메뉴 건너뛰기




Volumn 12, Issue 11, 2016, Pages 944-950

The role of protein dynamics in the evolution of new enzyme function

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; ARYLESTERASE; CARBOXYLESTERASE; PHOSPHOTRIESTERASE;

EID: 84987641979     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.2175     Document Type: Article
Times cited : (231)

References (60)
  • 3
    • 77957754309 scopus 로고    scopus 로고
    • Enzyme dynamics point to stepwise conformational selection in catalysis
    • Ma, B. & Nussinov, R. Enzyme dynamics point to stepwise conformational selection in catalysis. Curr. Opin. Chem. Biol. 14, 652-659 (2010).
    • (2010) Curr. Opin. Chem. Biol. , vol.14 , pp. 652-659
    • Ma, B.1    Nussinov, R.2
  • 4
    • 0041876227 scopus 로고    scopus 로고
    • Computer simulations of enzyme catalysis: Methods, progress, and insights
    • Warshel, A. Computer simulations of enzyme catalysis: methods, progress, and insights. Annu. Rev. Biophys. Biomol. Struct. 32, 425-443 (2003).
    • (2003) Annu. Rev. Biophys. Biomol. Struct. , vol.32 , pp. 425-443
    • Warshel, A.1
  • 6
    • 79953823548 scopus 로고    scopus 로고
    • A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
    • Bhabha, G. et al. A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332, 234-238 (2011).
    • (2011) Science , vol.332 , pp. 234-238
    • Bhabha, G.1
  • 7
    • 81755172909 scopus 로고    scopus 로고
    • Femtosecond dynamics coupled to chemical barrier crossing in a Born-Oppenheimer enzyme
    • Silva, R.G., Murkin, A.S. & Schramm, V.L. Femtosecond dynamics coupled to chemical barrier crossing in a Born-Oppenheimer enzyme. Proc. Natl. Acad. Sci. USA 108, 18661-18665 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 18661-18665
    • Silva, R.G.1    Murkin, A.S.2    Schramm, V.L.3
  • 8
    • 84887464612 scopus 로고    scopus 로고
    • Divergent evolution of protein conformational dynamics in dihydrofolate reductase
    • Bhabha, G. et al. Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nat. Struct. Mol. Biol. 20, 1243-1249 (2013).
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 1243-1249
    • Bhabha, G.1
  • 9
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • Fraser, J.S. et al. Hidden alternative structures of proline isomerase essential for catalysis. Nature 462, 669-673 (2009).
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1
  • 10
    • 84908329345 scopus 로고    scopus 로고
    • Maintenance of native-like protein dynamics may not be required for engineering functional proteins
    • Gobeil, S.M. et al. Maintenance of native-like protein dynamics may not be required for engineering functional proteins. Chem. Biol. 21, 1330-1340 (2014).
    • (2014) Chem. Biol. , vol.21 , pp. 1330-1340
    • Gobeil, S.M.1
  • 11
    • 76049124264 scopus 로고    scopus 로고
    • Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase
    • Jackson, C.J. et al. Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase. Proc. Natl. Acad. Sci. USA 106, 21631-21636 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 21631-21636
    • Jackson, C.J.1
  • 12
    • 84857542642 scopus 로고    scopus 로고
    • Taking Ockham's razor to enzyme dynamics and catalysis
    • Glowacki, D.R., Harvey, J.N. & Mulholland, A.J. Taking Ockham's razor to enzyme dynamics and catalysis. Nat. Chem. 4, 169-176 (2012).
    • (2012) Nat. Chem. , vol.4 , pp. 169-176
    • Glowacki, D.R.1    Harvey, J.N.2    Mulholland, A.J.3
  • 13
    • 77951226274 scopus 로고    scopus 로고
    • At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
    • Kamerlin, S.C. & Warshel, A. At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins 78, 1339-1375 (2010).
    • (2010) Proteins , vol.78 , pp. 1339-1375
    • Kamerlin, S.C.1    Warshel, A.2
  • 14
    • 77957750113 scopus 로고    scopus 로고
    • Hitting a moving target?-Understanding how conformational diversity impacts enzymatic catalysis
    • O'Brien, P.J. & Hollfelder, F. Hitting a moving target?-Understanding how conformational diversity impacts enzymatic catalysis. Curr. Opin. Chem. Biol. 14, 634-635 (2010).
    • (2010) Curr. Opin. Chem. Biol. , vol.14 , pp. 634-635
    • O'Brien, P.J.1    Hollfelder, F.2
  • 15
    • 79958207530 scopus 로고    scopus 로고
    • Mining electron density for functionally relevant protein polysterism in crystal structures
    • Fraser, J.S. & Jackson, C.J. Mining electron density for functionally relevant protein polysterism in crystal structures. Cell. Mol. Life Sci. 68, 1829-1841 (2011).
    • (2011) Cell. Mol. Life Sci. , vol.68 , pp. 1829-1841
    • Fraser, J.S.1    Jackson, C.J.2
  • 17
    • 84908624908 scopus 로고    scopus 로고
    • Evolutionary aspects of enzyme dynamics
    • Klinman, J.P. & Kohen, A. Evolutionary aspects of enzyme dynamics. J. Biol. Chem. 289, 30205-30212 (2014).
    • (2014) J. Biol. Chem. , vol.289 , pp. 30205-30212
    • Klinman, J.P.1    Kohen, A.2
  • 18
    • 84861359623 scopus 로고    scopus 로고
    • Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions
    • Colletier, J.P. et al. Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions. Mol. Biol. Evol. 29, 1683-1694 (2012).
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 1683-1694
    • Colletier, J.P.1
  • 19
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • Tokuriki, N. & Tawfik, D.S. Protein dynamism and evolvability. Science 324, 203-207 (2009).
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 20
    • 0038148710 scopus 로고    scopus 로고
    • Conformational diversity and protein evolution-A 60-year-old hypothesis revisited
    • James, L.C. & Tawfik, D.S. Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28, 361-368 (2003).
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 361-368
    • James, L.C.1    Tawfik, D.S.2
  • 21
    • 84871755504 scopus 로고    scopus 로고
    • Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme
    • Tokuriki, N. et al. Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme. Nat. Commun. 3, 1257 (2012).
    • (2012) Nat. Commun. , vol.3 , pp. 1257
    • Tokuriki, N.1
  • 22
    • 84949117325 scopus 로고    scopus 로고
    • Negative epistasis and evolvability in TEM-1 β-lactamase-The thin line between an enzyme's conformational freedom and disorder
    • Dellus-Gur, E. et al. Negative epistasis and evolvability in TEM-1 β-lactamase-the thin line between an enzyme's conformational freedom and disorder. J. Mol. Biol. 427, 2396-2409 (2015).
    • (2015) J. Mol. Biol. , vol.427 , pp. 2396-2409
    • Dellus-Gur, E.1
  • 23
    • 0025836538 scopus 로고
    • Limits of diffusion in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta
    • Caldwell, S.R., Newcomb, J.R., Schlecht, K.A. & Raushel, F.M. Limits of diffusion in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta. Biochemistry 30, 7438-7444 (1991).
    • (1991) Biochemistry , vol.30 , pp. 7438-7444
    • Caldwell, S.R.1    Newcomb, J.R.2    Schlecht, K.A.3    Raushel, F.M.4
  • 24
    • 84943792201 scopus 로고    scopus 로고
    • Reverse evolution leads to genotypic incompatibility despite functional and active site convergence
    • Kaltenbach, M., Jackson, C.J., Campbell, E.C., Hollfelder, F. & Tokuriki, N. Reverse evolution leads to genotypic incompatibility despite functional and active site convergence. eLife 4, e06492 (2015).
    • (2015) ELife , vol.4 , pp. e06492
    • Kaltenbach, M.1    Jackson, C.J.2    Campbell, E.C.3    Hollfelder, F.4    Tokuriki, N.5
  • 25
    • 84923917012 scopus 로고    scopus 로고
    • On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations
    • Bora, R.P., Mills, M.J., Frushicheva, M.P. & Warshel, A. On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations. J. Phys. Chem. B 119, 3434-3445 (2015).
    • (2015) J. Phys. Chem. B , vol.119 , pp. 3434-3445
    • Bora, R.P.1    Mills, M.J.2    Frushicheva, M.P.3    Warshel, A.4
  • 26
    • 84861779036 scopus 로고    scopus 로고
    • Topological analysis and interactive visualization of biological networks and protein structures
    • Doncheva, N.T., Assenov, Y., Domingues, F.S. & Albrecht, M. Topological analysis and interactive visualization of biological networks and protein structures. Nat. Protoc. 7, 670-685 (2012).
    • (2012) Nat. Protoc. , vol.7 , pp. 670-685
    • Doncheva, N.T.1    Assenov, Y.2    Domingues, F.S.3    Albrecht, M.4
  • 27
    • 84923853645 scopus 로고    scopus 로고
    • Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD
    • Fetics, S.K. et al. Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD. Structure 23, 505-516 (2015).
    • (2015) Structure , vol.23 , pp. 505-516
    • Fetics, S.K.1
  • 29
    • 37549047246 scopus 로고    scopus 로고
    • In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase
    • Jackson, C.J. et al. In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase. J. Mol. Biol. 375, 1189-1196 (2008).
    • (2008) J. Mol. Biol. , vol.375 , pp. 1189-1196
    • Jackson, C.J.1
  • 30
    • 84883403423 scopus 로고    scopus 로고
    • Automated identification of functional dynamic contact networks from X-ray crystallography
    • van den Bedem, H., Bhabha, G., Yang, K., Wright, P.E. & Fraser, J.S. Automated identification of functional dynamic contact networks from X-ray crystallography. Nat. Methods 10, 896-902 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 896-902
    • Van-Den-Bedem, H.1    Bhabha, G.2    Yang, K.3    Wright, P.E.4    Fraser, J.S.5
  • 32
    • 84908221627 scopus 로고    scopus 로고
    • Modelling dynamics in protein crystal structures by ensemble refinement
    • Burnley, B.T., Afonine, P.V., Adams, P.D. & Gros, P. Modelling dynamics in protein crystal structures by ensemble refinement. eLife 1, e00311 (2012).
    • (2012) ELife , vol.1 , pp. e00311
    • Burnley, B.T.1    Afonine, P.V.2    Adams, P.D.3    Gros, P.4
  • 33
    • 34548040966 scopus 로고    scopus 로고
    • Crystal structure of an ancient protein: Evolution by conformational epistasis
    • Ortlund, E.A., Bridgham, J.T., Redinbo, M.R. & Thornton, J.W. Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317, 1544-1548 (2007).
    • (2007) Science , vol.317 , pp. 1544-1548
    • Ortlund, E.A.1    Bridgham, J.T.2    Redinbo, M.R.3    Thornton, J.W.4
  • 34
    • 84872684145 scopus 로고    scopus 로고
    • Structure and dynamics of a primordial catalytic fold generated by in vitro evolution
    • Chao, F.A. et al. Structure and dynamics of a primordial catalytic fold generated by in vitro evolution. Nat. Chem. Biol. 9, 81-83 (2013).
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 81-83
    • Chao, F.A.1
  • 35
    • 84880920662 scopus 로고    scopus 로고
    • Evolution of a designed retro-aldolase leads to complete active site remodeling
    • Giger, L. et al. Evolution of a designed retro-aldolase leads to complete active site remodeling. Nat. Chem. Biol. 9, 494-498 (2013).
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 494-498
    • Giger, L.1
  • 36
    • 79952437832 scopus 로고    scopus 로고
    • Optimization of the in-silico-designed Kemp eliminase KE70 by computational design and directed evolution
    • Khersonsky, O. et al. Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution. J. Mol. Biol. 407, 391-412 (2011).
    • (2011) J. Mol. Biol. , vol.407 , pp. 391-412
    • Khersonsky, O.1
  • 37
    • 84901855811 scopus 로고    scopus 로고
    • Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase
    • Preiswerk, N. et al. Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase. Proc. Natl. Acad. Sci. USA 111, 8013-8018 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 8013-8018
    • Preiswerk, N.1
  • 38
    • 84901203399 scopus 로고    scopus 로고
    • Dynamics and hydration explain failed functional transformation in dehalogenase design
    • Sykora, J. et al. Dynamics and hydration explain failed functional transformation in dehalogenase design. Nat. Chem. Biol. 10, 428-430 (2014).
    • (2014) Nat. Chem. Biol. , vol.10 , pp. 428-430
    • Sykora, J.1
  • 39
    • 18144403554 scopus 로고    scopus 로고
    • Improving enzyme properties: When are closer mutations better?
    • Morley, K.L. & Kazlauskas, R.J. Improving enzyme properties: when are closer mutations better? Trends Biotechnol. 23, 231-237 (2005).
    • (2005) Trends Biotechnol. , vol.23 , pp. 231-237
    • Morley, K.L.1    Kazlauskas, R.J.2
  • 40
    • 0030591783 scopus 로고    scopus 로고
    • Stable high-copy-number bacteriophage lambda promoter vectors for overproduction of proteins in Escherichia coli
    • Love, C.A., Lilley, P.E. & Dixon, N.E. Stable high-copy-number bacteriophage lambda promoter vectors for overproduction of proteins in Escherichia coli. Gene 176, 49-53 (1996).
    • (1996) Gene , vol.176 , pp. 49-53
    • Love, C.A.1    Lilley, P.E.2    Dixon, N.E.3
  • 42
    • 0028103275 scopus 로고
    • Collaborative Computational Project, Number 4. The CCP4 suite: Programs for protein crystallography
    • Collaborative, C.P. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763 (1994).
    • (1994) Acta Crystallogr. D Biol. Crystallogr. , vol.50 , pp. 760-763
    • Collaborative, C.P.1
  • 43
    • 84861425552 scopus 로고    scopus 로고
    • Linking crystallographic model and data quality
    • Karplus, P.A. & Diederichs, K. Linking crystallographic model and data quality. Science 336, 1030-1033 (2012).
    • (2012) Science , vol.336 , pp. 1030-1033
    • Karplus, P.A.1    Diederichs, K.2
  • 44
    • 34447508216 scopus 로고    scopus 로고
    • Phaser crystallographic software
    • McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
    • (2007) J. Appl. Crystallogr. , vol.40 , pp. 658-674
    • McCoy, A.J.1
  • 45
    • 16644364842 scopus 로고    scopus 로고
    • REFMAC5 dictionary: Organization of prior chemical knowledge and guidelines for its use
    • Vagin, A.A. et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr. D Biol. Crystallogr. 60, 2184-2195 (2004).
    • (2004) Acta Crystallogr. D Biol. Crystallogr. , vol.60 , pp. 2184-2195
    • Vagin, A.A.1
  • 48
    • 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. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 4, 435-447 (2008).
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van-Der-Spoel, D.3    Lindahl, E.4
  • 49
    • 79959713919 scopus 로고    scopus 로고
    • Definition and testing of the GROMOS force-field versions 54A7 and 54B7
    • Schmid, N. et al. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur. Biophys. J. 40, 843-856 (2011).
    • (2011) Eur. Biophys. J. , vol.40 , pp. 843-856
    • Schmid, N.1
  • 52
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • Tironi, I.G., Sperb, R., Smith, P.E. & van Gunsteren, W.F. A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102, 5451 (1995).
    • (1995) J. Chem. Phys. , vol.102 , pp. 5451
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    Van-Gunsteren, W.F.4
  • 53
    • 0035878765 scopus 로고    scopus 로고
    • Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations
    • Heinz, T.N., van Gunsteren, W.F. & Hünenberger, P.H. Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations. J. Chem. Phys. 115, 1125 (2001).
    • (2001) J. Chem. Phys. , vol.115 , pp. 1125
    • Heinz, T.N.1    Van-Gunsteren, W.F.2    Hünenberger, P.H.3
  • 54
  • 55
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto, S. & Kollman, P.A. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13, 952-962 (1992).
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 56
    • 79957788878 scopus 로고    scopus 로고
    • ProDy: Protein dynamics inferred from theory and experiments
    • Bakan, A., Meireles, L.M. & Bahar, I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 27, 1575-1577 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1575-1577
    • Bakan, A.1    Meireles, L.M.2    Bahar, I.3
  • 58
    • 84894119536 scopus 로고    scopus 로고
    • Weighted Implementation of suboptimal paths (WISP): An optimized algorithm and tool for dynamical network analysis
    • Van Wart, A.T., Durrant, J., Votapka, L. & Amaro, R.E. Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis. J. Chem. Theory Comput. 10, 511-517 (2014).
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 511-517
    • Van-Wart, A.T.1    Durrant, J.2    Votapka, L.3    Amaro, R.E.4
  • 60
    • 3242875210 scopus 로고    scopus 로고
    • El Nemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
    • Suhre, K. & Sanejouand, Y.H. El Nemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 32, W610-W614 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. W610-W614
    • Suhre, K.1    Sanejouand, Y.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.