메뉴 건너뛰기




Volumn 18, Issue 10, 2010, Pages 1102-1108

Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

Author keywords

[No Author keywords available]

Indexed keywords

METAL ION; METALLOPROTEINASE; WATER; ZINC;

EID: 80054967217     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2120     Document Type: Article
Times cited : (181)

References (55)
  • 1
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specifcity to protein synthesis
    • Koshland, D.E. Application of a theory of enzyme specifcity to protein synthesis. Proc. Natl. Acad. Sci. USA 44, 98-104 (1958)
    • (1958) Proc. Natl. Acad. Sci. USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 2
    • 40849097646 scopus 로고    scopus 로고
    • Free-energy landscape of enzyme catalysis
    • DOI 10.1021/bi800049z
    • Benkovic, S.J., Hammes, G.G. & Hammes-Schiffer, S. Free-energy landscape of enzyme catalysis. Biochemistry 47, 3317-3321 (2008) (Pubitemid 351399220)
    • (2008) Biochemistry , vol.47 , Issue.11 , pp. 3317-3321
    • Benkovic, S.J.1    Hammes, G.G.2    Hammes-Schiffer, S.3
  • 3
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • DOI 10.1038/nature06407, PII NATURE06407
    • Henzler-Wildman, K.A. et al. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450, 913-916 (2007) (Pubitemid 350231333)
    • (2007) Nature , vol.450 , Issue.7171 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 4
    • 0041821836 scopus 로고    scopus 로고
    • A perspective on enzyme catalysis
    • DOI 10.1126/science.1085515
    • Benkovic, S.J. & Hammes-Schiffer, S. A perspective on enzyme catalysis. Science 301, 1196-1202 (2003) (Pubitemid 37052200)
    • (2003) Science , vol.301 , Issue.5637 , pp. 1196-1202
    • Benkovic, S.J.1    Hammes-Schiffer, S.2
  • 5
    • 25844521524 scopus 로고    scopus 로고
    • Advances in kinetic protein crystallography
    • DOI 10.1016/j.sbi.2005.08.002, PII S0959440X05001508, Carbohydrates and Glycoconjugates/Biophysical Methods
    • Bourgeois, D. & Royant, A. Advances in kinetic protein crystallography. Curr. Opin. Struct. Biol. 15, 538-547 (2005) (Pubitemid 41393485)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.5 , pp. 538-547
    • Bourgeois, D.1    Royant, A.2
  • 6
    • 38949151546 scopus 로고    scopus 로고
    • Molecular simulations of protein dynamics: New windows on mechanisms in biology
    • DOI 10.1038/sj.embor.7401160, PII 7401160
    • Dodson, G.G., Lane, D.P. & Verma, C.S. Molecular simulations of protein dynamics: new windows on mechanisms in biology. EMBO Rep. 9, 144-150 (2008) (Pubitemid 351223451)
    • (2008) EMBO Reports , vol.9 , Issue.2 , pp. 144-150
    • Dodson, G.G.1    Lane, D.P.2    Verma, C.S.3
  • 8
    • 33645834303 scopus 로고    scopus 로고
    • New tools provide new insights in NMR studies of protein dynamics
    • Mittermaier, A. & Kay, L.E. New tools provide new insights in NMR studies of protein dynamics. Science 312, 224-228 (2006)
    • (2006) Science , vol.312 , pp. 224-228
    • Mittermaier, A.1    Kay, L.E.2
  • 9
    • 35048839174 scopus 로고    scopus 로고
    • Temperature- and hydration-dependent protein dynamics in photosystem II of green plants studied by quasielastic neutron scattering
    • DOI 10.1021/bi700179s
    • Pieper, J. et al. Temperature-and hydration-dependent protein dynamics in photosystem II of green plants studied by quasielastic neutron scattering. Biochemistry 46, 11398-11409 (2007) (Pubitemid 47556767)
    • (2007) Biochemistry , vol.46 , Issue.40 , pp. 11398-11409
    • Pieper, J.1    Hauss, T.2    Buchsteiner, A.3    Baczynski, K.4    Adamiak, K.5    Lechner, R.E.6    Renger, G.7
  • 11
    • 0034595671 scopus 로고    scopus 로고
    • How soft is a protein? A protein dynamics force constant measured by neutron scattering
    • DOI 10.1126/science.288.5471.1604
    • Zaccai, G. How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science 288, 1604-1607 (2000) (Pubitemid 30387420)
    • (2000) Science , vol.288 , Issue.5471 , pp. 1604-1607
    • Zaccai, G.1
  • 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
    • 68049093016 scopus 로고    scopus 로고
    • Enzymatic transition states and dynamic motion in barrier crossing
    • Schwartz, S.D. & Schramm, V.L. Enzymatic transition states and dynamic motion in barrier crossing. Nat. Chem. Biol. 5, 551-558 (2009)
    • (2009) Nat. Chem. Biol , vol.5 , pp. 551-558
    • Schwartz, S.D.1    Schramm, V.L.2
  • 16
    • 0030853055 scopus 로고    scopus 로고
    • The lubricant of life: A proposal that solvent water promotes extremely fast conformational fluctuations in mobile heteropolypeptide structure
    • DOI 10.1021/bi971323j
    • Barron, L.D., Hecht, L. & Wilson, G. The lubricant of life: a proposal that solvent water promotes extremely fast conformational fuctuations in mobile heteropolypeptide structure. Biochemistry 36, 13143-13147 (1997) (Pubitemid 27473357)
    • (1997) Biochemistry , vol.36 , Issue.43 , pp. 13143-13147
    • Barron, L.D.1    Hecht, L.2    Wilson, G.3
  • 19
    • 33947391268 scopus 로고    scopus 로고
    • The dynamics of water-protein interaction studied by ultrafast optical Kerr-effect spectroscopy
    • DOI 10.1021/ja066289n
    • Hunt, N.T., Kattner, L., Shanks, R.P. & Wynne, K. The dynamics of water-protein interaction studied by ultrafast optical Kerr-effect spectroscopy. J. Am. Chem. Soc. 129, 3168-3172 (2007) (Pubitemid 46449349)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.11 , pp. 3168-3172
    • Hunt, N.T.1    Kattner, L.2    Shanks, R.P.3    Wynne, K.4
  • 22
    • 0035843166 scopus 로고    scopus 로고
    • Improving enzymes by using them in organic solvents
    • DOI 10.1038/35051719
    • Klibanov, A.M. Improving enzymes by using them in organic solvents. Nature 409, 241-246 (2001) (Pubitemid 32144293)
    • (2001) Nature , vol.409 , Issue.6817 , pp. 241-246
    • Klibanov, A.M.1
  • 23
    • 0027918556 scopus 로고
    • Water: Now you see it, now you don't
    • DOI 10.1016/0969-2126(93)90011-5
    • Levitt, M. & Park, B.H. Water: now you see it, now you don't. Structure 1, 223-226 (1993) (Pubitemid 2031109)
    • (1993) Structure , vol.1 , Issue.4 , pp. 223-226
    • Levitt, M.1    Park, B.H.2
  • 27
    • 33750286994 scopus 로고    scopus 로고
    • Do we underestimate the importance of water in cell biology?
    • DOI 10.1038/nrm2021, PII NRM2021
    • Chaplin, M. Do we underestimate the importance of water in cell biology? Nat. Rev. Mol. Cell Biol. 7, 861-866 (2006) (Pubitemid 44627479)
    • (2006) Nature Reviews Molecular Cell Biology , vol.7 , Issue.11 , pp. 861-866
    • Chaplin, M.1
  • 28
    • 0037154884 scopus 로고    scopus 로고
    • Enzyme dynamics during catalysis
    • DOI 10.1126/science.1066176
    • Eisenmesser, E.Z., Bosco, D.A., Akke, M. & Kern, D. Enzyme dynamics during catalysis. Science 295, 1520-1523 (2002) (Pubitemid 34174006)
    • (2002) Science , vol.295 , Issue.5559 , pp. 1520-1523
    • Eisenmesser, E.Z.1    Bosco, D.A.2    Akke, M.3    Kern, D.4
  • 30
    • 65549103917 scopus 로고    scopus 로고
    • Simultaneous measurements of solvent dynamics and functional kinetics in a light-activated enzyme
    • Durin, G. et al. Simultaneous measurements of solvent dynamics and functional kinetics in a light-activated enzyme. Biophys. J. 96, 1902-1910 (2009)
    • (2009) Biophys. J , vol.96 , pp. 1902-1910
    • Durin, G.1
  • 32
    • 0037312979 scopus 로고    scopus 로고
    • Active site electronic structure and dynamics during metalloenzyme catalysis
    • DOI 10.1038/nsb889
    • Kleifeld, O., Frenkel, A., Martin, J.M. & Sagi, I. Active site electronic structure and dynamics during metalloenzyme catalysis. Nat. Struct. Biol. 10, 98-103 (2003) (Pubitemid 36177088)
    • (2003) Nature Structural Biology , vol.10 , Issue.2 , pp. 98-103
    • Kleifeld, O.1    Frenkel, A.2    Martin, J.M.L.3    Sagi, I.4
  • 34
    • 52049105004 scopus 로고    scopus 로고
    • Real-time detection of protein-water dynamics upon protein folding by terahertz absorption spectroscopy
    • Kim, S.J., Born, B., Havenith, M. & Gruebele, M. Real-time detection of protein-water dynamics upon protein folding by terahertz absorption spectroscopy. Angew. Chem. Int. Edn Engl. 47, 6486-6489 (2008)
    • (2008) Angew. Chem. Int. Edn Engl , vol.47 , pp. 6486-6489
    • Kim, S.J.1    Born, B.2    Havenith, M.3    Gruebele, M.4
  • 35
    • 2642546699 scopus 로고    scopus 로고
    • Processing, shedding, and endocytosis of membrane type 1-Matrix metalloproteinase (MT1-MMP)
    • DOI 10.1002/jcp.20064
    • Osenkowski, P., Toth, M. & Fridman, R. Processing, shedding, and endocytosis of membrane type 1-matrix metalloproteinase (MT1-MMP). J. Cell. Physiol. 200, 2-10 (2004) (Pubitemid 38720616)
    • (2004) Journal of Cellular Physiology , vol.200 , Issue.1 , pp. 2-10
    • Osenkowski, P.1    Toth, M.2    Fridman, R.3
  • 36
    • 2142828483 scopus 로고    scopus 로고
    • 2, a fluorogenic substrate with increased specificity constants for collagenases and tumor necrosis factor converting enzyme
    • DOI 10.1016/j.ab.2003.12.035, PII S0003269704001319
    • Neumann, U., Kubota, H., Frei, K., Ganu, V. & Leppert, D. Characterization of Mca-Lys-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2, a fuorogenic substrate with increased specifcity constants for collagenases and tumor necrosis factor converting enzyme. Anal. Biochem. 328, 166-173 (2004) (Pubitemid 38542933)
    • (2004) Analytical Biochemistry , vol.328 , Issue.2 , pp. 166-173
    • Neumann, U.1    Kubota, H.2    Frei, K.3    Ganu, V.4    Leppert, D.5
  • 37
    • 38049115489 scopus 로고    scopus 로고
    • An extended dynamical hydration shell around proteins
    • Ebbinghaus, S. et al. An extended dynamical hydration shell around proteins. Proc. Natl. Acad. Sci. USA 104, 20749-20752 (2007)
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 20749-20752
    • Ebbinghaus, S.1
  • 39
    • 77955440237 scopus 로고    scopus 로고
    • Dissecting the THz spectrum of liquid water from frst principles through correlations in time and space
    • Heyden, M. et al. Dissecting the THz spectrum of liquid water from frst principles through correlations in time and space. Proc. Natl. Acad. Sci. USA 107, 12068-12073 (2010)
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 12068-12073
    • Heyden, M.1
  • 42
    • 43549111353 scopus 로고    scopus 로고
    • Characterizing hydration state in solution using terahertz time-domain attenuated total refection spectroscopy
    • Arikawa, T., Nagai, M. & Tanaka, K. Characterizing hydration state in solution using terahertz time-domain attenuated total refection spectroscopy. Chem. Phys. Lett. 457, 12-17 (2008)
    • (2008) Chem. Phys. Lett , vol.457 , pp. 12-17
    • Arikawa, T.1    Nagai, M.2    Tanaka, K.3
  • 43
    • 77956209545 scopus 로고    scopus 로고
    • Combining THz spectroscopy and MD simulations to study protein-hydration coupling
    • Heyden, M. & Havenith, M. Combining THz spectroscopy and MD simulations to study protein-hydration coupling. Methods 52, 74-83 (2010)
    • (2010) Methods , vol.52 , pp. 74-83
    • Heyden, M.1    Havenith, M.2
  • 44
    • 35948954456 scopus 로고    scopus 로고
    • Molecular structures and dynamics of the stepwise activation mechanism of a matrix metalloproteinase zymogen: Challenging the cysteine switch dogma
    • DOI 10.1021/ja073941l
    • Rosenblum, G. et al. Molecular structures and dynamics of the stepwise activation mechanism of a matrix metalloproteinase zymogen: challenging the cysteine switch dogma. J. Am. Chem. Soc. 129, 13566-13574 (2007) (Pubitemid 350071785)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.44 , pp. 13566-13574
    • Rosenblum, G.1    Meroueh, S.2    Toth, M.3    Fisher, J.F.4    Fridman, R.5    Mobashery, S.6    Sagi, I.7
  • 45
    • 0036607073 scopus 로고    scopus 로고
    • Phase speciation by extended x-ray absorption fine structure spectroscopy
    • DOI 10.1063/1.1473193
    • Frenkel, A.I., Kleifeld, O., Wasserman, S.R. & Sagi, I. Phase speciation by extended X-ray absorption fne structure spectroscopy. J. Chem. Phys. 116, 9449-9456 (2002) (Pubitemid 34632534)
    • (2002) Journal of Chemical Physics , vol.116 , Issue.21 , pp. 9449-9456
    • Frenkel, A.I.1    Kleifeld, O.2    Wasserman, S.R.3    Sagi, I.4
  • 46
    • 0028145441 scopus 로고
    • Design and characterization of a fluorogenic substrate selectively hydrolyzed by stromelysin 1 (matrix metalloproteinase-3)
    • Nagase, H., Fields, C.G. & Fields, G.B. Design and characterization of a fuorogenic substrate selectively hydrolyzed by stromelysin 1 (matrix metalloproteinase-3). J. Biol. Chem. 269, 20952-20957 (1994) (Pubitemid 24266460)
    • (1994) Journal of Biological Chemistry , vol.269 , Issue.33 , pp. 20952-20957
    • Nagase, H.1    Fields, C.G.2    Fields, G.B.3
  • 47
    • 0032167522 scopus 로고    scopus 로고
    • Crystal structure of the complex formed by the membrane type 1-matrix metalloproteinase with the tissue inhibitor of metalloproteinases-2, the soluble progelatinase A receptor
    • DOI 10.1093/emboj/17.17.5238
    • Fernandez-Catalan, C. et al. Crystal structure of the complex formed by the membrane type 1-matrix metalloproteinase with the tissue inhibitor of metalloproteinases-2, the soluble progelatinase A receptor. EMBO J. 17, 5238-5248 (1998) (Pubitemid 28408489)
    • (1998) EMBO Journal , vol.17 , Issue.17 , pp. 5238-5248
    • Fernandez-Catalan, C.1    Bode, W.2    Huber, R.3    Turk, D.4    Calvete, J.J.5    Lichte, A.6    Tschesche, H.7    Maskos, K.8
  • 48
    • 77954827231 scopus 로고    scopus 로고
    • The intrinsic protein fexibility of endogenous protease inhibitor TIMP-1 controls its binding interface and affects its function
    • Grossman, M. et al. The intrinsic protein fexibility of endogenous protease inhibitor TIMP-1 controls its binding interface and affects its function. Biochemistry 49, 6184-6192 (2010)
    • (2010) Biochemistry , vol.49 , pp. 6184-6192
    • Grossman, M.1
  • 49
    • 0040362704 scopus 로고    scopus 로고
    • Chemical basis for enzyme catalysis
    • DOI 10.1021/bi0003689
    • Bruice, T.C. & Benkovic, S.J. Chemical basis for enzyme catalysis. Biochemistry 39, 6267-6274 (2000) (Pubitemid 30347130)
    • (2000) Biochemistry , vol.39 , Issue.21 , pp. 6267-6274
    • Bruice, T.C.1    Benkovic, S.J.2
  • 50
    • 27544462342 scopus 로고    scopus 로고
    • Role of protein dynamics in reaction rate enhancement by enzymes
    • DOI 10.1021/ja055251s
    • Agarwal, P.K. Role of protein dynamics in reaction rate enhancement by enzymes. J. Am. Chem. Soc. 127, 15248-15256 (2005) (Pubitemid 41547393)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.43 , pp. 15248-15256
    • Agarwal, P.K.1
  • 51
    • 84975571748 scopus 로고
    • Terahertz time-domain spectroscopy of water vapor
    • Exter, M.V., Fattinger, C. & Grischkowsky, D. Terahertz time-domain spectroscopy of water vapor. Opt. Lett. 14, 1128-1130 (1989)
    • (1989) Opt. Lett , vol.14 , pp. 1128-1130
    • Exter, M.V.1    Fattinger, C.2    Grischkowsky, D.3
  • 52
    • 33748552723 scopus 로고    scopus 로고
    • Far-infrared dielectric properties of polar liquids probed by femtosecond terahertz pulse spectroscopy
    • Kindt, J.T. & Schmuttenmaer, C.A. Far-infrared dielectric properties of polar liquids probed by femtosecond terahertz pulse spectroscopy. J. Phys. Chem. 100, 10373-10379 (1996) (Pubitemid 126789365)
    • (1996) Journal of Physical Chemistry , vol.100 , Issue.24 , pp. 10373-10379
    • Kindt, J.T.1    Schmuttenmaer, C.A.2
  • 53
    • 2342427576 scopus 로고    scopus 로고
    • Threonine 98, the Pivotal Residue of Tissue Inhibitor of Metalloproteinases (TIMP)-1 in Metalloproteinase Recognition
    • DOI 10.1074/jbc.M312589200
    • Lee, M.H., Rapti, M., Knauper, V. & Murphy, G. Threonine 98, the pivotal residue of tissue inhibitor of metalloproteinases (TIMP)-1 in metalloproteinase recognition. J. Biol. Chem. 279, 17562-17569 (2004) (Pubitemid 38560520)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.17 , pp. 17562-17569
    • Lee, M.-H.1    Rapti, M.2    Knauper, V.3    Murphy, G.4
  • 54
    • 27344454932 scopus 로고    scopus 로고
    • GROMACS: Fast, fexible, and free
    • Spoel, D.V.D. et al. GROMACS: Fast, fexible, and free. J. Comput. Chem. 26, 1701-1718 (2005)
    • (2005) J. Comput. Chem , vol.26 , pp. 1701-1718
    • Spoel, D.V.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.