메뉴 건너뛰기




Volumn 8, Issue 1, 1998, Pages 80-85

Simplified proteins: Minimalist solutions to the 'protein folding problem'

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 0032005126     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80013-4     Document Type: Article
Times cited : (62)

References (48)
  • 1
    • 0029793096 scopus 로고    scopus 로고
    • Evidence for nonrandom hydrophobicity structures in protein chains
    • Irback A, Peterson C, Potthast F. Evidence for nonrandom hydrophobicity structures in protein chains. Proc Natl Acad Sci USA. 93:1996;9533-9538.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 9533-9538
    • Irback, A.1    Peterson, C.2    Potthast, F.3
  • 2
    • 0028846974 scopus 로고
    • Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins
    • West MW, Hecht MH. Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins. Protein Sci. 4:1995;2032-2039.
    • (1995) Protein Sci , vol.4 , pp. 2032-2039
    • West, M.W.1    Hecht, M.H.2
  • 3
    • 0028234347 scopus 로고
    • Sequences with 'unusual' amino acid compositions
    • Wootton JC. Sequences with 'unusual' amino acid compositions. Curr Opin Struct Biol. 4:1994;413-421.
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 413-421
    • Wootton, J.C.1
  • 4
    • 0031020765 scopus 로고    scopus 로고
    • How far can sequences diverge?
    • Chothia C, Gerstein M. How far can sequences diverge? Nature. 385:1997;579-581.
    • (1997) Nature , vol.385 , pp. 579-581
    • Chothia, C.1    Gerstein, M.2
  • 5
    • 0031029551 scopus 로고    scopus 로고
    • Protein design: The choice of de novo sequences
    • of outstanding interest. An excellent review of the sequence determinants of protein structure. The authors place particular emphasis on the role played by simple binary patterns in encoding the three-dimensional structure of the native state.
    • of outstanding interest Beasley JR, Hecht MH. Protein design: the choice of de novo sequences. J Biol Chem. 272:1997;2031-2034 An excellent review of the sequence determinants of protein structure. The authors place particular emphasis on the role played by simple binary patterns in encoding the three-dimensional structure of the native state.
    • (1997) J Biol Chem , vol.272 , pp. 2031-2034
    • Beasley, J.R.1    Hecht, M.H.2
  • 6
    • 0002983608 scopus 로고    scopus 로고
    • Protein folding from a combinatorial perspective
    • Sauer RT. Protein folding from a combinatorial perspective. Fold Des. 1:1996;R27-R30.
    • (1996) Fold des , vol.1
    • Sauer, R.T.1
  • 7
    • 0028247281 scopus 로고
    • Side-chain entropy and packing in proteins
    • Bromberg S, Dill KA. Side-chain entropy and packing in proteins. Protein Sci. 3:1994;997-1009.
    • (1994) Protein Sci , vol.3 , pp. 997-1009
    • Bromberg, S.1    Dill, K.A.2
  • 8
    • 0025759275 scopus 로고
    • The protein-folding problem: The native fold determines packing, but does packing determine the native fold?
    • Behe MJ, Lattman EE, Rose GD. The protein-folding problem: the native fold determines packing, but does packing determine the native fold? Proc Natl Acad Sci USA. 88:1991;4195-4199.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 4195-4199
    • Behe, M.J.1    Lattman, E.E.2    Rose, G.D.3
  • 9
    • 0023155210 scopus 로고
    • Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol. 193:1987;775-791.
    • (1987) J Mol Biol , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 10
    • 0000920828 scopus 로고
    • The packing of α-helices: Simple coiled-coils
    • Crick FHC. The packing of α-helices: simple coiled-coils. Acta Crystallogr. 6:1953;689-697.
    • (1953) Acta Crystallogr , vol.6 , pp. 689-697
    • Crick, F.H.C.1
  • 12
    • 0029980972 scopus 로고    scopus 로고
    • Active barnase variants with completely random hydrophobic cores
    • Axe DD, Foster NW, Fersht AR. Active barnase variants with completely random hydrophobic cores. Proc Natl Acad Sci USA. 93:1996;5590-5594.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 5590-5594
    • Axe, D.D.1    Foster, N.W.2    Fersht, A.R.3
  • 13
    • 0028982611 scopus 로고
    • Sequence 'minimization': Exploring the sequence landscape with simplified sequences
    • Clarke ND. Sequence 'minimization': exploring the sequence landscape with simplified sequences. Curr Opin Biotechnol. 6:1995;467-472.
    • (1995) Curr Opin Biotechnol , vol.6 , pp. 467-472
    • Clarke, N.D.1
  • 14
    • 0028608066 scopus 로고
    • Redesigning the hydrophobic core of a four-helix-bundle protein
    • Munson M, O'Brien R, Sturtevant JM, Regan L. Redesigning the hydrophobic core of a four-helix-bundle protein. Protein Sci. 3:1994;2015-2022.
    • (1994) Protein Sci , vol.3 , pp. 2015-2022
    • Munson, M.1    O'Brien, R.2    Sturtevant, J.M.3    Regan, L.4
  • 16
    • 0029958604 scopus 로고    scopus 로고
    • A test of the 'jigsaw puzzle' model for protein folding by multiple methionine substitutions within the core of T4 lysozyme
    • of outstanding interest. This crystallographic and thermodynamic study of T4 lysozyme variants with significantly simplified hydrophobic cores demonstrates clearly the extraordinary degree of core compositional simplicity that a globular protein can accommodate and poses a serious challenge to the 'jigsaw puzzle' model of core packing and protein structure.
    • of outstanding interest Gassner NC, Baase WA, Matthews BW. A test of the 'jigsaw puzzle' model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc Natl Acad Sci USA. 93:1996;12155-12158 This crystallographic and thermodynamic study of T4 lysozyme variants with significantly simplified hydrophobic cores demonstrates clearly the extraordinary degree of core compositional simplicity that a globular protein can accommodate and poses a serious challenge to the 'jigsaw puzzle' model of core packing and protein structure.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 12155-12158
    • Gassner, N.C.1    Baase, W.A.2    Matthews, B.W.3
  • 17
    • 0028858499 scopus 로고
    • De novo design of the hydrophobic cores of proteins
    • Desjarlais JR, Handel TM. De novo design of the hydrophobic cores of proteins. Protein Sci. 4:1995;2006-2018.
    • (1995) Protein Sci , vol.4 , pp. 2006-2018
    • Desjarlais, J.R.1    Handel, T.M.2
  • 19
    • 0028168562 scopus 로고
    • Design of a 'minimAl' homeodomain: The N-terminal arm modulates DNA binding affinity and stabilizes homeodomain structure
    • Shang Z, Isaac VE, Li H, Patel L, Catron KM, Curran T, Montelione GT, Abate C. Design of a 'minimAl' homeodomain: the N-terminal arm modulates DNA binding affinity and stabilizes homeodomain structure. Proc Natl Acad Sci USA. 91:1994;8373-8377.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 8373-8377
    • Shang, Z.1    Isaac, V.E.2    Li, H.3    Patel, L.4    Catron, K.M.5    Curran, T.6    Montelione, G.T.7    Abate, C.8
  • 20
    • 23444436172 scopus 로고
    • Protein design by binary patterning of polar and nonpolar amino acids
    • Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH. Protein design by binary patterning of polar and nonpolar amino acids. Science. 265:1993;1680-1685.
    • (1993) Science , vol.265 , pp. 1680-1685
    • Kamtekar, S.1    Schiffer, J.M.2    Xiong, H.3    Babik, J.M.4    Hecht, M.H.5
  • 21
    • 0030623317 scopus 로고    scopus 로고
    • Detecting native-like properties in combinatorial libraries of de novo proteins
    • of special interest. NMR is used in this study to investigate the nativeness of representative proteins derived from a library of random sequences that conform to a binary pattern thought to encode four-helix bundle proteins.
    • of special interest Roy S, Helmer KJ, Hecht MH. Detecting native-like properties in combinatorial libraries of de novo proteins. Fold Des. 2:1997;89-92 NMR is used in this study to investigate the nativeness of representative proteins derived from a library of random sequences that conform to a binary pattern thought to encode four-helix bundle proteins.
    • (1997) Fold des , vol.2 , pp. 89-92
    • Roy, S.1    Helmer, K.J.2    Hecht, M.H.3
  • 22
  • 23
    • 0023812695 scopus 로고
    • Characterization of a helical protein designed from first principles
    • Regan L, DeGrado WF. Characterization of a helical protein designed from first principles. Science. 241:1988;976-978.
    • (1988) Science , vol.241 , pp. 976-978
    • Regan, L.1    Degrado, W.F.2
  • 24
    • 0027177971 scopus 로고
    • Metal ion-dependent modulation of the dynamics of a designed protein
    • Handel TM, Williams SA, DeGrado WF. Metal ion-dependent modulation of the dynamics of a designed protein. Science. 261:1993;879-885.
    • (1993) Science , vol.261 , pp. 879-885
    • Handel, T.M.1    Williams, S.A.2    Degrado, W.F.3
  • 25
    • 0029004982 scopus 로고
    • A phage display system for studying the sequence determinants of protein folding
    • Gu H, Yi Q, Bray ST, Riddle DS, Shiau AK, 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.1    Yi, Q.2    Bray, S.T.3    Riddle, D.S.4    Shiau, A.K.5    Baker, D.6
  • 26
    • 0030852463 scopus 로고    scopus 로고
    • Functional rapidly folding proteins from simplified amino acid sequences
    • of outstanding interest. A phage display technique was used to select for significantly simplified proteins that adopt an SH3 domain fold. These studies suggest that a five-letter alphabet is the minimal compositional complexity required to generate this predominantly β-sheet fold. The rapid folding of the highly simplified variants recovered in this work (one folds 50% more rapidly than the wild-type sequence from which it was derived) suggests that sequence complexity of naturally occurring proteins is not required to generate rapidly folding species.
    • of outstanding interest Riddle DS, Santiago JV, Bray ST, Doshi N, Grantcharova V, Yi Q, Baker D. Functional rapidly folding proteins from simplified amino acid sequences. Nat Struct Biol. 4:1997;805-809 A phage display technique was used to select for significantly simplified proteins that adopt an SH3 domain fold. These studies suggest that a five-letter alphabet is the minimal compositional complexity required to generate this predominantly β-sheet fold. The rapid folding of the highly simplified variants recovered in this work (one folds 50% more rapidly than the wild-type sequence from which it was derived) suggests that sequence complexity of naturally occurring proteins is not required to generate rapidly folding species.
    • (1997) Nat Struct Biol , vol.4 , pp. 805-809
    • Riddle, D.S.1    Santiago, J.V.2    Bray, S.T.3    Doshi, N.4    Grantcharova, V.5    Yi, Q.6    Baker, D.7
  • 28
    • 0028218304 scopus 로고
    • Folded proteins occur frequently in libraries of random amino acid sequences
    • Davidson AR, Sauer RT. Folded proteins occur frequently in libraries of random amino acid sequences. Proc Natl Acad Sci USA. 91:1994;2146-2150.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 2146-2150
    • Davidson, A.R.1    Sauer, R.T.2
  • 29
    • 0029120253 scopus 로고
    • Cooperatively folded proteins in random sequence libraries
    • Davidson AR, Lumb KJ, Sauer RT. Cooperatively folded proteins in random sequence libraries. Nat Struct Biol. 2:1995;856-864.
    • (1995) Nat Struct Biol , vol.2 , pp. 856-864
    • Davidson, A.R.1    Lumb, K.J.2    Sauer, R.T.3
  • 30
    • 0000648204 scopus 로고
    • On the structure of native, denatured, and coagulated proteins
    • Mirsky AK, Pauling L. On the structure of native, denatured, and coagulated proteins. Proc Natl Acad Sci USA. 22:1936;439-447.
    • (1936) Proc Natl Acad Sci USA , vol.22 , pp. 439-447
    • Mirsky, A.K.1    Pauling, L.2
  • 31
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB. Principles that govern the folding of protein chains. Science. 181:1973;223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 32
    • 0029864379 scopus 로고    scopus 로고
    • Collapse and cooperativity in protein folding
    • Miranker AD, Dobson CM. Collapse and cooperativity in protein folding. Curr Opin Struct Biol. 6:1996;31-42.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 31-42
    • Miranker, A.D.1    Dobson, C.M.2
  • 33
    • 0028917296 scopus 로고
    • Structures of folding intermediates
    • Ptitsyn OB. Structures of folding intermediates. Curr Opin Struct Biol. 5:1995;74-78.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 74-78
    • Ptitsyn, O.B.1
  • 34
    • 0031055942 scopus 로고    scopus 로고
    • Kinetic role of early intermediates in protein folding
    • of special interest. An excellent review of collapse and cooperativity in protein folding and the role of collapse as a rate-limiting step in the folding process.
    • of special interest Roder H, Colón W. Kinetic role of early intermediates in protein folding. Curr Opin Struct Biol. 7:1997;15-28 An excellent review of collapse and cooperativity in protein folding and the role of collapse as a rate-limiting step in the folding process.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 15-28
    • Roder, H.1    Colón, W.2
  • 35
    • 0029883960 scopus 로고    scopus 로고
    • From structure to sequence and back again
    • of special interest. This theoretical study explores some potential structural pitfalls faced by proteins composed of reduced amino acid alphabets.
    • of special interest Hinds DA, Levitt M. From structure to sequence and back again. J Mol Biol. 258:1996;201-209 This theoretical study explores some potential structural pitfalls faced by proteins composed of reduced amino acid alphabets.
    • (1996) J Mol Biol , vol.258 , pp. 201-209
    • Hinds, D.A.1    Levitt, M.2
  • 36
    • 0003155594 scopus 로고    scopus 로고
    • Comparing folding codes for proteins and polymers
    • Chan HS, Dill KA. Comparing folding codes for proteins and polymers. Proteins. 24:1996;335-344.
    • (1996) Proteins , vol.24 , pp. 335-344
    • Chan, H.S.1    Dill, K.A.2
  • 37
    • 0030627747 scopus 로고    scopus 로고
    • Speeding up protein folding: Mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude
    • of outstanding interest. This investigation into the folding rates of core-simplified variants of Rop suggests that the potential packing redundancy of simplified hydrophobic cores does not reduce protein folding rates. Indeed, all of the simplified variants investigated fold more rapidly than the wild-type sequence from which they were derived, potentially due to the removal of buried hydrophilic residues.
    • of outstanding interest Munson M, Anderson KS, Regan L. Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude. Fold Des. 2:1997;77-87 This investigation into the folding rates of core-simplified variants of Rop suggests that the potential packing redundancy of simplified hydrophobic cores does not reduce protein folding rates. Indeed, all of the simplified variants investigated fold more rapidly than the wild-type sequence from which they were derived, potentially due to the removal of buried hydrophilic residues.
    • (1997) Fold des , vol.2 , pp. 77-87
    • Munson, M.1    Anderson, K.S.2    Regan, L.3
  • 38
    • 0029966342 scopus 로고    scopus 로고
    • Barriers to protein folding: Formation of buried polar interactions is a slow step in acquisition of structure
    • Waldburger CD, Jonsson T, Sauer RT. Barriers to protein folding: formation of buried polar interactions is a slow step in acquisition of structure. Proc Natl Acad Sci USA. 93:1996;2629-2634.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 2629-2634
    • Waldburger, C.D.1    Jonsson, T.2    Sauer, R.T.3
  • 39
    • 0002006297 scopus 로고
    • Are there pathways for protein folding?
    • Levinthal C. Are there pathways for protein folding? J Chem Phys. 65:1968;44-45.
    • (1968) J Chem Phys , vol.65 , pp. 44-45
    • Levinthal, C.1
  • 40
    • 0014378880 scopus 로고
    • The origin of the genetic code
    • Crick FHC. The origin of the genetic code. J Mol Biol. 38:1968;367-379.
    • (1968) J Mol Biol , vol.38 , pp. 367-379
    • Crick, F.H.C.1
  • 41
    • 0001437696 scopus 로고
    • Directed Panspermia
    • Crick FHC, Orgel L. Directed Panspermia. Icarus. 19:1973;341-346.
    • (1973) Icarus , vol.19 , pp. 341-346
    • Crick, F.H.C.1    Orgel, L.2
  • 42
    • 0001155613 scopus 로고
    • A co-evolution theory of the genetic code
    • Wong JT. A co-evolution theory of the genetic code. Proc Natl Acad Sci USA. 72:1975;1909-1912.
    • (1975) Proc Natl Acad Sci USA , vol.72 , pp. 1909-1912
    • Wong, J.T.1
  • 43
    • 0028037914 scopus 로고
    • On the origin of the genetic code
    • Kuhn H, Waser J. On the origin of the genetic code. FEBS Lett. 352:1994;259-264.
    • (1994) FEBS Lett , vol.352 , pp. 259-264
    • Kuhn, H.1    Waser, J.2
  • 44
    • 0025339596 scopus 로고
    • Transfer RNAs for primordial amino acids contain remnants of a primitive code at position 3 to 5
    • Moller W, Janssen GM. Transfer RNAs for primordial amino acids contain remnants of a primitive code at position 3 to 5. Biochimie. 72:1990;361-368.
    • (1990) Biochimie , vol.72 , pp. 361-368
    • Moller, W.1    Janssen, G.M.2
  • 46
    • 0029013417 scopus 로고
    • Ice-binding structure and mechanism of an antifreeze protein from winter flounder
    • Sicheri F, Yang DS. Ice-binding structure and mechanism of an antifreeze protein from winter flounder. Nature. 375:1995;427-431.
    • (1995) Nature , vol.375 , pp. 427-431
    • Sicheri, F.1    Yang, D.S.2
  • 47
    • 0031467812 scopus 로고    scopus 로고
    • Antifreeze proteins
    • of special interest. A comprehensive review of the structures and activities of some of the simplest naturally occurring proteins.
    • of special interest Davies PL, Sykes BD. Antifreeze proteins. Curr Opin Struct Biol. 7:1997;828-834 A comprehensive review of the structures and activities of some of the simplest naturally occurring proteins.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 828-834
    • Davies, P.L.1    Sykes, B.D.2
  • 48
    • 0030779405 scopus 로고    scopus 로고
    • A designed four helix bundle protein with native-like structure
    • of outstanding interest. This crystallographic study of a de novo designed, seven-residue type, 108 residue, four-helix bundle clearly demonstrates that only limited compositional and pattern complexity are required to generate truly native proteins
    • of outstanding interest Schafmeister CE, LaPorte SL, Miercke LJW, Stroud RM. A designed four helix bundle protein with native-like structure. Nat Struct Biol. 4:1997;1039-1042 This crystallographic study of a de novo designed, seven-residue type, 108 residue, four-helix bundle clearly demonstrates that only limited compositional and pattern complexity are required to generate truly native proteins.
    • (1997) Nat Struct Biol , vol.4 , pp. 1039-1042
    • Schafmeister, C.E.1    Laporte, S.L.2    Miercke, L.J.W.3    Stroud, R.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.