메뉴 건너뛰기




Volumn 70, Issue 3, 2008, Pages 915-924

New insight into long-range nonadditivity within protein double-mutant cycles

Author keywords

Cooperativity; Double mutant cycle; Free energy nonadditivity; Network rigidity; Protein structure

Indexed keywords

MUTANT PROTEIN;

EID: 38549120278     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21620     Document Type: Article
Times cited : (44)

References (34)
  • 1
    • 0019407381 scopus 로고
    • On the attribution and additivity of binding energies
    • Jencks WP. On the attribution and additivity of binding energies. Proc Natl Acad Sci USA 1981;78:4046-4050.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 4046-4050
    • Jencks, W.P.1
  • 2
    • 0021891887 scopus 로고
    • Effects of site-specific amino acid modification on protein interactions and biological function
    • Ackers GK, Smith FR. Effects of site-specific amino acid modification on protein interactions and biological function. Annu Rev Biochem 1985;54:597-629.
    • (1985) Annu Rev Biochem , vol.54 , pp. 597-629
    • Ackers, G.K.1    Smith, F.R.2
  • 3
    • 0025082684 scopus 로고
    • Additivity of mutational effects in proteins
    • Wells JA. Additivity of mutational effects in proteins. Biochemistry 1990;29:8509-8517.
    • (1990) Biochemistry , vol.29 , pp. 8509-8517
    • Wells, J.A.1
  • 4
    • 0027383834 scopus 로고
    • Patterns of nonadditivity between pairs of stability mutations in staphylococcal nuclease
    • Green SM, Shortle D. Patterns of nonadditivity between pairs of stability mutations in staphylococcal nuclease. Biochemistry 1993;32:10131-10139.
    • (1993) Biochemistry , vol.32 , pp. 10131-10139
    • Green, S.M.1    Shortle, D.2
  • 5
    • 0027211894 scopus 로고
    • Additivity of mutant effects assessed by binomial mutagenesis
    • Gregoret LM, Sauer RT. Additivity of mutant effects assessed by binomial mutagenesis. Proc Natl Acad Sci USA 1993;90:4246-4250.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 4246-4250
    • Gregoret, L.M.1    Sauer, R.T.2
  • 6
    • 0028037407 scopus 로고
    • Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase
    • Huang Z, Wagner CR, Benkovic SJ. Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase. Biochemistry 1994;33:11576-11585.
    • (1994) Biochemistry , vol.33 , pp. 11576-11585
    • Huang, Z.1    Wagner, C.R.2    Benkovic, S.J.3
  • 7
    • 8744220371 scopus 로고    scopus 로고
    • Inverse thinking about double mutants of enzymes
    • Mildvan AS. Inverse thinking about double mutants of enzymes. Biochemistry 2004;43:14517-14520.
    • (2004) Biochemistry , vol.43 , pp. 14517-14520
    • Mildvan, A.S.1
  • 8
    • 0029785464 scopus 로고    scopus 로고
    • Potential use of additivity of mutational effects in simplifying protein engineering
    • Skinner MM, Terwilliger TC. Potential use of additivity of mutational effects in simplifying protein engineering. Proc Natl Acad Sci USA 1996;93:10753-10757.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 10753-10757
    • Skinner, M.M.1    Terwilliger, T.C.2
  • 10
    • 0027248706 scopus 로고
    • Engineering multiple properties of a protein by combinatorial mutagenesis
    • Sandberg WS, Terwilliger TC. Engineering multiple properties of a protein by combinatorial mutagenesis. Proc Natl Acad Sci USA 1993;90:8367-8371.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 8367-8371
    • Sandberg, W.S.1    Terwilliger, T.C.2
  • 11
    • 0031715867 scopus 로고    scopus 로고
    • Nonadditivity of mutational effects on the properties of catalase I and its application to efficient directed evolution
    • Matsuura T, Yomo T, Trakulmalemsai S, Ohashi Y, Yamamoto K, Urabe I. Nonadditivity of mutational effects on the properties of catalase I and its application to efficient directed evolution. Prot Engineering 1998;11:789-795.
    • (1998) Prot Engineering , vol.11 , pp. 789-795
    • Matsuura, T.1    Yomo, T.2    Trakulmalemsai, S.3    Ohashi, Y.4    Yamamoto, K.5    Urabe, I.6
  • 12
    • 0026681635 scopus 로고
    • Quantitative interpretations of double mutations of enzymes
    • Mildvan AS, Weber DJ, Kuliopulos A. Quantitative interpretations of double mutations of enzymes. Arch Biochem Biophys 1992;294:327-340.
    • (1992) Arch Biochem Biophys , vol.294 , pp. 327-340
    • Mildvan, A.S.1    Weber, D.J.2    Kuliopulos, A.3
  • 13
    • 0028362702 scopus 로고
    • Prediction of an inter-residue interaction in the chaperonin GroEL from multiple sequence alignment is confirmed by double-mutant cycle analysis
    • Horovitz A, Bochkareva ES, Yifrach O, Girshovich AS. Prediction of an inter-residue interaction in the chaperonin GroEL from multiple sequence alignment is confirmed by double-mutant cycle analysis. J Mol Biol 1994;238:133-138.
    • (1994) J Mol Biol , vol.238 , pp. 133-138
    • Horovitz, A.1    Bochkareva, E.S.2    Yifrach, O.3    Girshovich, A.S.4
  • 14
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless SW, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999;286:295-299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 15
    • 2442498470 scopus 로고    scopus 로고
    • On evolutionary conservation of thermodynamic coupling in proteins
    • Fodor A, Aldrich R. On evolutionary conservation of thermodynamic coupling in proteins. J Biol Chem 2004;279:19046-19050.
    • (2004) J Biol Chem , vol.279 , pp. 19046-19050
    • Fodor, A.1    Aldrich, R.2
  • 16
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • Suel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003;10:59-69.
    • (2003) Nat Struct Biol , vol.10 , pp. 59-69
    • Suel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 18
    • 1642304065 scopus 로고    scopus 로고
    • Structural determinants of allosteric ligand activation in RXR heterodimers
    • Shulman A, Larson C, Mangelsdorf D, Ranganathan R. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 2004;116:417-429.
    • (2004) Cell , vol.116 , pp. 417-429
    • Shulman, A.1    Larson, C.2    Mangelsdorf, D.3    Ranganathan, R.4
  • 19
    • 0028965496 scopus 로고
    • Long-range, small magnitude nonadditivity of mutational effects in proteins
    • LiCata VJ, Ackers GK. Long-range, small magnitude nonadditivity of mutational effects in proteins. Biochemistry 1995;34:3133-3139.
    • (1995) Biochemistry , vol.34 , pp. 3133-3139
    • LiCata, V.J.1    Ackers, G.K.2
  • 20
    • 0031022887 scopus 로고    scopus 로고
    • Additivity principles in biochemistry
    • Dill KA. Additivity principles in biochemistry. J Biol Chem 1997;272:701-704.
    • (1997) J Biol Chem , vol.272 , pp. 701-704
    • Dill, K.A.1
  • 21
    • 0038810233 scopus 로고    scopus 로고
    • Correlated motion and the effect of distal mutations in dihydrofolate reductase
    • Rod TH, Radkiewicz JL, Brooks CL III. Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc Natl Acad Sci USA 2003;100:6980-6985.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 6980-6985
    • Rod, T.H.1    Radkiewicz, J.L.2    Brooks III, C.L.3
  • 22
    • 84923260008 scopus 로고    scopus 로고
    • Jacobs DJ, Dallakyan S, Wood GG, Heckathorne A. Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems. Phys Rev E 2003;68:061109, 1-21.
    • Jacobs DJ, Dallakyan S, Wood GG, Heckathorne A. Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems. Phys Rev E 2003;68:061109, 1-21.
  • 23
    • 6344223617 scopus 로고    scopus 로고
    • A flexible approach for understanding protein stability
    • Livesay DR, Dallakyan S, Wood GG, Jacobs DJ. A flexible approach for understanding protein stability. FEBS Lett 2004;576:468-476.
    • (2004) FEBS Lett , vol.576 , pp. 468-476
    • Livesay, D.R.1    Dallakyan, S.2    Wood, G.G.3    Jacobs, D.J.4
  • 24
    • 21244483843 scopus 로고    scopus 로고
    • Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity
    • Jacobs DJ, Dallakyan S. Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity. Biophys J 2005;88:903-915.
    • (2005) Biophys J , vol.88 , pp. 903-915
    • Jacobs, D.J.1    Dallakyan, S.2
  • 25
    • 33646033429 scopus 로고    scopus 로고
    • Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model
    • Jacobs DJ, Livesay DR, Hules J, Tasayco M-L. Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model. J Mol Biol 2006;358:882-904.
    • (2006) J Mol Biol , vol.358 , pp. 882-904
    • Jacobs, D.J.1    Livesay, D.R.2    Hules, J.3    Tasayco, M.-L.4
  • 26
    • 30344476409 scopus 로고    scopus 로고
    • Conserved quantified stability/flexibility relationships (QSFR) in an orthologous RNase H pair
    • Livesay DR, Jacobs DJ. Conserved quantified stability/flexibility relationships (QSFR) in an orthologous RNase H pair. Proteins 2006;62:130-143.
    • (2006) Proteins , vol.62 , pp. 130-143
    • Livesay, D.R.1    Jacobs, D.J.2
  • 29
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs DJ, Rader AJ, Thorpe MF, Kuhn LA. Protein flexibility predictions using graph theory. Proteins 2001;44:150-165.
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Thorpe, M.F.3    Kuhn, L.A.4
  • 31
    • 3042806330 scopus 로고    scopus 로고
    • Gohlke H, Kuhn LA, Case DA. Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins 2004;56:322-337.
    • Gohlke H, Kuhn LA, Case DA. Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins 2004;56:322-337.
  • 32
    • 33646742004 scopus 로고    scopus 로고
    • Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
    • Zheng W, Brooks BR, Thirumalai D. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci USA 2006;103:7664-7669.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 7664-7669
    • Zheng, W.1    Brooks, B.R.2    Thirumalai, D.3
  • 34
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • Ponder JW, Case DA. Force fields for protein simulations. Adv Prot Chem 2003;66:27-85.
    • (2003) Adv Prot Chem , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.