메뉴 건너뛰기




Volumn 7, Issue 4, 2012, Pages

Role of active site rigidity in activity: Md simulation and fluorescence study on a lipase mutant

Author keywords

[No Author keywords available]

Indexed keywords

MUTANT PROTEIN; TRIACYLGLYCEROL LIPASE;

EID: 84859722834     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035188     Document Type: Article
Times cited : (74)

References (48)
  • 1
    • 0025822794 scopus 로고
    • Relation between stability, dynamics and enzyme activity in 3-phosphoglycerate kinases from yeast and Thermus thermophilus
    • Varley PG, Pain RH, (1991) Relation between stability, dynamics and enzyme activity in 3-phosphoglycerate kinases from yeast and Thermus thermophilus. J Mol Biol 220: 531-538.
    • (1991) J Mol Biol , vol.220 , pp. 531-538
    • Varley, P.G.1    Pain, R.H.2
  • 2
    • 0031467464 scopus 로고    scopus 로고
    • Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin
    • Lazaridis T, Lee I, Karplus M, (1997) Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin. Protein Sci 6: 2589-2605.
    • (1997) Protein Sci , vol.6 , pp. 2589-2605
    • Lazaridis, T.1    Lee, I.2    Karplus, M.3
  • 3
    • 0032560505 scopus 로고    scopus 로고
    • Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins
    • Zavodszky P, Kardos J, Svingor A, Petsko GA, (1998) Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. Proc Natl Acad Sci U S A 95: 7406-7411.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 7406-7411
    • Zavodszky, P.1    Kardos, J.2    Svingor, A.3    Petsko, G.A.4
  • 4
    • 0033598719 scopus 로고    scopus 로고
    • Structural distribution of stability in a thermophilic enzyme
    • Hollien J, Marqusee S, (1999) Structural distribution of stability in a thermophilic enzyme. Proc Natl Acad Sci U S A 96: 13674-13678.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 13674-13678
    • Hollien, J.1    Marqusee, S.2
  • 6
    • 0037424370 scopus 로고    scopus 로고
    • Activity-stability relationships in extremophilic enzymes
    • D'Amico S, Marx JC, Gerday C, Feller G, (2003) Activity-stability relationships in extremophilic enzymes. J Biol Chem 278: 7891-7896.
    • (2003) J Biol Chem , vol.278 , pp. 7891-7896
    • D'Amico, S.1    Marx, J.C.2    Gerday, C.3    Feller, G.4
  • 8
    • 0032973026 scopus 로고    scopus 로고
    • Directed evolution converts subtilisin E into a functional equivalent of thermitase
    • Zhao H, Arnold FH, (1999) Directed evolution converts subtilisin E into a functional equivalent of thermitase. Protein Eng 12: 47-53.
    • (1999) Protein Eng , vol.12 , pp. 47-53
    • Zhao, H.1    Arnold, F.H.2
  • 10
    • 0034731381 scopus 로고    scopus 로고
    • The consensus concept for thermostability engineering of proteins
    • Lehmann M, Pasamontes L, Lassen SF, Wyss M, (2000) The consensus concept for thermostability engineering of proteins. Biochim Biophys Acta 1543: 408-415.
    • (2000) Biochim Biophys Acta , vol.1543 , pp. 408-415
    • Lehmann, M.1    Pasamontes, L.2    Lassen, S.F.3    Wyss, M.4
  • 12
    • 0031935580 scopus 로고    scopus 로고
    • Serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution
    • Akanuma S, Yamagishi A, Tanaka N, Oshima T, (1998) Serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution. Protein Sci 7: 698-705.
    • (1998) Protein Sci , vol.7 , pp. 698-705
    • Akanuma, S.1    Yamagishi, A.2    Tanaka, N.3    Oshima, T.4
  • 13
    • 25444463283 scopus 로고    scopus 로고
    • Structural perturbation and compensation by directed evolution at physiological temperature leads to thermostabilization of beta-lactamase
    • Hecky J, Muller KM, (2005) Structural perturbation and compensation by directed evolution at physiological temperature leads to thermostabilization of beta-lactamase. Biochemistry 44: 12640-12654.
    • (2005) Biochemistry , vol.44 , pp. 12640-12654
    • Hecky, J.1    Muller, K.M.2
  • 14
    • 80054692390 scopus 로고    scopus 로고
    • In Vitro Evolved Non-Aggregating and Thermostable Lipase: Structural and Thermodynamic Investigation
    • Kamal MZ, Ahmad S, Molugu TR, Vijayalakshmi A, Deshmukh MV, et al. (2011) In Vitro Evolved Non-Aggregating and Thermostable Lipase: Structural and Thermodynamic Investigation. J Mol Biol 413: 726-741.
    • (2011) J Mol Biol , vol.413 , pp. 726-741
    • Kamal, M.Z.1    Ahmad, S.2    Molugu, T.R.3    Vijayalakshmi, A.4    Deshmukh, M.V.5
  • 15
    • 4143110558 scopus 로고    scopus 로고
    • Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase
    • Acharya P, Rajakumara E, Sankaranarayanan R, Rao NM, (2004) Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase. J Mol Biol 341: 1271-1281.
    • (2004) J Mol Biol , vol.341 , pp. 1271-1281
    • Acharya, P.1    Rajakumara, E.2    Sankaranarayanan, R.3    Rao, N.M.4
  • 16
    • 47049084664 scopus 로고    scopus 로고
    • Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight
    • Ahmad S, Kamal MZ, Sankaranarayanan R, Rao NM, (2008) Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight. J Mol Biol 381: 324-340.
    • (2008) J Mol Biol , vol.381 , pp. 324-340
    • Ahmad, S.1    Kamal, M.Z.2    Sankaranarayanan, R.3    Rao, N.M.4
  • 17
    • 66349117989 scopus 로고    scopus 로고
    • Thermally denatured state determines refolding in lipase: mutational analysis
    • Ahmad S, Rao NM, (2009) Thermally denatured state determines refolding in lipase: mutational analysis. Protein Sci 18: 1183-1196.
    • (2009) Protein Sci , vol.18 , pp. 1183-1196
    • Ahmad, S.1    Rao, N.M.2
  • 18
    • 0035946913 scopus 로고    scopus 로고
    • The crystal structure of Bacillus subtilis lipase: a minimal alpha/beta hydrolase fold enzyme
    • van PG, Eggert T, Jaeger KE, Dijkstra BW, (2001) The crystal structure of Bacillus subtilis lipase: a minimal alpha/beta hydrolase fold enzyme. J Mol Biol 309: 215-226.
    • (2001) J Mol Biol , vol.309 , pp. 215-226
    • van, P.G.1    Eggert, T.2    Jaeger, K.E.3    Dijkstra, B.W.4
  • 19
    • 40149103604 scopus 로고    scopus 로고
    • Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases
    • Papaleo E, Pasi M, Riccardi L, Sambi I, Fantucci P, de GL, (2008) Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases. FEBS Lett 582: 1008-1018.
    • (2008) FEBS Lett , vol.582 , pp. 1008-1018
    • Papaleo, E.1    Pasi, M.2    Riccardi, L.3    Sambi, I.4    Fantucci, P.5    de, G.L.6
  • 20
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, van der Spoel D, Lindahl E, (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theo Comp 4: 435-447.
    • (2008) J Chem Theo Comp , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 21
    • 77954495192 scopus 로고    scopus 로고
    • Fluorescence Dynamics of Double- and Single-Stranded DNA Bound to Histone and Micellar Surfaces
    • Goel T, Mukherjee T, Rao BJ, Krishnamoorthy G, (2010) Fluorescence Dynamics of Double- and Single-Stranded DNA Bound to Histone and Micellar Surfaces. J Phys Chem B 114: 8986-8993.
    • (2010) J Phys Chem B , vol.114 , pp. 8986-8993
    • Goel, T.1    Mukherjee, T.2    Rao, B.J.3    Krishnamoorthy, G.4
  • 22
    • 0032586678 scopus 로고    scopus 로고
    • Solvent-exposed tryptophans probe the dynamics at protein surfaces
    • Lakshmikanth GS, Krishnamoorthy G, (1999) Solvent-exposed tryptophans probe the dynamics at protein surfaces. Biophys J 77: 1100-1106.
    • (1999) Biophys J , vol.77 , pp. 1100-1106
    • Lakshmikanth, G.S.1    Krishnamoorthy, G.2
  • 23
    • 33845994767 scopus 로고    scopus 로고
    • Influence of agonists and antagonists on the segmental motion of residues near the agonist binding pocket of the acetylcholine-binding protein
    • Hibbs RE, Radic Z, Taylor P, Johnson DA, (2006) Influence of agonists and antagonists on the segmental motion of residues near the agonist binding pocket of the acetylcholine-binding protein. J Biol Chem 281: 39708-39718.
    • (2006) J Biol Chem , vol.281 , pp. 39708-39718
    • Hibbs, R.E.1    Radic, Z.2    Taylor, P.3    Johnson, D.A.4
  • 25
    • 33745039756 scopus 로고    scopus 로고
    • Characterization of the formation of amyloid protofibrils from barstar by mapping residue-specific fluorescence dynamics
    • Mukhopadhyay S, Nayak PK, Udgaonkar JB, Krishnamoorthy G, (2006) Characterization of the formation of amyloid protofibrils from barstar by mapping residue-specific fluorescence dynamics. J Mol Biol 358: 935-942.
    • (2006) J Mol Biol , vol.358 , pp. 935-942
    • Mukhopadhyay, S.1    Nayak, P.K.2    Udgaonkar, J.B.3    Krishnamoorthy, G.4
  • 26
    • 70350134740 scopus 로고    scopus 로고
    • Characterization of the heterogeneity and specificity of interpolypeptide interactions in amyloid protofibrils by measurement of site-specific fluorescence anisotropy decay kinetics
    • Jha A, Udgaonkar JB, Krishnamoorthy G, (2009) Characterization of the heterogeneity and specificity of interpolypeptide interactions in amyloid protofibrils by measurement of site-specific fluorescence anisotropy decay kinetics. J Mol Biol 393: 735-752.
    • (2009) J Mol Biol , vol.393 , pp. 735-752
    • Jha, A.1    Udgaonkar, J.B.2    Krishnamoorthy, G.3
  • 27
    • 33751423377 scopus 로고    scopus 로고
    • How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding
    • Gunasekaran K, Nussinov R, (2007) How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. J Mol Biol 365: 257-273.
    • (2007) J Mol Biol , vol.365 , pp. 257-273
    • Gunasekaran, K.1    Nussinov, R.2
  • 28
    • 12344307441 scopus 로고    scopus 로고
    • Conformational changes observed in enzyme crystal structures upon substrate binding
    • Gutteridge A, Thornton J, (2005) Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol 346: 21-28.
    • (2005) J Mol Biol , vol.346 , pp. 21-28
    • Gutteridge, A.1    Thornton, J.2
  • 30
    • 56449128760 scopus 로고    scopus 로고
    • Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle
    • Smith AJ, Muller R, Toscano MD, Kast P, Hellinga HW, et al. (2008) Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle. J Am Chem Soc 130: 15361-15373.
    • (2008) J Am Chem Soc , vol.130 , pp. 15361-15373
    • Smith, A.J.1    Muller, R.2    Toscano, M.D.3    Kast, P.4    Hellinga, H.W.5
  • 31
    • 30444439246 scopus 로고    scopus 로고
    • Directed evolution of Bacillus subtilis lipase A by use of enantiomeric phosphonate inhibitors: crystal structures and phage display selection
    • Droge MJ, Boersma YL, van PG, Vrenken TE, Ruggeberg CJ, et al. (2006) Directed evolution of Bacillus subtilis lipase A by use of enantiomeric phosphonate inhibitors: crystal structures and phage display selection. Chembiochem 7: 149-157.
    • (2006) Chembiochem , vol.7 , pp. 149-157
    • Droge, M.J.1    Boersma, Y.L.2    van, P.G.3    Vrenken, T.E.4    Ruggeberg, C.J.5
  • 33
    • 36849048228 scopus 로고    scopus 로고
    • Intrinsic motions along an enzymatic reaction trajectory
    • Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, et al. (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450: 838-844.
    • (2007) Nature , vol.450 , pp. 838-844
    • Henzler-Wildman, K.A.1    Thai, V.2    Lei, M.3    Ott, M.4    Wolf-Watz, M.5
  • 37
    • 0141993702 scopus 로고    scopus 로고
    • Protein conformational dynamics probed by single-molecule electron transfer
    • Yang H, Luo GB, Karnchanaphanurach P, Louie TM, Rech I, et al. (2003) Protein conformational dynamics probed by single-molecule electron transfer. Science 302: 262-266.
    • (2003) Science , vol.302 , pp. 262-266
    • Yang, H.1    Luo, G.B.2    Karnchanaphanurach, P.3    Louie, T.M.4    Rech, I.5
  • 38
    • 79953823548 scopus 로고    scopus 로고
    • A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
    • Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, et al. (2011) A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332: 234-238.
    • (2011) Science , vol.332 , pp. 234-238
    • Bhabha, G.1    Lee, J.2    Ekiert, D.C.3    Gam, J.4    Wilson, I.A.5
  • 39
    • 70350453758 scopus 로고    scopus 로고
    • Enzyme millisecond conformational dynamics do not catalyze the chemical step
    • Pisliakov AV, Cao J, Kamerlin SC, Warshel A, (2009) Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc Natl Acad Sci U S A 106: 17359-17364.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 17359-17364
    • Pisliakov, A.V.1    Cao, J.2    Kamerlin, S.C.3    Warshel, A.4
  • 40
    • 77951226274 scopus 로고    scopus 로고
    • At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
    • Kamerlin SC, Warshel A, (2010) At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins 78: 1339-1375.
    • (2010) Proteins , vol.78 , pp. 1339-1375
    • Kamerlin, S.C.1    Warshel, A.2
  • 41
    • 80052149070 scopus 로고    scopus 로고
    • Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
    • Adamczyk AJ, Cao J, Kamerlin SC, Warshel A, (2011) Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. Proc Natl Acad Sci U S A 108: 14115-14120.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 14115-14120
    • Adamczyk, A.J.1    Cao, J.2    Kamerlin, S.C.3    Warshel, A.4
  • 42
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, et al. (2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature 462: 669-673.
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1    Clarkson, M.W.2    Degnan, S.C.3    Erion, R.4    Kern, D.5
  • 44
    • 62449293337 scopus 로고    scopus 로고
    • Rational stabilization of enzymes by computational redesign of surface charge-charge interactions
    • Gribenko AV, Patel MM, Liu J, McCallum SA, Wang C, et al. (2009) Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. Proc Natl Acad Sci U S A 106: 2601-2606.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 2601-2606
    • Gribenko, A.V.1    Patel, M.M.2    Liu, J.3    McCallum, S.A.4    Wang, C.5
  • 45
  • 46
    • 0019751507 scopus 로고
    • Protein determination in membrane and lipoprotein samples: Manual and automated prosedures
    • Markwell MAKHSMTNEaBLL
    • Markwell MAKHSMTNEaBLL (1981) Protein determination in membrane and lipoprotein samples: Manual and automated prosedures. Methods Enzymol 72: 296-303.
    • (1981) Methods Enzymol , vol.72 , pp. 296-303
  • 47
    • 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: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.