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Volumn 373, Issue 1749, 2018, Pages

A non-equilibrium approach to allosteric communication

Author keywords

Allosteric transition; Downhill folding; Dynamic content; Free energy landscape; Non equilibrium molecular dynamics simulations; Time resolved vibrational spectroscopy

Indexed keywords

CHEMICAL BINDING; EXPERIMENTAL DESIGN; EXPERIMENTAL STUDY; HIERARCHICAL SYSTEM; LIGAND; MODEL VALIDATION; MOLECULAR ANALYSIS; PROBE; PROTEIN;

EID: 85046705129     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2017.0187     Document Type: Article
Times cited : (49)

References (85)
  • 1
    • 0346220393 scopus 로고    scopus 로고
    • The role of dynamics in allosteric regulation
    • Kern D, Zuiderweg E. 2003 The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13, 748–757. (doi:10.1016/j.sbi.2003.10.008)
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 748-757
    • Kern, D.1    Zuiderweg, E.2
  • 2
    • 6344219895 scopus 로고    scopus 로고
    • Is allostery an intrinsic property of all dynamic proteins?
    • Gunasekaran K, Ma B, Nussinov R. 2004 Is allostery an intrinsic property of all dynamic proteins? Proteins 57, 433–443. (doi:10.1002/prot.20232)
    • (2004) Proteins , vol.57 , pp. 433-443
    • Gunasekaran, K.1    Ma, B.2    Nussinov, R.3
  • 3
    • 48249141040 scopus 로고    scopus 로고
    • Allostery and cooperativity revisited
    • Cui Q, Karplus M. 2008 Allostery and cooperativity revisited. Protein. Sci. 17, 1295–1307. (doi:10. 1110/ps.03259908)
    • (2008) Protein. Sci. , vol.17 , pp. 1295-1307
    • Cui, Q.1    Karplus, M.2
  • 4
    • 84861219631 scopus 로고    scopus 로고
    • Allostery and the Monod- Wyman-Changeux model after 50 years
    • Changeux J-P. 2012 Allostery and the Monod- Wyman-Changeux model after 50 years. Ann. Rev. Biophys. 41, 103–133. (doi:10.1146/annurev-biophys-050511-102222)
    • (2012) Ann. Rev. Biophys. , vol.41 , pp. 103-133
    • Changeux, J.-P.1
  • 5
    • 84898993517 scopus 로고    scopus 로고
    • The ensemble nature of allostery
    • Motlagh HN, Wrabl JO, Li J, Hilser VJ. 2014 The ensemble nature of allostery. Nature 508, 331–339. (doi:10.1038/nature13001)
    • (2014) Nature , vol.508 , pp. 331-339
    • Motlagh, H.N.1    Wrabl, J.O.2    Li, J.3    Hilser, V.J.4
  • 6
    • 84974555787 scopus 로고    scopus 로고
    • Special issue on protein ensembles and allostery
    • Nussinov R. 2016 Special issue on protein ensembles and allostery. Chem. Rev. 116, 6263–6266. (doi:10.1021/acs.chemrev.6b00283)
    • (2016) Chem. Rev. , vol.116 , pp. 6263-6266
    • Nussinov, R.1
  • 7
    • 84974627299 scopus 로고    scopus 로고
    • Protein allostery and conformational dynamics
    • Guo J, Zhou H-X. 2016 Protein allostery and conformational dynamics. Chem. Rev. 116, 6503–6515. (doi:10.1021/acs.chemrev.5b00590)
    • (2016) Chem. Rev. , vol.116 , pp. 6503-6515
    • Guo, J.1    Zhou, H.-X.2
  • 8
    • 84974577224 scopus 로고    scopus 로고
    • Controlling allosteric networks in proteins
    • Dokholyan NV. 2016 Controlling allosteric networks in proteins. Chem. Rev. 116, 6463–6487. (doi:10. 1021/acs.chemrev.5b00544)
    • (2016) Chem. Rev. , vol.116 , pp. 6463-6487
    • Dokholyan, N.V.1
  • 9
    • 84984865333 scopus 로고    scopus 로고
    • Computational approaches to investigating allostery
    • Schueler-Furman O, Wodak SJ. 2016 Computational approaches to investigating allostery. Curr. Opin. Struct. Biol. 41, 159–171. (doi:10.1016/j.sbi. 2016.06.017)
    • (2016) Curr. Opin. Struct. Biol. , vol.41 , pp. 159-171
    • Schueler-Furman, O.1    Wodak, S.J.2
  • 11
    • 84886954019 scopus 로고    scopus 로고
    • Single-molecule fluorescence probes dynamics of barrier crossing
    • Chung HS, Eaton WA. 2013 Single-molecule fluorescence probes dynamics of barrier crossing. Nature 502, 685–688. (doi:10.1038/nature12649)
    • (2013) Nature , vol.502 , pp. 685-688
    • Chung, H.S.1    Eaton, W.A.2
  • 12
    • 77955505542 scopus 로고    scopus 로고
    • Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation
    • Hub JS, Kubitzki M, de Groot BL. 2010 Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation. PLoS Comput. Biol. 6, e1000774. (doi:10.1371/journal. pcbi.1000774)
    • (2010) Plos Comput. Biol. , vol.6
    • Hub, J.S.1    Kubitzki, M.2    de Groot, B.L.3
  • 13
    • 84931287895 scopus 로고    scopus 로고
    • Free energy landscape of activation in a signalling protein at atomic resolution
    • Pontiggia F, Pachov D, Clarkson M, Villali J, Hagan M, Pande V, Kern D. 2015 Free energy landscape of activation in a signalling protein at atomic resolution. Nat. Commun. 6, 7284. (doi:10.1038/ncomms8284)
    • (2015) Nat. Commun , vol.6 , pp. 7284
    • Pontiggia, F.1    Pachov, D.2    Clarkson, M.3    Villali, J.4    Hagan, M.5    Pande, V.6    Kern, D.7
  • 17
    • 70450228044 scopus 로고    scopus 로고
    • Fast protein folding
    • (ed. R Schweitzer-Stenner, London, UK: The Royal Society of Chemistry
    • Gruebele M 2008 Fast protein folding. In Protein folding, misfolding and aggregation (ed. R Schweitzer-Stenner), pp. 106–138. London, UK: The Royal Society of Chemistry.
    • (2008) Protein Folding, Misfolding and Aggregation , pp. 106-138
    • Gruebele, M.1
  • 18
    • 0030628825 scopus 로고    scopus 로고
    • Theory of protein folding: The energy landscape perspective
    • Onuchic JN, Schulten ZL, Wolynes PG. 1997 Theory of protein folding: the energy landscape perspective. Annu. Rev. Phys. Chem. 48, 545–600. (doi:10.1146/annurev.physchem.48.1.545)
    • (1997) Annu. Rev. Phys. Chem. , vol.48 , pp. 545-600
    • Onuchic, J.N.1    Schulten, Z.L.2    Wolynes, P.G.3
  • 20
    • 84903302956 scopus 로고    scopus 로고
    • An introduction to Markov state models
    • Germany: Springer
    • Bowman GR, Pande VS, Noe F 2013 An introduction to Markov state models. Heidelberg, Germany: Springer.
    • (2013) Heidelberg
    • Bowman, G.R.1    Pande, V.S.2    Noe, F.3
  • 21
    • 0021658956 scopus 로고
    • Allostery without conformational change—a plausible model
    • Cooper A, Dryden D. 1984 Allostery without conformational change—a plausible model. Europ. Biophys. J. Biophys. Lett. 11, 103–109. (doi:10. 1007/BF00276625)
    • (1984) Europ. Biophys. J. Biophys. Lett. , vol.11 , pp. 103-109
    • Cooper, A.1    Dryden, D.2
  • 22
    • 84887037245 scopus 로고    scopus 로고
    • Allostery without conformational change: Modelling protein dynamics at multiple scales
    • McLeish TCB, Rodgers TL, Wilson MR. 2013 Allostery without conformational change: modelling protein dynamics at multiple scales. Phys. Biol. 10, 056004. (doi:10.1088/1478-3975/10/ 5/056004)
    • (2013) Phys. Biol. , vol.10
    • McLeish, T.C.B.1    Rodgers, T.L.2    Wilson, M.R.3
  • 23
    • 0033723528 scopus 로고    scopus 로고
    • Femtochemistry: Atomic-scale dynamics of the chemical bond
    • Zewail AH. 2000 Femtochemistry: atomic-scale dynamics of the chemical bond. J. Phys. Chem. A 104, 5660–5694. (doi:10.1021/jp001460h)
    • (2000) J. Phys. Chem. A , vol.104 , pp. 5660-5694
    • Zewail, A.H.1
  • 24
    • 0030789351 scopus 로고    scopus 로고
    • Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpreted with a ‘kinetic zipper’ model
    • Thompson PA, Eaton WA, Hofrichter J. 1997 Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpreted with a ‘kinetic zipper’ model. Biochemistry 36, 9200–9210. (doi:10.1021/bi9704764)
    • (1997) Biochemistry , vol.36 , pp. 9200-9210
    • Thompson, P.A.1    Eaton, W.A.2    Hofrichter, J.3
  • 25
    • 84874227957 scopus 로고    scopus 로고
    • Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy
    • Jones KC, Peng CS, Tokmakoff A. 2013 Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy. Proc. Natl Acad. Sci. USA 110, 2828–2833. (doi:10.1073/pnas. 1211968110)
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 2828-2833
    • Jones, K.C.1    Peng, C.S.2    Tokmakoff, A.3
  • 26
    • 33645399069 scopus 로고    scopus 로고
    • Nonequilibrium protein folding dynamics: Laser induced pH-jump studies of the helix-coil transition
    • Causgrove TP, Dyer RB. 2006 Nonequilibrium protein folding dynamics: laser induced pH-jump studies of the helix-coil transition. Chem. Phys. 323, 2–10. (doi:10.1016/j.chemphys. 2005.08.032)
    • (2006) Chem. Phys. , vol.323 , pp. 2-10
    • Causgrove, T.P.1    Dyer, R.B.2
  • 27
    • 84921915792 scopus 로고    scopus 로고
    • PH-jump induced leucine zipper folding beyond the diffusion limit
    • Donten ML, Hassan S, Popp A, Halter J, Hauser K, Hamm P. 2015 pH-jump induced leucine zipper folding beyond the diffusion limit. J. Phys. Chem. B 119, 1425–1432. (doi:10.1021/jp511539c)
    • (2015) J. Phys. Chem. B , vol.119 , pp. 1425-1432
    • Donten, M.L.1    Hassan, S.2    Popp, A.3    Halter, J.4    Hauser, K.5    Hamm, P.6
  • 28
    • 33745294757 scopus 로고    scopus 로고
    • Azobenzene as conformational switch in model peptides
    • Renner C, Moroder L. 2006 Azobenzene as conformational switch in model peptides. Chem. Biol. Chem. 7, 869–878. (doi:10.1002/cbic. 200500531)
    • (2006) Chem. Biol. Chem. , vol.7 , pp. 869-878
    • Renner, C.1    Moroder, L.2
  • 29
    • 43949092430 scopus 로고    scopus 로고
    • Two-dimensional infrared spectroscopy of photoswitchable peptides
    • Hamm P, Helbing J, Bredenbeck J. 2008 Two-dimensional infrared spectroscopy of photoswitchable peptides. Annu. Rev. Phys. Chem. 59, 291–317. (doi:10.1146/annurev.physchem.59. 032607.093757)
    • (2008) Annu. Rev. Phys. Chem. , vol.59 , pp. 291-317
    • Hamm, P.1    Helbing, J.2    Bredenbeck, J.3
  • 31
    • 84880355882 scopus 로고    scopus 로고
    • Kinetic response of a photoperturbed allosteric protein
    • Buchli B et al. 2013 Kinetic response of a photoperturbed allosteric protein. Proc. Natl Acad. Sci. USA 110, 11725–11730. (doi:10.1073/pnas. 1306323110)
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 11725-11730
    • Buchli, B.1
  • 32
    • 85027402370 scopus 로고    scopus 로고
    • Time-resolved observation of protein allosteric communication
    • Buchenberg S, Sittel F, Stock G. 2017 Time-resolved observation of protein allosteric communication. Proc. Natl Acad. Sci. USA 114, E6804–E6811. (doi:10.1073/pnas.1707694114)
    • (2017) Proc. Natl Acad. Sci. USA , vol.114 , pp. E6804-E6811
    • Buchenberg, S.1    Sittel, F.2    Stock, G.3
  • 33
    • 0347753736 scopus 로고    scopus 로고
    • Ligand-dependent dynamics and intramolecular signaling in a PDZ domain
    • Fuentes E, Der C, Lee A. 2004 Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J. Mol. Biol. 335, 1105–1115. (doi:10. 1016/j.jmb.2003.11.010)
    • (2004) J. Mol. Biol , vol.335 , pp. 1105-1115
    • Fuentes, E.1    Der, C.2    Lee, A.3
  • 35
    • 77952705907 scopus 로고    scopus 로고
    • PDZ domains and their binding partners: Structure, specificity
    • Lee H-J, Zheng JJ. 2010 PDZ domains and their binding partners: structure, specificity, and modification. Cell Commun. Signal. 8, 8. (doi:10. 1186/1478-811X-8-8)
    • (2010) And Modification. Cell Commun. Signal , vol.8 , pp. 8
    • Lee, H.-J.1    Zheng, J.J.2
  • 36
    • 84884245462 scopus 로고    scopus 로고
    • Structures and target recognition modes of PDZ domains: Recurring themes and emerging pictures
    • Ye F, Zhang M. 2013 Structures and target recognition modes of PDZ domains: recurring themes and emerging pictures. Biochem. J. 455, 1–14. (doi:10.1042/BJ20130783)
    • (2013) Biochem. J. , vol.455 , pp. 1-14
    • Ye, F.1    Zhang, M.2
  • 37
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless SW, Ranganathan R. 1999 Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286, 295–299. (doi:10. 1126/science.286.5438.295)
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 38
    • 22444450449 scopus 로고    scopus 로고
    • Intramolecular signaling pathways revealed by molecular anisotropic thermal diffusion
    • Ota N, Agard DA. 2005 Intramolecular signaling pathways revealed by molecular anisotropic thermal diffusion. J. Mol. Biol. 351, 345–354. (doi:10.1016/j.jmb.2005.05.043)
    • (2005) J. Mol. Biol. , vol.351 , pp. 345-354
    • Ota, N.1    Agard, D.A.2
  • 39
    • 58949102247 scopus 로고    scopus 로고
    • Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis
    • Kong Y, Karplus M. 2009 Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins 74, 145–154. (doi:10. 1002/prot.22139)
    • (2009) Proteins , vol.74 , pp. 145-154
    • Kong, Y.1    Karplus, M.2
  • 40
    • 80055066238 scopus 로고    scopus 로고
    • Change in allosteric network affects binding affinities of PDZ domains: Analysis through perturbation response scanning
    • Gerek ZN, Ozkan SB. 2011 Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning. PLoS Comput. Biol. 7, e1002154. (doi:10.1371/journal.pcbi.1002154)
    • (2011) Plos Comput. Biol. , vol.7
    • Gerek, Z.N.1    Ozkan, S.B.2
  • 41
    • 84937040398 scopus 로고    scopus 로고
    • Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study
    • Ishikura T, Iwata Y, Hatano T, Yamato T. 2015 Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: a computational study. J. Comput. Chem. 36, 1709–1718. (doi:10.1002/jcc.23989)
    • (2015) J. Comput. Chem. , vol.36 , pp. 1709-1718
    • Ishikura, T.1    Iwata, Y.2    Hatano, T.3    Yamato, T.4
  • 42
    • 85024408796 scopus 로고    scopus 로고
    • Hidden electrostatic basis of dynamic allostery in a PDZ domain
    • Kumawat A, Chakrabarty S. 2017 Hidden electrostatic basis of dynamic allostery in a PDZ domain. Proc. Natl Acad. Sci. USA 114, E5825–E5834. (doi:10.1073/pnas.1705311114)
    • (2017) Proc. Natl Acad. Sci. USA , vol.114 , pp. E5825-E5834
    • Kumawat, A.1    Chakrabarty, S.2
  • 43
    • 33750795402 scopus 로고    scopus 로고
    • Evaluation of energetic and dynamic coupling networks in a PDZ domain protein
    • Fuentes EJ, Gilmore SA, Mauldin RV, Lee AL. 2006 Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. J. Mol. Biol. 364, 337–351. (doi:10.1016/j.jmb.2006.08.076)
    • (2006) J. Mol. Biol. , vol.364 , pp. 337-351
    • Fuentes, E.J.1    Gilmore, S.A.2    Mauldin, R.V.3    Lee, A.L.4
  • 44
    • 33845186553 scopus 로고    scopus 로고
    • Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering
    • Gianni S et al. 2006 Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering. Structure 14, 1801–1809. (doi:10.1016/j.str.2006.10.010)
    • (2006) Structure , vol.14 , pp. 1801-1809
    • Gianni, S.1
  • 45
    • 78049307619 scopus 로고    scopus 로고
    • Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E
    • Zhang J, Sapienza PJ, Ke H, Chang A, Hengel SR, Wang H, PhillipsJr GN, Lee AL. 2010 Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E. Biochemistry 49, 9280–9291. (doi:10.1021/bi101131f)
    • (2010) Biochemistry , vol.49 , pp. 9280-9291
    • Zhang, J.1    Sapienza, P.J.2    Ke, H.3    Chang, A.4    Hengel, S.R.5    Wang, H.6    Phillipsjr, G.N.7    Lee, A.L.8
  • 46
    • 77957937199 scopus 로고    scopus 로고
    • Atomic-level characterization of the structural dynamics of proteins
    • Shaw DE et al. 2010 Atomic-level characterization of the structural dynamics of proteins. Science 330, 341–346. (doi:10.1126/science.1187409)
    • (2010) Science , vol.330 , pp. 341-346
    • Shaw, D.E.1
  • 48
    • 78650901019 scopus 로고    scopus 로고
    • A current-transient methodology for trap analysis for GaN high electron mobility transistors
    • Joh J, Alamo JAD. 2011 A current-transient methodology for trap analysis for GaN high electron mobility transistors. IEEE Trans. Electron Devices 58, 132–140. (doi:10.1109/TED.2010.2087339)
    • (2011) IEEE Trans. Electron Devices , vol.58 , pp. 132-140
    • Joh, J.1    Alamo, J.A.D.2
  • 49
    • 84978933867 scopus 로고    scopus 로고
    • Advances in Data Mining. Applications and Theoretical Aspects. ICDM 2016 (ed. P Perner). Lecture Notes in Computer Science, Cham, Switzerland: Springer
    • Knyazev A, Gao Q, Teo K 2016 Multi-exponential lifetime extraction in time-logarithmic scale. In Advances in Data Mining. Applications and Theoretical Aspects. ICDM 2016 (ed. P Perner). Lecture Notes in Computer Science, vol. 9728, pp. 282–296. Cham, Switzerland: Springer.
    • (2016) Multi-Exponential Lifetime Extraction in Time-Logarithmic Scale , vol.9728 , pp. 282-296
    • Knyazev, A.1    Gao, Q.2    Teo, K.3
  • 50
    • 0035899723 scopus 로고    scopus 로고
    • On the rate distribution analysis of kinetic data using the maximum entropy method: Applications to myoglobin relaxation on the nanosecond and femtosecond timescales
    • Kumar ATN, Zhu L, Christian JF, Demidov AA, Champion PM. 2001 On the rate distribution analysis of kinetic data using the maximum entropy method: applications to myoglobin relaxation on the nanosecond and femtosecond timescales. J. Phys. Chem. B 105, 7847–7856. (doi:10.1021/jp0101209)
    • (2001) J. Phys. Chem. B , vol.105 , pp. 7847-7856
    • Kumar, A.T.N.1    Zhu, L.2    Christian, J.F.3    Demidov, A.A.4    Champion, P.M.5
  • 51
    • 0032989351 scopus 로고    scopus 로고
    • Observation of strange kinetics in protein folding
    • Sabelko J, Ervin J, Gruebele M. 1999 Observation of strange kinetics in protein folding. Proc. Natl Acad. Sci. USA 96, 6031–6036. (doi:10.1073/pnas.96.11.6031)
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 6031-6036
    • Sabelko, J.1    Ervin, J.2    Gruebele, M.3
  • 52
    • 34347218159 scopus 로고    scopus 로고
    • Conformational dynamics and ensembles in protein folding
    • Munoz V. 2007 Conformational dynamics and ensembles in protein folding. Annu. Rev. Biophys. Biomol. Struct. 36, 395–412. (doi:10.1146/annurev. biophys.36.040306.132608)
    • (2007) Annu. Rev. Biophys. Biomol. Struct. , vol.36 , pp. 395-412
    • Munoz, V.1
  • 53
    • 84941807000 scopus 로고    scopus 로고
    • Dynamic transmission of protein allostery without structural change: Spatial pathways or global modes?
    • McLeish T, Cann M, Rogers T. 2015 Dynamic transmission of protein allostery without structural change: spatial pathways or global modes? Biophys. J. 109, 1240–1250. (doi:10.1016/j.bpj.2015.08.009)
    • (2015) Biophys. J. , vol.109 , pp. 1240-1250
    • McLeish, T.1    Cann, M.2    Rogers, T.3
  • 54
    • 0036880493 scopus 로고    scopus 로고
    • What vibrations tell us about proteins
    • Barth A, Zscherp C. 2002 What vibrations tell us about proteins. Q. Rev. Biophys. 35, 369–430. (doi:10.1017/S0033583502003815)
    • (2002) Q. Rev. Biophys. , vol.35 , pp. 369-430
    • Barth, A.1    Zscherp, C.2
  • 55
    • 0000171168 scopus 로고    scopus 로고
    • Vibrational cooling after ultrafast photoisomerization of azobenzene measured by femtosecond infrared spectroscopy
    • Hamm P, Ohline SM, Zinth W. 1997 Vibrational cooling after ultrafast photoisomerization of azobenzene measured by femtosecond infrared spectroscopy. J. Chem. Phys. 106, 519–529. (doi:10.1063/1.473392)
    • (1997) J. Chem. Phys. , vol.106 , pp. 519-529
    • Hamm, P.1    Ohline, S.M.2    Zinth, W.3
  • 56
    • 72949111782 scopus 로고    scopus 로고
    • Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent
    • Park SM, Nguyen PH, Stock G. 2009 Molecular dynamics simulation of cooling: heat transfer from a photoexcited peptide to the solvent. J. Chem. Phys. 131, 184503. (doi:10.1063/1.3259971)
    • (2009) J. Chem. Phys. , vol.131
    • Park, S.M.1    Nguyen, P.H.2    Stock, G.3
  • 57
    • 33645387985 scopus 로고    scopus 로고
    • Nonequilibrium molecular dynamics simulation of a photoswitchable peptide
    • Nguyen PH, Stock G. 2006 Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem. Phys. 323, 36–44. (doi:10.1016/j.chemphys.2005.08.047)
    • (2006) Chem. Phys. , vol.323 , pp. 36-44
    • Nguyen, P.H.1    Stock, G.2
  • 58
    • 84914161401 scopus 로고    scopus 로고
    • Long-range conformational transition in a photoswitchable allosteric protein: A molecular dynamics simulation study
    • Buchenberg S, Knecht V, Walser R, Hamm P, Stock G. 2014 Long-range conformational transition in a photoswitchable allosteric protein: a molecular dynamics simulation study. J. Phys. Chem. B 118, 13468–13476. (doi:10.1021/jp506873y)
    • (2014) J. Phys. Chem. B , vol.118 , pp. 13468-13476
    • Buchenberg, S.1    Knecht, V.2    Walser, R.3    Hamm, P.4    Stock, G.5
  • 59
    • 84958019931 scopus 로고    scopus 로고
    • Long-range conformational response of a PDZ domain to ligand binding and release: A molecular dynamics study
    • Cheng L, Knecht V, Stock G. 2016 Long-range conformational response of a PDZ domain to ligand binding and release: a molecular dynamics study. J. Chem. Theory Comp. 12, 1627–1638. (doi:10. 1021/acs.jctc.5b01009)
    • (2016) J. Chem. Theory Comp. , vol.12 , pp. 1627-1638
    • Cheng, L.1    Knecht, V.2    Stock, G.3
  • 60
    • 84960361119 scopus 로고    scopus 로고
    • Protein structural memory influences ligand binding mode(S) and unbinding rates
    • Xu M, Caflisch A, Hamm P. 2016 Protein structural memory influences ligand binding mode(s) and unbinding rates. J. Chem. Theory Comput. 12, 1393–1399. (doi:10.1021/acs.jctc.5b01052)
    • (2016) J. Chem. Theory Comput. , vol.12 , pp. 1393-1399
    • Xu, M.1    Caflisch, A.2    Hamm, P.3
  • 62
    • 84969601898 scopus 로고    scopus 로고
    • Robust density-based clustering to identify metastable conformational states of proteins
    • Sittel F, Stock G. 2016 Robust density-based clustering to identify metastable conformational states of proteins. J. Chem. Theory Comp. 12, 2426–2435. (doi:10.1021/acs.jctc.5b01233)
    • (2016) J. Chem. Theory Comp. , vol.12 , pp. 2426-2435
    • Sittel, F.1    Stock, G.2
  • 63
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H, Sligar S, Wolynes P. 1991 The energy landscapes and motions of proteins. Science 254, 1598–1603. (doi:10.1126/science.1749933)
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.2    Wolynes, P.3
  • 64
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M, Kern D. 2007 A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450, 913–916. (doi:10.1038/nature06407)
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 65
    • 84924352528 scopus 로고    scopus 로고
    • Hierarchical biomolecular dynamics: Picosecond hydrogen bonding regulates microsecond conformational transitions
    • Buchenberg S, Schaudinnus N, Stock G. 2015 Hierarchical biomolecular dynamics: picosecond hydrogen bonding regulates microsecond conformational transitions. J. Chem. Theory Comp. 11, 1330–1336. (doi:10.1021/ct501156t)
    • (2015) J. Chem. Theory Comp. , vol.11 , pp. 1330-1336
    • Buchenberg, S.1    Schaudinnus, N.2    Stock, G.3
  • 66
    • 46249127902 scopus 로고    scopus 로고
    • Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis
    • Altis A, Otten M, Nguyen PH, Hegger R, Stock G. 2008 Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis. J. Chem. Phys. 128, 245102. (doi:10.1063/1.2945165)
    • (2008) J. Chem. Phys. , vol.128
    • Altis, A.1    Otten, M.2    Nguyen, P.H.3    Hegger, R.4    Stock, G.5
  • 67
    • 85031046473 scopus 로고    scopus 로고
    • Principal component analysis on a torus: Theory and application to protein dynamics
    • Sittel F, Filk T, Stock G. 2017 Principal component analysis on a torus: theory and application to protein dynamics. J. Chem. Phys. 147, 244101. (doi:10.1063/1.4998259)
    • (2017) J. Chem. Phys. , vol.147
    • Sittel, F.1    Filk, T.2    Stock, G.3
  • 68
  • 70
    • 36549043024 scopus 로고    scopus 로고
    • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    • Bahar I, Chennubhotla C, Tobi D. 2007 Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr. Opin. Struct. Biol. 17, 633–640. (doi:10.1016/j.sbi.2007.09.011)
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 633-640
    • Bahar, I.1    Chennubhotla, C.2    Tobi, D.3
  • 72
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • Atilgan A, Durell S, Jernigan R, Demirel M, Keskin O, Bahar I. 2001 Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80, 505–515. (doi:10.1016/S0006-3495(01) 76033-X)
    • (2001) Biophys. J. , vol.80 , pp. 505-515
    • Atilgan, A.1    Durell, S.2    Jernigan, R.3    Demirel, M.4    Keskin, O.5    Bahar, I.6
  • 73
    • 34848882812 scopus 로고    scopus 로고
    • Signal propagation in proteins and relation to equilibrium fluctuations
    • Chennubhotla C, Bahar I. 2007 Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput. Biol. 9, 1716–1726. (doi:10.1371/journal.pcbi.0030172)
    • (2007) Plos Comput. Biol. , vol.9 , pp. 1716-1726
    • Chennubhotla, C.1    Bahar, I.2
  • 74
    • 18744387720 scopus 로고    scopus 로고
    • Reaction coordinates and rates from transition paths
    • Best RB, Hummer G. 2005 Reaction coordinates and rates from transition paths. Proc. Natl Acad. Sci. USA 102, 6732–6737. (doi:10.1073/pnas.0408098102)
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 6732-6737
    • Best, R.B.1    Hummer, G.2
  • 75
    • 6944235051 scopus 로고    scopus 로고
    • Hidden complexity of free energy surfaces for peptide (Protein) folding
    • Krivov SV, Karplus M. 2004 Hidden complexity of free energy surfaces for peptide (protein) folding. Proc. Natl Acad. Sci. USA 101, 14766–14770. (doi:10.1073/pnas.0406234101)
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 14766-14770
    • Krivov, S.V.1    Karplus, M.2
  • 76
    • 11244328062 scopus 로고    scopus 로고
    • Protein folding in high-dimensional spaces: Hypergutters and the role of nonnative interactions
    • McLeish T. 2005 Protein folding in high-dimensional spaces: hypergutters and the role of nonnative interactions. Biophys. J. 88, 172–183. (doi:10.1529/biophysj.103.036616)
    • (2005) Biophys. J. , vol.88 , pp. 172-183
    • McLeish, T.1
  • 77
    • 33846382040 scopus 로고    scopus 로고
    • How complex is the dynamics of peptide folding?
    • Hegger R, Altis A, Nguyen PH, Stock G. 2007 How complex is the dynamics of peptide folding? Phys. Rev. Lett. 98, 028102. (doi:10.1103/PhysRevLett. 98.028102)
    • (2007) Phys. Rev. Lett. , vol.98 , pp. 28102
    • Hegger, R.1    Altis, A.2    Nguyen, P.H.3    Stock, G.4
  • 78
    • 56249105081 scopus 로고    scopus 로고
    • Advillin folding takes place on a hypersurface of small dimensionality
    • Piana S, Laio A. 2008 Advillin folding takes place on a hypersurface of small dimensionality. Phys. Rev. Lett. 101, 208101. (doi:10.1103/PhysRevLett.101. 208101)
    • (2008) Phys. Rev. Lett. , vol.101 , pp. 208101
    • Piana, S.1    Laio, A.2
  • 79
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • Isralewitz B, Gao M, Schulten K. 2001 Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11, 224–230. (doi:10.1016/S0959-440X(00)00194-9)
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 80
    • 0028455053 scopus 로고
    • Targeted molecular dynamics—a new approach for searching pathways of conformational transitions
    • Schlitter J, Engels M, Krüger P. 1994 Targeted molecular dynamics—a new approach for searching pathways of conformational transitions. J. Mol. Graph. 12, 84–89. (doi:10.1016/0263-7855(94)80072-3)
    • (1994) J. Mol. Graph. , vol.12 , pp. 84-89
    • Schlitter, J.1    Engels, M.2    Krüger, P.3
  • 81
    • 62849098480 scopus 로고    scopus 로고
    • Free energy calculations (eds C Chipot, A Pohorille), Berlin, Germany: Springer
    • Hummer G 2007 Nonequilibrium methods for free energy calculations. In Free energy calculations (eds C Chipot, A Pohorille) pp. 171–198. Berlin, Germany: Springer.
    • (2007) Nonequilibrium Methods for Free Energy Calculations , pp. 171-198
    • Hummer, G.1
  • 84
    • 85019753673 scopus 로고    scopus 로고
    • Quantifying biomolecular recognition with site-specific 2D infrared probes
    • Johnson PJM, Koziol KL, Hamm P. 2017 Quantifying biomolecular recognition with site-specific 2D infrared probes. J. Phys. Chem. Lett. 8, 2280–2284. (doi:10.1021/acs.jpclett.7b00742)
    • (2017) J. Phys. Chem. Lett. , vol.8 , pp. 2280-2284
    • Johnson, P.J.M.1    Koziol, K.L.2    Hamm, P.3
  • 85
    • 33645405109 scopus 로고    scopus 로고
    • Stretched versus compressed exponential kinetics in α-helix folding
    • Hamm P, Helbing J, Bredenbeck J. 2006 Stretched versus compressed exponential kinetics in α-helix folding. Chem. Phys. 323, 54–65. (doi:10.1016/j.chemphys.2005.08.035)
    • (2006) Chem. Phys. , vol.323 , pp. 54-65
    • Hamm, P.1    Helbing, J.2    Bredenbeck, J.3


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