메뉴 건너뛰기




Volumn 332, Issue 3, 2003, Pages 741-756

Repacking the core of T4 lysozyme by automated design

Author keywords

ORBIT; Repacking; Single site revertants; T4 lysozyme

Indexed keywords

AMINO ACID; CORE PROTEIN; LYSOZYME; WATER;

EID: 0043238060     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00856-8     Document Type: Article
Times cited : (48)

References (52)
  • 2
    • 0027815614 scopus 로고
    • An analysis of packing in the protein folding problem
    • Richards F.M., Lim W.A. An analysis of packing in the protein folding problem. Quart. Rev. Biophys. 26:1994;423-498.
    • (1994) Quart. Rev. Biophys. , vol.26 , pp. 423-498
    • Richards, F.M.1    Lim, W.A.2
  • 3
    • 0027716138 scopus 로고
    • The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme
    • Baldwin E.P., Hajiseyedjavadi O., Baase W.A., Matthews B.W. The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme. Science. 262:1993;1715-1718.
    • (1993) Science , vol.262 , pp. 1715-1718
    • Baldwin, E.P.1    Hajiseyedjavadi, O.2    Baase, W.A.3    Matthews, B.W.4
  • 4
    • 0029892667 scopus 로고    scopus 로고
    • Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme
    • Baldwin E.P., Xu J., Hajiseyedjavadi O., Baase W.A., Matthews B.W. Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme. J. Mol. Biol. 259:1996;542-559.
    • (1996) J. Mol. Biol. , vol.259 , pp. 542-559
    • Baldwin, E.P.1    Xu, J.2    Hajiseyedjavadi, O.3    Baase, W.A.4    Matthews, B.W.5
  • 5
    • 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
    • Gassner N.C., Baase W.A., Matthews B.W. 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.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 12155-12158
    • Gassner, N.C.1    Baase, W.A.2    Matthews, B.W.3
  • 6
    • 0034901412 scopus 로고    scopus 로고
    • Are proteins well-packed?
    • Liang J., Dill K.A. Are proteins well-packed? Biophys. J. 81:2001;751-766.
    • (2001) Biophys. J. , vol.81 , pp. 751-766
    • Liang, J.1    Dill, K.A.2
  • 8
    • 0018115846 scopus 로고
    • Conformation of amino acid side-chains in proteins
    • Janin J., Wodak S., Levitt M., Maigret B. Conformation of amino acid side-chains in proteins. J. Mol. Biol. 125:1978;357-386.
    • (1978) J. Mol. Biol. , vol.125 , pp. 357-386
    • Janin, J.1    Wodak, S.2    Levitt, M.3    Maigret, B.4
  • 9
    • 0023155210 scopus 로고
    • Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder J.W., Richards F.M. 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
    • 0026532266 scopus 로고
    • Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme
    • Hurley J.H., Baase W.A., Matthews B.W. Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme. J. Mol. Biol. 224:1992;1143-1159.
    • (1992) J. Mol. Biol. , vol.224 , pp. 1143-1159
    • Hurley, J.H.1    Baase, W.A.2    Matthews, B.W.3
  • 11
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet J., De Maeyer M., Hazes B., Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature. 356:1992;539-542.
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    De Maeyer, M.2    Hazes, B.3    Lasters, I.4
  • 12
    • 0028212927 scopus 로고
    • Efficient rotamer elimination applied to protein side-chains and related spin glasses
    • Goldstein R.F. Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys. J. 66:1994;1335-1340.
    • (1994) Biophys. J. , vol.66 , pp. 1335-1340
    • Goldstein, R.F.1
  • 13
    • 0029920337 scopus 로고    scopus 로고
    • Protein design automation
    • Dahiyat B.I., Mayo S.L. Protein design automation. Protein Sci. 5:1996;895-903.
    • (1996) Protein Sci. , vol.5 , pp. 895-903
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 14
    • 0030987610 scopus 로고    scopus 로고
    • Probing the role of packing specificity in protein design
    • Dahiyat B.I., Mayo S.L. Probing the role of packing specificity in protein design. Proc. Natl Acad. Sci. USA. 94:1997;10172-10177.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 10172-10177
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 15
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat B.I., Mayo S.L. De novo protein design: fully automated sequence selection. Science. 278:1997;82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 16
    • 0343742614 scopus 로고    scopus 로고
    • Automated design of the surface positions of protein helices
    • Dahiyat B.I., Gordon B.D., Mayo S.L. Automated design of the surface positions of protein helices. Protein Sci. 6:1997;1333-1337.
    • (1997) Protein Sci. , vol.6 , pp. 1333-1337
    • Dahiyat, B.I.1    Gordon, B.D.2    Mayo, S.L.3
  • 17
    • 0030762021 scopus 로고    scopus 로고
    • Coupling backbone flexibility and amino acid sequence selection in protein design
    • Su A., Mayo S.L. Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci. 6:1997;1701-1707.
    • (1997) Protein Sci. , vol.6 , pp. 1701-1707
    • Su, A.1    Mayo, S.L.2
  • 18
    • 0031779918 scopus 로고    scopus 로고
    • Design, structure and stability of a hyperthermophilic protein variant
    • Malakauskas S.M., Mayo S.L. Design, structure and stability of a hyperthermophilic protein variant. Nature Struct. Biol. 5:1998;470-475.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 470-475
    • Malakauskas, S.M.1    Mayo, S.L.2
  • 19
    • 0028820703 scopus 로고
    • Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding
    • Myers J.K., Pace C.N., Scholtz J.M. Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4:1995;2138-2148.
    • (1995) Protein Sci. , vol.4 , pp. 2138-2148
    • Myers, J.K.1    Pace, C.N.2    Scholtz, J.M.3
  • 20
    • 0018784438 scopus 로고
    • Surface and inside volumes in globular proteins
    • Janin J. Surface and inside volumes in globular proteins. Nature. 277:1979;491-492.
    • (1979) Nature , vol.277 , pp. 491-492
    • Janin, J.1
  • 22
  • 23
    • 0024564552 scopus 로고
    • Control of enzyme activity by an engineered disulfide bond
    • Matsumura M., Matthews B.W. Control of enzyme activity by an engineered disulfide bond. Science. 243:1989;792-794.
    • (1989) Science , vol.243 , pp. 792-794
    • Matsumura, M.1    Matthews, B.W.2
  • 26
    • 0025234587 scopus 로고
    • PH-induced denaturation of proteins: A single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme
    • Anderson D.E., Becktel W.J., Dahlquist F.W. pH-induced denaturation of proteins: a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme. Biochemistry. 29:1990;2403-2408.
    • (1990) Biochemistry , vol.29 , pp. 2403-2408
    • Anderson, D.E.1    Becktel, W.J.2    Dahlquist, F.W.3
  • 27
    • 0016634772 scopus 로고
    • Phage T4 lysozyme. Physical properties and reversible unfolding
    • Elwell M., Schellman J.A. Phage T4 lysozyme. Physical properties and reversible unfolding. Biochim. Biophys. Acta. 386:1975;309-323.
    • (1975) Biochim. Biophys. Acta , vol.386 , pp. 309-323
    • Elwell, M.1    Schellman, J.A.2
  • 28
    • 0023660935 scopus 로고
    • Structural studies of mutants of the lysozyme of bacteriophage T4. The temperature sensitive mutant protein Thr157→Ile
    • Grütter M.G., Gray T.M., Weaver L.H., Alber T., Wilson K., Matthews B.W. Structural studies of mutants of the lysozyme of bacteriophage T4. The temperature sensitive mutant protein Thr157→Ile. J. Mol. Biol. 197:1987;315-329.
    • (1987) J. Mol. Biol. , vol.197 , pp. 315-329
    • Grütter, M.G.1    Gray, T.M.2    Weaver, L.H.3    Alber, T.4    Wilson, K.5    Matthews, B.W.6
  • 29
    • 0028178528 scopus 로고
    • Determination of α-helix propensity within the context of a folded protein: Sites 44 and 131 in bacteriophage T4 lysozyme
    • Blaber M., Zhang X.-J., Lindstrom J.D., Pepiot S.D., Baase W.A., Matthews B.W. Determination of α-helix propensity within the context of a folded protein: sites 44 and 131 in bacteriophage T4 lysozyme. J. Mol. Biol. 235:1994;600-624.
    • (1994) J. Mol. Biol. , vol.235 , pp. 600-624
    • Blaber, M.1    Zhang, X.-J.2    Lindstrom, J.D.3    Pepiot, S.D.4    Baase, W.A.5    Matthews, B.W.6
  • 30
    • 0023104358 scopus 로고
    • Structure of bacteriophage T4 lysozyme refined at 1.7 Å resolution
    • Weaver L.H., Matthews B.W. Structure of bacteriophage T4 lysozyme refined at 1.7 Å resolution. J. Mol. Biol. 193:1987;189-199.
    • (1987) J. Mol. Biol. , vol.193 , pp. 189-199
    • Weaver, L.H.1    Matthews, B.W.2
  • 31
    • 0035059356 scopus 로고    scopus 로고
    • Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme
    • Xu J., Baase W.A., Quillin M.L., Baldwin E.P., Matthews B.W. Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme. Protein Sci. 10:2001;1067-1078.
    • (2001) Protein Sci. , vol.10 , pp. 1067-1078
    • Xu, J.1    Baase, W.A.2    Quillin, M.L.3    Baldwin, E.P.4    Matthews, B.W.5
  • 32
    • 0037438594 scopus 로고    scopus 로고
    • Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability
    • Gassner N.C., Baase W.A., Mooers B.H.M., Busam R.D., Weaver L.H., Lindstrom J.D., et al. Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability. Biophys. Chem. 100:2003;325-340.
    • (2003) Biophys. Chem. , vol.100 , pp. 325-340
    • Gassner, N.C.1    Baase, W.A.2    Mooers, B.H.M.3    Busam, R.D.4    Weaver, L.H.5    Lindstrom, J.D.6
  • 33
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly M.L. Analytical molecular surface calculation. J. Appl. Crystallog. 16:1983;548-558.
    • (1983) J. Appl. Crystallog. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 34
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Application to side-chain prediction
    • Dunbrack R.L. Jr, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J. Mol. Biol. 230:1993;543-574.
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-574
    • Dunbrack R.L., Jr.1    Karplus, M.2
  • 35
    • 0001114311 scopus 로고    scopus 로고
    • Conformational splitting: A more powerful criterion for dead-end elimination
    • Pierce N.A., Spriet J.A., Desmet J., Mayo S.L. Conformational splitting: a more powerful criterion for dead-end elimination. J. Comput. Chem. 21:2000;999-1009.
    • (2000) J. Comput. Chem. , vol.21 , pp. 999-1009
    • Pierce, N.A.1    Spriet, J.A.2    Desmet, J.3    Mayo, S.L.4
  • 36
    • 0031844416 scopus 로고    scopus 로고
    • Pairwise calculation of protein solvent-accessible surface areas
    • Street A.G., Mayo S.L. Pairwise calculation of protein solvent-accessible surface areas. Fold Des. 3:1998;253-258.
    • (1998) Fold Des. , vol.3 , pp. 253-258
    • Street, A.G.1    Mayo, S.L.2
  • 37
    • 0025643362 scopus 로고
    • A general method for rapid site-directed mutagenesis using the polymerase chain reaction
    • Landt O., Grunert H., Hahn U. A general method for rapid site-directed mutagenesis using the polymerase chain reaction. Gene. 96:1990;125-128.
    • (1990) Gene , vol.96 , pp. 125-128
    • Landt, O.1    Grunert, H.2    Hahn, U.3
  • 38
    • 0024357799 scopus 로고
    • A simple method for site-directed mutagenesis using the polymerase chain reaction
    • Hemsley A., Arnheim N., Toney M.D., Cortopassi G., Galas D.J. A simple method for site-directed mutagenesis using the polymerase chain reaction. Nucl. Acids Res. 17:1989;6545-6551.
    • (1989) Nucl. Acids Res. , vol.17 , pp. 6545-6551
    • Hemsley, A.1    Arnheim, N.2    Toney, M.D.3    Cortopassi, G.4    Galas, D.J.5
  • 39
    • 0023668221 scopus 로고
    • Temperature-sensitive mutation of bacteriophage T4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein
    • Alber T., Matthews B.W. Temperature-sensitive mutation of bacteriophage T4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein. Biochemistry. 26:1987;3754-3758.
    • (1987) Biochemistry , vol.26 , pp. 3754-3758
    • Alber, T.1    Matthews, B.W.2
  • 41
    • 0025761294 scopus 로고
    • Second-site revertants of an inactive T4 lysozyme mutant restore activity structuring the active site cleft
    • Poteete A.R., Dao-pin S., Nicholson H., Matthews B.W. Second-site revertants of an inactive T4 lysozyme mutant restore activity structuring the active site cleft. Biochemistry. 30:1991;1425-1432.
    • (1991) Biochemistry , vol.30 , pp. 1425-1432
    • Poteete, A.R.1    Dao-pin, S.2    Nicholson, H.3    Matthews, B.W.4
  • 42
    • 0027394606 scopus 로고
    • Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences
    • Eriksson A.E., Baase W.A., Matthews B.W. Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences. J. Mol. Biol. 229:1993;747-769.
    • (1993) J. Mol. Biol. , vol.229 , pp. 747-769
    • Eriksson, A.E.1    Baase, W.A.2    Matthews, B.W.3
  • 43
    • 0029585945 scopus 로고
    • Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive
    • Zhang X.-J., Baase W.A., Shoichet B.K., Wilson K.P., Matthews B.W. Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive. Protein Eng. 8:1995;1017-1022.
    • (1995) Protein Eng. , vol.8 , pp. 1017-1022
    • Zhang, X.-J.1    Baase, W.A.2    Shoichet, B.K.3    Wilson, K.P.4    Matthews, B.W.5
  • 44
    • 0021749888 scopus 로고
    • Thermodynamic stability and point mutations of bacteriophage T4 lysozyme
    • Hawkes R., Grutter M.G., Schellman J. Thermodynamic stability and point mutations of bacteriophage T4 lysozyme. J. Mol. Biol. 175:1984;195-212.
    • (1984) J. Mol. Biol. , vol.175 , pp. 195-212
    • Hawkes, R.1    Grutter, M.G.2    Schellman, J.3
  • 48
    • 84913050729 scopus 로고
    • An efficient general-purpose least-squares refinement program for macromolecular structures
    • Tronrud D.E., Ten Eyck L.F., Matthews B.W. An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallog. sect. A. 43:1987;489-501.
    • (1987) Acta Crystallog. sect. A , vol.43 , pp. 489-501
    • Tronrud, D.E.1    Ten Eyck, L.F.2    Matthews, B.W.3
  • 49
    • 0030757720 scopus 로고    scopus 로고
    • TNT refinement package
    • Tronrud D.E. TNT refinement package. Methods Enzymol. 277:1997;306-319.
    • (1997) Methods Enzymol. , vol.277 , pp. 306-319
    • Tronrud, D.E.1
  • 50
    • 0002705842 scopus 로고
    • A visual protein crystallographic software system for X11/Xview
    • MacRee D.E. A visual protein crystallographic software system for X11/Xview. J. Mol. Graph. 10:1992;44-46.
    • (1992) J. Mol. Graph. , vol.10 , pp. 44-46
    • MacRee, D.E.1
  • 51
    • 0033517740 scopus 로고    scopus 로고
    • Methionine and alanine substitutions show that the formation of wild-type-like structure in the carboxy-terminal domain of T4 lysozyme is a rate-limiting step in folding
    • Gassner N.C., Baase W.A., Lindstrom J.D., Lu J., Dalqusit F.W., Matthews B.W. Methionine and alanine substitutions show that the formation of wild-type-like structure in the carboxy-terminal domain of T4 lysozyme is a rate-limiting step in folding. Biochemistry. 38:1999;14451-14460.
    • (1999) Biochemistry , vol.38 , pp. 14451-14460
    • Gassner, N.C.1    Baase, W.A.2    Lindstrom, J.D.3    Lu, J.4    Dalqusit, F.W.5    Matthews, B.W.6
  • 52
    • 0028878767 scopus 로고
    • EDPDB: A multi-functional tool for protein structure analysis
    • Zhang X.-J., Matthews B.W. EDPDB: a multi-functional tool for protein structure analysis. J. Appl. Crystallog. 28:1995;624-630.
    • (1995) J. Appl. Crystallog. , vol.28 , pp. 624-630
    • Zhang, X.-J.1    Matthews, B.W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.