Top

Published in:

2012 | OriginalPaper | Chapter

Applications of Computational Methods to Simulations of Proteins Dynamics

Author : Wieslaw Nowak

Published in: Handbook of Computational Chemistry

Publisher: Springer Netherlands

Activate our intelligent search to find suitable subject content or patents.

search-config

AI-assisted search

Off

Abstract

Advances in computer technology offer great opportunities for new explorations of protein structure and dynamics. Sound and well-established theoretical models may be successfully used for searching new biochemical phenomena, correlations, and protein properties. In this review the fast-growing field of computer simulations of protein dynamics is presented. The principles of currently used computational methods are outlined and representative examples of their recent advanced applications are given. In particular, protein folding studies, protein-drug interactions, transport phenomena, ion channels activity, molecular machines mechanics, origins of molecular diseases, and simulations of single molecule AFM experiments are addressed.

Experimentalists and management will not only become used to accepting the use of molecular modeling, but they will expect it. (Phillip R. Westmoreland)

WTEC Panel Report on Applications of Molecular and Materials Modeling,NIST 2002 (USA)

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

previous chapter Protein Modeling

next chapter Molecular Dynamics and Advanced Sampling Simulations of Nucleic Acids

Achary, M. S., & Nagarajaram, H. A. (2009). Effects of disease causing mutations on the essential motions in proteins. Journal of Biomolecular Structure and Dynamics, 26, 609.

Adcock, S. A., & McCammon, J. A. (2006). Molecular dynamics: Survey of methods for simulating the activity of proteins. Chemical Reviews, 106, 1589.

Aksimentiev, A., Balabin, I. A., Fillingame, R. H., & Schulten, K. (2004). Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Biophysical Journal, 86, 1332.

Aksimentiev, A., Brunner, R., Cohen, J., Comer, J., Cruz-Chu, E., Hardy, D., et al. (2008). Computer modeling in biotechnology: A partner in development. Methods in Molecular Biology, 474, 181.

Alder, B. J., & Wainwright, T. E. (1957). Phase transition for a hard sphere system. Journal of Chemical Physics, 27, 1208.

Aleksandrov, A., Thompson, D., & Simonson, T. (2010). Alchemical free energy simulations for biological complexes: Powerful but temperamental. Journal of Molecular Recognition, 23, 117.

Aliev, A. E., & Courtier-Murias, D. (2010). Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly. The Journal of Physical Chemistry B, 114, 12358.

Allen, M. P., & Tildesley, D. J. (1987). Computer simulation of liquids. Oxford: Clarendon Press.

Alvarez-Paggi, D., Martin, D. F., DeBiase, P. M., Hildebrandt, P., Marti, M. A., & Murgida, D. H. (2010). Molecular basis of coupled protein and electron transfer dynamics of cytochrome c in biomimetic complexes. Journal of the American Chemical Society, 132, 5769.

Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins, 17, 412.

Aqvist, J., Luzhkov, V. B., & Brandsdal, B. O. (2002). Ligand binding affinities from MD simulations. Accounts of Chemical Research, 35, 358.

Ash, W. L., Zlomislic, M. R., Oloo, E. O., & Tieleman, D. P. (2004). Computer simulations of membrane proteins. Biochimica et Biophysica Acta, 1666, 158.

Avila, C. L., Drechsel, N. J., Alcantara, R., & Ville-Freixa, J. (2011). Multiscale molecular dynamics of protein aggregation. Current Protein & Peptide Science, 12(3), 221–234.

Ayton, G. S., Noid, W. G., & Voth, G. A. (2007). Multiscale modeling of biomolecular systems: In serial and in parallel. Current Opinion in Structural Biology, 17, 192.

Ayton, G. S., Lyman, E., & Voth, G. A. (2010). Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. Faraday Discuss, 144, 347.

Bahar, I., & Rader, A. J. (2005). Coarse-grained normal mode analysis in structural biology. Current Opinion in Structural Biology, 15, 586.

Banci, L. (2003). Molecular dynamics simulations of metalloproteins. Current Opinion in Chemical Biology, 7, 143.

Bashford, D., & Case, D. A. (2000). Generalized born models of macromolecular solvation effects. Annual Review of Physical Chemistry, 51, 129.

Becker, O. M., & Karplus, M. (2006). A guide to biomolecular simulations (Vol. 4). Dordrecht: Springer.

Becker, T., Bhushan, S., Jarasch, A., Armache, J. P., Funes, S., Jossinet, F., et al. (2009). Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science, 326, 1369.

Beckstein, O., Biggin, P. C., Bond, P., Bright, J. N., Domene, C., Grottesi, A., et al. (2003). Ion channel gating: Insights via molecular simulations. FEBS Letters, 555, 85.

Berendsen, H. J. C. E. (1976). Proceedings of the CECAM workshop on models for protein dynamics. Orsay: University of Paris.

Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., et al. (2000). The protein data bank. Nucleic Acids Research, 28, 235.

Biarnes, X., Bongarzone, S., Vargiu, A. V., Carloni, P., & Ruggerone, P. (2011). Molecular motions in drug design: The coming age of the metadynamics method. Journal of Computer-Aided Molecular Design, 25, 395.

Bikiel, D. E., Boechi, L., Capece, L., Crespo, A., De Biase, P. M., Di Lella, S., et al. (2006). Modeling heme proteins using atomistic simulations. Physical Chemistry Chemical Physics, 8, 5611.

Boas, F. E., & Harbury, P. B. (2007). Potential energy functions for protein design. Current Opinion in Structural Biology, 17, 199.

Boiteux, C., Kraszewski, S., Ramseyer, C., & Girardet, C. (2007). Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives. Journal of Molecular Modeling, 13, 699.

Borell B. (2008). Chemistry: Power play. Nature, 451, 240.

Brooks, B. R., Brooks, C. L., 3rd, Mackerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., et al. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30, 1545.

Buda, F. (2009). Introduction to theory/modeling methods in photosynthesis, Photosynthesis Research, 102(2–3), 437–441.

Carnevale, V., Raugei, S., Neri, M., Pantano, S., Micheletti, C., & Carloni, P. (2009). Multi-scale modeling of HIV-1 proteins. Journal of Molecular Structure-Theochem, 898, 97.

Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., et al. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26, 1668.

Chen, J., & Brooks, C. L., 3rd. (2008). Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Physical Chemistry Chemical Physics, 10, 471.

Chen, J., Brooks, C. L., 3rd, & Khandogin, J. (2008). Recent advances in implicit solvent-based methods for biomolecular simulations. Current Opinion in Structural Biology, 18, 140.

Chou, K. C. (2004). Structural bioinformatics and its impact to biomedical science. Current Medicinal Chemistry, 11, 2105.

Christ, C. D., Mark, A. E., & van Gunsteren, W. F. (2010). Basic ingredients of free energy calculations: A review. Journal of Computational Chemistry, 31, 1569.

Christen, M., Hunenberger, P. H., Bakowies, D., Baron, R., Burgi, R., Geerke, D. P., et al. (2005). The GROMOS software for biomolecular simulation: GROMOS05. Journal of Computational Chemistry, 26, 1719.

Chu, J.-W., Ayton, G. S., Izvekov, S., & Voth, G. A. (2007). Emerging methods for multiscale simulation of biomolecular systems. Molecular Physics, 105, 167.

Clementi, C. (2008). Coarse-grained models of protein folding: Toy models or predictive tools? Current Opinion in Structural Biology, 18, 10.

Cohen, J., Olsen, K. W., & Schulten, K. (2008). Finding gas migration pathways in proteins using implicit ligand sampling. Methods in Enzymology, 437, 439.

Cornell, W., & Nam, K. (2009). Steroid hormone binding receptors: Application of homology modeling, induced fit docking, and molecular dynamics to study structure-function relationships. Current Topics in Medicinal Chemistry, 9, 844.

Cukier, R. I. (2004). Theory and simulation of proton-coupled electron transfer, hydrogen-atom transfer, and proton translocation in proteins. Biochimica et Biophysica Acta, 1655, 37.

Dahl, J. P. (2001). Introduction to the quantum world of atoms and molecules. Singapore: World Scientific Publishing Co.

Dal Peraro, M., Ruggerone, P., Raugei, S., Gervasi, F., & Elber, R. (2005). Long-timescale simulation methods. Current Opinion in Structural Biology, 15, 151.

Dal Peraro, M., Ruggerone, P., Raugei, S., Gervasio, F. L., & Carloni, P. (2007). Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Current Opinion in Structural Biology, 17, 149.

DeMarco, M. L., & Daggett, V. (2009). Characterization of cell-surface prion protein relative to its recombinant analogue: Insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein. Journal of Neurochemistry, 109, 60.

Deng, Y., & Roux, B. (2009). Computations of standard binding free energies with molecular dynamics simulations. The Journal of Physical Chemistry B, 113, 2234.

Dittrich, M., Freddolino, P. L., & Schulten, K. (2005). When light falls in LOV: A quantum mechanical/ molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii. The Journal of Physical Chemistry B, 109, 13006.

Dittrich, M., & Schulten, K. (2006). PcrA helicase, a prototype ATP-driven molecular motor. Structure, 14, 1345.

Dodson, G. G., Lane, D. P., & Verma, C. S. (2008). Molecular simulations of protein dynamics: New windows on mechanisms in biology. EMBO Reports, 9, 144.

Duan, Y., & Kollman, P. A. (1998). Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science, 282, 740.

Ekonomiuk, D., Kielbasinski, M., & Kolinski, A. (2005). Protein modeling with reduced representation: Statistical potentials and protein folding mechanism. Acta Biochimica Polonica, 52, 741.

Elber, R., Ghosh, A., & Cardenas, A. (2002). Long time dynamics of complex systems. Accounts of Chemical Research, 35, 396.

Elcock, A. H., Sept, D., & McCammon, J. A. (2001). Computer simulation of protein–protein interactions. The Journal of Physical Chemistry B, 105, 1504.

Ensign, D. L., Kasson, P. M., & Pande, V. S. (2007). Heterogeneity even at the speed limit of folding: Large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. Journal of Molecular Biology, 374, 806.

Flechsig, H., & Mikhailov, A. S. (2010). Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations. Proceedings of the National Academy of Sciences of the United States of America, 107, 20875.

Frankel, D., & Smit, B. (2001). Understanding molecular simulation (2nd ed.). San Diego: Academic.

Freddolino, P. L., Arkhipov, A. S., Larson, S. B., McPherson, A., & Schulten, K. (2006a). Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure, 14, 437.

Freddolino, P. L., Dittrich, M., & Schulten, K. (2006b). Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophysical Journal, 91, 3630.

Freddolino, P. L., Liu, F., Gruebele, M., & Schulten, K. (2008). Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophysical Journal, 94, L75.

Freddolino, P. L., Park, S., Roux, B., & Schulten, K. (2009). Force field bias in protein folding simulations. Biophysical Journal, 96, 3772.

Freddolino, P. L., Harrison, C. B., Liu, Y., & Schulten, K. (2010). Challenges in protein folding simulations: Timescale, representation, and analysis. Nature Physics, 6, 751.

Freddolino, P. L., & Schulten, K. (2009). Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophysical Journal, 97, 2338.

Galeazzi, R. (2009). Molecular dynamics as a tool in rational drug design: Current status and some major applications. Current Computer-Aided Drug Design, 5, 225.

Galera-Prat, A., Gomez-Sicilia, A., Oberhauser, A. F., Cieplak, M., & Carrion-Vazquez, M. (2010). Understanding biology by stretching proteins: Recent progress. Current Opinion in Structural Biology, 20, 63.

Gallicchio, E., & Levy, R. M. (2011). Advances in all atom sampling methods for modeling protein-ligand binding affinities. Current Opinion in Structural Biology, 161, 161–166.

Gao, M., Sotomayor, M., Villa, E., Lee, E. H., & Schulten, K. (2006). Molecular mechanisms of cellular mechanics. Physical Chemistry Chemical Physics, 8, 3692.

Grubmueller, H. (2004). “Proteins as molecular machines: Force probe simulations” published in Computational soft matter: From synthetic polymers to proteins, lecture notes. In N. Attig, K. Binder, H. Grubmueller & K. Kremer (Eds.), NIC series (Vol. 23, pp. 401–422). Julich: John von Neumann Institute for Computing. ISBN 3-00-012641-4.

Gu, J., & Bourne, P. E. (Eds.). (2009). Structural bioinformatics (2nd ed.). Hoboken: Wiley-Blackwell.

Gumbart, J., Wang, Y., Aksimentiev, A., Tajkhorshid, E., & Schulten, K. (2005). Molecular dynamics simulations of proteins in lipid bilayers. Current Opinion in Structural Biology, 15, 423.

Guvench, O., & MacKerell, A. D., Jr. (2008). Comparison of protein force fields for molecular dynamics simulations. Methods in Molecular Biology, 443, 63.

Haile, M. (1992). Molecular dynamics simulation: Elementary methods. New York: Wiley.

Hansson, T. O. C., & van Gunsteren, W. (2002). Molecular dynamics simulations. Current Opinion in Structural Biology, 12, 190.

Hardy, D. J., Stone, J. E., & Schulten, K. (2009). Multilevel summation of electrostatic potentials using graphics processing units. Parallel Computing, 35, 164.

Hayashi, S., Tajkhorshid, E., & Schulten, K. (2009). Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation. Biophysical Journal, 96, 403.

Henzler-Wildman, K., & Kern, D. (2007). Dynamic personalities of proteins. Nature, 450, 964.

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, 435.

Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65, 712.

Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51, 69.

Houriez, C., Ferre, N., Masella, M., & Siri, D. (2008). Prediction of nitroxide hyperfine coupling constants in solution from combined nanosecond scale simulations and quantum computations. Journal of Chemical Physics, 128, 244504.

Hsin, J., Arkhipov, A., Yin, Y., Stone, J. E., & Schulten, K. (2008). Using VMD: An introductory tutorial. Current Protocols in Bioinformatics, Chapter 5, p. Unit 5 7.

Hub, J. S., & de Groot, B. L. (2009). Detection of functional modes in protein dynamics. PLoS Computational Biology, 5, e1000480.

Hub, J. S., Grubmuller, H., & de Groot, B. L. (2009). Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? Handbook of Experimental Pharmacology, 190, 57.

Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33.

Ikeguchi, M. (2009). Water transport in aquaporins: Molecular dynamics simulations. Frontiers in Bioscience, 14, 1283.

Jorgensen, W. L., & Tiradorives, J. (1988). The OPLS potential functions for proteins – energy minimizations for crystals of cyclic-peptides and crambin. Journal of the American Chemical Society, 110, 1657.

Kannan, S., & Zacharias, M. (2009). Simulated annealing coupled replica exchange molecular dynamics – an efficient conformational sampling method. Journal of Structural Biology, 166, 288.

Karplus, M. (2003). Molecular dynamics of biological macromolecules: A brief history and perspective. Biopolymers, 68, 350.

Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9, 646.

Kassler, K., Horn, A. H. C., & Sticht, H. (2010). Effect of pathogenic mutations on the structure and dynamics of Alzheimer’s A beta(42)-amyloid oligomers. Journal of Molecular Modeling, 16, 1011.

Khafizov, K., Lattanzi, G., & Carloni, P. (2009). G protein inactive and active forms investigated by simulation methods. Proteins-Structure Function and Bioinformatics, 75, 919.

Khalili-Araghi, F., Gumbart, J., Wen, P. C., Sotomayor, M., Tajkhorshid, E., & Schulten, K. (2009). Molecular dynamics simulations of membrane channels and transporters. Current Opinion in Structural Biology, 19, 128.

Kholmurodov, K. T., Altaisky, M. V., Puzynin, I. V., Darden, T., & Filatov, F. P. (2003). Methods of molecular dynamics for simulation of physical and biological processes. Physics of Particles and Nuclei, 34, 244.

Khurana, E., Devane, R. H., Dal Peraro, M., & Klein, M. L. (2011). Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus. Biochimica et Biophysica Acta, 1808, 530.

Klein, M. L., & Shinoda, W. (2008). Large-scale molecular dynamics simulations of self- assembling systems. Science, 321, 798.

Klepeis, J. L., Pieja, M. J., & Floudas, C. A. (2003). Hybrid global optimization algorithms for protein structure prediction: Alternating hybrids. Biophysical Journal, 84, 869.

Klepeis, J. L., Lindorff-Larsen, K., Dror, R. O., & Shaw, D. E. (2009). Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology, 19, 120.

Kmiecik, S., Gront, D., & Kolinski, A. (2007). Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Structural Biology, 7, 43.

Knapp, B., & Schreiner, W. (2009). Graphical user interfaces for molecular dynamics-quo vadis? Bioinformatics and Biology Insights, 3, 103.

Knoll, P., & Mirzaei, S. (2003). Development of an interactive molecular dynamics simulation software package. Review of Scientific Instruments, 74, 2483.

Kolomeisky, A. B., & Fisher, M. E. (2007). Molecular motors: A theorist’s perspective. Annual Review of Physical Chemistry, 58, 675.

Kremer, K. (2003). Computer simulations for macromolecular science. Macromolecular Chemistry and Physics, 204, 257.

Kubiak, K., & Nowak, W. (2008). Molecular dynamics simulations of the photoactive protein nitrile hydratase. Biophysical Journal, 94, 3824.

Kuczera, K., Jas, G. S., & Elber, R. (2009). Kinetics of helix unfolding: Molecular dynamics simulations with milestoning. The Journal of Physical Chemistry A, 113, 7461.

Kupfer, L., Hinrichs, W., & Groschup, M. H. (2009). Prion protein misfolding. Current Molecular Medicine, 9, 826.

Lange, O. E., Schafer, L. V., & Grubmuller, H. (2006). Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics. Journal of Computational Chemistry, 27, 1693.

Lauria, A., Tutone, M., Ippolito, M., Pantano, L., & Almerico, A. M. (2010). Molecular modeling approaches in the discovery of new drugs for anti-cancer therapy: The investigation of p53-MDM2 interaction and its inhibition by small molecules. Current Medicinal Chemistry, 17, 3142.

Le, L., Lee, E., Schulten, K., & Truong, T. N. (2009). Molecular modeling of swine influenza A/H1N1, Spanish H1N1, and avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza. PLoS Currents: Influenza, 1, RRN1015.

Leach, A. (2001). Molecular modelling: Principles and applications (2nd ed.). Harlow: Prentice Hall.

Lee, E. H., Hsin, J., Sotomayor, M., Comellas, G., & Schulten, K. (2009). Discovery through the computational microscope. Structure, 17, 1295.

Lee, G., Nowak, W., Jaroniec, J., Zhang, Q., & Marszalek, P. E. (2004). Nanomechanical control of glucopyranose rotamers. Journal of the American Chemical Society, 126, 6218.

Lee, K. H., Kuczera, K., & Banaszak Holl, M. M. (2011). The severity of osteogenesis imperfecta: A comparison to the relative free energy differences of collagen model peptides. Biopolymers, 95, 182.

Levitt, M., & Lifson, S. (1969). Refinement of protein conformation using a macromolecular energy minimization procedure. Journal of Molecular Biology, 46, 269.

Liu, J., & Nussinov, R. (2010). Molecular dynamics reveal the essential role of Linker motions in the function of Cullin-RING E3 ligases. Journal of Molecular Biology, 396, 1508.

Liwo, A., Czaplewski, C., Oldziej, S., & Scheraga, H. A. (2008). Computational techniques for efficient conformational sampling of proteins. Current Opinion in Structural Biology, 18, 134.

Lonsdale, R., Ranaghan, K. E., & Mulholland, A. J. (2010). Computational enzymology. Chemical Communications, 46, 2354.

Ma, J., Flynn, T. C., Cui, Q., Leslie, A. G., Walker, J. E., & Karplus, M. (2002). A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure, 10, 921.

Ma, J. P., & Karplus, M. (1997). Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21. Proceedings of the National Academy of Sciences of the United States of America, 94, 11905.

Ma, B., & Levine, A. J. (2007). Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements. Nucleic Acids Research, 35, 7733.

MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., et al. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry B, 102, 3586.

Mackerell, A. D., Jr., & Nilsson, L. (2008). Molecular dynamics simulations of nucleic acid-protein complexes. Current Opinion in Structural Biology, 18, 194.

Marti, M. A., Capece, L., Bidon-Chanal, A., Crespo, A., Guallar, V., Luque, F. J., & Estrin, D. A. (2008). Nitric oxide reactivity with globins as investigated through computer simulation. Methods in Enzymology, 437, 477.

Mayor, U., Guydosh, N. R., Johnson, C. M., Grossmann, J. G., Sato, S., Jas, G. S., et al. (2003). The complete folding pathway of a protein from nanoseconds to microseconds. Nature, 421, 863.

McCammon, J. A., Gelin, B. R., & Karplus, M. (1977). Dynamics of folded proteins. Nature, 267, 585.

Meirovitch, H. (2007). Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation. Current Opinion in Structural Biology, 17, 181.

Miao, L., & Schulten, K. (2009). Transport-related structures and processes of the nuclear pore complex studied through molecular dynamics. Structure, 17, 449.

Miller, B. T., Singh, R. P., Klauda, J. B., Hodoscek, M., Brooks, B. R., & Woodcock, H. L. (2008). CHARMMing: A new, flexible web portal for CHARMM. Journal of Chemical Information and Modeling, 48, 1920.

Moraitakis, G., Purkiss, A. G., & Goodfellow, J. M. (2003). Simulated dynamics and biological molecules. Reports on Progress in Physics, 66, 483.

Morra, G., Meli, M., & Colombo, G. (2008). Molecular dynamics simulations of proteins and peptides: From folding to drug design. Current Protein & Peptide Science, 9, 181.

Morra, G., Genoni, A., Neves, M. A., Merz, K. M., Jr., & Colombo, G (2010) Molecular recognition and drug-lead identification: What can molecular simulations tell us? Current Medicinal Chemistry, 17, 25.

Nielsen, S. O., Bulo, R. E., Moore, P. B., & Ensing, B. (2010). Recent progress in adaptive multiscale molecular dynamics simulations of soft matter. Physical Chemistry Chemical Physics, 12, 12401.

Nowak, W., Czerminski, R., & Elber, R. (1991). Reaction path study of ligand diffusion in proteins: Application of the self penalty walk (SPW) method to calculate reaction coordinates for the motion of CO through leghemoglobin. Journal of the American Chemical Society, 113, 5627.

Nowak, W., & Marszalek, P. (2005). Molecular dynamics simulations of single molecule atomic force microscope experiments. In J. Leszczynski (Ed.), Current trends in computational chemistry (pp. 47–83). Singapore: World Scientific.

Nowak, W., Wasilewski, S., & Peplowski, L. (2007). Steered molecular dynamics as a virtual atomic force microscope. In H. E. Ulrich, J. M. Hansmann, S. Mohanty & O. Zimmermann (Eds.), From computational biophysics to systems biology (CBSB07), Proceedings of the NIC Workshop 2007 (p. 251). Julich: John von Neumann Institute for Computing.

Olsen, S., Lamothe, K., & Martinez, T. J. (2010). Protonic gating of excited-state twisting and charge localization in GFP chromophores: A mechanistic hypothesis for reversible photoswitching. Journal of the American Chemical Society, 132, 1192.

Orlowski, S., & Nowak, W. (2007). Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin. Journal of Molecular Modeling, 13, 715.

Orlowski, S., & Nowak, W. (2008). Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin. Biosystems, 94, 263.

Paci, E. (2002). High pressure simulations of biomolecules. BBA-Protein Structure and Molecular Enzymology, 1595, 185.

Paci, E., Caflisch, A., Pluckthun, A., & Karplus, M. (2001). Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. Journal of Molecular Biology, 314, 589.

Pande, V. S., Baker, I., Chapman, J., Elmer, S. P., Khaliq, S., Larson, S. M., et al. (2003). Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers, 68, 91.

Papaleo, E., & Invernizzi, G. (2011). Conformational diseases: Structural studies of aggregation of polyglutamine proteins. Current Computer-Aided Drug Design, 7, 23.

Peplowski, L., Kubiak, K., & Nowak, W. (2008). Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095. Chemical Physics Letters, 467, 144.

Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., et al. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26, 1781.

Piana, S., Sarkar, K., Lindorff-Larsen, K., Guo, M., Gruebele, M., & Shaw, D. E. (2011). Computational design and experimental testing of the fastest-folding beta-sheet protein. Journal of Molecular Biology, 405, 43.

Pohorille, A., Jarzynski, C., & Chipot, C. (2010). Good practices in free-energy calculations. The Journal of Physical Chemistry B, 114, 10235.

Rahman, A., & Stillinger, F. H. (1971). Molecular dynamics study of liquid water. Journal of Chemical Physics, 55, 3336.

Rapaport, D. C. (1995). The art of molecular dynamics simulation. Cambridge, MA: Cambridge University Press.

Rehm, S., Trodler, P., & Pleiss, J. (2010). Solvent-induced lid opening in lipases: A molecular dynamics study. Protein Science, 19, 2122.

Rief, M., & Grubmuller, H. (2002). Force spectroscopy of single biomolecules. A EuropeanJournal of Chemical Physics and Physical Chemistry, 3, 255.

Rodrigues, J. R., Simoes, C. J. V., Silva, C. G., & Brito, R. M. M. (2010). Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations. Protein Science, 19, 202.

Romanowska, J., Setny, P., & Trylska, J. (2008). Molecular dynamics study of the ribosomal A-site. The Journal of Physical Chemistry B, 112, 15227.

Rosales-Hernandez, M. C., Bermudez-Lugo, J., Garcia, J., Trujillo-Ferrara, J., & Correa-Basurto, J. (2009). Molecular modeling applied to anti-cancer drug development. Anti-Cancer Agents in Medicinal Chemistry, 9, 230.

Rossle, S. C., & Frank, I. (2009). First-principles simulation of photoreactions in biological systems. Frontiers in Bioscience, 14, 4862.

Roux, B., & Schulten, K. (2004). Computational studies of membrane channels. Structure, 12, 1343.

Russel, D., Lasker, K., Phillips, J., Schneidman-Duhovny, D., Velazquez-Muriel, J. A., & Sali, A. (2009). The structural dynamics of macromolecular processes. Current Opinion in Cell Biology, 21, 97.

Sakudo, A., Xue, G. A., Kawashita, N., Ano, Y., Takagi, T., Shintani, H., et al. (2010). Structure of the prion protein and its gene: An analysis using bioinformatics and computer simulation. Current Protein & Peptide Science, 11, 166.

Sanbonmatsu, K. Y., & Tung, C. S. (2007). High performance computing in biology: Multimillion atom simulations of nanoscale systems. Journal of Structural Biology, 157, 470.

Sansom, M. S., Scott, K. A., & Bond, P. J. (2008). Coarse-grained simulation: A high-throughput computational approach to membrane proteins. Biochemical Society Transactions, 36, 27.

Schaeffer, R. D., Fersht, A., & Daggett, V. (2008). Combining experiment and simulation in protein folding: Closing the gap for small model systems. Current Opinion in Structural Biology, 18, 4.

Scheraga, H. A., Khalili, M., & Liwo, A. (2007). Protein-folding dynamics: Overview of molecular simulation techniques. Annual Review of Physical Chemistry, 58, 57.

Scheres, S. H. (2010). Visualizing molecular machines in action: Single-particle analysis with structural variability. Advances in Protein Chemistry and Structural Biology, 81, 89.

Schlegel, H. B. (2003). Exploring potential energy surfaces for chemical reactions: An overview of some practical methods. Journal of Computational Chemistry, 24, 1514.

Schlick, T. (2002). Molecular modeling and simulation – an interdisciplinary guide. New York: Springer.

Schuyler, A. D., Carlson, H. A., & Feldman, E. L. (2009). Computational methods for predicting sites of functionally important dynamics. The Journal of Physical Chemistry B, 113, 6613.

Schwede, T., & Peitsch, M. C. (2008). Computational structural biology: Methods and applications. Hackensack, NJ: World Scientific.

Sellis, D., Vlachakis, D., & Vlassi, M. (2009). Gromita: A fully integrated graphical user interface to Gromacs 4. Bioinformatics and Biology Insights, 3, 99.

Sen, S., Andreatta, D., Ponomarev, S. Y., Beveridge, D. L., & Berg, M. A. (2009). Dynamics of water and ions near DNA: Comparison of simulation to time-resolved stokes-shift experiments. Journal of the American Chemical Society, 131, 1724.

Shakhnovich, E. (2006). Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chemical Reviews, 106, 1559.

Sherwood, P., Brooks, B. R., & Sansom, M. S. (2008). Multiscale methods for macromolecular simulations. Current Opinion in Structural Biology, 18, 630.

Shi, S., Pei, J., Sadreyev, R. I., Kinch, L. N., Majumdar, I., Tong, J., et al. (2009). Analysis of CASP8 targets, predictions and assessment methods. Database (Oxford), 2009, bap003.

Showalter, S. A., & Bruschweiler, R. (2007). Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: Application to the AMBER99SB force field. Journal of Chemical Theory and Computation, 3, 961.

Simms A. M., Toofanny R. D., Kehl C., Benson N. C., and Daggett, V. (2008). Dynameomics: Design of a computational lab workflow and scientific data repository for protein simulations. Protein Engineering, Design and Selection, 21, 369.

Simonson, T., Archontis, G., & Karplus, M. (2002). Free energy simulations come of age: Protein-ligand recognition. Accounts of Chemical Research, 35, 430.

Sotomayor, M., & Schulten, K. (2007). Single-molecule experiments in vitro and in silico. Science, 316, 1144.

Spyrakis, F., BidonChanal, A., Barril, X., & Luque, F. J. (2011). Protein flexibility and ligand recognition: Challenges for molecular modeling. Current Topics in Medicinal Chemistry, 11, 192.

Stone, J. E., Phillips, J. C., Freddolino, P. L., Hardy, D. J., Trabuco, L. G., & Schulten, K. (2007). Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry, 28, 2618.

Straatsma, T. P., & McCammon, J. A. (1992). Computational alchemy. Annual Review of Physical Chemistry, 43, 407.

Straub, J. E., & Thirumalai, D. (2010). Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annual Review of Physical Chemistry, 62, 437.

Strzelecki, J., Mikulska, K., Lekka, M., Kulik, A., Balter, A., & Nowak, W. (2009). AFM force spectroscopy and steered molecular dynamics simulation of protein contactin 4. Acta Physica Polonica A, 116, S156.

Sugita, Y. (2009). Free-energy landscapes of proteins in solution by generalized-ensemble simulations. Frontiers in Bioscience, 14, 1292.

Sugita, Y., & Okamoto, Y. (1999). Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters, 314, 141.

Sun, Q., Doerr, M., Li, Z., Smith, S. C., & Thiel, W. (2010). QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed. Physical Chemistry Chemical Physics, 12, 2450.

Tajkhorshid, E., Aksimentiev, A., Balabin, I., Gao, M., Isralewitz, B., Phillips, J. C., et al. (2003). Large scale simulation of protein mechanics and function. Advances in Protein Chemistry, 66, 195.

Tatke, S. S., Loong, C. K., D’Souza, N., Schoephoerster, R. T., & Prabhakaran, M. (2008). Large scale motions in a biosensor protein glucose oxidase: A combined approach by DENS, normal mode analysis, and molecular dynamics studies. Biopolymers, 89, 582.

Tozzini, V. (2010). Multiscale modeling of proteins. Accounts of Chemical Research, 43, 220.

Tozzini, V., Trylska, J., Chang, C. E., & McCammon, J. A. (2007). Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. Journal of Structural Biology, 157, 606.

Trabuco, L. G., Villa, E., Schreiner, E., Harrison, C. B., & Schulten, K. (2009). Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods, 49, 174.

Trylska, J. (2010). Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome. Journal of Physics: Condensed Matter, 22, 453101.

Urbanc, B., Betnel, M., Cruz, L., Bitan, G., & Teplow, D. B. (2010). Elucidation of amyloid beta-protein oligomerization mechanisms: Discrete molecular dynamics study. Journal of the American Chemical Society, 132, 4266.

Van Der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J. (2008). Biomolecular simulation and modelling: Status, progress and prospects. Journal of the Royal Society Interface, 5, 173.

Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701.

Van Gunsteren, W. F., Bakowies, D., Baron, R., Chandrasekhar, I. C. M., Daura, X., Gee, P., et al. (2006). Biomolecular modeling: Goals, problems, perspectives. Angewandte Chemie International Edition, 45, 4064.

van Oijen, A. M. (2007). Single-molecule studies of complex systems: The replisome. Molecular BioSystems, 3, 117.

van Speybroeck, V., & Meier, R. J. (2003). A recent development in computational chemistry: Chemical reactions from first principles molecular dynamics simulations. Chemical Society Reviews, 32, 151.

Vasquez, V., Sotomayor, M., Cordero-Morales, J., Schulten, K., & Perozo, E. (2008). A structural mechanism for MscS gating in lipid bilayers. Science, 321, 1210.

Vemparala, S., Domene, C., & Klein, M. L. (2010). Computational studies on the interactions of inhalational anesthetics with proteins. Accounts of Chemical Research, 43, 103.

Villa, E., Balaeff, A., & Schulten, K. (2005). Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proceedings of the National Academy of Sciences of the United States of America, 102, 6783.

Vreede, J., Juraszek, J., & Bolhuis, P. G. (2010). Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Proceedings of the National Academy of Sciences of the United States of America, 107, 2397.

Wang, T., & Duan, Y. (2011). Retinal release from opsin in molecular dynamics simulations. Journal of Molecular Recognition, 24, 350.

Wanko, M., Hoffmann, M., Frauenheim, T., & Elstner, M. (2006). Computational photochemistry of retinal proteins. Journal of Computer-Aided Molecular Design, 20, 511.

Warshel, A. (2002). Molecular dynamics simulations of biological reactions. Accounts of Chemical Research, 35, 385.

Warshel, A. (2003). Computer simulations of enzyme catalysis: Methods, progress, and insights. Annual Review of Biophysics and Biomolecular Structure, 32, 425.

Warshel A., Kato M., & Pisliakov A.V. (2007). Polarizable force fields: History, test cases, and prospects. Journal of Chemical Theory and Computation, 3, 2034.

Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., & Weiner, P. (1984). A new force-field for molecular mechanical simulation of nucleic-acids and proteins. Journal of the American Chemical Society, 106, 765.

Wong, V., & Case, D. A. (2008). Evaluating rotational diffusion from protein MD simulations. The Journal of Physical Chemistry B, 112, 6013.

Yu, J., Ha, T., & Schulten, K. (2007). How directional translocation is regulated in a DNA helicase motor. Biophysical Journal, 93, 3783.

Zhang, J., Li, W., Wang, J., Qin, M., Wu, L., Yan, Z., et al. (2009). Protein folding simulations: From coarse-grained model to all-atom model. IUBMB Life, 61, 627.

Zhmurov, A., Dima, R. I., Kholodov, Y., & Barsegov, V. (2010). SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors. Proteins, 78, 2984.

Zhu, F., Tajkhorshid, E., & Schulten, K. (2004). Theory and simulation of water permeation in aquaporin-1. Biophysical Journal, 86, 50.

Zink, M., & Grubmuller, H. (2009). Mechanical properties of the icosahedral shell of Southern bean mosaic virus: A molecular dynamics study. Biophysical Journal, 96, 1350.

Title: Applications of Computational Methods to Simulations of Proteins Dynamics
Author: Wieslaw Nowak
Publisher: Springer Netherlands
Book: Handbook of Computational Chemistry
Print ISBN: 978-94-007-0710-8

Electronic ISBN: 978-94-007-0711-5

Copyright Year: 2012
DOI: https://doi.org/10.1007/978-94-007-0711-5_31

Springer Professional

Abstract

Please log in to get access to your license.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Premium Partner