Observing reorientation dynamics with Time-Resolved fluorescence and molecular dynamics in varying periodic boundary conditions

Reference

• Berne, B. J., & Pecora, R. (2000). Dynamic light scattering: With applications to chemistry, biology, and physics. Dover Publications. ISBN 978-1-4613-2389-1.
   Google Scholar
• Boisbouvier, J., Wu, Z., Ono, A., Kainosho, M., & Bax, A. (2003). Rotational diffusion tensor of nucleic acids from 13C NMR relaxation. Journal of Biomolecular NMR, 27(2), 133–142. https://doi.org/10.1023/a:1024931619957
   PubMed Web of Science ®Google Scholar
• Bowman, G. R., Pande, V. S., & Noe, F. Eds. (2014). An introduction to Markov state models and their applications to long timescale molecular simulation. Springer. ISBN 978-94-007-7606-7
   Google Scholar
• Brooks, B. R., Brooks, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30 (10), 1545–1614. https://doi.org/10.1002/jcc.21287
   PubMed Web of Science ®Google Scholar
• Brüschweiler, R., Liao, X., & Wright, P. E. (1995). Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling. Science (New York, N.Y.), 268 (5212), 886–889. https://doi.org/10.1126/science.7754375
   PubMed Web of Science ®Google Scholar
• Debye, P. J. W. (1929). Polar Molecules. Angew. Chemi, 42 (41), 995–995. https://doi.org/10.1002/ange.19290424112
   Google Scholar
• Duchardt, E., Nilsson, L., & Schleucher, J. (2008). Cytosine ribose flexibility in DNA: A combined NMR 13C spin relaxation and molecular dynamics simulation study. Nucleic Acids Research, 36 (12), 4211–4219. https://doi.org/10.1093/nar/gkn375
   PubMed Web of Science ®Google Scholar
• Dünweg, B., & Kremer, K. (1993). Molecular dynamics simulation of a polymer chain in solution. Journal of Chemical Physics., 99 (9), 6983–6997. https://doi.org/10.1063/1.465445
   Web of Science ®Google Scholar
• Ghose, R., Fushman, D., & Cowburn, D. (2001). Determination of the rotational diffusion tensor of macromolecules in solution from NMR relaxation data with a combination of exact and approximate methods-application to the determination of interdomain orientation in multidomain proteins. Journal of Magnetic Resonance (San Diego, Calif. : 1997), 149 (2), 204–217. https://doi.org/10.1006/jmre.2001.2295
   PubMed Web of Science ®Google Scholar
• Hasimoto, H. (1959). On the periodic fundamental solutions of the stokes equations and their application to viscous flow past a cubic array of spheres. Journal of Fluid Mechanics, 5 (02), 317–328. https://doi.org/10.1017/S0022112059000222
   Google Scholar
• Heinz, T. N., Van Gunsteren, W. F., & Hunenberger, P. H. (2001). Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations. Journal of Chemical Physics., 115(3), 1125–1136. https://doi.org/10.1063/1.1379764
   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
• Horn, H. W., Swope, W. C., Pitera, J. W., Madura, J. D., Dick, T. J., Hura, G. L., & Head-Gordon, T. (2004). Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. The Journal of Chemical Physics, 120 (20), 9665–9678. https://doi.org/10.1063/1.1683075
   PubMed Web of Science ®Google Scholar
• Hummer, G., & Szabo, A. (2015). Optimal dimensionality reduction of multistate kinetic and Markov state models. The Journal of Physical Chemistry. B, 119(29), 9029–9037. 2015, https://doi.org/10.1021/jp508375q
   PubMed Web of Science ®Google Scholar
• Hummer, G., & Szabo, A. (2017). Dynamics of the orientational factor in fluorescence resonance energy transfer. The Journal of Physical Chemistry. B, 121 (15), 3331–3339. https://doi.org/10.1021/acs.jpcb.6b08345
   PubMed Web of Science ®Google Scholar
• Ilie, I. M., den Otter, W. K., & Briels, W. J. (2014). Rotational Brownian dynamics simulations of Clathrin cage formation. The Journal of Chemical Physics, 141 (6), 065101. https://doi.org/10.1063/1.4891306
   PubMed Web of Science ®Google Scholar
• Jas, G. S., Childs, E. W., & Kuczera, K. (2021). Probing coupled motions of peptides in solution with fluorescence anisotropy and molecular dynamics simulation. Chemical Physics, 541, 111018. https://doi.org/10.1016/j.chemphys.2020.111018
   Web of Science ®Google Scholar
• Jas, G. S., Eaton, W. A., & Hofrichter, J. (2001). Effect of viscosity on the kinetics of α-helix and β-hairpin formation. The Journal of Physical Chemistry B, 105(1), 261–272. https://doi.org/10.1021/jp0022048
   Web of Science ®Google Scholar
• Jas, G. S., Middaugh, C. R., & Kuczera, K. (2016). Probing selection mechanism of the most favorable conformation of a dipeptide in chaotropic and kosmotropic solution. The Journal of Physical Chemistry. B, 120 (28), 6939–6950. https://doi.org/10.1021/acs.jpcb.6b04528
   PubMed Web of Science ®Google Scholar
• Jas, G. S., Rentchler, E. C., Słowicka, A. M., Hermansen, J. R., Johnson, C. K., Middaugh, C. R., & Kuczera, K. (2016). Reorientation motion and preferential interactions of a peptide in denaturants and osmolyte. The Journal of Physical Chemistry. B, 120(12), 3089–3099. https://doi.org/10.1021/acs.jpcb.6b00028
   PubMed Web of Science ®Google Scholar
• Jas, G. S., Vallejo-Calzada, R., Johnson, C. K., & Kuczera, K. (2019). Dynamic elements and kinetics: Most favorable conformations of peptides in solution with measurements and simulations. The Journal of Chemical Physics, 151 (22), 225102 https://doi.org/10.1063/1.5131782
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., & Jenson, C. (1998). Temperature dependence of TIP3P, SPC and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density. Journal of Computational Chemistry, 19 (10), 1179–1186. https://doi.org/10.1002/(SICI)1096-987X(19980730)19:10<1179::AID-JCC6>3.0.CO;2-J
   Web of Science ®Google Scholar
• Juszczak, L. J., Zhang, Z.-Y., Wu, L., Gottfried, D. S., & Eads, D. D. (1997). Rapid Loop dynamics of Yersinia protein tyrosine phosphatases. Biochemistry, 36 (8), 2227–2236. https://doi.org/10.1021/bi9622130
   PubMed Web of Science ®Google Scholar
• Kaminski, G., & Jorgensen, W. L. (1996). Performance of the AMBER94, MMFF94, and OPLS-AA force fields for modeling organic liquids. the Journal of Physical Chemistry, 100 (46), 18010–18013. https://doi.org/10.1021/jp9624257
   Web of Science ®Google Scholar
• Klein, H. C., & Schwarz, U. S. (2014). Studying protein assembly with reversible Brownian dynamics of patchy particles. The Journal of Chemical Physics, 140 (18), 184112 https://doi.org/10.1063/1.4873708
   PubMed Web of Science ®Google Scholar
• Kube, S., & Weber, M. A. (2007). Coarse Graining method for the identification of transition rates between molecular conformations. The Journal of Chemical Physics, 126(2), 024103. https://doi.org/10.1063/1.2404953
   PubMed Web of Science ®Google Scholar
• Lakowicz, J. R. (1999). Principles of flourescence spectroscopy. Springer. ISBN 978-0-387-46312-4
   Google Scholar
• Lee, L. K., Rance, M., Chazin, W. J., & Palmer, A. G. III (1997). Rotational diffusion anisotropy of proteins from simultaneous analysis of 15n and 13cα nuclear spin relaxation. Journal of Biomolecular NMR, 9(3), 287–298. − https://doi.org/10.1023/A:1018631009583
   PubMed Web of Science ®Google Scholar
• Li, P., Roberts, B. P., Chakravorty, D. K., & Merz, K. M. Jr. (2013). Rational design of particle mesh Ewald compatible Lennard-Jones parameters for +2 metal cations in explicit solvent. Journal of Chemical Theory and Computation, 9(6), 2733–2748. 2013, https://doi.org/10.1021/ct400146w
   PubMed Web of Science ®Google Scholar
• Linke, M., Köfinger, J., & Hummer, G. (2018). Rotational diffusion depends on box size in molecular dynamics simulations. The Journal of Physical Chemistry Letters, 9 (11), 2874–2878. https://doi.org/10.1021/acs.jpclett.8b01090
   PubMed Web of Science ®Google Scholar
• Lipari, G., & Szabo, A. (1982). Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. Journal of the American Chemical Society, 104 (17), 4546–4559. https://doi.org/10.1021/ja00381a009
   Web of Science ®Google Scholar
• Loman, A., Gregor, I., Stutz, C., Mund, M., & Enderlein, J. (2010). Measuring rotational diffusion of macromolecules by fluorescence correlation spectroscopy. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology, 9 (5), 627–636. https://doi.org/10.1039/b9pp00029a
   PubMed Web of Science ®Google Scholar
• Margittai, M., Widengren, J., Schweinberger, E., Schröder, G. F., Felekyan, S., Haustein, E., KöNig, M., Fasshauer, D., GrubmüLler, H., Jahn, R., & Seidel, C. A. M. (2003). Single-molecule fluorescence resonance energy transfer reveals a dynamic equilibrium between closed and open conformations of syntaxin 1. Proceedings of the National Academy of Sciences of the United States of America, 100 (26), 15516–15521. https://doi.org/10.1073/pnas.2331232100
   PubMed Web of Science ®Google Scholar
• McKinney, S. A., DéClais, A.-C., Lilley, D. M. J., & Ha, T. (2003). Structural dynamics of individual Holliday junctions. Nature Structural Biology, 10(2), 93–97. https://doi.org/10.1038/nsb883
   PubMedGoogle Scholar
• Morelli, M. J., & Ten Wolde, P. R. (2008). Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network. The Journal of Chemical Physics, 129 (5), 054112 https://doi.org/10.1063/1.2958287
   PubMed Web of Science ®Google Scholar
• Munro, I., Pecht, I., & Stryer, L. (1979). Subnanosecond motions of tryptophan residues in proteins. Proceedings of the National Academy of Sciences of the United States of America, 76 (1), 56–60. https://doi.org/10.1073/pnas.76.1.56
   PubMed Web of Science ®Google Scholar
• Northrup, S. H., Allison, S. A., & McCammon, J. A. (1984). Brownian dynamics simulation of diffusion-influenced biomolecular reactions. Journal of Chemical Physics, 80 (4), 1517–1524. https://doi.org/10.1063/1.446900
   Web of Science ®Google Scholar
• Ortega, A., Amoros, D., & Garcia De La Torre, J. (2011). Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models. Biophysical Journal, 101 (4), 892–898. https://doi.org/10.1016/j.bpj.2011.06.046
   PubMed Web of Science ®Google Scholar
• Perrin, F. (1934). Mouvement Brownien d’un Ellipsoide - I. Dispersion Dielectrique pour des Mole ́ cules Ellipsoidales. ́ Journal de Physique et le Radium, 5 (10), 497–511. https://doi.org/10.1051/jphysrad:01934005010049700
   Google Scholar
• Perrin, F. (1936). Mouvement Brownien d’un ellipsoide (II). (1936) rotation libre et depolarisation des fluorescences. Translation et diffusion de ́ molecules ellipsoidales. ́Journal de Physique et le Radium, 7(1), 1–11. − https://doi.org/10.1051/jphysrad:01936007010100
   Google Scholar
• Schröder, G. F., & Grubmüller, H. (2003). Maximum likelihood trajectories from single molecule fluorescence resonance energy transfer. Journal of Chemical Physics., 119 (18), 9920. https://doi.org/10.1063/1.1616511
   Web of Science ®Google Scholar
• Schröder, G. F., Alexiev, U., & Grubmüller, H. (2005). Simulation of fluorescence anisotropy experiments: probing protein dynamics. Biophysical Journal, 89 (6), 3757–3770. https://doi.org/10.1529/biophysj.105.069500
   PubMed Web of Science ®Google Scholar
• Schuler, B., Lipman, A., & Eaton, W. A. (2002). Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature, 419 (6908), 743–747. https://doi.org/10.1038/nature01060
   PubMed Web of Science ®Google Scholar
• Senne, M., Trendelkamp-Schroer, B., Mey, A. S. J. S., Schütte, C., & Noé, F. (2012). EMMA: A software package for Markov model building and analysis. Journal of Chemical Theory and Computation, 8 (7), 2223–2238. https://doi.org/10.1021/ct300274u
   PubMed Web of Science ®Google Scholar
• Shoup, D., & Szabo, A. (1982). Role of diffusion in ligand binding to macromolecules and cell-bound receptors. Biophysical Journal, 40 (1), 33–39. https://doi.org/10.1016/S0006-3495(82)84455-X
   PubMed Web of Science ®Google Scholar
• Szabo, A. (1980). Theory of polarized fluorescent emission in uniaxial liquid crystals. Journal of Chemical Physics., 72 (8), 4620–4626. https://doi.org/10.1063/1.439704
   Web of Science ®Google Scholar
• Tjandra, N., Feller, S. E., Pastor, R. W., & Bax, A. (1995). Rotational diffusion anisotropy of human ubiquitin FROM NMR relaxation. Journal of the American Chemical Society, 117 (50), 12562–12566. https://doi.org/10.1021/ja00155a020
   Web of Science ®Google Scholar
• Venable, R. M., Ingólfsson, H. I., Lerner, M. G., Perrin, B. S., Camley, B. A., Marrink, S. J., Brown, F. L. H., & Pastor, R. W. (2017). Lipid and peptide diffusion in bilayers: The Saffman-Delbrück model and periodic boundary conditions. The Journal of Physical Chemistry. B, 121 (15), 3443–3457. https://doi.org/10.1021/acs.jpcb.6b09111
   PubMed Web of Science ®Google Scholar
• Vögele, M., & Hummer, G. (2016). Divergent diffusion coefficients in simulations of fluids and lipid membranes. The Journal of Physical Chemistry. B, 120 (33), 8722–8732. https://doi.org/10.1021/acs.jpcb.6b05102
   PubMed Web of Science ®Google Scholar
• Wang, D., Kreutzer, U., Chung, Y., & Jue, T. (1997). Myoglobin and hemoglobin rotational diffusion in the cell. Biophysical Journal, 73 (5), 2764–2770. https://doi.org/10.1016/S0006-3495(97)78305-X
   PubMed Web of Science ®Google Scholar
• Weiss, S. (1999). Fluorescence spectroscopy of single biomolecules. Science (New York, N.Y.), 283 (5408), 1676–1683. 2. https://doi.org/10.1126/science.283.5408.1676
   PubMed Web of Science ®Google Scholar
• Woessner, D. E. (1962a). Nuclear spin relaxation in ellipsoids undergoing rotational Brownian motion. Journal of Chemical Physics., 37 (3), 647–654. https://doi.org/10.1063/1.1701390
   Web of Science ®Google Scholar
• Woessner, D. E. (1962b). Spin relaxation processes in a two-proton system undergoing anisotropic reorientation. Journal of Chemical Physics., 36 (1), 1–4. https://doi.org/10.1063/1.1732274
   Web of Science ®Google Scholar
• Wolf, M., Gulich, R., Lunkenheimer, P., & Loidl, A. (2012). Relaxation dynamics of a protein solution investigated by dielectric spectroscopy. Biochimica et Biophysica Acta, 1824 (5), 723–730. https://doi.org/10.1016/j.bbapap.2012.02.008
   PubMed Web of Science ®Google Scholar
• Yamamoto, Y., & Tanaka, J. (1972). Polarized absorption spectra of indole and its related compounds. Bulletin of the Chemical Society of Japan, 45 (5), 1362–1366. https://doi.org/10.1246/bcsj.45.1362
   Web of Science ®Google Scholar
• Yeh, I.-C., & Hummer, G. (2004). System-Size dependence of diffusion coefficients and viscosities from molecular dynamics simulations with periodic boundary conditions. The Journal of Physical Chemistry B, 108 (40), 15873–15879. https://doi.org/10.1021/jp0477147
   Web of Science ®Google Scholar