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Volumn 10, Issue 1, 2013, Pages

Interplay between native topology and non-native interactions in the folding of tethered proteins

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EID: 84873377406     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/10/1/016002     Document Type: Article
Times cited : (13)

References (59)
  • 1
    • 66849106554 scopus 로고    scopus 로고
    • An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms
    • 10.1038/nsmb.1592 1545-9993
    • Bartlett A I and Radford S E 2009 An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms Nature Struct. Mol. Biol. 16 582-8
    • (2009) Nature Struct. Mol. Biol. , vol.16 , Issue.6 , pp. 582-588
    • Bartlett, A.I.1    Radford, S.E.2
  • 2
    • 79551682100 scopus 로고    scopus 로고
    • Taming the complexity of protein folding
    • 10.1016/j.sbi.2010.10.006 0959-440X
    • Bowman G R, Voelz V A and Pande V S 2011 Taming the complexity of protein folding Curr. Opin. Struct. Biol. 21 4-11
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , Issue.1 , pp. 4-11
    • Bowman, G.R.1    Voelz, V.A.2    Pande, V.S.3
  • 4
    • 78149495375 scopus 로고    scopus 로고
    • From protein folding to protein function and biomolecular binding by energy landscape theory
    • 10.1016/j.coph.2010.09.012 1471-4892
    • Schug A and Onuchic J N 2010 From protein folding to protein function and biomolecular binding by energy landscape theory Curr. Opin. Pharmacol. 10 709-14
    • (2010) Curr. Opin. Pharmacol. , vol.10 , Issue.6 , pp. 709-714
    • Schug, A.1    Onuchic, J.N.2
  • 6
    • 77957937199 scopus 로고    scopus 로고
    • Atomic-level characterization of the structural dynamics of proteins
    • 10.1126/science.1187409 0036-8075
    • Shaw D E et al 2010 Atomic-level characterization of the structural dynamics of proteins Science 330 341-6
    • (2010) Science , vol.330 , Issue.6002 , pp. 341-346
    • Shaw, D.E.1
  • 8
    • 65549112634 scopus 로고    scopus 로고
    • Biology, one molecule at a time
    • 10.1016/j.tibs.2009.01.008 0968-0004
    • Kapanidis A N and Strick T 2009 Biology, one molecule at a time Trends Biochem. Sci. 34 234-43
    • (2009) Trends Biochem. Sci. , vol.34 , Issue.5 , pp. 234-243
    • Kapanidis, A.N.1    Strick, T.2
  • 10
    • 62449169742 scopus 로고    scopus 로고
    • The effect of surface tethering on the folding of the src-SH3 protein domain
    • 1478-3975 015004
    • Zhuang Z Y, Jewett A I, Soto P and Shea J E 2009 The effect of surface tethering on the folding of the src-SH3 protein domain Phys. Biol. 6 015004
    • (2009) Phys. Biol. , vol.6 , Issue.1
    • Zhuang, Z.Y.1    Jewett, A.I.2    Soto, P.3    Shea, J.E.4
  • 12
  • 14
    • 62449160383 scopus 로고    scopus 로고
    • What have we learned from the studies of two-state folders, and what are the unanswered questions about two-state protein folding
    • 1478-3975 015001
    • Barrick D 2009 What have we learned from the studies of two-state folders, and what are the unanswered questions about two-state protein folding Phys. Biol. 6 015001
    • (2009) Phys. Biol. , vol.6 , Issue.1
    • Barrick, D.1
  • 16
    • 14744273112 scopus 로고    scopus 로고
    • Native geometry and the dynamics of protein folding
    • DOI 10.1016/j.bpc.2004.12.022
    • Faisca P F N and da Gama M M T 2005 Native geometry and the dynamics of protein folding Biophys. Chem. 115 169-75 (Pubitemid 40327053)
    • (2005) Biophysical Chemistry , vol.115 , Issue.2 , pp. 169-175
    • Faisca, P.F.N.1    Telo Da Gama, M.M.2
  • 17
    • 84871062621 scopus 로고    scopus 로고
    • Why do protein folding rates correlate with metrics of native topology
    • 10.1371/journal.pone.0035599 1932-6203
    • Faísca P F N, Travasso R D M, Parisi A and Rey A 2012 Why do protein folding rates correlate with metrics of native topology PLoS One 7 e35599
    • (2012) PLoS One , vol.7 , Issue.4 , pp. 35599
    • Faísca, P.F.N.1    Travasso, R.D.M.2    Parisi, A.3    Rey, A.4
  • 18
    • 0043093689 scopus 로고    scopus 로고
    • Getting a grip on non-native proteins
    • DOI 10.1038/sj.embor.embor869
    • Stirling P C, Lundin V F and Leroux M R 2003 Getting a grip on non-native proteins EMBO Rep. 4 565-70 (Pubitemid 36939946)
    • (2003) EMBO Reports , vol.4 , Issue.6 , pp. 565-570
    • Stirling, P.C.1    Lundin, V.F.2    Leroux, M.R.3
  • 19
    • 0034112774 scopus 로고    scopus 로고
    • Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
    • DOI 10.1038/74111
    • Li L, Mirny L A and Shakhnovich E I 2000 Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus Nature Struct. Biol. 7 336-42 (Pubitemid 30194459)
    • (2000) Nature Structural Biology , vol.7 , Issue.4 , pp. 336-342
    • Li, L.1    Mirny, L.A.2    Shakhnovich, E.I.3
  • 20
    • 78349295630 scopus 로고    scopus 로고
    • Non-native interactions play an effective role in protein folding dynamics
    • 10.1002/pro.498 0961-8368
    • Faisca P F N, Nunes A, Travasso R D M and Shakhnovich E I 2010 Non-native interactions play an effective role in protein folding dynamics Protein Sci. 19 2196-209
    • (2010) Protein Sci. , vol.19 , Issue.11 , pp. 2196-2209
    • Faisca, P.F.N.1    Nunes, A.2    Travasso, R.D.M.3    Shakhnovich, E.I.4
  • 21
    • 48249138078 scopus 로고    scopus 로고
    • Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding
    • 10.1073/pnas.0801874105 0027-8424
    • Zarrine-Afsar A et al 2008 Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding Proc. Natl Acad. Sci. USA 105 9999-10004
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , Issue.29 , pp. 9999-10004
    • Zarrine-Afsar, A.1
  • 22
    • 84856789405 scopus 로고    scopus 로고
    • Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain
    • 10.1002/prot.23243 0887-3585
    • Zarrine-Afsar A et al 2012 Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain Proteins 80 858-70
    • (2012) Proteins , vol.80 , Issue.3 , pp. 858-870
    • Zarrine-Afsar, A.1
  • 23
    • 77649264931 scopus 로고    scopus 로고
    • Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins
    • 10.1073/pnas.0911844107 0027-8424
    • Zhang Z Q and Chan H S 2010 Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins Proc. Natl Acad. Sci. USA 107 2920-5
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , Issue.7 , pp. 2920-2925
    • Zhang, Z.Q.1    Chan, H.S.2
  • 24
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • DOI 10.1006/jmbi.1998.1645
    • Plaxco K W, Simons K T and Baker D 1998 Contact order, transition state placement and the refolding rates of single domain proteins J. Mol. Biol. 277 985-94 (Pubitemid 28195995)
    • (1998) Journal of Molecular Biology , vol.277 , Issue.4 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 25
    • 0028174310 scopus 로고
    • How does a protein fold
    • 10.1038/369248a0 0028-0836
    • Sali A, Shakhnovich E and Karplus M 1994 How does a protein fold Nature 369 248-51
    • (1994) Nature , vol.369 , Issue.6477 , pp. 248-251
    • Sali, A.1    Shakhnovich, E.2    Karplus, M.3
  • 26
    • 0028024928 scopus 로고
    • Specific nucleus as the transition state for protein folding: Evidence from the lattice model
    • Abkevich V I, Gutin A M and Shakhnovich E I 1994 Specific nucleus as the transition-state for protein-folding - evidence from the lattice model Biochemistry 33 10026-36 (Pubitemid 24286081)
    • (1994) Biochemistry , vol.33 , Issue.33 , pp. 10026-10036
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 27
    • 0032544484 scopus 로고    scopus 로고
    • Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism
    • DOI 10.1006/jmbi.1998.1997
    • Klimov D K and Thirumalai D 1998 Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism J. Mol. Biol. 282 471-92 (Pubitemid 28418797)
    • (1998) Journal of Molecular Biology , vol.282 , Issue.2 , pp. 471-492
    • Klimov, D.K.1    Thirumalai, D.2
  • 28
    • 0028929556 scopus 로고
    • Principles of protein-folding - A perspective from simple exact models
    • 10.1002/pro.5560040401 0961-8368
    • Dill K A et al 1995 Principles of protein-folding - a perspective from simple exact models Protein Sci. 4 561-602
    • (1995) Protein Sci. , vol.4 , Issue.4 , pp. 561-602
    • Dill, K.A.1
  • 30
    • 4243416989 scopus 로고    scopus 로고
    • Chain length scaling of protein folding time
    • DOI 10.1103/PhysRevLett.77.5433, 5433
    • Gutin A M, Abkevich V I and Shakhnovich E I 1996 Chain length scaling of protein folding time Phys. Rev. Lett. 77 5433-6 (Pubitemid 40620115)
    • (1996) Physical Review Letters , vol.77 , Issue.27 , pp. 5433-5436
    • Gutin, A.M.1    Abkevich, V.I.2    Shakhnovich, E.I.3
  • 32
    • 77957731766 scopus 로고    scopus 로고
    • The protein folding transition state: Insights from kinetics and thermodynamics
    • 10.1063/1.3485286 0021-9606 125102
    • Travasso R D M, Faisca P F N and Rey A 2010 The protein folding transition state: insights from kinetics and thermodynamics J. Chem. Phys. 133 125102
    • (2010) J. Chem. Phys. , vol.133 , Issue.12
    • Travasso, R.D.M.1    Faisca, P.F.N.2    Rey, A.3
  • 33
    • 33745698759 scopus 로고    scopus 로고
    • Cooperativity and the origins of rapid, single-exponential kinetics in protein folding
    • 10.1110/ps.062180806 0961-8368
    • Faisca P F N and Plaxco K W 2006 Cooperativity and the origins of rapid, single-exponential kinetics in protein folding Protein Sci. 15 1608-18
    • (2006) Protein Sci. , vol.15 , Issue.7 , pp. 1608-1618
    • Faisca, P.F.N.1    Plaxco, K.W.2
  • 34
    • 51349086269 scopus 로고    scopus 로고
    • Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis
    • 10.1063/1.2973624 0021-9606 095108
    • Faisca P F N, Travasso R D M, Ball R C and Shakhnovich E I 2008 Identifying critical residues in protein folding: insights from phi-value and P(fold) analysis J. Chem. Phys. 129 095108
    • (2008) J. Chem. Phys. , vol.129 , Issue.9
    • Faisca, P.F.N.1    Travasso, R.D.M.2    Ball, R.C.3    Shakhnovich, E.I.4
  • 35
    • 78349267139 scopus 로고    scopus 로고
    • Factors governing fibrillogenesis of polypeptide chains revealed by lattice models
    • 10.1103/PhysRevLett.105.218101 0031-9007 218101
    • Li M S et al 2010 Factors governing fibrillogenesis of polypeptide chains revealed by lattice models Phys. Rev. Lett. 105 218101
    • (2010) Phys. Rev. Lett. , vol.105 , Issue.21
    • Li, M.S.1
  • 36
    • 84856694618 scopus 로고    scopus 로고
    • Coupled folding-binding in a hydrophobic/polar protein model: Impact of synergistic folding and disordered flanks
    • 10.1016/j.bpj.2011.12.008 0006-3495
    • Bhattacherjee A and Wallin S 2012 Coupled folding-binding in a hydrophobic/polar protein model: impact of synergistic folding and disordered flanks Biophys. J. 102 569-78
    • (2012) Biophys. J. , vol.102 , Issue.3 , pp. 569-578
    • Bhattacherjee, A.1    Wallin, S.2
  • 38
    • 38549131880 scopus 로고    scopus 로고
    • Lattice simulations of cotranslational folding of single domain proteins
    • DOI 10.1002/prot.21547
    • Wang P Y and Klimov D K 2008 Lattice simulations of cotranslational folding of single domain proteins Proteins 70 925-37 (Pubitemid 351161951)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.3 , pp. 925-937
    • Wang, P.1    Klimov, D.K.2
  • 39
    • 37849006746 scopus 로고    scopus 로고
    • A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues
    • 10.1002/prot.21575 0887-3585
    • Lu H M and Liang J 2008 A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues Proteins 70 442-9
    • (2008) Proteins , vol.70 , Issue.2 , pp. 442-449
    • Lu, H.M.1    Liang, J.2
  • 40
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer-simulation :1. Effect of specific amino-acid sequence represented by specific inter-unit interactions
    • 10.1111/j.1399-3011.1975.tb02465.x 0367-8377
    • Taketomi H, Ueda Y and Go N 1975 Studies on protein folding, unfolding and fluctuations by computer-simulation :1. Effect of specific amino-acid sequence represented by specific inter-unit interactions Int. J. Pept. Protein Res. 7 445-59
    • (1975) Int. J. Pept. Protein Res. , vol.7 , Issue.6 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 41
    • 4243392673 scopus 로고
    • Proteins with selected sequences fold into unique native conformation
    • Shakhnovich E I 1994 Proteins with selected sequences fold into unique native conformation Phys. Rev. Lett. 72 3907-10 (Pubitemid 24975549)
    • (1994) Physical Review Letters , vol.72 , Issue.24 , pp. 3907-3910
    • Shakhnovich, E.I.1
  • 42
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal-structures - Quasi-chemical approximation
    • 10.1021/ma00145a039 0024-9297
    • Miyazawa S and Jernigan R L 1985 Estimation of effective interresidue contact energies from protein crystal-structures - quasi-chemical approximation Macromolecules 18 534-52
    • (1985) Macromolecules , vol.18 , Issue.3 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 43
    • 0028957666 scopus 로고
    • Evolution-like selection of fast-folding model proteins
    • 10.1073/pnas.92.5.1282 0027-8424
    • Gutin A M, Abkevich V I and Shakhnovich E I 1995 Evolution-like selection of fast-folding model proteins Proc. Natl Acad. Sci. USA 92 1282-6
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , Issue.5 , pp. 1282-1286
    • Gutin, A.M.1    Abkevich, V.I.2    Shakhnovich, E.I.3
  • 46
    • 0037156117 scopus 로고    scopus 로고
    • Thermodynamic control and dynamical regimes in protein folding
    • DOI 10.1063/1.1466833
    • Faisca P F N and Ball R C 2002 Thermodynamic control and dynamical regimes in protein folding J. Chem. Phys. 116 7231-7 (Pubitemid 34537102)
    • (2002) Journal of Chemical Physics , vol.116 , Issue.16 , pp. 7231-7237
    • Faisca, P.F.N.1    Ball, R.C.2
  • 49
    • 0016224361 scopus 로고
    • Thermodynamic approach to problem of stabilization of globular protein structure - Calorimetric study
    • 10.1016/0022-2836(74)90188-0 0022-2836
    • Privalov P L and Khechina N n 1974 Thermodynamic approach to problem of stabilization of globular protein structure - calorimetric study J. Mol. Biol. 86 665-84
    • (1974) J. Mol. Biol. , vol.86 , Issue.3 , pp. 665-684
    • Privalov, P.L.1    Khechina, N.N.2
  • 50
    • 1542319916 scopus 로고    scopus 로고
    • Cooperativity principles in protein folding
    • DOI 10.1016/S0076-6879(04)80016-8
    • Chan H S, Shimizu S and Kaya H 2004 Energetics of Biological Macromolecules, Pt E (Methods in Enzymology vol 380) ed J M Holt, M L Johnson and G K Ackers (Amsterdam: Elsevier) pp 350-79 (Pubitemid 38297503)
    • (2004) Methods in Enzymology , vol.380 , pp. 350-379
    • Chan, H.S.1    Shimizu, S.2    Kaya, H.3
  • 51
    • 33947398571 scopus 로고    scopus 로고
    • Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations
    • 10.1021/ct0502864 1549-9618
    • Chodera J D, Swope W C, Pitera J W, Seok C and Dill K A 2007 Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations J. Chem. Theory Comput. 3 26-41
    • (2007) J. Chem. Theory Comput. , vol.3 , Issue.1 , pp. 26-41
    • Chodera, J.D.1    Swope, W.C.2    Pitera, J.W.3    Seok, C.4    Dill, K.A.5
  • 52
    • 0001720011 scopus 로고    scopus 로고
    • Molecular dynamics of folding of secondary structures in Go-type models of proteins
    • DOI 10.1063/1.481261
    • Hoang T X and Cieplak M 2000 Molecular dynamics of folding of secondary structures in Go-type models of proteins J. Chem. Phys. 112 6851-62 (Pubitemid 33638906)
    • (2000) Journal of Chemical Physics , vol.112 , Issue.15 , pp. 6851-6862
    • Hoang, T.X.1    Cieplak, M.2
  • 53
    • 42749107023 scopus 로고    scopus 로고
    • Folding and form: Insights from lattice simulations
    • 10.1103/PhysRevE.69.051917 1539-3755 E 051917
    • Faisca P F N, da Gama M M T and Ball R C 2004 Folding and form: insights from lattice simulations Phys. Rev. E 69 051917
    • (2004) Phys. Rev. , vol.69 , Issue.5
    • Faisca, P.F.N.1    Da Gama, M.M.T.2    Ball, R.C.3
  • 54
    • 77953231020 scopus 로고    scopus 로고
    • The folding cooperativity of a protein is controlled by its chain topology
    • 10.1038/nature09021 0028-0836
    • Shank E A, Cecconi C, Dill J W, Marqusee S and Bustamante C 2010 The folding cooperativity of a protein is controlled by its chain topology Nature 465 637-40
    • (2010) Nature , vol.465 , Issue.7298 , pp. 637-640
    • Shank, E.A.1    Cecconi, C.2    Dill, J.W.3    Marqusee, S.4    Bustamante, C.5
  • 56
    • 34547507851 scopus 로고    scopus 로고
    • Effects of crowding and confinement on the structures of the transition state ensemble in proteins
    • DOI 10.1021/jp068201y
    • Cheung M S and Thirumalai D 2007 Effects of crowding and confinement on the structures of the transition state ensemble in proteins J. Phys. Chem. B 111 8250-7 (Pubitemid 47184401)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.28 , pp. 8250-8257
    • Cheung, M.S.1    Thirumalai, D.2
  • 57
    • 21444458916 scopus 로고    scopus 로고
    • The shape of a flexible polymer in a cylindrical pore
    • DOI 10.1063/1.1903923, 194907
    • Morrison G and Thirumalai D 2005 The shape of a flexible polymer in a cylindrical pore J. Chem. Phys. 122 194907 (Pubitemid 40914355)
    • (2005) Journal of Chemical Physics , vol.122 , Issue.19 , pp. 1-5
    • Morrison, G.1    Thirumalai, D.2
  • 58
    • 54849440101 scopus 로고    scopus 로고
    • Effects of confinement and crowding on folding of model proteins
    • 10.1016/j.biosystems.2008.06.016 0303-2647
    • Wojciehowski M and Cieplak M 2008 Effects of confinement and crowding on folding of model proteins Biosystems 94 248-52
    • (2008) Biosystems , vol.94 , Issue.3 , pp. 248-252
    • Wojciehowski, M.1    Cieplak, M.2
  • 59
    • 78751481478 scopus 로고    scopus 로고
    • The influence of hydrodynamic interactions on protein dynamics in confined and crowded spaces - Assessment in simple models
    • 1478-3975 046011
    • Wojciechowski M, Szymczak P and Cieplak M 2010 The influence of hydrodynamic interactions on protein dynamics in confined and crowded spaces - assessment in simple models Phys. Biol. 7 046011
    • (2010) Phys. Biol. , vol.7 , Issue.4
    • Wojciechowski, M.1    Szymczak, P.2    Cieplak, M.3


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