy analysis for small natural molecules against cyclin-dependent kinase 5 for Alzheimer’s disease. Journal of Biomolecular Structure and Dynamics, 1–15. doi:10.1080/07391102.2019.1571947
   Google Scholar
• Singh, A., Goyal, S., Jamal, S., Subramani, B., Das, M., Admane, N., & Grover, A. (2016). Computational identification of novel piperidine derivatives as potential HDM2 inhibitors designed by fragment-based QSAR, molecular docking and molecular dynamics simulations. Structural Chemistry, 27(3), 993–1003. doi:10.1007/s11224-015-0697-2
   Web of Science ®Google Scholar
• Singh, A., Grover, S., Sinha, S., Das, M., Somvanshi, P., & Grover, A. (2017). Mechanistic principles behind molecular mechanism of Rifampicin resistance in mutant RNA polymerase beta subunit of Mycobacterium tuberculosis. Journal of Cellular Biochemistry, 118(12), 4594–4606. doi:10.1002/jcb.26124
   Web of Science ®Google Scholar
• Singh, A., Singh, A., Grover, S., Pandey, B., Kumari, A., & Grover, A. (2018). Wild-type catalase peroxidase vs G279D mutant type: Molecular basis of Isoniazid drug resistance in Mycobacterium tuberculosis. Gene, 641, 226–234. doi:10.1016/j.gene.2017.10.047
   PubMed Web of Science ®Google Scholar
• Singh, A., Somvanshi, P., & Grover, A. (2018). Pyrazinamide drug resistance in RpsA mutant (Δ 438A) of Mycobacterium tuberculosis: Dynamics of essential motions and free‐energy landscape analysis. Journal of Cellular Biochemistry.
   Web of Science ®Google Scholar
• Singh, A., Somvanshi, P., & Grover, A. (2019). Drug repurposing against arabinosyl transferase (EmbC) of Mycobacterium tuberculosis: Essential dynamics and free energy minima based binding mechanics analysis. Gene, 693, 114–126. doi:10.1016/j.gene.2019.01.029.
   Google Scholar
• Spiekermann, P., Rehm, B. H., Kalscheuer, R., Baumeister, D., & Steinbüchel, A. (1999). A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Archives of Microbiology, 171(2), 73–80. doi:10.1007/s002030050681
   PubMed Web of Science ®Google Scholar
• Sudesh, K., Abe, H., & Doi, Y. (2000). Synthesis, structure and properties of polyhydroxyalkanoates: Biological polyesters. Progress in Polymer Science, 25(10), 1503–1555. doi:10.1016/S0079-6700(00)00035-6
   Web of Science ®Google Scholar
• van Gunsteren, W. F., Billeter, S., Eising, A., Hünenberger, P. H., Krüger, P., Mark, A. E., …., Tironi, I. G. (1996). Biomolecular simulation: The GROMOS 96 manual and user guide (pp. 1–1042) . Zürich: VDF Hochschulverlag AG an der ETH Zürich.
   Google Scholar
• Wang, L., Zhang, L., Feng, R. R., Dong, X., Lu, H. Z., & Zhang, J. J. (2019). Unravelling the binding affinity between model transport protein and a prospective tuberculosis therapeutic agent: A spectroscopic and theoretical simulation exploration. Journal of Biomolecular Structure and Dynamics, 1–15. doi:10.1080/07391102.2018.1552624
   PubMed Web of Science ®Google Scholar
• Warner, D. R., & Weinstein, L. S. (1999). A mutation in the heterotrimeric stimulatory guanine nucleotide binding protein α-subunit with impaired receptor-mediated activation because of elevated GTPase activity. Proceedings of the National Academy of Sciences United States of America, 96(8), 4268–4272. doi:10.1073/pnas.96.8.4268
   PubMed Web of Science ®Google Scholar
• Zhu, C., Nomura, C. T., Perrotta, J. A., Stipanovic, A. J., & Nakas, J. P. (2010). Production and characterization of poly‐3‐hydroxybutyrate from biodiesel‐glycerol by Burkholderia cepacia ATCC 17759. Biotechnology Progress, 26(2), 424–30. doi:10.1002/btpr.355
   Web of Science ®Google Scholar