메뉴 건너뛰기




Volumn 48, Issue 6, 2009, Pages 1305-1314

Functional impact of polar and acidic substitutions in the lactose repressor hydrophobic monomer · monomer interface with a buried lysine

Author keywords

[No Author keywords available]

Indexed keywords

ACIDIC RESIDUES; BURIED CHARGES; CHARGED RESIDUES; CONFORMATIONAL CHANGES; DRIVING FORCES; FUNCTIONAL CHANGES; FUNCTIONAL PROPERTIES; HYDROPHOBIC INTERACTIONS; HYDROPHOBIC MONOMERS; ION-PAIR FORMATIONS; ION-PAIR INTERACTIONS; LYSINE SIDE CHAINS; MONOMER-MONOMER INTERFACES; POSITIVE CHARGES; PROTEIN STABILITIES; SALT BRIDGES; SIDE CHAINS; STRUCTURAL STABILIZATIONS;

EID: 63749117665     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801357f     Document Type: Article
Times cited : (10)

References (45)
  • 1
    • 34447297323 scopus 로고    scopus 로고
    • Energetics of protein folding
    • Baldwin, R. L. (2007) Energetics of protein folding. J. Mol. Biol. 371, 283-301.
    • (2007) J. Mol. Biol , vol.371 , pp. 283-301
    • Baldwin, R.L.1
  • 2
    • 84962439356 scopus 로고    scopus 로고
    • Roles of electrostatic interaction in proteins
    • Nakamura, H. (1996) Roles of electrostatic interaction in proteins. Q. Rev. Biophys. 29, 1-90.
    • (1996) Q. Rev. Biophys , vol.29 , pp. 1-90
    • Nakamura, H.1
  • 4
    • 0028204490 scopus 로고
    • Do salt bridges stabilize proteins? A continuum electrostatic analysis
    • Hendsch, Z. S., and Tidor, B. (1994) Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3, 211-226.
    • (1994) Protein Sci , vol.3 , pp. 211-226
    • Hendsch, Z.S.1    Tidor, B.2
  • 6
    • 0035850794 scopus 로고    scopus 로고
    • Structure of a variant of lac repressor with increased thermostability and decreased affinity for operator
    • Bell, C. E., Barry, J., Matthews, K. S., and Lewis, M. (2001) Structure of a variant of lac repressor with increased thermostability and decreased affinity for operator. J. Mol. Biol. 313, 99-109.
    • (2001) J. Mol. Biol , vol.313 , pp. 99-109
    • Bell, C.E.1    Barry, J.2    Matthews, K.S.3    Lewis, M.4
  • 7
    • 0034089394 scopus 로고    scopus 로고
    • A closer view of the conformation of the Lac repressor bound to operator
    • Bell, C. E., and Lewis, M. (2000) A closer view of the conformation of the Lac repressor bound to operator. Nat. Struct. Biol. 7, 209-214.
    • (2000) Nat. Struct. Biol , vol.7 , pp. 209-214
    • Bell, C.E.1    Lewis, M.2
  • 8
    • 23944464891 scopus 로고    scopus 로고
    • Integrated insights from simulation, experiment, and mutational analysis yield new details of LacI function
    • Swint-Kruse, L., Zhan, H., and Matthews, K. S. (2005) Integrated insights from simulation, experiment, and mutational analysis yield new details of LacI function. Biochemistry 44, 11201-11213.
    • (2005) Biochemistry , vol.44 , pp. 11201-11213
    • Swint-Kruse, L.1    Zhan, H.2    Matthews, K.S.3
  • 9
    • 0031961672 scopus 로고    scopus 로고
    • Lactose repressor protein: Functional properties and structure
    • Matthews, K. S., and Nichols, J. C. (1998) Lactose repressor protein: Functional properties and structure. Prog. Nucleic Acid Res. Mol. Biol. 58, 127-164.
    • (1998) Prog. Nucleic Acid Res. Mol. Biol , vol.58 , pp. 127-164
    • Matthews, K.S.1    Nichols, J.C.2
  • 10
    • 0033580635 scopus 로고    scopus 로고
    • Thermodynamic analysis of unfolding and dissociation in lactose repressor protein
    • Barry, J. K., and Matthews, K. S. (1999) Thermodynamic analysis of unfolding and dissociation in lactose repressor protein. Biochemistry 38, 6520-6528.
    • (1999) Biochemistry , vol.38 , pp. 6520-6528
    • Barry, J.K.1    Matthews, K.S.2
  • 11
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • Monod, J., Wyman, J., and Changeux, J. P. (1965) On the nature of allosteric transitions: A plausible model. J. Mol. Biol. 12, 88-118.
    • (1965) J. Mol. Biol , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 12
    • 26844536032 scopus 로고    scopus 로고
    • The experimental folding landscape of monomeric lactose repressor, a large two-domain protein, involves two kinetic intermediates
    • Wilson, C. J., Das, P., Clementi, C, Matthews, K. S., and Wittung-Stafshede, P. (2005) The experimental folding landscape of monomeric lactose repressor, a large two-domain protein, involves two kinetic intermediates. Proc. Natl. Acad. Sci. U.S.A. 102, 14563-14568.
    • (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , pp. 14563-14568
    • Wilson, C.J.1    Das, P.2    Clementi, C.3    Matthews, K.S.4    Wittung-Stafshede, P.5
  • 13
    • 33846516797 scopus 로고    scopus 로고
    • The lactose repressor system: Paradigms for regulation, allosteric behavior and protein folding
    • Wilson, C. J., Zhan, H., Swint-Kruse, L., and Matthews, K. S. (2007) The lactose repressor system: Paradigms for regulation, allosteric behavior and protein folding. Cell. Mol. Life Sci. 64, 3-16.
    • (2007) Cell. Mol. Life Sci , vol.64 , pp. 3-16
    • Wilson, C.J.1    Zhan, H.2    Swint-Kruse, L.3    Matthews, K.S.4
  • 15
    • 0029004903 scopus 로고
    • Crystal structure of lac repressor core tetramer and its implications for DNA looping
    • Friedman, A. M., Fischmann, T. O., and Steitz, T. A. (1995) Crystal structure of lac repressor core tetramer and its implications for DNA looping. Science 268, 1721-1727.
    • (1995) Science , vol.268 , pp. 1721-1727
    • Friedman, A.M.1    Fischmann, T.O.2    Steitz, T.A.3
  • 16
    • 0142179045 scopus 로고    scopus 로고
    • Allosteric transition pathways in the lactose repressor protein core domain: Asymmetric motions in homodimer
    • Flynn, T. C., Swint-Kruse, L., Kong, Y., Booth, C., Matthews, K. S., and Ma, J. (2003) Allosteric transition pathways in the lactose repressor protein core domain: Asymmetric motions in homodimer. Protein Sci. 12, 2523-2541.
    • (2003) Protein Sci , vol.12 , pp. 2523-2541
    • Flynn, T.C.1    Swint-Kruse, L.2    Kong, Y.3    Booth, C.4    Matthews, K.S.5    Ma, J.6
  • 17
    • 0344412958 scopus 로고    scopus 로고
    • Perturbation from a distance: Mutations that alter LacI function through long-range effects
    • Swint-Kruse, L., Zhan, H., Fairbanks, B. M., Maheshwari, A., and Matthews, K. S. (2003) Perturbation from a distance: Mutations that alter LacI function through long-range effects. Biochemistry 42, 14004-14016.
    • (2003) Biochemistry , vol.42 , pp. 14004-14016
    • Swint-Kruse, L.1    Zhan, H.2    Fairbanks, B.M.3    Maheshwari, A.4    Matthews, K.S.5
  • 18
    • 0033596862 scopus 로고    scopus 로고
    • Substitutions at Histidine 74 and Aspartate 278 alter ligand binding and allostery in lactose repressor protein
    • Barry, J. K., and Matthews, K. S. (1999) Substitutions at Histidine 74 and Aspartate 278 alter ligand binding and allostery in lactose repressor protein. Biochemistry 38, 3579-3590.
    • (1999) Biochemistry , vol.38 , pp. 3579-3590
    • Barry, J.K.1    Matthews, K.S.2
  • 19
    • 0027236781 scopus 로고
    • Lysine 84 is at the subunit interface of lac repressor protein
    • Chang, W.-I., Olson, J. S., and Matthews, K. S. (1993) Lysine 84 is at the subunit interface of lac repressor protein. J. Biol. Chem. 268, 17613-17622.
    • (1993) J. Biol. Chem , vol.268 , pp. 17613-17622
    • Chang, W.-I.1    Olson, J.S.2    Matthews, K.S.3
  • 20
    • 0030806865 scopus 로고    scopus 로고
    • Combinatorial mutations of lac repressor. Stability of monomer-monomer interface is increased by apolar substitution at position 84
    • Nichols, J. C., and Matthews, K. S. (1997) Combinatorial mutations of lac repressor. Stability of monomer-monomer interface is increased by apolar substitution at position 84. J. Biol. Chem. 272, 18550-18557.
    • (1997) J. Biol. Chem , vol.272 , pp. 18550-18557
    • Nichols, J.C.1    Matthews, K.S.2
  • 21
    • 0033987659 scopus 로고    scopus 로고
    • Generation of an AraC-araBAD promoter-regulated T7 expression system
    • Wycuff, D. R., and Matthews, K. S. (2000) Generation of an AraC-araBAD promoter-regulated T7 expression system. Anal. Biochem. 277, 67-73.
    • (2000) Anal. Biochem , vol.277 , pp. 67-73
    • Wycuff, D.R.1    Matthews, K.S.2
  • 22
    • 0026723976 scopus 로고
    • Deletion of lactose repressor carboxyl-terminal domain affects tetramer formation
    • Chen, J., and Matthews, K. S. (1992) Deletion of lactose repressor carboxyl-terminal domain affects tetramer formation. J. Biol. Chem. 267, 13843-13850.
    • (1992) J. Biol. Chem , vol.267 , pp. 13843-13850
    • Chen, J.1    Matthews, K.S.2
  • 23
    • 0028059578 scopus 로고
    • Subunit dissociation affects DNA binding in a dimeric lac repressor produced by C-terminal deletion
    • Chen, J., and Matthews, K. S. (1994) Subunit dissociation affects DNA binding in a dimeric lac repressor produced by C-terminal deletion. Biochemistry 33, 8728-8735.
    • (1994) Biochemistry , vol.33 , pp. 8728-8735
    • Chen, J.1    Matthews, K.S.2
  • 24
    • 33646472260 scopus 로고    scopus 로고
    • Extrinsic interactions dominate helical propensity in coupled binding and folding of lactose repressor protein hinge helix
    • Zhan, H., Swint-Kruse, L., and Matthews, K. S. (2006) Extrinsic interactions dominate helical propensity in coupled binding and folding of lactose repressor protein hinge helix. Biochemistry 45, 5896-5906.
    • (2006) Biochemistry , vol.45 , pp. 5896-5906
    • Zhan, H.1    Swint-Kruse, L.2    Matthews, K.S.3
  • 25
    • 0027172789 scopus 로고
    • A double-filter method for nitrocellulose-filter binding: Application to protein-nucleic acid interactions
    • Wong, I., and Lohman, T. M. (1993) A double-filter method for nitrocellulose-filter binding: Application to protein-nucleic acid interactions. Proc. Natl. Acad. Sci. U.S.A. 90, 5428-5432.
    • (1993) Proc. Natl. Acad. Sci. U.S.A , vol.90 , pp. 5428-5432
    • Wong, I.1    Lohman, T.M.2
  • 26
    • 0035951105 scopus 로고    scopus 로고
    • Engineered disulfide linking the hinge regions within lactose repressor dimer increases operator affinity, decreases sequence selectivity, and alters allostery
    • Falcon, C. M., and Matthews, K. S. (2001) Engineered disulfide linking the hinge regions within lactose repressor dimer increases operator affinity, decreases sequence selectivity, and alters allostery. Biochemistry 40, 15650-15659.
    • (2001) Biochemistry , vol.40 , pp. 15650-15659
    • Falcon, C.M.1    Matthews, K.S.2
  • 27
    • 0015526977 scopus 로고
    • Equilibrium and kinetic studies of Escherichia coli lac repressorinducer interactions
    • Laiken, S. L., Gross, C. A., and von Hippel, P. H. (1972) Equilibrium and kinetic studies of Escherichia coli lac repressorinducer interactions. J. Mol. Biol. 66, 143-155.
    • (1972) J. Mol. Biol , vol.66 , pp. 143-155
    • Laiken, S.L.1    Gross, C.A.2    von Hippel, P.H.3
  • 28
    • 0008084783 scopus 로고
    • Techniques to assay repressors
    • Bourgeois, S. (1971) Techniques to assay repressors. Methods Enzymol. 21, 491-500.
    • (1971) Methods Enzymol , vol.21 , pp. 491-500
    • Bourgeois, S.1
  • 29
    • 33947332551 scopus 로고
    • On the refractive indices of aqueous solutions of urea
    • Warren, J. R., and Gordon, J. A. (1966) On the refractive indices of aqueous solutions of urea. J. Phys. Chem. 70, 297-300.
    • (1966) J. Phys. Chem , vol.70 , pp. 297-300
    • Warren, J.R.1    Gordon, J.A.2
  • 30
    • 0022555885 scopus 로고
    • Determination and analysis of urea and guanidine hydrochloride denaturation curves
    • Pace, C. N. (1986) Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 131, 266-280.
    • (1986) Methods Enzymol , vol.131 , pp. 266-280
    • Pace, C.N.1
  • 31
    • 0023697408 scopus 로고
    • Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants
    • Santoro, M. M., and Bolen, D. W. (1988) Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants. Biochemistry 27, 8063-8068.
    • (1988) Biochemistry , vol.27 , pp. 8063-8068
    • Santoro, M.M.1    Bolen, D.W.2
  • 32
    • 2342519701 scopus 로고    scopus 로고
    • Genetic studies of the Lac repressor XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure
    • Suckow, J., Markiewicz, P., Kleina, L. G., Miller, J., Kisters-Woike, B., and Müller-Hill, B. (1996) Genetic studies of the Lac repressor XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure. J. Mol. Biol. 261, 509-523.
    • (1996) J. Mol. Biol , vol.261 , pp. 509-523
    • Suckow, J.1    Markiewicz, P.2    Kleina, L.G.3    Miller, J.4    Kisters-Woike, B.5    Müller-Hill, B.6
  • 33
    • 0036708467 scopus 로고    scopus 로고
    • Relationship between ion pair geometries and electrostatic strengths in proteins
    • Kumar, S., and Nussinov, R. (2002) Relationship between ion pair geometries and electrostatic strengths in proteins. Biophys. J. 83, 1595-1612.
    • (2002) Biophys. J , vol.83 , pp. 1595-1612
    • Kumar, S.1    Nussinov, R.2
  • 34
    • 33645235083 scopus 로고    scopus 로고
    • Hydration of the folding transition state ensemble of a protein
    • Brun, L., Isom, D. G., Velu, P., Garcia-Moreno, B., and Royer, C. A. (2006) Hydration of the folding transition state ensemble of a protein. Biochemistry 45, 3473-3480.
    • (2006) Biochemistry , vol.45 , pp. 3473-3480
    • Brun, L.1    Isom, D.G.2    Velu, P.3    Garcia-Moreno, B.4    Royer, C.A.5
  • 36
    • 18144394277 scopus 로고    scopus 로고
    • Are acidic and basic groups in buried proteins predicted to be ionized?
    • Kim, J., Mao, J., and Gunner, M. R. (2005) Are acidic and basic groups in buried proteins predicted to be ionized? J. Mol. Biol. 348, 1283-1298.
    • (2005) J. Mol. Biol , vol.348 , pp. 1283-1298
    • Kim, J.1    Mao, J.2    Gunner, M.R.3
  • 37
    • 43049126500 scopus 로고    scopus 로고
    • A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein-water interface as a determinant of pKa values
    • Harms, M. J., Schlessman, J. L., Chimenti, M. S., Sue, G. R., Damjanovic, A., and Garcia-Moreno, B. (2008) A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein-water interface as a determinant of pKa values. Protein Sci. 17, 833-845.
    • (2008) Protein Sci , vol.17 , pp. 833-845
    • Harms, M.J.1    Schlessman, J.L.2    Chimenti, M.S.3    Sue, G.R.4    Damjanovic, A.5    Garcia-Moreno, B.6
  • 38
    • 21244469736 scopus 로고    scopus 로고
    • Molecular dynamics study of water penetration in staphylococcal nuclease
    • Damjanovic, A., Garcia-Moreno, B., Lattman, E. E., and Garcia, A. E. (2005) Molecular dynamics study of water penetration in staphylococcal nuclease. Proteins 60, 433-449.
    • (2005) Proteins , vol.60 , pp. 433-449
    • Damjanovic, A.1    Garcia-Moreno, B.2    Lattman, E.E.3    Garcia, A.E.4
  • 39
    • 58149160375 scopus 로고    scopus 로고
    • Backbone relaxation coupled to the ionization of internal groups in proteins: A self-guided Langevin dynamics study
    • Damjanovic, A., Wu, X., Garcia-Moreno, E. B., and Brooks, B. R. (2008) Backbone relaxation coupled to the ionization of internal groups in proteins: A self-guided Langevin dynamics study. Biophys. J. 95, 4091-4101.
    • (2008) Biophys. J , vol.95 , pp. 4091-4101
    • Damjanovic, A.1    Wu, X.2    Garcia-Moreno, E.B.3    Brooks, B.R.4
  • 40
    • 0035901483 scopus 로고    scopus 로고
    • Contribution of polar groups in the interior of a protein to the conformational stability
    • Takano, K., Yamagata, Y., and Yutani, K. (2001) Contribution of polar groups in the interior of a protein to the conformational stability. Biochemistry 40, 4853-4858.
    • (2001) Biochemistry , vol.40 , pp. 4853-4858
    • Takano, K.1    Yamagata, Y.2    Yutani, K.3
  • 41
    • 0029564595 scopus 로고
    • Are buried salt bridges important for protein stability and conformational specificity?
    • Waldburger, C. D., Schildbach, J. F., and Sauer, R. T. (1995) Are buried salt bridges important for protein stability and conformational specificity? Nat. Struct. Biol. 2, 122-128.
    • (1995) Nat. Struct. Biol , vol.2 , pp. 122-128
    • Waldburger, C.D.1    Schildbach, J.F.2    Sauer, R.T.3
  • 42
    • 0033550299 scopus 로고    scopus 로고
    • Salt bridge stability in monomeric proteins
    • Kumar, S., and Nussinov, R. (1999) Salt bridge stability in monomeric proteins. J. Mol. Biol. 293, 1241-1255.
    • (1999) J. Mol. Biol , vol.293 , pp. 1241-1255
    • Kumar, S.1    Nussinov, R.2
  • 44
    • 0034855858 scopus 로고    scopus 로고
    • How do thermophilic proteins deal with heat?
    • Kumar, S., and Nussinov, R. (2001) How do thermophilic proteins deal with heat? Cell. Mol. Life Sci. 58, 1216-1233.
    • (2001) Cell. Mol. Life Sci , vol.58 , pp. 1216-1233
    • Kumar, S.1    Nussinov, R.2
  • 45
    • 0028574137 scopus 로고
    • Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in lambda repressor
    • Marqusee, S., and Sauer, R. T. (1994) Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in lambda repressor. Protein Sci. 3, 2217-2225.
    • (1994) Protein Sci , vol.3 , pp. 2217-2225
    • Marqusee, S.1    Sauer, R.T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.