메뉴 건너뛰기




Volumn 305, Issue , 2005, Pages 493-515

Force Probe Molecular Dynamics Simulations

Author keywords

enforced protein unfolding; force probe simulation; ligand receptor unbinding; Molecular dynamics simulation; nonequilibrium statistical mechanics; protein dynamics; rescaling of loading rates; rupture force calculation; steered molecular dynamics; unfolding forces

Indexed keywords

BIOTIN; LIGAND; MOLECULAR MOTOR; PROTEIN; STREPTAVIDIN;

EID: 21344467900     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1385/1-59259-912-5_493     Document Type: Chapter
Times cited : (33)

References (75)
  • 1
    • 0030059225 scopus 로고    scopus 로고
    • Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
    • Grubmüller, H., Heymann, B., and Tavan, P. (1996) Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 271, 997– 999.
    • (1996) Science , vol.271 , pp. 997-999
    • Grubmüller, H.1    Heymann, B.2    Tavan, P.3
  • 2
    • 0030987036 scopus 로고    scopus 로고
    • Molecular dynamics study of unbinding of the avidin-biotin complex
    • Izrailev, S., Stepaniants, S., Balsera, M., Oono, Y., and Schulten, K. (1997) Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J. 72, 1568–1581.
    • (1997) Biophys. J. , vol.72 , pp. 1568-1581
    • Izrailev, S.1    Stepaniants, S.2    Balsera, M.3    Oono, Y.4    Schulten, K.5
  • 4
    • 0017258698 scopus 로고
    • Single-channel currents recorded from membrane of denervated frog muscle fibres
    • Neher, E. and Sakmann, B. (1976) Single-channel currents recorded from membrane of denervated frog muscle fibres. Nature 260, 799–802.
    • (1976) Nature , vol.260 , pp. 799-802
    • Neher, E.1    Sakmann, B.2
  • 5
    • 85152480774 scopus 로고    scopus 로고
    • Rugged LV Trench IGBT with Extreme Stability in Continuous SOA Operation: Next Generation LV Technology at Hitachi ABB Powergrids
    • Sakmann, B. and Neher, E., eds. (1995) Single-Channel Recording. 2nd Ed., Plenum Press.
    • PCIM Europe Digital Days 2021
  • 6
    • 0037026489 scopus 로고    scopus 로고
    • The voltage-gated potassium channels and their relatives
    • Yellen, G. (2002) The voltage-gated potassium channels and their relatives. Nature 419, 35–42.
    • (2002) Nature , vol.419 , pp. 35-42
    • Yellen, G.1
  • 8
    • 0023140044 scopus 로고
    • Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin
    • Elber, R. and Karplus, M. (1987) Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science 235, 318–321.
    • (1987) Science , vol.235 , pp. 318-321
    • Elber, R.1    Karplus, M.2
  • 9
    • 0030021471 scopus 로고    scopus 로고
    • Bio-molecular dynamics comes of age
    • Berendsen, H. J. C. (1996) Bio-molecular dynamics comes of age. Science 271, 954–955.
    • (1996) Science , vol.271 , pp. 954-955
    • Berendsen, H.J.C.1
  • 11
    • 0035861454 scopus 로고    scopus 로고
    • Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF
    • de Groot, B. L. and Grubmüller, H. (2001) Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF. Science 294, 2353–2357.
    • (2001) Science , vol.294 , pp. 2353-2357
    • de Groot, B.L.1    Grubmüller, H.2
  • 12
    • 0035812426 scopus 로고    scopus 로고
    • Simulation of the spontaneous aggregation of phospholipids into bilayers
    • Marrink, S. J., Lindahl, E., Edholm, O., and Mark, A. E. (2001) Simulation of the spontaneous aggregation of phospholipids into bilayers. J. Am. Chem. Soc. 123, 8638–8639.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 8638-8639
    • Marrink, S.J.1    Lindahl, E.2    Edholm, O.3    Mark, A.E.4
  • 14
    • 0036499409 scopus 로고    scopus 로고
    • Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations
    • Colombo, G., Roccatano, D., and Mark, A. E. (2002) Folding and stability of the three-stranded beta-sheet peptide betanova: insights from molecular dynamics simulations. Proteins 46, 380–392.
    • (2002) Proteins , vol.46 , pp. 380-392
    • Colombo, G.1    Roccatano, D.2    Mark, A.E.3
  • 16
    • 0017776823 scopus 로고
    • Dynamics of folded proteins
    • McCammon, J. A., Gelin, B. R., and Karplus, M. (1977) Dynamics of folded proteins. Nature 267, 585–590.
    • (1977) Nature , vol.267 , pp. 585-590
    • McCammon, J.A.1    Gelin, B.R.2    Karplus, M.3
  • 17
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • van Gunsteren, W. F. and Berendsen, H. J. C. (1977) Algorithms for macromolecular dynamics and constraint dynamics. Molec. Phys. 34, 1311–1327.
    • (1977) Molec. Phys. , vol.34 , pp. 1311-1327
    • van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 18
    • 0035861430 scopus 로고    scopus 로고
    • Reality simulation—observe while it happens
    • Berendsen, H. J. C. (2001) Reality simulation—observe while it happens. Science 294, 2304–2305.
    • (2001) Science , vol.294 , pp. 2304-2305
    • Berendsen, H.J.C.1
  • 21
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus, M. and McCammon, J. A. (2002) Molecular dynamics simulations of biomolecules. Nature Struct. Biol. 9, 646–652.
    • (2002) Nature Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 22
    • 76549252207 scopus 로고
    • The structure of proteins: Two hydrogen-bonded helical configurations of polypeptide chain
    • Pauling, L., Corey, R. B., and Branson, H. R. (1951) The structure of proteins: two hydrogen-bonded helical configurations of polypeptide chain. Proc. Natl. Acad. Sci. USA 37, 205.
    • (1951) Proc. Natl. Acad. Sci. USA , vol.37 , pp. 205
    • Pauling, L.1    Corey, R.B.2    Branson, H.R.3
  • 24
    • 2142813682 scopus 로고
    • Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry
    • van Gunsteren, W. F. and Berendsen, H. J. C. (1990) Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew. Chem. Int. Ed. 29, 992–1023.
    • (1990) Angew. Chem. Int. Ed. , vol.29 , pp. 992-1023
    • van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 25
    • 0001994422 scopus 로고    scopus 로고
    • Simulating complex systems without adjustable parameters
    • Parrinello, M. (2000) Simulating complex systems without adjustable parameters. IEEE Comput. Sci. Eng. 2, 22–27.
    • (2000) IEEE Comput. Sci. Eng. , vol.2 , pp. 22-27
    • Parrinello, M.1
  • 26
    • 0000695782 scopus 로고    scopus 로고
    • Understanding modern molecular dynamics: Techniques and applications
    • Tuckerman, M. E. and Martyna, G. J. (2000) Understanding modern molecular dynamics: techniques and applications. J. Phys. Chem. B. 104, 159–178.
    • (2000) J. Phys. Chem. B. , vol.104 , pp. 159-178
    • Tuckerman, M.E.1    Martyna, G.J.2
  • 27
    • 85152480774 scopus 로고    scopus 로고
    • Rugged LV Trench IGBT with Extreme Stability in Continuous SOA Operation: Next Generation LV Technology at Hitachi ABB Powergrids
    • van Gunsteren, W. F., Weiner, P. K., and Wilkinson, A. J., eds. (1989–1997) Computer Simulation of Biomolecular Systems: Theoretical and Experimiental Applications, vol. 1–3, Escom, Leiden, The Netherlands.
    • PCIM Europe Digital Days 2021
  • 29
    • 0028309424 scopus 로고
    • Adhesion forces between individual ligand-receptor pairs
    • Florin, E.-L., Moy, V. T., and Gaub, H. E. (1994) Adhesion forces between individual ligand-receptor pairs. Science 264, 415–417.
    • (1994) Science , vol.264 , pp. 415-417
    • Florin, E.-L.1    Moy, V.T.2    Gaub, H.E.3
  • 30
    • 0028381539 scopus 로고
    • Sensing discrete streptavidin-biotin interactions with atomic force microscopy
    • Lee, G. U., Kidwell, D. A., and Colton, R. J. (1994) Sensing discrete streptavidin-biotin interactions with atomic force microscopy. Langmuir 10, 354–357.
    • (1994) Langmuir , vol.10 , pp. 354-357
    • Lee, G.U.1    Kidwell, D.A.2    Colton, R.J.3
  • 31
    • 0028261701 scopus 로고
    • Single myosin molecule mechanics: Piconewton forces and nanometer steps
    • Finer, J. T., Simmons, R. M., and Spudich, J. A. (1994) Single myosin molecule mechanics: piconewton forces and nanometer steps. Nature 368, 113–119.
    • (1994) Nature , vol.368 , pp. 113-119
    • Finer, J.T.1    Simmons, R.M.2    Spudich, J.A.3
  • 33
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: Conformational flooding
    • Grubmüller, H. (1995) Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys. Rev. E. 52, 2893.
    • (1995) Phys. Rev. E. , vol.52 , pp. 2893
    • Grubmüller, H.1
  • 34
    • 0037080723 scopus 로고    scopus 로고
    • Predicting unimolecular chemical reactions: Chemical flooding
    • Müller, E. M., de Meijere, A., and Grubmüller, H. (2002) Predicting unimolecular chemical reactions: Chemical flooding. Biophys. J. 116, 897–905.
    • (2002) Biophys. J. , vol.116 , pp. 897-905
    • Müller, E.M.1    de Meijere, A.2    Grubmüller, H.3
  • 35
    • 0031011695 scopus 로고    scopus 로고
    • Reversible unfolding of individual titin immunoglobulin domains by AFM
    • Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J. M., and Gaub, H. E. (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276, 1109–1112.
    • (1997) Science , vol.276 , pp. 1109-1112
    • Rief, M.1    Gautel, M.2    Oesterhelt, F.3    Fernandez, J.M.4    Gaub, H.E.5
  • 37
    • 0037066262 scopus 로고    scopus 로고
    • Force spectroscopy of single biomolecules
    • Rief, M. and Grubmüller, H. (2002) Force spectroscopy of single biomolecules. Chem. Phys. Chem. 3, 255–261.
    • (2002) Chem. Phys. Chem. , vol.3 , pp. 255-261
    • Rief, M.1    Grubmüller, H.2
  • 38
    • 0031848099 scopus 로고    scopus 로고
    • Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
    • Lu, H., Isralewitz, B., Krammer, A., Vogel, V., and Schulten, K. (1998) Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys. J. 75, 662–671.
    • (1998) Biophys. J. , vol.75 , pp. 662-671
    • Lu, H.1    Isralewitz, B.2    Krammer, A.3    Vogel, V.4    Schulten, K.5
  • 40
    • 0033531973 scopus 로고    scopus 로고
    • Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
    • Paci, E. and Karplus, M. (1999) Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J. Molec. Biol. 288, 441–459.
    • (1999) J. Molec. Biol. , vol.288 , pp. 441-459
    • Paci, E.1    Karplus, M.2
  • 41
    • 0033917135 scopus 로고    scopus 로고
    • The key event in force-induced unfolding of titin’s immunoglubin domains
    • Lu, H. and Schulten, K. (2000) The key event in force-induced unfolding of titin’s immunoglubin domains. Biophys. J. 79, 51–65.
    • (2000) Biophys. J. , vol.79 , pp. 51-65
    • Lu, H.1    Schulten, K.2
  • 42
    • 0034804341 scopus 로고    scopus 로고
    • Can non-me-chanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation
    • Best, R. B., Li, B., Steward, A., Daggett, V., and Clarke, J. (2001) Can non-me-chanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophys. J. 81, 2344–2356.
    • (2001) Biophys. J. , vol.81 , pp. 2344-2356
    • Best, R.B.1    Li, B.2    Steward, A.3    Daggett, V.4    Clarke, J.5
  • 43
    • 0035976752 scopus 로고    scopus 로고
    • Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study
    • Paci, E., Caflisch, A., Plückthun, A., and Karplus, M. (2001) Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. J. Molec. Biol. 314, 589–605.
    • (2001) J. Molec. Biol. , vol.314 , pp. 589-605
    • Paci, E.1    Caflisch, A.2    Plückthun, A.3    Karplus, M.4
  • 44
    • 0036389817 scopus 로고    scopus 로고
    • Mechanical unfolding of a titin Ig domain: Structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering
    • Fowlere, S. B., Best, R. B., Herrera, J. L. T., Rutherford, T. J., Steward, A., Paci, E., Karplus, M., and Clarke, J. (2002) Mechanical unfolding of a titin Ig domain: Structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J. Mol. Biol. 322, 841–849.
    • (2002) J. Mol. Biol. , vol.322 , pp. 841-849
    • Fowlere, S.B.1    Best, R.B.2    Herrera, J.L.T.3    Rutherford, T.J.4    Steward, A.5    Paci, E.6    Karplus, M.7    Clarke, J.8
  • 45
    • 0031042739 scopus 로고    scopus 로고
    • Single molecule force spectroscopy reveals conformational change in polysaccharides
    • Rief, M., Oesterhelt, F., Heymann, B., and Gaub, H. E. (1997) Single molecule force spectroscopy reveals conformational change in polysaccharides. Science 275, 1295–1297.
    • (1997) Science , vol.275 , pp. 1295-1297
    • Rief, M.1    Oesterhelt, F.2    Heymann, B.3    Gaub, H.E.4
  • 46
    • 0344327079 scopus 로고    scopus 로고
    • Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads
    • MacKerell, A. D. and Lee, G. U. (1999) Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads. Europ. Biophys. J. 28, 415–426.
    • (1999) Europ. Biophys. J. , vol.28 , pp. 415-426
    • Mackerell, A.D.1    Lee, G.U.2
  • 47
    • 0002688989 scopus 로고    scopus 로고
    • Elastic properties of poly(Ethylene-gly-col) studied by molecular dynamics stretching simulations
    • Heymann, B. and Grubmüller, H. (1999) Elastic properties of poly(ethylene-gly-col) studied by molecular dynamics stretching simulations. Chem. Phys. Lett. 307, 425–432.
    • (1999) Chem. Phys. Lett. , vol.307 , pp. 425-432
    • Heymann, B.1    Grubmüller, H.2
  • 48
    • 0042852135 scopus 로고    scopus 로고
    • Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations
    • Gullingsrud, J., Braun, R., and Schulten, K. (1999) Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J. Comp. Phys. 151, 190–211.
    • (1999) J. Comp. Phys. , vol.151 , pp. 190-211
    • Gullingsrud, J.1    Braun, R.2    Schulten, K.3
  • 49
    • 0042885340 scopus 로고    scopus 로고
    • Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality
    • Park, S., Khalili-Araghi, F., Tajkhorshid, E., and Schulten, K. (2003) Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality. J. Chem. Phys. 119, 3559–3566.
    • (2003) J. Chem. Phys. , vol.119 , pp. 3559-3566
    • Park, S.1    Khalili-Araghi, F.2    Tajkhorshid, E.3    Schulten, K.4
  • 50
    • 4143087050 scopus 로고    scopus 로고
    • Calculating potentials of mean force from steered molecular dynamics simulations
    • Park, S. and Schulten, K. (2004) Calculating potentials of mean force from steered molecular dynamics simulations. J. Chem. Phys. 120, 5946–5961.
    • (2004) J. Chem. Phys. , vol.120 , pp. 5946-5961
    • Park, S.1    Schulten, K.2
  • 51
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • Isralewitz, B., Gao, M., and Schulten, K. (2001) Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11, 224–230.
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 52
    • 1442328108 scopus 로고    scopus 로고
    • Advances in biomolecular simulations: Methodology and recent applications
    • Norberg, J. and Nilsson, L. (2003) Advances in biomolecular simulations: methodology and recent applications. Q. Rev. Biophys. 36, 257–306.
    • (2003) Q. Rev. Biophys. , vol.36 , pp. 257-306
    • Norberg, J.1    Nilsson, L.2
  • 53
    • 0018101150 scopus 로고
    • Models for specific adhesion of cells to cells
    • Bell, G. I. (1978) Models for specific adhesion of cells to cells. Science 200, 618–627.
    • (1978) Science , vol.200 , pp. 618-627
    • Bell, G.I.1
  • 54
    • 0031001349 scopus 로고    scopus 로고
    • Dynamic strength of molecular adhesion bonds
    • Evans, E. and Ritchie, K. (1997) Dynamic strength of molecular adhesion bonds. Biophys. J. 72, 1541–1555.
    • (1997) Biophys. J. , vol.72 , pp. 1541-1555
    • Evans, E.1    Ritchie, K.2
  • 55
    • 0034688856 scopus 로고    scopus 로고
    • Rupture of multiple parallel molecular bonds under dynamic loading
    • Seifert, U. (2000) Rupture of multiple parallel molecular bonds under dynamic loading. Phys. Rev. Lett. 84, 2750–2753.
    • (2000) Phys. Rev. Lett. , vol.84 , pp. 2750-2753
    • Seifert, U.1
  • 56
    • 0342350248 scopus 로고    scopus 로고
    • Dynamic force spectroscopy of molecular adhesion bonds
    • Heymann, B. and Grubmüller, H. (2000) Dynamic force spectroscopy of molecular adhesion bonds. Phys. Rev. Lett. 84, 6126–6129.
    • (2000) Phys. Rev. Lett. , vol.84 , pp. 6126-6129
    • Heymann, B.1    Grubmüller, H.2
  • 57
    • 0038650860 scopus 로고    scopus 로고
    • Kinetics from nonequilibrium single-molecule pulling experiments
    • Hummer, G. and Szabo, A. (2003) Kinetics from nonequilibrium single-molecule pulling experiments. Biophys. J. 85, 5–15.
    • (2003) Biophys. J. , vol.85 , pp. 5-15
    • Hummer, G.1    Szabo, A.2
  • 58
    • 2142746284 scopus 로고
    • The activated complex in chemical reactions
    • Eyring, H. (1935) The activated complex in chemical reactions. J. Chem. Phys. 3, 107–115.
    • (1935) J. Chem. Phys. , vol.3 , pp. 107-115
    • Eyring, H.1
  • 59
    • 34547275473 scopus 로고
    • Brownian motion in a field of force and the diffusion model of chemical reactions
    • Kramers, H. A. (1940) Brownian motion in a field of force and the diffusion model of chemical reactions. Physica (Utrecht) VII, 284–304.
    • (1940) Physica (Utrecht) VII , pp. 284-304
    • Kramers, H.A.1
  • 60
    • 0347193736 scopus 로고
    • Reaction-rate theory: Fifty years after Kramers
    • Hänggi, P., Talkner, P., and Borkovec, M. (1990) Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62, 251–341.
    • (1990) Rev. Mod. Phys. , vol.62 , pp. 251-341
    • Hänggi, P.1    Talkner, P.2    Borkovec, M.3
  • 61
    • 0013412734 scopus 로고    scopus 로고
    • AN02/DNP unbinding forces studied by molecular dynamics AFM simulations
    • Heymann, B. and Grubmüller, H. (1999) AN02/DNP unbinding forces studied by molecular dynamics AFM simulations. Chem. Phys. Lett. 303, 1–9.
    • (1999) Chem. Phys. Lett. , vol.303 , pp. 1-9
    • Heymann, B.1    Grubmüller, H.2
  • 62
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., Hess, B., and van der Spoel, D. (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7, 306–317.
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 63
    • 85152480774 scopus 로고    scopus 로고
    • Rugged LV Trench IGBT with Extreme Stability in Continuous SOA Operation: Next Generation LV Technology at Hitachi ABB Powergrids
    • Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kalé, L., Skeel, R. D., and Schulten, K. (1995) NAMD–a parallel, object-oriented molecular dynamics program. Technical report, Beckman Institute.
    • PCIM Europe Digital Days 2021
  • 64
    • 85147446965 scopus 로고    scopus 로고
    • EGO—An efficient molecular dynamics program and its application to protein dynamics simulations, in: Workshop on Molecular Dynamics on Parallel Computers, John von Neumann Institute for Computing (NIC) Research Centre Jülich, Germany, 8–10 February 1999, (Esser, R., Grassberger, P., Grotendorst, J., and Lewerenz, M., eds.), pp. 154–174, World Scientific
    • Eichinger, M., Heller, H., and Grubmüller, H. (2000) EGO—An efficient molecular dynamics program and its application to protein dynamics simulations, in: Workshop on Molecular Dynamics on Parallel Computers, John von Neumann Institute for Computing (NIC) Research Centre Jülich, Germany, 8–10 February 1999, (Esser, R., Grassberger, P., Grotendorst, J., and Lewerenz, M., eds.), pp. 154–174, World Scientific, Singapore 912805.
    • (2000) Singapore 912805
    • Eichinger, M.1    Heller, H.2    Grubmüller, H.3
  • 67
    • 0028071373 scopus 로고
    • Entropic elasticity of lambda-phage DNA
    • Bustamante, C., Marko, J. F., Siggia, E. D., and Smith, S. (1994) Entropic elasticity of lambda-phage DNA. Science 265, 1599–1600.
    • (1994) Science , vol.265 , pp. 1599-1600
    • Bustamante, C.1    Marko, J.F.2    Siggia, E.D.3    Smith, S.4
  • 68
    • 0034500645 scopus 로고    scopus 로고
    • Similarities between principal components of protein dynamics and random diffusion
    • Hess, B. (2000) Similarities between principal components of protein dynamics and random diffusion. Phys. Rev. E. 62, 8438–8448.
    • (2000) Phys. Rev. E. , vol.62 , pp. 8438-8448
    • Hess, B.1
  • 69
    • 0032584783 scopus 로고    scopus 로고
    • Reversible peptide folding in solution by molecular dynamics simulation
    • Daura, X., Jaun, B., Seebach, D., van Gunsteren, W. F., and Mark, A. E. (1998) Reversible peptide folding in solution by molecular dynamics simulation. J. Molec. Biol. 280, 925–932.
    • (1998) J. Molec. Biol. , vol.280 , pp. 925-932
    • Daura, X.1    Jaun, B.2    Seebach, D.3    van Gunsteren, W.F.4    Mark, A.E.5
  • 71
    • 0034825161 scopus 로고    scopus 로고
    • A strategy for analysis of (Molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization
    • Hamprecht, F. A., Peter, C., Daura, X., Thiel, W., and van Gunsteren, W. F. (2001) A strategy for analysis of (molecular) equilibrium simulations: configuration space density estimation, clustering, and visualization. J. Chem. Phys. 114, 2079–2089.
    • (2001) J. Chem. Phys. , vol.114 , pp. 2079-2089
    • Hamprecht, F.A.1    Peter, C.2    Daura, X.3    Thiel, W.4    van Gunsteren, W.F.5
  • 72
    • 0035946983 scopus 로고    scopus 로고
    • Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds
    • de Groot, B. L., Daura, X., Mark, A. E., and Grubmüller, H. (2001) Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. J. Molec. Biol. 309, 299–313.
    • (2001) J. Molec. Biol. , vol.309 , pp. 299-313
    • de Groot, B.L.1    Daura, X.2    Mark, A.E.3    Grubmüller, H.4
  • 74
    • 0041305824 scopus 로고    scopus 로고
    • Structural transitions and elasticity from torque measurements on DNA
    • Bryant, Z., Stone, M. D., Gore, J., Smith, S. B., Cozzarelli, N. R., and Bustamante, C. (2003) Structural transitions and elasticity from torque measurements on DNA. Nature 424, 338–341.
    • (2003) Nature , vol.424 , pp. 338-341
    • Bryant, Z.1    Stone, M.D.2    Gore, J.3    Smith, S.B.4    Cozzarelli, N.R.5    Bustamante, C.6
  • 75
    • 0034874258 scopus 로고    scopus 로고
    • Molecular dynamics force probe simulations of antibody/antigen unbinding: Entropic control and non-additivity of unbinding forces
    • Heymann, B. and Grubmüller, H. (2001) Molecular dynamics force probe simulations of antibody/antigen unbinding: entropic control and non-additivity of unbinding forces. Biophys. J. 81, 1295–1313.
    • (2001) Biophys. J. , vol.81 , pp. 1295-1313
    • Heymann, B.1    Grubmüller, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.