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Research Articles

Computational analysis of protein conformational heterogeneity

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Pages 12100-12105 | Received 15 Feb 2021, Accepted 10 Aug 2021, Published online: 23 Aug 2021

References

  • Abraham, M. J., van der Spoel, D., Lindahl, E., Hess, B., & GROMACS development team. (2016). GROMACS 5.1.2 documentation. http://manual.gromacs.org/documentation/5.1.2/index.html
  • Bowman, G. R., & Geissler, P. L. (2014). Extensive conformational heterogeneity within protein cores. Journal of Physical Chemistry B, 19, 6417–6423.
  • Caldararu, O., Kumar, R., Oksanen, E., Logan, T., & Ulf Ryde, D. (2019). Are crystallographic B-factors suitable for calculating protein conformational entropy? Physical Chemistry Chemical Physics: PCCP, 21(33), 18149–18160. https://doi.org/10.1039/c9cp02504a
  • Childers, M. C., & Daggett, V. (2018). Validating molecular dynamics simulations against experimental observables in light of underlying conformational ensembles. The Journal of Physical Chemistry B, 122(26), 6673–6689. https://doi.org/10.1021/acs.jpcb.8b02144
  • de Gennes, P.-G. (1979). Scaling concepts in polymer physics. Cornel University Press. https://books.google.com/books/about/Scaling_Concepts_in_Polymer_Physics.html?id=ApzfJ2LYwGUC
  • de Kreij, A., van den Burg, B., Venema, G., Vriend, G., Eijsink, V. G. H., & Nielsen, J. E. (2002). The effects of modifying the surface charge on the catalytic activity of a thermolysin-like protease. The Journal of Biological Chemistry, 277(18), 15432–15438. https://doi.org/10.1074/jbc.M200807200
  • Dong, M., Lauro, M. L., Koblish, T. J., & Bahnson, B. J. (2020). Conformational sampling and kinetics changes across a non-Arrhenius break point in the enzyme thermolysin. Structural Dynamics, 7, 014101.
  • Doster, W., Cusack, S., & Petry, W. (1989). Dynamical transition of myoglobin revealed by inelastic neutron scattering. Nature, 337(6209), 754–756. https://doi.org/10.1038/337754a0
  • Fraser, J. S., Clarkson, M. W., Degnan, S. C., Erion, R., Kern, D., & Alber, T. (2009). Hidden alternative structures of proline isomerase essential for catalysis. Nature, 462(7273), 669–673. https://doi.org/10.1038/nature08615
  • Fujii, M., Takagi, M., Imanaka, T., & Aiba, S. (1983). Molecular cloning of a thermostable neutral protease gene from Bacillus stearothermophilus in a vector plasmid and its expression in Bacillus stearothermophilus and Bacillus subtilis. Journal of Bacteriology, 154(2), 831–837. https://doi.org/10.1128/jb.154.2.831-837.1983
  • Glass, D. C., Krishnan, M., Nutt, D. R., & Smith, J. C. (2010). Temperature dependence of protein dynamics simulated with three different water models. Journal of Chemical Theory and Computation, 6(4), 1390–1400. https://doi.org/10.1021/ct9006508
  • Hu, S., Sharma, S. C., Scouras, A. D., Soudackov, A. V., Carr, C. A. M., Hammes-Schiffer, S., Alber, T., & Klinman, J. P. (2014). Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation. Journal of the American Chemical Society, 136(23), 8157–8160. https://doi.org/10.1021/ja502726s
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38.
  • Inouye, K., Lee, S.-B., & Tonomura, B. (1996). Effect of amino acid residues at the cleavable site of substrates on the remarkable activation of thermolysin by salts. Biochemical Journal, 315(1), 133–138. https://doi.org/10.1042/bj3150133
  • Jephthah, S., Staby, L., Kragelund, B. B., & Skepö, M. (2019). Temperature dependence of intrinsically disordered proteins in simulations: What are we missing? Journal of Chemical Theory and Computation, 15(4), 2672–2683. https://doi.org/10.1021/acs.jctc.8b01281
  • Keedy, D. A. (2015). Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Elife, 4, 1–26. https://doi.org/10.7554/eLife.07574
  • Keedy, D. A., Fraser, J. S., & van den Bedem, H. (2015). Exposing hidden alternative backbone conformations in x-ray crystallography using qFit. PLoS Computational Biology, 11, 1–22.
  • Lang, P. T., Ng, H.-L., Fraser, J. S., Corn, J. E., Echols, N., Sales, M., Holton, J. M., & Alber, T. (2010). Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Science, 19(7), 1420–1431. https://doi.org/10.1002/pro.423
  • Liang, Z.-X., Tsigos, I., Lee, T., Bouriotis, V., Resing, K. A., Ahn, N. G., & Klinman, J. P. (2004). Evidence for increased local flexibility in psychrophilic alcohol dehydrogenase relative to its thermophilic homologue. Biochemistry, 43(46), 14676–14683. https://doi.org/10.1021/bi049004x
  • Liu, Y.-H Y., & Konermann, L. (2008). Conformational dynamics of free and catalytically active thermolysin are indistinguishable by hydrogen/deuterium exchange mass spectrometry. Biochemistry, 47(24), 6342–6351. https://doi.org/10.1021/bi800463q
  • Menach, E., Yasukawa, K., & Inouye, K. (2012). Effects of site-directed mutagenesis of the loop residue of the N-terminal domain Gly117 of thermolysin on its catalytic activity. Journal of Biochemistry, 152(3), 231–239. https://doi.org/10.1093/jb/mvs064
  • Merkley, E. D., Parson, W. W., & Daggett, V. (2010). Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold. Protein Engineering, Design & Selection: PEDS, 23(5), 327–336. https://doi.org/10.1093/protein/gzp090
  • Michetti, D., Brandsdal, B. O., Bon, D., Isaksen, G. V., Tiberti, M., & Papaleo, E. (2017). A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular Dynamics simulations. PLoS One, 12(2), e0169586. https://doi.org/10.1371/journal.pone.0169586
  • Nagel, Z. D., Dong, M., Bahnson, B. J., & Klinman, J. P. (2011). Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors. Proceedings of the National Academy of Sciences of the United States of America, 108(26), 10520–10525. https://doi.org/10.1073/pnas.1104989108
  • Nagel, Z. D., Meadows, C. W., Dong, M., Bahnson, B. J., & Klinman, J. P. (2012). Active site hydrophobic residues impact hydrogen tunneling differently in a thermophilic alcohol dehydrogenase at optimal versus nonoptimal temperatures. Biochemistry, 51(20), 4147–4156. https://doi.org/10.1021/bi3001352
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
  • Petsko, G. A., & Ringe, D. (1984). Fluctuations in protein structure from X-ray diffraction. Annual Review of Biophysics and Bioengineering, 13, 331–371. https://doi.org/10.1146/annurev.bb.13.060184.001555
  • Réat, V., Patzelt, H., Ferrand, M., Pfister, C., Oesterhelt, D., & Zaccai, G. (1998). Dynamics of different functional parts of bacteriorhodopsin: H-2H labeling and neutron scattering. Proceedings of the National Academy of Sciences of the United States of America, 95(9), 4970–4975. https://doi.org/10.1073/pnas.95.9.4970
  • Sang, P., Liu, S. Q., & Yang, L. Q. (2020). New insight into mechanisms of protein adaptation to high temperatures: A comparative molecular dynamics simulation study of thermophilic and mesophilic subtilisin-like serine proteases. International Journal of Molecular Sciences, 21, 3128–3140.
  • Tilton, R. F., Dewan, J. C., & Petsko, G. (1992). A. Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. Biochemistry, 31(9), 2469–2481. https://doi.org/10.1021/bi00124a006
  • Zaccai, G. (2000). How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science (New York, N.Y.), 288(5471), 1604–1607. https://doi.org/10.1126/science.288.5471.1604
  • Zhang, X., & Bruice, T. C. (2007). Temperature-dependent structure of the E x S complex of Bacillus stearothermophilus alcohol dehydrogenase. Biochemistry, 46, 837–843.

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