메뉴 건너뛰기




Volumn 30, Issue , 2015, Pages 57-62

What protein folding teaches us about biological function and molecular machines

Author keywords

[No Author keywords available]

Indexed keywords

INTERLEUKIN 1BETA; TRANSFER RNA; MACROMOLECULE;

EID: 84920140834     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2014.12.003     Document Type: Review
Times cited : (30)

References (43)
  • 1
    • 0024733407 scopus 로고
    • Intermediates and barrier crossing in a random energy-model (with applications to protein folding)
    • Bryngelson J.D., Wolynes P.G. Intermediates and barrier crossing in a random energy-model (with applications to protein folding). J Phys Chem-US 1989, 93:6902-6915.
    • (1989) J Phys Chem-US , vol.93 , pp. 6902-6915
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 2
    • 0026723063 scopus 로고
    • Protein folding funnels-a kinetic approach to the sequence structure relationship
    • Leopold P.E., Montal M., Onuchic J.N. Protein folding funnels-a kinetic approach to the sequence structure relationship. Proc Natl Acad Sci U S A 1992, 89:8721-8725.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 8721-8725
    • Leopold, P.E.1    Montal, M.2    Onuchic, J.N.3
  • 3
    • 84904968329 scopus 로고    scopus 로고
    • Predictive energy landscapes for folding helical transmembrane proteins
    • Kim B.L., Schafer N.P., Wolynes P.G. Predictive energy landscapes for folding helical transmembrane proteins. Proc Natl Acad Sci U S A 2014, 111:11031-11036.
    • (2014) Proc Natl Acad Sci U S A , vol.111 , pp. 11031-11036
    • Kim, B.L.1    Schafer, N.P.2    Wolynes, P.G.3
  • 4
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    • Clementi C., Nymeyer H., Onuchic J.N. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 2000, 298:937-953. 10.1006/jmbi.2000.3693.
    • (2000) J Mol Biol , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 5
    • 63449135082 scopus 로고    scopus 로고
    • An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields
    • Whitford P.C., Noel J.K., Gosavi S., Schug A., Sanbonmatsu K.Y., Onuchic J.N. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins 2009, 75:430-441. 10.1002/prot.22253.
    • (2009) Proteins , vol.75 , pp. 430-441
    • Whitford, P.C.1    Noel, J.K.2    Gosavi, S.3    Schug, A.4    Sanbonmatsu, K.Y.5    Onuchic, J.N.6
  • 6
    • 33645030244 scopus 로고    scopus 로고
    • Topological frustration and the folding of interleukin-1β
    • Gosavi S., Chavez L.L., Jennings P.A., Onuchic J.N. Topological frustration and the folding of interleukin-1β. J Mol Biol 2006, 357:986-996. 10.1016/j.jmb.2005.11.074.
    • (2006) J Mol Biol , vol.357 , pp. 986-996
    • Gosavi, S.1    Chavez, L.L.2    Jennings, P.A.3    Onuchic, J.N.4
  • 11
    • 84887117718 scopus 로고    scopus 로고
    • Native contacts determine protein folding mechanisms in atomistic simulations
    • Best R.B., Hummer G., Eaton W.A. Native contacts determine protein folding mechanisms in atomistic simulations. Proc Natl Acad Sci U S A 2013, 110:17874-17879.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 17874-17879
    • Best, R.B.1    Hummer, G.2    Eaton, W.A.3
  • 13
    • 80855128904 scopus 로고    scopus 로고
    • Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I
    • Samiotakis A., Cheung M.S. Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I. J Chem Phys 2011, 135:175101. 10.1063/1.3656691.
    • (2011) J Chem Phys , vol.135 , pp. 175101
    • Samiotakis, A.1    Cheung, M.S.2
  • 14
    • 84886670980 scopus 로고    scopus 로고
    • Force-induced unzipping transitions in an athermal crowded environment
    • Pincus D.L., Thirumalai D. Force-induced unzipping transitions in an athermal crowded environment. J Phys Chem B 2013, 117:13107-13114.
    • (2013) J Phys Chem B , vol.117 , pp. 13107-13114
    • Pincus, D.L.1    Thirumalai, D.2
  • 15
    • 84864206909 scopus 로고    scopus 로고
    • Influence of the shape of crowding particles on the structural transitions in a polymer
    • Kudlay A., Cheung M.S., Thirumalai D. Influence of the shape of crowding particles on the structural transitions in a polymer. J Phys Chem B 2012, 116:8513-8522.
    • (2012) J Phys Chem B , vol.116 , pp. 8513-8522
    • Kudlay, A.1    Cheung, M.S.2    Thirumalai, D.3
  • 16
    • 77952717308 scopus 로고    scopus 로고
    • Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways
    • Whitford P.C., Geggier P., Altman R.B., Blanchard S.C., Onuchic J.N., Sanbonmatsu K.Y. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA 2010, 16:1196-1204. 10.1261/rna.2035410.
    • (2010) RNA , vol.16 , pp. 1196-1204
    • Whitford, P.C.1    Geggier, P.2    Altman, R.B.3    Blanchard, S.C.4    Onuchic, J.N.5    Sanbonmatsu, K.Y.6
  • 17
    • 84885459860 scopus 로고    scopus 로고
    • Simulating movement of tRNA through the ribosome during hybrid-state formation
    • Whitford P.C., Sanbonmatsu K.Y. Simulating movement of tRNA through the ribosome during hybrid-state formation. J Chem Phys 2013, 139:121919.
    • (2013) J Chem Phys , vol.139 , pp. 121919
    • Whitford, P.C.1    Sanbonmatsu, K.Y.2
  • 18
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity proteinquakes and the energy landscapes of functional transitions in proteins
    • Miyashita O., Onuchic J.N., Wolynes P.G. Nonlinear elasticity proteinquakes and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci U S A 2003, 100:12570-12575. 10.1073/pnas.2135471100.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 12570-12575
    • Miyashita, O.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 20
    • 33846847773 scopus 로고    scopus 로고
    • Conformational transitions of adenylate kinase: switching by cracking
    • Whitford P.C., Miyashita O., Levy Y., Onuchic J.N. Conformational transitions of adenylate kinase: switching by cracking. J Mol Biol 2007, 366:1661-1671. 10.1016/j.jmb.2006.11.085.
    • (2007) J Mol Biol , vol.366 , pp. 1661-1671
    • Whitford, P.C.1    Miyashita, O.2    Levy, Y.3    Onuchic, J.N.4
  • 21
    • 78650049311 scopus 로고    scopus 로고
    • Overlap between folding and functional energy landscapes for adenylate kinase conformational change
    • Olsson U., Wolf-Watz M. Overlap between folding and functional energy landscapes for adenylate kinase conformational change. Nat Commun 2010, 1:111. 10.1038/ncomms1106.
    • (2010) Nat Commun , vol.1 , pp. 111
    • Olsson, U.1    Wolf-Watz, M.2
  • 22
    • 79951986441 scopus 로고    scopus 로고
    • Strategies for the thermodynamic characterization of linked binding/local folding reactions within the native state application to the LID domain of adenylate
    • Schrank T., Elam W., Li J., Hilser V. Strategies for the thermodynamic characterization of linked binding/local folding reactions within the native state application to the LID domain of adenylate. Methods in Enzymology 2011.
    • (2011) Methods in Enzymology
    • Schrank, T.1    Elam, W.2    Li, J.3    Hilser, V.4
  • 23
    • 33847770916 scopus 로고    scopus 로고
    • Internal strain regulates the nucleotide binding site of the kinesin leading head
    • Hyeon C., Onuchic J.N. Internal strain regulates the nucleotide binding site of the kinesin leading head. Proc Natl Acad Sci U S A 2007, 104:2175-2180. 10.1073/pnas.0610939104.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 2175-2180
    • Hyeon, C.1    Onuchic, J.N.2
  • 24
    • 60549089572 scopus 로고    scopus 로고
    • Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin
    • Tripathi S., Portman J.J. Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin. Proc Natl Acad Sci U S A 2009, 106:2104-2109. 10.1073/pnas.0806872106.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 2104-2109
    • Tripathi, S.1    Portman, J.J.2
  • 25
    • 62549167040 scopus 로고    scopus 로고
    • Ligand-induced global transitions in the catalytic domain of protein kinase A
    • Hyeon C., Jennings P.A., Adams J.A., Onuchic J.N. Ligand-induced global transitions in the catalytic domain of protein kinase A. Proc Natl Acad Sci U S A 2009, 106:3023-3028. 10.1073/pnas.0813266106.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 3023-3028
    • Hyeon, C.1    Jennings, P.A.2    Adams, J.A.3    Onuchic, J.N.4
  • 27
    • 84876925215 scopus 로고    scopus 로고
    • Disorder guides protein function
    • Whitford P.C. Disorder guides protein function. Proc Natl Acad Sci U S A 2013, 110:7114-7115.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 7114-7115
    • Whitford, P.C.1
  • 28
    • 84920118389 scopus 로고    scopus 로고
    • Capturing transition paths and transition states for conformational rearrangements in the ribosome
    • Noel J.K., Chahine J., Veite V.B.P., Whitford P.C. Capturing transition paths and transition states for conformational rearrangements in the ribosome. Biophys J 2014, 10.1016/j.bpj.2014.10.022.
    • (2014) Biophys J
    • Noel, J.K.1    Chahine, J.2    Veite, V.B.P.3    Whitford, P.C.4
  • 29
    • 84872164266 scopus 로고    scopus 로고
    • On reaction coordinate optimality
    • Krivov S.V. On reaction coordinate optimality. J Chem Theory Comput 2013, 9:135-146.
    • (2013) J Chem Theory Comput , vol.9 , pp. 135-146
    • Krivov, S.V.1
  • 30
    • 31444452031 scopus 로고    scopus 로고
    • P versus Q: structural reaction coordinates capture protein folding on smooth landscapes
    • Cho S.S., Levy Y., Wolynes P.G. P versus Q: structural reaction coordinates capture protein folding on smooth landscapes. Proc Natl Acad Sci U S A 2006, 103:586-591. 10.1073/pnas.0509768103.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 586-591
    • Cho, S.S.1    Levy, Y.2    Wolynes, P.G.3
  • 31
    • 23244438863 scopus 로고    scopus 로고
    • Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
    • Hummer G. Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations. New J Phys 2005, 7:34. 10.1088/1367-2630/7/1/034.
    • (2005) New J Phys , vol.7 , pp. 34
    • Hummer, G.1
  • 32
    • 79953320021 scopus 로고    scopus 로고
    • Determination of reaction coordinates via locally scaled diffusion map
    • Rohrdanz M., Zheng W., ldots M.M., Clementi C. Determination of reaction coordinates via locally scaled diffusion map. J Chem Phys 2011, 134:124116.
    • (2011) J Chem Phys , vol.134 , pp. 124116
    • Rohrdanz, M.1    Zheng, W.2    Ldots, M.M.3    Clementi, C.4
  • 33
    • 18744387720 scopus 로고    scopus 로고
    • Reaction coordinates and rates from transition paths
    • Best R.B., Hummer G. Reaction coordinates and rates from transition paths. Proc Natl Acad Sci U S A 2005, 102:6732-6737.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 6732-6737
    • Best, R.B.1    Hummer, G.2
  • 34
    • 84875969059 scopus 로고    scopus 로고
    • Connecting the kinetics and energy landscape of tRNA translocation on the ribosome
    • Whitford P.C., Blanchard S.C., Cate J.H.D., Sanbonmatsu K.Y. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comput Biol 2013, 9:e1003003.
    • (2013) PLoS Comput Biol , vol.9 , pp. e1003003
    • Whitford, P.C.1    Blanchard, S.C.2    Cate, J.H.D.3    Sanbonmatsu, K.Y.4
  • 35
    • 34548273698 scopus 로고    scopus 로고
    • Folding time predictions from all-atom replica exchange simulations
    • Yang S., Onuchic J.N., Garcia A.E., Levine H. Folding time predictions from all-atom replica exchange simulations. J Mol Biol 2007, 372:756-763. 10.1016/j.jmb.2007.07.010.
    • (2007) J Mol Biol , vol.372 , pp. 756-763
    • Yang, S.1    Onuchic, J.N.2    Garcia, A.E.3    Levine, H.4
  • 36
    • 77955200083 scopus 로고    scopus 로고
    • The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding
    • Oliveira R.J., Whitford P.C., Chahine J., Wang J., Onuchic J.N., Leite V.B.P. The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding. Biophys J 2010, 99:600-608. 10.1016/j.bpj.2010.04.041.
    • (2010) Biophys J , vol.99 , pp. 600-608
    • Oliveira, R.J.1    Whitford, P.C.2    Chahine, J.3    Wang, J.4    Onuchic, J.N.5    Leite, V.B.P.6
  • 37
    • 0041335634 scopus 로고    scopus 로고
    • Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?
    • Hyeon C., Thirumalai D. Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?. Proc Natl Acad Sci U S A 2003, 100:10249-10253. 10.1073/pnas.1833310100.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 10249-10253
    • Hyeon, C.1    Thirumalai, D.2
  • 38
    • 33847254454 scopus 로고    scopus 로고
    • Ultrafast dynamics of protein collapse from single-molecule photon statistics
    • Nettels D., Gopich I.V., Hoffmann A., Schuler B. Ultrafast dynamics of protein collapse from single-molecule photon statistics. Proc Natl Acad Sci U S A 2007, 104:2655-2660. 10.1073/pnas.0611093104.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 2655-2660
    • Nettels, D.1    Gopich, I.V.2    Hoffmann, A.3    Schuler, B.4
  • 40
    • 16344371778 scopus 로고    scopus 로고
    • RNA and protein folding: common themes and variations
    • Thirumalai D., Hyeon C. RNA and protein folding: common themes and variations. Biochemistry 2005, 44:4957-4970. 10.1021/bi047314+.
    • (2005) Biochemistry , vol.44 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 41
    • 77957159348 scopus 로고    scopus 로고
    • Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome
    • Whitford P.C., Onuchic J.N., Sanbonmatsu K.Y. Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. J Am Chem Soc 2010, 132:13170-13171. 10.1021/ja1061399.
    • (2010) J Am Chem Soc , vol.132 , pp. 13170-13171
    • Whitford, P.C.1    Onuchic, J.N.2    Sanbonmatsu, K.Y.3
  • 42
    • 84863522650 scopus 로고    scopus 로고
    • Biomolecular dynamics: order-disorder transitions and energy landscapes
    • Whitford P.C., Sanbonmatsu K.Y., Onuchic J.N. Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys 2012, 75:076601.
    • (2012) Rep Prog Phys , vol.75 , pp. 076601
    • Whitford, P.C.1    Sanbonmatsu, K.Y.2    Onuchic, J.N.3
  • 43
    • 77957259237 scopus 로고    scopus 로고
    • Slipknotting upon native-like loop formation in a trefoil knot protein
    • Noel J.K., Sułkowska J.I., Onuchic J.N. Slipknotting upon native-like loop formation in a trefoil knot protein. Proc Natl Acad Sci U S A 2010, 107:15403-15408. 10.1073/pnas.1009522107.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 15403-15408
    • Noel, J.K.1    Sułkowska, J.I.2    Onuchic, J.N.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.