메뉴 건너뛰기




Volumn 13, Issue 2, 2003, Pages 160-167

Minimalist models for protein folding and design

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE;

EID: 0037398844     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(03)00030-7     Document Type: Review
Times cited : (113)

References (64)
  • 2
    • 0000019986 scopus 로고
    • Protein folding as a stochastic process
    • Go N: Protein folding as a stochastic process. J Stat Phys 1983:413-423.
    • (1983) J Stat Phys , pp. 413-423
    • Go, N.1
  • 3
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill K.A., Chan H.S. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4:1997;10-19.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 4
    • 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. 93:1989;6902-6915.
    • (1989) J. Phys. Chem. , vol.93 , pp. 6902-6915
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 6
    • 0030443105 scopus 로고    scopus 로고
    • Factors governing the foldability of proteins
    • Klimov D.K., Thirumalai D. Factors governing the foldability of proteins. Proteins. 26:1996;411-441.
    • (1996) Proteins , vol.26 , pp. 411-441
    • Klimov, D.K.1    Thirumalai, D.2
  • 8
    • 0000301323 scopus 로고    scopus 로고
    • Scaling of folding properties in simple models of proteins
    • Cieplak M., Hoang T.X., Li M.S. Scaling of folding properties in simple models of proteins. Phys. Rev. Lett. 83:1999;1684-1687.
    • (1999) Phys. Rev. Lett. , vol.83 , pp. 1684-1687
    • Cieplak, M.1    Hoang, T.X.2    Li, M.S.3
  • 9
    • 0033607208 scopus 로고    scopus 로고
    • Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A
    • Shea J.E., Onuchic J.N., Brooks C.L. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc. Natl. Acad. Sci. USA. 96:1999;12512-12517.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 12512-12517
    • Shea, J.E.1    Onuchic, J.N.2    Brooks, C.L.3
  • 10
    • 0035943433 scopus 로고    scopus 로고
    • Prediction of folding mechanism for circular-permuted proteins
    • This paper substantiates the role of topological frustration in a joint experimental/theoretical study of circularly permuted proteins.
    • Clementi C., Jennings P.A., Onuchic J.N. Prediction of folding mechanism for circular-permuted proteins. J. Mol. Biol. 311:2001;879-890 This paper substantiates the role of topological frustration in a joint experimental/theoretical study of circularly permuted proteins.
    • (2001) J. Mol. Biol. , vol.311 , pp. 879-890
    • Clementi, C.1    Jennings, P.A.2    Onuchic, J.N.3
  • 11
    • 0035850732 scopus 로고    scopus 로고
    • Roles of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model
    • This paper analyzes folding rate constants and characteristics of the transition state ensemble and the denatured states in terms of native topology and chain length for 18 different proteins using a sequence-independent Gō model. The transition state ensemble of the model is consistent with experimental Φ-values for approximately half of the proteins, indicating that sequence dependence is important to folding for the other half.
    • Koga N., Takada S. Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. J. Mol. Biol. 313:2001;171-180 This paper analyzes folding rate constants and characteristics of the transition state ensemble and the denatured states in terms of native topology and chain length for 18 different proteins using a sequence-independent Gō model. The transition state ensemble of the model is consistent with experimental Φ-values for approximately half of the proteins, indicating that sequence dependence is important to folding for the other half.
    • (2001) J. Mol. Biol. , vol.313 , pp. 171-180
    • Koga, N.1    Takada, S.2
  • 12
    • 0034687123 scopus 로고    scopus 로고
    • Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics
    • The authors make the important observation that the magnitude of the folding rate for simple two-state folders is strongly correlated with the average sequence separation between contacting residues in the native state. This emphasizes the role of native topology in determining the kinetics of folding, at least for small proteins.
    • Plaxco K.W., Simons K.T., Ruczinski I., David B. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry. 39:2000;11177-11183 The authors make the important observation that the magnitude of the folding rate for simple two-state folders is strongly correlated with the average sequence separation between contacting residues in the native state. This emphasizes the role of native topology in determining the kinetics of folding, at least for small proteins.
    • (2000) Biochemistry , vol.39 , pp. 11177-11183
    • Plaxco, K.W.1    Simons, K.T.2    Ruczinski, I.3    David, B.4
  • 13
    • 0037133574 scopus 로고    scopus 로고
    • How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
    • Makarov D.E., Keller C.A., Plaxco K.W., Metiu H. How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc. Natl. Acad. Sci. USA. 99:2002;3535-3539.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 3535-3539
    • Makarov, D.E.1    Keller, C.A.2    Plaxco, K.W.3    Metiu, H.4
  • 14
    • 12444316042 scopus 로고    scopus 로고
    • Formation of a compact structured ensemble without fluorescence signature early during ubiquitin folding
    • in press
    • Qin Z, Ervin J, Larios E, Gruebele M, Kihara H: Formation of a compact structured ensemble without fluorescence signature early during ubiquitin folding. J Phys Chem 2003, in press.
    • (2003) J Phys Chem
    • Qin, Z.1    Ervin, J.2    Larios, E.3    Gruebele, M.4    Kihara, H.5
  • 15
    • 0036440985 scopus 로고    scopus 로고
    • Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding
    • The authors argue that the finding of early intermediates (extra barrier(s) that precede the rate-limiting barrier to folding) is an artifact of interpreting ultrafast experimental techniques.
    • Krantz B.A., Mayne L., Rumbley J., Englander S.W., Sosnick T.R. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J. Mol. Biol. 324:2002;359-371 The authors argue that the finding of early intermediates (extra barrier(s) that precede the rate-limiting barrier to folding) is an artifact of interpreting ultrafast experimental techniques.
    • (2002) J. Mol. Biol. , vol.324 , pp. 359-371
    • Krantz, B.A.1    Mayne, L.2    Rumbley, J.3    Englander, S.W.4    Sosnick, T.R.5
  • 16
    • 0036280693 scopus 로고    scopus 로고
    • Protein and peptide folding explored with molecular simulations
    • Molecular simulations with emphasis on models with full atomic detail of polypeptide and solvent.
    • Brooks C.L. Protein and peptide folding explored with molecular simulations. Acc. Chem. Res. 35:2002;447-454 Molecular simulations with emphasis on models with full atomic detail of polypeptide and solvent.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 447-454
    • Brooks, C.L.1
  • 17
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y., Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:1998;740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 18
    • 0034623787 scopus 로고    scopus 로고
    • Computing - Screen savers of the world unite!
    • The authors describe using world-wide distributed computing in the spirit of the SETI project to overcome the sampling problem for high-resolution protein folding models.
    • Shirts M., Pande V.S. Computing - Screen savers of the world unite! Science. 290:2000;1903-1904 The authors describe using world-wide distributed computing in the spirit of the SETI project to overcome the sampling problem for high-resolution protein folding models.
    • (2000) Science , vol.290 , pp. 1903-1904
    • Shirts, M.1    Pande, V.S.2
  • 19
    • 0034958341 scopus 로고    scopus 로고
    • Blue Gene: A vision for protein science using a petaflop supercomputer
    • This paper describes the design of special-purpose computer hardware and software for application to protein science.
    • Allen F., Almasi G., Andreoni W., Beece D., Berne B.J., Bright A., Brunheroto J., Cascaval C., Castanos J., Coteus P.et al. Blue Gene: a vision for protein science using a petaflop supercomputer. IBM Systems Journal. 40:2001;310-327 This paper describes the design of special-purpose computer hardware and software for application to protein science.
    • (2001) IBM Systems Journal , vol.40 , pp. 310-327
    • Allen, F.1    Almasi, G.2    Andreoni, W.3    Beece, D.4    Berne, B.J.5    Bright, A.6    Brunheroto, J.7    Cascaval, C.8    Castanos, J.9    Coteus, P.10
  • 20
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • A comparison of kinetics determined from experiment and simulation. The folding@home simulation predicted that protein BBA5 would fold in 6 μs, whereas experiment revealed an actual folding time of 7.5 μs.
    • Snow C.D., Nguyen N., Pande V.S., Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature. 420:2002;102-106 A comparison of kinetics determined from experiment and simulation. The folding@home simulation predicted that protein BBA5 would fold in 6 μs, whereas experiment revealed an actual folding time of 7.5 μs.
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, N.2    Pande, V.S.3    Gruebele, M.4
  • 21
    • 0034963883 scopus 로고    scopus 로고
    • Computational challenges in structural and functional genomics
    • A blueprint for computational biology research over the next several decades.
    • Head-Gordon T., Wooley J.C. Computational challenges in structural and functional genomics. IBM Systems Journal. 40:2001;265-296 A blueprint for computational biology research over the next several decades.
    • (2001) IBM Systems Journal , vol.40 , pp. 265-296
    • Head-Gordon, T.1    Wooley, J.C.2
  • 22
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco K.W., Simons K.T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277:1998;985-994.
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 23
    • 0034681133 scopus 로고    scopus 로고
    • Landscape approaches for determining the ensemble of folding transition states: Success and failure hinge on the degree of frustration
    • This paper shows that the connection between the folding kinetics and the thermodynamics of the transition state ensemble depends on the degree of energetic frustration. It also shows that interpretation of experimentally measured Φ-values as changes in free energy differences for a simple transition state ensemble is accurate and useful only for those proteins that are minimally frustrated and whose folding can be characterized by simple reaction coordinates.
    • Nymeyer H., Socci N.D., Onuchic J.N. Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration. Proc Natl Acad Sci USA. 97:2000;634-639 This paper shows that the connection between the folding kinetics and the thermodynamics of the transition state ensemble depends on the degree of energetic frustration. It also shows that interpretation of experimentally measured Φ-values as changes in free energy differences for a simple transition state ensemble is accurate and useful only for those proteins that are minimally frustrated and whose folding can be characterized by simple reaction coordinates.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 634-639
    • Nymeyer, H.1    Socci, N.D.2    Onuchic, J.N.3
  • 24
    • 0037143694 scopus 로고    scopus 로고
    • The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation
    • A recent extension of minimalist bead models to all-atom Gō potentials to characterize the folding of protein G. This paper shows that the presence of intermediates in folding may be lost when doing ensemble dynamics.
    • Shimada J., Shakhnovich E.I. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc. Natl. Acad. Sci. USA. 99:2002;11175-11180 A recent extension of minimalist bead models to all-atom Gō potentials to characterize the folding of protein G. This paper shows that the presence of intermediates in folding may be lost when doing ensemble dynamics.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11175-11180
    • Shimada, J.1    Shakhnovich, E.I.2
  • 25
    • 0037459022 scopus 로고    scopus 로고
    • Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: An all-atom representation study
    • A study using an all-atom Gō potential to characterize the folding of proteins G and L. The addition of sidechain packing results in greater cooperativity of folding relative to sequence-independent Gō models.
    • Clementi C., Garcia A., Onuchic J.N. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: an all-atom representation study. J. Mol. Biol. 326:2003;933-954 A study using an all-atom Gō potential to characterize the folding of proteins G and L. The addition of sidechain packing results in greater cooperativity of folding relative to sequence-independent Gō models.
    • (2003) J. Mol. Biol. , vol.326 , pp. 933-954
    • Clementi, C.1    Garcia, A.2    Onuchic, J.N.3
  • 26
    • 0025368288 scopus 로고
    • Metastability of the folded states of globular proteins
    • Honeycutt J.D., Thirumalai D. Metastability of the folded states of globular proteins. Proc. Natl. Acad. Sci. USA. 87:1990;3526-3529.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 3526-3529
    • Honeycutt, J.D.1    Thirumalai, D.2
  • 28
    • 0030601851 scopus 로고    scopus 로고
    • Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein
    • Guo Z., Thirumalai D. Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J. Mol. Biol. 263:1996;323-343.
    • (1996) J. Mol. Biol. , vol.263 , pp. 323-343
    • Guo, Z.1    Thirumalai, D.2
  • 29
    • 0032726519 scopus 로고    scopus 로고
    • Redesigning the hydrophobic core of a model beta-sheet protein: Destabilizing traps through a threading approach
    • Sorenson J.M., Head-Gordon T. Redesigning the hydrophobic core of a model beta-sheet protein: destabilizing traps through a threading approach. Proteins. 37:1999;582-591.
    • (1999) Proteins , vol.37 , pp. 582-591
    • Sorenson, J.M.1    Head-Gordon, T.2
  • 30
    • 0033693141 scopus 로고    scopus 로고
    • Matching simulation and experiment: A new simplified model for simulating protein folding
    • The first physico-chemical model for the α/β topology, based on the ubiquitin fold family.
    • Sorenson J.M., Head-Gordon T. Matching simulation and experiment: a new simplified model for simulating protein folding. J. Comput. Biol. 7:2000;469-481 The first physico-chemical model for the α/β topology, based on the ubiquitin fold family.
    • (2000) J. Comput. Biol. , vol.7 , pp. 469-481
    • Sorenson, J.M.1    Head-Gordon, T.2
  • 31
    • 0036207492 scopus 로고    scopus 로고
    • Protein engineering study of protein L by simulation
    • The authors validated the folding of the minimalist protein L/G model by comparison with sequence mutation data and Φ-value analysis. This paper emphasizes the ability of minimalist models to fully analyze and characterize folding.
    • Sorenson J.M., Head-Gordon T. Protein engineering study of protein L by simulation. J. Comput. Biol. 9:2002;35-54 The authors validated the folding of the minimalist protein L/G model by comparison with sequence mutation data and Φ-value analysis. This paper emphasizes the ability of minimalist models to fully analyze and characterize folding.
    • (2002) J. Comput. Biol. , vol.9 , pp. 35-54
    • Sorenson, J.M.1    Head-Gordon, T.2
  • 32
    • 0036499417 scopus 로고    scopus 로고
    • Toward minimalist models of larger proteins: A ubiquitin-like protein
    • The extension of the physico-chemical model for protein L/G to investigate the folding of ubiquitin.
    • Sorensen J.M., Head-Gordon T. Toward minimalist models of larger proteins: a ubiquitin-like protein. Proteins. 46:2002;368-379 The extension of the physico-chemical model for protein L/G to investigate the folding of ubiquitin.
    • (2002) Proteins , vol.46 , pp. 368-379
    • Sorensen, J.M.1    Head-Gordon, T.2
  • 33
    • 12444281071 scopus 로고    scopus 로고
    • Sequence design for determining proteins that fold by alternative folding mechanisms
    • in press
    • Brown S, Head-Gordon T: Sequence design for determining proteins that fold by alternative folding mechanisms. Protein Sci 2003, in press.
    • (2003) Protein Sci
    • Brown, S.1    Head-Gordon, T.2
  • 34
    • 0033117762 scopus 로고    scopus 로고
    • Designing potential energy functions for protein folding
    • Hao M.H., Scheraga H.A. Designing potential energy functions for protein folding. Curr. Opin. Struct. Biol. 9:1999;184-188.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 184-188
    • Hao, M.H.1    Scheraga, H.A.2
  • 35
    • 0032606941 scopus 로고    scopus 로고
    • Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer
    • Takada S., Luthey-Schulten Z., Wolynes P.G. Folding dynamics with nonadditive forces: a simulation study of a designed helical protein and a random heteropolymer. J. Chem. Phys. 110:1999;11616-11629.
    • (1999) J. Chem. Phys. , vol.110 , pp. 11616-11629
    • Takada, S.1    Luthey-Schulten, Z.2    Wolynes, P.G.3
  • 36
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa S., Jernigan R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256:1996;623-644.
    • (1996) J. Mol. Biol. , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 37
    • 0036785556 scopus 로고    scopus 로고
    • The origins of asymmetry in the folding transition states of protein L and protein G
    • The development of a minimalist protein model that includes physical interactions using an MJ statistical potential on top of a Gō potential to realize a sequence-dependent model for characterizing proteins G and L.
    • Karanicolas J., Brooks C.L. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci. 11:2002;2351-2361 The development of a minimalist protein model that includes physical interactions using an MJ statistical potential on top of a Gō potential to realize a sequence-dependent model for characterizing proteins G and L.
    • (2002) Protein Sci. , vol.11 , pp. 2351-2361
    • Karanicolas, J.1    Brooks, C.L.2
  • 39
    • 0037154268 scopus 로고    scopus 로고
    • Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
    • This paper describes the mechanism of folding of a simple SH3 model with explicit inclusion of a water reaction coordinate.
    • Cheung M.S., Garcia A.E., Onuchic J.N. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. USA. 99:2002;685-690 This paper describes the mechanism of folding of a simple SH3 model with explicit inclusion of a water reaction coordinate.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 685-690
    • Cheung, M.S.1    Garcia, A.E.2    Onuchic, J.N.3
  • 40
    • 0029004982 scopus 로고
    • A phage display system for studying the sequence determinants of protein folding
    • Gu H.D., Yi Q.A., Bray S.T., Riddle D.S., Shiau A.K., Baker D. A phage display system for studying the sequence determinants of protein folding. Protein Sci. 4:1995;1108-1117.
    • (1995) Protein Sci. , vol.4 , pp. 1108-1117
    • Gu, H.D.1    Yi, Q.A.2    Bray, S.T.3    Riddle, D.S.4    Shiau, A.K.5    Baker, D.6
  • 41
    • 0030664958 scopus 로고    scopus 로고
    • An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core
    • Park S.H., Oneil K.T., Roder H. An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core. Biochemistry. 36:1997;14277-14283.
    • (1997) Biochemistry , vol.36 , pp. 14277-14283
    • Park, S.H.1    Oneil, K.T.2    Roder, H.3
  • 42
    • 0031565981 scopus 로고    scopus 로고
    • Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein
    • Gu H.D., Kim D., Baker D. Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. J. Mol. Biol. 274:1997;588-596.
    • (1997) J. Mol. Biol. , vol.274 , pp. 588-596
    • Gu, H.D.1    Kim, D.2    Baker, D.3
  • 43
    • 0032978994 scopus 로고    scopus 로고
    • Chain collapse can occur concomitantly with the rate-limiting step in protein folding
    • Plaxco K.W., Millett I.S., Segel D.J., Doniach S., Baker D. Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nat. Struct. Biol. 6:1999;554-556.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 554-556
    • Plaxco, K.W.1    Millett, I.S.2    Segel, D.J.3    Doniach, S.4    Baker, D.5
  • 44
    • 0030900533 scopus 로고    scopus 로고
    • Kinetics of folding of the IgG binding domain of peptostreptoccocal protein L
    • Scalley M.L., Yi Q., Gu H.D., McCormack A., Yates J.R., Baker D. Kinetics of folding of the IgG binding domain of peptostreptoccocal protein L. Biochemistry. 36:1997;3373-3382.
    • (1997) Biochemistry , vol.36 , pp. 3373-3382
    • Scalley, M.L.1    Yi, Q.2    Gu, H.D.3    McCormack, A.4    Yates, J.R.5    Baker, D.6
  • 45
    • 0034964196 scopus 로고    scopus 로고
    • Computer-based redesign of a protein folding pathway
    • Computational redesign and experimental verification of a switch in the folding pathway of protein G to favor the formation of the first β hairpin, similar to protein L.
    • Nauli S., Kuhlman B., Baker D. Computer-based redesign of a protein folding pathway. Nat. Struct. Biol. 8:2001;602-605 Computational redesign and experimental verification of a switch in the folding pathway of protein G to favor the formation of the first β hairpin, similar to protein L.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 602-605
    • Nauli, S.1    Kuhlman, B.2    Baker, D.3
  • 46
    • 0032080053 scopus 로고    scopus 로고
    • Calculations on folding of segment B1 of streptococcal protein G
    • Sheinerman F.B., Brooks C.L. Calculations on folding of segment B1 of streptococcal protein G. J. Mol. Biol. 278:1998;439-456.
    • (1998) J. Mol. Biol. , vol.278 , pp. 439-456
    • Sheinerman, F.B.1    Brooks, C.L.2
  • 47
    • 0031697733 scopus 로고    scopus 로고
    • The burst phase in ribonuclease A folding and solvent dependence of the unfolded state
    • Qi P.X., Sosnick T.R., Englander S.W. The burst phase in ribonuclease A folding and solvent dependence of the unfolded state. Nat. Struct. Biol. 5:1998;882-884.
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 882-884
    • Qi, P.X.1    Sosnick, T.R.2    Englander, S.W.3
  • 48
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann W. Some factors in the interpretation of protein denaturation. Adv. Protein. Chem. 14:1959;1-59.
    • (1959) Adv. Protein. Chem. , vol.14 , pp. 1-59
    • Kauzmann, W.1
  • 49
    • 0037459035 scopus 로고    scopus 로고
    • Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
    • This paper critically examines whether the use of Gō potentials, even when supplemented by physical hydration forces, is adequate for robust and predictive protein folding studies.
    • Kaya H., Chan H.S. Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling? J. Mol. Biol. 326:2003;911-931 This paper critically examines whether the use of Gō potentials, even when supplemented by physical hydration forces, is adequate for robust and predictive protein folding studies.
    • (2003) J. Mol. Biol. , vol.326 , pp. 911-931
    • Kaya, H.1    Chan, H.S.2
  • 50
    • 0032437795 scopus 로고    scopus 로고
    • The importance of hydration for the kinetics and thermodynamics of protein folding: Simplified lattice models
    • Sorenson J.M., Head-Gordon T. The importance of hydration for the kinetics and thermodynamics of protein folding: simplified lattice models. Fold Des. 3:1998;523-534.
    • (1998) Fold Des. , vol.3 , pp. 523-534
    • Sorenson, J.M.1    Head-Gordon, T.2
  • 51
    • 36749120002 scopus 로고
    • Theory of the hydrophobic effect
    • Pratt L.R., Chandler D. Theory of the hydrophobic effect. J. Chem. Phys. 67:1977;3683-3704.
    • (1977) J. Chem. Phys. , vol.67 , pp. 3683-3704
    • Pratt, L.R.1    Chandler, D.2
  • 53
    • 0031052147 scopus 로고    scopus 로고
    • A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding
    • Rank J.A., Baker D. A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding. Protein Sci. 6:1997;347-354.
    • (1997) Protein Sci. , vol.6 , pp. 347-354
    • Rank, J.A.1    Baker, D.2
  • 55
    • 0033529908 scopus 로고    scopus 로고
    • Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G
    • Pande V.S., Rokhsar D.S. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc. Natl. Acad. Sci. USA. 96:1999;9062-9067.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9062-9067
    • Pande, V.S.1    Rokhsar, D.S.2
  • 56
    • 0032539561 scopus 로고    scopus 로고
    • Molecular picture of folding of a small alpha/beta protein
    • Sheinerman F.B., Brooks C.L. Molecular picture of folding of a small alpha/beta protein. Proc. Natl. Acad. Sci. USA. 95:1998;1562-1567.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 1562-1567
    • Sheinerman, F.B.1    Brooks, C.L.2
  • 58
    • 0030900199 scopus 로고    scopus 로고
    • NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions
    • Zhang O.W., Formankay J.D. NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions. Biochemistry. 36:1997;3959-3970.
    • (1997) Biochemistry , vol.36 , pp. 3959-3970
    • Zhang, O.W.1    Formankay, J.D.2
  • 59
    • 0029772552 scopus 로고    scopus 로고
    • Emergence of preferred structures in a simple model of protein folding
    • Li H., Helling R., Tang C., Wingreen N. Emergence of preferred structures in a simple model of protein folding. Science. 273:1996;666-669.
    • (1996) Science , vol.273 , pp. 666-669
    • Li, H.1    Helling, R.2    Tang, C.3    Wingreen, N.4
  • 61
    • 0037110580 scopus 로고    scopus 로고
    • Designability of protein structures: A lattice-model study using the Miyazawa-Jernigan matrix
    • This theoretical study suggests that the most common folds of real proteins are the most atypical in the space of all possible structures and are more designable (defined as the number of sequences that have that structure as their unique lowest energy state), with enhanced thermodynamic stability. This paper confirms that these conclusions are sound whether using a hydrophobic-polar (HP) or MJ model.
    • Li H., Tang C., Wingreen N.S. Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix. Proteins. 49:2002;403-412 This theoretical study suggests that the most common folds of real proteins are the most atypical in the space of all possible structures and are more designable (defined as the number of sequences that have that structure as their unique lowest energy state), with enhanced thermodynamic stability. This paper confirms that these conclusions are sound whether using a hydrophobic-polar (HP) or MJ model.
    • (2002) Proteins , vol.49 , pp. 403-412
    • Li, H.1    Tang, C.2    Wingreen, N.S.3
  • 63
    • 0036892389 scopus 로고    scopus 로고
    • Thoroughly sampling sequence space: Large-scale protein design of structural ensembles
    • The authors, using distributed computing, broadly explore sequence space with backbone flexibility to achieve large-scale protein design of structural ensembles.
    • Larson S.M., England J.L., Desjarlais J.R., Pande V.S. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci. 11:2002;2804-2813 The authors, using distributed computing, broadly explore sequence space with backbone flexibility to achieve large-scale protein design of structural ensembles.
    • (2002) Protein Sci. , vol.11 , pp. 2804-2813
    • Larson, S.M.1    England, J.L.2    Desjarlais, J.R.3    Pande, V.S.4
  • 64
    • 0028109545 scopus 로고
    • Three-dimensional solution structure of an immunoglobulin light chain-binding domain of protein l - comparison with the IgG-binding domains of protein G
    • Wikstrom M., Drakenberg T., Forsen S., Sjobring U., Bjorck L. Three-dimensional solution structure of an immunoglobulin light chain-binding domain of protein l - comparison with the IgG-binding domains of protein G. Biochemistry. 33:1994;14011-14017.
    • (1994) Biochemistry , vol.33 , pp. 14011-14017
    • Wikstrom, M.1    Drakenberg, T.2    Forsen, S.3    Sjobring, U.4    Bjorck, L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.