Investigation of the conformation of human prion protein in ethanol solution using molecular dynamics simulations

References

• Aguzzi, A., & Calella, A. M. (2009). Prions: Protein aggregation and infectious diseases. Physiological Reviews, 89(4), 1105–1152. https://doi.org/10.1152/physrev.00006.2009
   PubMed Web of Science ®Google Scholar
• Alred, E. J., Lodangco, I., Gallaher, J., & Hansmann, U. (2018). Mutations alter RNA-mediated conversion of human prions. ACS Omega, 3(4), 3936–3944. https://doi.org/10.1021/acsomega.7b02007
   PubMed Web of Science ®Google Scholar
• Amin, M. A., Halder, R., Ghosh, C., Jana, B., & Bhattacharyya, K. (2016). Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations. The Journal of Chemical Physics, 145(23), 235102. https://doi.org/10.1063/1.4972065
   PubMed Web of Science ®Google Scholar
• Benetti, F., Biarnes, X., Attanasio, F., Giachin, G., Rizzarelli, E., & Legname, G. (2014). Structural determinants in prion protein folding and stability. Journal of Molecular Biology, 426(22), 3796–3810. https://doi.org/10.1016/j.jmb.2014.09.017
   PubMed Web of Science ®Google Scholar
• Bermudez, M., Mortier, J., Rakers, C., Sydow, D., & Wolber, G. (2016). More than a look into a crystal ball: Protein structure elucidation guided by molecular dynamics simulations. Drug Discovery Today. 21(11), 1799–1805. https://doi.org/10.1016/j.drudis.2016.07.001
   PubMed Web of Science ®Google Scholar
• Borgohain, G., Dan, N., & Paul, S. (2016). Use of molecular dynamics simulation to explore structural facets of human prion protein with pathogenic mutations. Biophysical Chemistry, 213, 32–39. https://doi.org/10.1016/j.bpc.2016.03.004
   PubMed Web of Science ®Google Scholar
• Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995). Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins, 21(3), 167–195. https://doi.org/10.1002/prot.340210302
   PubMed Web of Science ®Google Scholar
• Buck, T., Jansen, C. H. P., Levine, R. A., & Handschumacher, M. D. (1998). Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins. Quarterly Reviews of Biophysics, 31(3), 297–355.
   PubMed Web of Science ®Google Scholar
• Buck, M., Radford, S. E., & Dobson, C. M. (1993). A partially folded state of hen egg white lysozyme in trifluoroethanol: Structural characterization and implications for protein folding. Biochemistry, 32(2), 669–678. https://doi.org/10.1021/bi00053a036
   PubMed Web of Science ®Google Scholar
• Calzolai, L., & Zahn, R. (2003). Influence of pH on NMR structure and stability of the human prion protein globular domain. The Journal of Biological Chemistry, 278(37), 35592–35596. https://doi.org/10.1074/jbc.M303005200
   PubMed Web of Science ®Google Scholar
• Canchi, D. R., & Garcia, A. E. (2013). Cosolvent effects on protein stability. Annual Review of Physical Chemistry, 64, 273–293. https://doi.org/10.1146/annurev-physchem-040412-110156
   PubMed Web of Science ®Google Scholar
• Caughey, B., & Chesebro, B. (2001). Transmissible spongiform encephalopathies and prion protein interconversions. Advances in Virus Research, 56, 277–311. https://doi.org/10.1016/s0065-3527(01)56031-5
   PubMed Web of Science ®Google Scholar
• Chamachi, N. G., & Chakrabarty, S. (2017). Temperature-induced misfolding in prion protein: Evidence of multiple partially disordered states stabilized by non-native hydrogen bonds. Biochemistry, 56(6), 833–844. https://doi.org/10.1021/acs.biochem.6b01042
   PubMed Web of Science ®Google Scholar
• Chen, X., Duan, D. H., Zhu, S. Y., & Zhang, J. L. (2013). Molecular dynamics simulation of temperature induced unfolding of animal prion protein. Journal of Molecular Modeling, 19(10), 4433–4441. https://doi.org/10.1007/s00894-013-1955-0
   PubMed Web of Science ®Google Scholar
• Chu, Y. P., & Kordower, J. H. (2015). The prion hypothesis of Parkinson’s disease. Current Neurology and Neuroscience Reports, 15(5), 3045–3054.
   Web of Science ®Google Scholar
• Collinge, J. (1999). Variant Creutzfeldt-Jakob disease. Lancet (London, England), 354(9175), 317–323. https://doi.org/10.1016/S0140-6736(99)05128-4
   PubMed Web of Science ®Google Scholar
• Collins, S. J., Lawson, V. A., & Masters, C. L. (2004). Transmissible spongiform encephalopathies. Lancet, 363(9402), 51–61.
   PubMed Web of Science ®Google Scholar
• DeMarco, M. L., & Daggett, V. (2007). Molecular mechanism for low pH triggered misfolding of the human prion protein. Biochemistry, 46(11), 3045–3054., https://doi.org/10.1021/bi0619066
   PubMed Web of Science ®Google Scholar
• Eghiaian, F., Daubenfeld, T., Quenet, Y., van Audenhaege, M., Bouin, A. P., van der Rest, G., Grosclaude, J., & Rezaei, H. 2007. Diversity in prion protein oligomerization pathways results from domain expansion as revealed by hydrogen/deuterium exchange and disulfide linkage. Proceedings of the National Academy of Sciences, 104(18), 7414–7419.
   PubMed Web of Science ®Google Scholar
• Gu, W., Wang, T., Zhu, J., Shi, Y., & Liu, H. (2003). Molecular dynamics simulation of the unfolding of the human prion protein domain under low pH and high temperature conditions. Biophysical Chemistry, 104(1), 79–94.
   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. https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Honda, R. (2018). Role of the disulfide bond in prion protein amyloid formation: A thermodynamic and kinetic analysis. Biophysical Journal, 114(4), 885–892. https://doi.org/10.1016/j.bpj.2017.12.031
   PubMed Web of Science ®Google Scholar
• Jaspe, J., & Hagen, S. J. (2006). Do protein molecules unfold in a simple shear flow? Biophysical Journal, 91(9), 3415–3424.
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935., ).
   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. https://doi.org/10.1002/bip.360221211
   PubMed Web of Science ®Google Scholar
• Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105(28), 6474–6487.
   Web of Science ®Google Scholar
• Lee, B., & Richards, F. M. (1971). The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology, 55(3), 379–400.
   PubMed Web of Science ®Google Scholar
• Lugaresi, E., Medori, R., Montagna, P., Baruzzi, A., Cortelli, P., Lugaresi, A., Tinuper, P., Zucconi, M., & Gambetti, P. (1986). Fatal familial insomnia and dysautonomia with selective degeneration of thalamic nuclei. The New England Journal of Medicine, 315(16), 997–1003. https://doi.org/10.1056/NEJM198610163151605
   PubMed Web of Science ®Google Scholar
• Lysek, D. A., Schorn, C., Nivon, L. G., Esteve-Moya, V., Christen, B., Calzolai, L., von Schroetter, C., Fiorito, F., Herrmann, T., Guntert, P., & Wuthrich, K. (2005). Prion protein NMR structures of cats, dogs, pigs, and sheep. Proceedings of the National Academy of Sciences of the United States of America, 102(3), 640–645. https://doi.org/10.1073/pnas.0408937102
   PubMed Web of Science ®Google Scholar
• Mu, Y. G., Nguyen, P. H., & Stock, G. (2004). Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins: Structure, Function, and Bioinformatics, 58(1), 45–52.
   Web of Science ®Google Scholar
• Okumura, H. (2012). Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric-multithermal molecular dynamics method. Proteins, 80(10), 2397–2416. https://doi.org/10.1002/prot.24125
   PubMed Web of Science ®Google Scholar
• Onuchic, J. N., Luthey-Schulten, Z., & Wolynes, P. G. (1997). Theory of protein folding: The energy landscape perspective. Annual Review of Physical Chemistry, 48, 545–600. https://doi.org/10.1146/annurev.physchem.48.1.545
   PubMed Web of Science ®Google Scholar
• Palaniappan, C., Narayanan, R. C., & Sekar, K. (2021). Mutation-dependent refolding of prion protein unveils amyloidogenic-related structural ramifications: Insights from molecular dynamics simulations. ACS Chemical Neuroscience, 12(15), 2810–2819. https://doi.org/10.1021/acschemneuro.1c00142
   PubMed Web of Science ®Google Scholar
• Pan, K. M., Baldwin, M., Nguyen, J., Gasset, M., Serban, A., Groth, D., Mehlhorn, I., Huang, Z., Fletterick, R. J., & Cohen, F. E. (1993). Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins. Proceedings of the National Academy of Sciences of the United States of America, 90(23), 10962–10966. https://doi.org/10.1073/pnas.90.23.10962
   PubMed Web of Science ®Google Scholar
• Pan, A. C., Jacobson, D., Yatsenko, K., Sritharan, D., Weinreich, T. M., & Shaw, D. E. (2019). Atomic-level characterization of protein-protein association. Proceedings of the National Academy of Sciences of the United States of America, 116(10), 4244–4249. https://doi.org/10.1073/pnas.1815431116
   PubMed Web of Science ®Google Scholar
• Perezzan, R., & Rey, A. (2012). Simulating protein unfolding under pressure with a coarse-grained model. The Journal of Chemical Physics, 137(18), 185102. https://doi.org/10.1063/1.4765057
   PubMed Web of Science ®Google Scholar
• Plattner, N., Doerr, S., Fabritiis, G. D., & Noe, F. (2017). Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nature Chemistry, 9(10), 1005–1011. https://doi.org/10.1038/nchem.2785
   PubMed Web of Science ®Google Scholar
• Polymenidou, M., & Cleveland, D. W. (2011). The seeds of neurodegeneration: Prion-like spreading in ALS. Cell, 147(3), 498–508. https://doi.org/10.1016/j.cell.2011.10.011
   PubMed Web of Science ®Google Scholar
• Prasad, A., Bharathi, V., Sivalingam, V., Girdhar, A., & Patel, B. K. (2019). Frontiers in molecular neuroscience. Frontiers in Molecular Neuroscience, 12, 25. ( https://doi.org/10.3389/fnmol.2019.00025
   PubMed Web of Science ®Google Scholar
• Prusiner, S. B. (1982). Novel proteinaceous infectious particles cause scrapie. Science (New York, N.Y.), 216(4542), 136–144. https://doi.org/10.1126/science.6801762
   PubMed Web of Science ®Google Scholar
• Prusiner, S. B. (1996). Molecular biology and pathogenesis of prion diseases. Trends in Biochemical Sciences, 21(12), 482–487.
   PubMed Web of Science ®Google Scholar
• Prusiner, S. B. (1997). Prion diseases and the BSE crisis. Science (New York, N.Y.), 278(5336), 245–251. https://doi.org/10.1126/science.278.5336.245
   PubMed Web of Science ®Google Scholar
• Prusiner, S. B. (1998). Prions. Proceedings of the National Academy of Sciences of the United States of America, 95(23), 13363–13383. https://doi.org/10.1073/pnas.95.23.13363
   PubMed Web of Science ®Google Scholar
• Sengupta, I., Bhate, S. H., Das, R., & Udgaonkar, J. B. (2017). Salt-mediated oligomerization of the mouse prion protein monitored by real-time NMR. Journal of Molecular Biology, 429(12), 1852–1872.
   PubMed Web of Science ®Google Scholar
• Shao, Q., Fan, Y., Yang, L., & Gao, Y. Q. (2012). From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions. The Journal of Chemical Physics, 136(11), 115101. https://doi.org/10.1063/1.3692801
   PubMed Web of Science ®Google Scholar
• Singh, R. K., Chamachi, N. G., Chakrabarty, S., & Mukherjee, A. (2017). Mechanism of unfolding of human prion protein. The Journal of Physical Chemistry. B, 121(3), 550–564. https://doi.org/10.1021/acs.jpcb.6b11416
   PubMed Web of Science ®Google Scholar
• Tang, J. L., Wu, P. J., Wang, S. C., & Lee, C. I. (2012). Insights into structural properties of denatured human prion 121-230 at melting temperature studied by replica exchange molecular dynamics. The Journal of Physical Chemistry. B, 116(10), 3305–3312. https://doi.org/10.1021/jp208433w
   PubMed Web of Science ®Google Scholar
• Thompson, H. N., Thompson, C. E., Caceres, R. A., Dardenne, L. E., Netz, P. A., & Stassen, H. (2018). Prion protein conversion triggered by acidic condition: A molecular dynamics study through different force fields. Journal of Computational Chemistry, 39(24), 2000–2011. https://doi.org/10.1002/jcc.25380
   PubMed Web of Science ®Google Scholar
• Uversky, V. N., Narizhneva, N. V., Kirschstein, S. O., Winter, S., & Lober, G. (1997). Fold Des. Mismatch, 2(3), 163–172.
   Google Scholar
• Weissmann, C. (1996). The Ninth Datta Lecture. Molecular biology of transmissible spongiform encephalopathies. FEBS Letters, 389(1), 3–11.
   PubMed Web of Science ®Google Scholar
• Wen, Y., Li, J., Yao, W., Xiong, M., Hong, J., Peng, Y., Xiao, G., & Lin, D. (2010). Unique structural characteristics of the rabbit prion protein. The Journal of Biological Chemistry, 285(41), 31682–31693. https://doi.org/10.1074/jbc.M110.118844
   PubMed Web of Science ®Google Scholar
• Zahn, R., Liu, A., Luhrs, T., Riek, R., von Schroetter, C., Lopez Garcia, F., Billeter, M., Calzolai, L., Wider, G., & Wuthrich, K. (2000). NMR solution structure of the human prion protein. Proceedings of the National Academy of Sciences of the United States of America, 97(1), 145–150. https://doi.org/10.1073/pnas.97.1.145
   PubMed Web of Science ®Google Scholar
• Zhou, S., Liu, X., An, X., Yao, X., & Liu, H. (2017). Molecular dynamics simulation study on the binding and stabilization mechanism of antiprion compounds to the "hot spot" region of PrPC. ACS Chemical Neuroscience, 8(11), 2446–2456. https://doi.org/10.1021/acschemneuro.7b00214
   PubMed Web of Science ®Google Scholar
• Ziaunys, M., Sakalauskas, A., Mikalauskaite, K., Snieckute, R., & Smirnovas, V. (2021). Temperature-dependent structural variability of prion protein amyloid fibrils. International Journal of Molecular Sciences, 22(10), 5075. )https://doi.org/10.3390/ijms22105075
   PubMed Web of Science ®Google Scholar