메뉴 건너뛰기




Volumn 11, Issue 2, 2010, Pages 101-111

Enhanced crystal packing due to solvent reorganization through reductive methylation of lysine residues in oxidoreductase from Streptococcus pneumoniae

Author keywords

Methylated lysine; Protein crystallization; Protein interactions; Protein modification; Reductive methylation

Indexed keywords

LYSINE; OXIDOREDUCTASE; SOLVENT;

EID: 77953985821     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10969-010-9079-6     Document Type: Article
Times cited : (10)

References (43)
  • 1
    • 0033794367 scopus 로고    scopus 로고
    • High-throughput protein crystallization
    • Stevens RC (2000) High-throughput protein crystallization. Curr Opin Struct Biol 10(5):558-563
    • (2000) Curr Opin Struct Biol , vol.10 , Issue.5 , pp. 558-563
    • Stevens, R.C.1
  • 2
    • 0026206788 scopus 로고
    • Sparse matrix sampling: A screening method for crystallization of proteins
    • Jancarik J, Kim SH (1991) Sparse matrix sampling: A screening method for crystallization of proteins. J Appl Crystallogr 24:409-411
    • (1991) J Appl Crystallogr , vol.24 , pp. 409-411
    • Jancarik, J.1    Kim, S.H.2
  • 3
    • 0035501932 scopus 로고    scopus 로고
    • Efficiency analysis of sampling protocols used in protein crystallization screening
    • Segelke BW (2001) Efficiency analysis of sampling protocols used in protein crystallization screening. J Cryst Growth 232(1-4):553-562
    • (2001) J Cryst Growth , vol.232 , Issue.1-4 , pp. 553-562
    • Segelke, B.W.1
  • 5
    • 0035024436 scopus 로고    scopus 로고
    • Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of Rho- GDI
    • Longenecker KL, Garrard SM, Sheffield PJ, Derewenda ZS (2001) Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of Rho- GDI. Acta Crystallogr D Biol Crystallogr 57(Pt 5):679-688
    • (2001) Acta Crystallogr D Biol Crystallogr , vol.57 , Issue.PART 5 , pp. 679-688
    • Longenecker, K.L.1    Garrard, S.M.2    Sheffield, P.J.3    Derewenda, Z.S.4
  • 8
    • 0345096595 scopus 로고    scopus 로고
    • Solvent entropy effects in the formation of protein solid phases
    • Vekilov PG (2003) Solvent entropy effects in the formation of protein solid phases. Methods Enzymol 368:84-105
    • (2003) Methods Enzymol , vol.368 , pp. 84-105
    • Vekilov, P.G.1
  • 9
    • 0036794760 scopus 로고    scopus 로고
    • Petsev D solvent entropy contribution to the free energy of protein crystallization
    • Pt 1
    • Vekilov PG, Feeling-Taylor AR, Yau ST (2002) Petsev D solvent entropy contribution to the free energy of protein crystallization. Acta Crystallogr D Biol Crystallogr 58(Pt 10 Pt 1):1611-1616
    • (2002) Acta Crystallogr D Biol Crystallogr , vol.58 , Issue.PART 10 , pp. 1611-1616
    • Vekilov, P.G.1    Feeling-Taylor, A.R.2    Yau, S.T.3
  • 10
    • 1842555070 scopus 로고    scopus 로고
    • Rational protein crystallization by mutational surface engineering
    • Derewenda ZS (2004) Rational protein crystallization by mutational surface engineering. Structure 12(4):529-535
    • (2004) Structure , vol.12 , Issue.4 , pp. 529-535
    • Derewenda, Z.S.1
  • 12
    • 33644874674 scopus 로고    scopus 로고
    • Entropy and surface engineering in protein crystallization
    • Derewenda ZS, Vekilov PG (2006) Entropy and surface engineering in protein crystallization. Acta Crystallogr D Biol Crystallogr 62(Pt 1):116-124
    • (2006) Acta Crystallogr D Biol Crystallogr , vol.62 , Issue.PART 1 , pp. 116-124
    • Derewenda, Z.S.1    Vekilov, P.G.2
  • 13
    • 33745122241 scopus 로고    scopus 로고
    • Lysine methylation goes global
    • Morgunkova A, Barlev NA (2006) Lysine methylation goes global. Cell Cycle 5(12):1308-1312
    • (2006) Cell Cycle , vol.5 , Issue.12 , pp. 1308-1312
    • Morgunkova, A.1    Barlev, N.A.2
  • 14
    • 67650461956 scopus 로고    scopus 로고
    • A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf-Hirschhorn syndrome
    • Nimura K, Ura K, Shiratori H, Ikawa M, Okabe M, Schwartz RJ, Kaneda Y (2009) A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf-Hirschhorn syndrome. Nature 460(7252): 287-291
    • (2009) Nature , vol.460 , Issue.7252 , pp. 287-291
    • Nimura, K.1    Ura, K.2    Shiratori, H.3    Ikawa, M.4    Okabe, M.5    Schwartz, R.J.6    Kaneda, Y.7
  • 17
    • 0025728614 scopus 로고
    • OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform
    • Pranata J, Wierschke SG, Jorgensen WL (1991) OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform. J Am Chem Soc 113(8):2810-2819
    • (1991) J Am Chem Soc , vol.113 , Issue.8 , pp. 2810-2819
    • Pranata, J.1    Wierschke, S.G.2    Jorgensen, W.L.3
  • 18
    • 0034250744 scopus 로고    scopus 로고
    • An improved empirical potential energy function for molecular simulations of phospholipids
    • Feller SE, MacKerell AD (2000) An improved empirical potential energy function for molecular simulations of phospholipids. J Phys Chem B 104(31):7510-7515
    • (2000) J Phys Chem B , vol.104 , Issue.31 , pp. 7510-7515
    • Feller, S.E.1    MacKerell, A.D.2
  • 19
    • 0000628743 scopus 로고
    • Conformational flexibility of ophosphorylcholine and o- phosphorylethanolamine: A molecular dynamics study of solvation effects
    • Woolf TB, Roux B (1994) Conformational flexibility of ophosphorylcholine and o-phosphorylethanolamine: A molecular dynamics study of solvation effects. J Am Chem Soc 116(13): 5916-5926
    • (1994) J Am Chem Soc , vol.116 , Issue.13 , pp. 5916-5926
    • Woolf, T.B.1    Roux, B.2
  • 20
    • 0027370168 scopus 로고
    • Determination of the side chain pKa values of the lysine residues in calmodulin
    • Zhang M, Vogel HJ (1993) Determination of the side chain pKa values of the lysine residues in calmodulin. J Biol Chem 268(30):22420-22428
    • (1993) J Biol Chem , vol.268 , Issue.30 , pp. 22420-22428
    • Zhang, M.1    Vogel, H.J.2
  • 22
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N × log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N × log(N) method for Ewald sums in large systems. J Chem Phys 98(12):10089-10092
    • (1993) J Chem Phys , vol.98 , Issue.12 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 23
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput Phys 23(3):327-341
    • (1977) J Comput Phys , vol.23 , Issue.3 , pp. 327-341
    • Ryckaert, J-.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 25
    • 0027166270 scopus 로고
    • Empirical scale of side-chain conformational entropy in protein folding
    • Pickett SD, Sternberg MJ (1993) Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 231(3): 825-839
    • (1993) J Mol Biol , vol.231 , Issue.3 , pp. 825-839
    • Pickett, S.D.1    Sternberg, M.J.2
  • 26
    • 0028174101 scopus 로고
    • Protein side-chain conformational entropy derived from fusion data-comparison with other empirical scales
    • Sternberg MJ, Chickos JS (1994) Protein side-chain conformational entropy derived from fusion data-comparison with other empirical scales. Protein Eng 7(2):149-155
    • (1994) Protein Eng , vol.7 , Issue.2 , pp. 149-155
    • Sternberg, M.J.1    Chickos, J.S.2
  • 27
    • 19644385843 scopus 로고    scopus 로고
    • Prion and water: Tight and dynamical hydration sites have a key role in structural stability
    • De Simone A, Dodson GG, Verma CS, Zagari A, Fraternali F (2005) Prion and water: Tight and dynamical hydration sites have a key role in structural stability. Proc Natl Acad Sci U S A 102(21):7535-7540
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.21 , pp. 7535-7540
    • De Simone, A.1    Dodson, G.G.2    Verma, C.S.3    Zagari, A.4    Fraternali, F.5
  • 29
    • 33845554708 scopus 로고
    • Crystallographic evidence for the existence of CH ⋯ O, CH ⋯ N and CH ⋯ Cl hydrogen bonds
    • Taylor R, Kennard O (1982) Crystallographic evidence for the existence of CH ⋯ O, CH ⋯ N and CH ⋯ Cl hydrogen bonds. J Am Chem Soc 104(19):5063-5070
    • (1982) J Am Chem Soc , vol.104 , Issue.19 , pp. 5063-5070
    • Taylor, R.1    Kennard, O.2
  • 30
    • 0034679011 scopus 로고    scopus 로고
    • How strong is the Calpha-H ⋯ O=C hydrogen bond?
    • Vargas R, Garza J, Dixon DA, Hay BP (2000) How strong is the Calpha-H ⋯ O=C hydrogen bond? J Am Chem Soc 122(19): 4750-4755
    • (2000) J Am Chem Soc , vol.122 , Issue.19 , pp. 4750-4755
    • Vargas, R.1    Garza, J.2    Dixon, D.A.3    Hay, B.P.4
  • 31
    • 0035971221 scopus 로고    scopus 로고
    • Strength of the Calpha H ⋯ O hydrogen bond of amino acid residues
    • Scheiner S, Kar T, Gu Y (2001) Strength of the Calpha H ⋯ O hydrogen bond of amino acid residues. J Biol Chem 276(13): 9832-9837
    • (2001) J Biol Chem , vol.276 , Issue.13 , pp. 9832-9837
    • Scheiner, S.1    Kar, T.2    Gu, Y.3
  • 32
    • 0036286851 scopus 로고    scopus 로고
    • Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment
    • Makarov V, Pettitt BM, Feig M (2002) Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment. Acc Chem Res 35(6):376-384
    • (2002) Acc Chem Res , vol.35 , Issue.6 , pp. 376-384
    • Makarov, V.1    Pettitt, B.M.2    Feig, M.3
  • 33
    • 33645983232 scopus 로고    scopus 로고
    • Water structure and interactions with protein surfaces
    • Raschke TM (2006) Water structure and interactions with protein surfaces. Curr Opin Struct Biol 16(2):152-159
    • (2006) Curr Opin Struct Biol , vol.16 , Issue.2 , pp. 152-159
    • Raschke, T.M.1
  • 34
    • 0024292355 scopus 로고
    • Effect of hydrostatic pressure on the solvent in crystals of hen egg-white lysozyme
    • Kundrot CE, Richards FM (1988) Effect of hydrostatic pressure on the solvent in crystals of hen egg-white lysozyme. J Mol Biol 200(2):401-410
    • (1988) J Mol Biol , vol.200 , Issue.2 , pp. 401-410
    • Kundrot, C.E.1    Richards, F.M.2
  • 35
    • 33646083683 scopus 로고    scopus 로고
    • Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5
    • Han Z, Guo L, Wang H, Shen Y, Deng XW, Chai J (2006) Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell 22(1):137-144
    • (2006) Mol Cell , vol.22 , Issue.1 , pp. 137-144
    • Han, Z.1    Guo, L.2    Wang, H.3    Shen, Y.4    Deng, X.W.5    Chai, J.6
  • 36
    • 0000207211 scopus 로고    scopus 로고
    • Thermodynamic constants of complexes of crown ethers and uncharged molecules and x-ray structure of the 18-crown-6. (MeNO2)2 complex
    • De Boer JAA, Reinhoudt DN, Harkema S, Van Hummel GJ, De Jong F (2002) Thermodynamic constants of complexes of crown ethers and uncharged molecules and x-ray structure of the 18-crown-6. (MeNO2)2 complex. J Am Chem Soc 104(15):4073-4076
    • (2002) J Am Chem Soc , vol.104 , Issue.15 , pp. 4073-4076
    • De Boer, J.A.A.1    Reinhoudt, D.N.2    Harkema, S.3    Van Hummel, G.J.4    De Jong, F.5
  • 37
    • 33748415525 scopus 로고    scopus 로고
    • Theoretical calculation of hydrogen-bonding strength for drug molecules
    • Hao M-H (2006) Theoretical calculation of hydrogen-bonding strength for drug molecules. J Chem Theory Comput 2(3):863-872
    • (2006) J Chem Theory Comput , vol.2 , Issue.3 , pp. 863-872
    • Hao, M.-H.1
  • 38
    • 34547566008 scopus 로고    scopus 로고
    • Toward rational protein crystallization: A web server for the design of crystallizable protein variants
    • Goldschmidt L, Cooper DR, Derewenda ZS, Eisenberg D (2007) Toward rational protein crystallization: A web server for the design of crystallizable protein variants. Protein Sci 16(8):1569-1576
    • (2007) Protein Sci , vol.16 , Issue.8 , pp. 1569-1576
    • Goldschmidt, L.1    Cooper, D.R.2    Derewenda, Z.S.3    Eisenberg, D.4
  • 40
    • 0028228418 scopus 로고
    • The entropic cost of bound water in crystals and biomolecules
    • Dunitz JD (1994) The entropic cost of bound water in crystals and biomolecules. Science 264(5159):670
    • (1994) Science , vol.264 , Issue.5159 , pp. 670
    • Dunitz, J.D.1
  • 42
    • 35748955512 scopus 로고    scopus 로고
    • Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein sex comb on midleg
    • Grimm C, de Ayala Alonso AG, Rybin V, Steuerwald U, Ly- Hartig N, Fischle W, Muller J, Muller CW (2007) Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein sex comb on midleg. EMBO Rep 8(11):1031-1037
    • (2007) EMBO Rep , vol.8 , Issue.11 , pp. 1031-1037
    • Grimm, C.1    De Ayala Alonso, A.G.2    Rybin, V.3    Steuerwald, U.4    Ly- Hartig, N.5    Fischle, W.6    Muller, J.7    Muller, C.W.8
  • 43
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280(1):1-9
    • (1998) J Mol Biol , vol.280 , Issue.1 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.