메뉴 건너뛰기




Volumn 375, Issue 2, 2008, Pages 529-546

Molecular Crowding Inhibits Intramolecular Breathing Motions in Proteins

Author keywords

crowding; protein conformation; protein stability; rigid body motion; X ray scattering

Indexed keywords

ARTICLE; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEOMICS; RADIATION SCATTERING; STRUCTURE ANALYSIS;

EID: 36549080494     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.07.075     Document Type: Article
Times cited : (89)

References (52)
  • 1
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H., Sligar S.G., and Wolynes P.G. The energy landscapes and motions of proteins. Science 254 (1991) 1598-1603
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 2
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M., and McCammon J.A. Molecular dynamics simulations of biomolecules. Nature Struct. Biol. 9 (2002) 646-652
    • (2002) Nature Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 3
    • 0041821836 scopus 로고    scopus 로고
    • A perspective on enzyme catalysis
    • Benkovic S.J., and Hammes-Schiffer S. A perspective on enzyme catalysis. Science 301 (2003) 1196-1202
    • (2003) Science , vol.301 , pp. 1196-1202
    • Benkovic, S.J.1    Hammes-Schiffer, S.2
  • 5
    • 0346365084 scopus 로고    scopus 로고
    • Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange
    • Vendruscolo M., Paci E., Dobson C.M., and Karplus M. Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange. J. Am. Chem. Soc. 125 (2003) 15686-15687
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 15686-15687
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 6
    • 0018793861 scopus 로고
    • Temperature-dependent X-ray diffraction as a probe of protein structural dynamics
    • Fraunfelder H., Petsko G.A., and Tsernoglou D. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 280 (1979) 558-563
    • (1979) Nature , vol.280 , pp. 558-563
    • Fraunfelder, H.1    Petsko, G.A.2    Tsernoglou, D.3
  • 7
    • 0021191208 scopus 로고
    • Fluctuations in Protein structure from x-ray diffraction
    • Petsko G.A., and Ringe D. Fluctuations in Protein structure from x-ray diffraction. Annu. Rev. Biophys. Bioeng. 13 (1984) 331-371
    • (1984) Annu. Rev. Biophys. Bioeng. , vol.13 , pp. 331-371
    • Petsko, G.A.1    Ringe, D.2
  • 8
    • 0023924794 scopus 로고
    • Liquid-like movements in crystalline insulin
    • Caspar D.L., Clarage J., Salunke D.M., and Clarage M. Liquid-like movements in crystalline insulin. Nature 332 (1988) 659-662
    • (1988) Nature , vol.332 , pp. 659-662
    • Caspar, D.L.1    Clarage, J.2    Salunke, D.M.3    Clarage, M.4
  • 9
    • 0034595671 scopus 로고    scopus 로고
    • How soft is a protein? A protein dynamics force constant measured by neutron scattering
    • Zaccai G. How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science 288 (2000) 1604-1607
    • (2000) Science , vol.288 , pp. 1604-1607
    • Zaccai, G.1
  • 10
    • 0141918782 scopus 로고    scopus 로고
    • Proteins in action: the physics of structural fluctuations and conformational changes
    • Parak F.G. Proteins in action: the physics of structural fluctuations and conformational changes. Curr. Opin. Struct. Biol. 13 (2003) 552-557
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 552-557
    • Parak, F.G.1
  • 11
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • Isralewitz B., Gao M., and Schulten K. Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11 (2001) 224-230
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 12
    • 0036721233 scopus 로고    scopus 로고
    • Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic
    • Krebs W.G., Alexandrov V., Wilson C.A., Echols N., Yu H., and Gerstein M. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins: Struct. Funct.Genet. 48 (2002) 682-695
    • (2002) Proteins: Struct. Funct.Genet. , vol.48 , pp. 682-695
    • Krebs, W.G.1    Alexandrov, V.2    Wilson, C.A.3    Echols, N.4    Yu, H.5    Gerstein, M.6
  • 13
    • 0022555894 scopus 로고
    • Protein dynamics investigated by neutron diffraction
    • Kossiakoff A.A. Protein dynamics investigated by neutron diffraction. Methods Enzymol. 131 (1986) 433-447
    • (1986) Methods Enzymol. , vol.131 , pp. 433-447
    • Kossiakoff, A.A.1
  • 14
    • 0025037796 scopus 로고
    • Comparison of the dynamics of myoglobin in different crystal forms
    • Phillips G.N.J. Comparison of the dynamics of myoglobin in different crystal forms. Biophys. J. 57 (1990) 381-383
    • (1990) Biophys. J. , vol.57 , pp. 381-383
    • Phillips, G.N.J.1
  • 16
    • 0035478585 scopus 로고    scopus 로고
    • Macromolecular crowding: obvious but underappreciated
    • Ellis R.J. Macromolecular crowding: obvious but underappreciated. Trends Biochem. Sci. 26 (2001) 597-604
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 597-604
    • Ellis, R.J.1
  • 17
    • 0027310845 scopus 로고
    • The control of protein stability and association by weak interactions with water: how do solvents affect these processes?
    • Timasheff S.N. The control of protein stability and association by weak interactions with water: how do solvents affect these processes?. Annu. Rev. Biophys. Biomol. Struct. 22 (1993) 67-97
    • (1993) Annu. Rev. Biophys. Biomol. Struct. , vol.22 , pp. 67-97
    • Timasheff, S.N.1
  • 18
    • 0037470574 scopus 로고    scopus 로고
    • Effect of dextran on protein stability and conformation attributed to macromolecular crowding
    • Sasahara K., McPhie P., and Minton A.P. Effect of dextran on protein stability and conformation attributed to macromolecular crowding. J. Mol. Biol. 326 (2003) 1227-1237
    • (2003) J. Mol. Biol. , vol.326 , pp. 1227-1237
    • Sasahara, K.1    McPhie, P.2    Minton, A.P.3
  • 19
    • 16344389134 scopus 로고    scopus 로고
    • Molecular crowding enhances native state stability and refolding rates of globular proteins
    • Cheung M.S., Klimov D., and Thirumalai D. Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc. Natl. Acad. Sci. USA 102 (2005) 4753-4758
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 4753-4758
    • Cheung, M.S.1    Klimov, D.2    Thirumalai, D.3
  • 20
    • 33646536078 scopus 로고    scopus 로고
    • The influence of macromolecular crowding on HIV-1 protease internal dynamics
    • Minh D.D., Chang C.E., Trylska J., Tozzini V., and McCammon J.A. The influence of macromolecular crowding on HIV-1 protease internal dynamics. J. Am. Chem. Soc. 128 (2006) 6006-6007
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 6006-6007
    • Minh, D.D.1    Chang, C.E.2    Trylska, J.3    Tozzini, V.4    McCammon, J.A.5
  • 21
    • 0033572725 scopus 로고    scopus 로고
    • Effects of macromolecular crowding on protein folding and aggregation
    • van den Berg B., Ellis R.J., and Dobson C.M. Effects of macromolecular crowding on protein folding and aggregation. EMBO J. 18 (1999) 6927-6933
    • (1999) EMBO J. , vol.18 , pp. 6927-6933
    • van den Berg, B.1    Ellis, R.J.2    Dobson, C.M.3
  • 22
    • 0034254189 scopus 로고    scopus 로고
    • Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell
    • van den Berg B., Wain R., Dobson C., and Ellis R.J. Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell. EMBO J. 19 (2000) 3870-3875
    • (2000) EMBO J. , vol.19 , pp. 3870-3875
    • van den Berg, B.1    Wain, R.2    Dobson, C.3    Ellis, R.J.4
  • 23
    • 0041931122 scopus 로고    scopus 로고
    • Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges
    • Hall D., and Minton A.P. Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges. Biochim. Biophys. Acta 1649 (2003) 127-139
    • (2003) Biochim. Biophys. Acta , vol.1649 , pp. 127-139
    • Hall, D.1    Minton, A.P.2
  • 24
    • 0037907487 scopus 로고    scopus 로고
    • Effects of sucrose on conformational equilibria and fluctuations within the native-state ensemble of proteins
    • Kim Y.S., Jones L.S., Dong A., Kendrick B.S., Chang B.S., Manning M.C., et al. Effects of sucrose on conformational equilibria and fluctuations within the native-state ensemble of proteins. Protein Sci. 12 (2003) 1252-1261
    • (2003) Protein Sci. , vol.12 , pp. 1252-1261
    • Kim, Y.S.1    Jones, L.S.2    Dong, A.3    Kendrick, B.S.4    Chang, B.S.5    Manning, M.C.6
  • 25
    • 5444263418 scopus 로고    scopus 로고
    • Wide-angle X-ray solution scattering as a probe of ligand-induced conformational changes in proteins
    • Fischetti R.F., Rodi D.J., Gore D.B., and Makowski L. Wide-angle X-ray solution scattering as a probe of ligand-induced conformational changes in proteins. Chem. Biol. 11 (2004) 1431-1443
    • (2004) Chem. Biol. , vol.11 , pp. 1431-1443
    • Fischetti, R.F.1    Rodi, D.J.2    Gore, D.B.3    Makowski, L.4
  • 26
    • 0037188386 scopus 로고    scopus 로고
    • Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C
    • Tiede D.M., Zhang R., and Siefert S. Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C. Biochemistry 41 (2002) 6605-6614
    • (2002) Biochemistry , vol.41 , pp. 6605-6614
    • Tiede, D.M.1    Zhang, R.2    Siefert, S.3
  • 27
    • 0036657545 scopus 로고    scopus 로고
    • Structural hierarchy of several proteins observed by wide-angle solution scattering
    • Hirai M., Iwase H., Hayakawa T., Miura K., and Inoue K. Structural hierarchy of several proteins observed by wide-angle solution scattering. J. Synchotron Radiat. 9 (2002) 202-205
    • (2002) J. Synchotron Radiat. , vol.9 , pp. 202-205
    • Hirai, M.1    Iwase, H.2    Hayakawa, T.3    Miura, K.4    Inoue, K.5
  • 28
    • 0141571313 scopus 로고    scopus 로고
    • High-resolution wide-angle X-ray scattering of protein solutions: effect of beam dose on protein integrity
    • Fischetti R.F., Rodi D.J., Mirza A., Irving T.C., Kondrashkina E., and Makowski L. High-resolution wide-angle X-ray scattering of protein solutions: effect of beam dose on protein integrity. J. Synchrotron Radiat. 10 (2003) 398-404
    • (2003) J. Synchrotron Radiat. , vol.10 , pp. 398-404
    • Fischetti, R.F.1    Rodi, D.J.2    Mirza, A.3    Irving, T.C.4    Kondrashkina, E.5    Makowski, L.6
  • 29
    • 7444260852 scopus 로고    scopus 로고
    • Structural characterization of modular supramolecular architectures in solution
    • Tiede D.M., Zhang R., Chen L.X., Yu L., and Lindsey J.S. Structural characterization of modular supramolecular architectures in solution. J .Am. Chem. Soc. 126 (2004) 14054-14062
    • (2004) J .Am. Chem. Soc. , vol.126 , pp. 14054-14062
    • Tiede, D.M.1    Zhang, R.2    Chen, L.X.3    Yu, L.4    Lindsey, J.S.5
  • 30
    • 33644861376 scopus 로고    scopus 로고
    • X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation
    • Zuo X., Cui G., Mertz K.M.J., Zhang L., Lewis F.D., and Tiede D.M. X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. Proc. Natl. Acad. Sci. USA 103 (2006) 3534-3539
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 3534-3539
    • Zuo, X.1    Cui, G.2    Mertz, K.M.J.3    Zhang, L.4    Lewis, F.D.5    Tiede, D.M.6
  • 32
    • 0018863001 scopus 로고
    • Recent developments in solution X-ray scattering
    • Luzzati V., and Tardieu A. Recent developments in solution X-ray scattering. Annu. Rev. Biophys. Bioeng. 9 (1980) 1-29
    • (1980) Annu. Rev. Biophys. Bioeng. , vol.9 , pp. 1-29
    • Luzzati, V.1    Tardieu, A.2
  • 34
    • 33646931175 scopus 로고    scopus 로고
    • NMR residual dipolar couplings as probes of biomolecular dynamics
    • Tolman J.R., and Ruan K. NMR residual dipolar couplings as probes of biomolecular dynamics. Chem. Rev. 106 (2006) 1720-1736
    • (2006) Chem. Rev. , vol.106 , pp. 1720-1736
    • Tolman, J.R.1    Ruan, K.2
  • 36
    • 0035925113 scopus 로고    scopus 로고
    • Structural and dynamic analysis of residual dipolar coupling data for proteins
    • Tolman J.R., Al-Hashimi H.M., Kay L.E., and Prestegard J.H. Structural and dynamic analysis of residual dipolar coupling data for proteins. J. Am. Chem. Soc. 123 (2001) 1416-1424
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 1416-1424
    • Tolman, J.R.1    Al-Hashimi, H.M.2    Kay, L.E.3    Prestegard, J.H.4
  • 37
    • 4143079167 scopus 로고    scopus 로고
    • Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements
    • Clore G.M., and Schwieters C.D. Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry 43 (2004) 10678-10691
    • (2004) Biochemistry , vol.43 , pp. 10678-10691
    • Clore, G.M.1    Schwieters, C.D.2
  • 40
    • 0034821018 scopus 로고    scopus 로고
    • Cross-correlated chemical shift modulation: a signature of slow internal motions in proteins
    • Fruh D., Tolman J.R., Bodenhausen G., and Zwahlen C. Cross-correlated chemical shift modulation: a signature of slow internal motions in proteins. J. Am. Chem. Soc. 123 (2001) 4810-4816
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 4810-4816
    • Fruh, D.1    Tolman, J.R.2    Bodenhausen, G.3    Zwahlen, C.4
  • 41
    • 1242331371 scopus 로고    scopus 로고
    • Evidence of slow motions by cross-correlated chemical shift modulation in deuterated and protonated proteins
    • Vugmeyster L., Perazzolo C., Wist J., Frueh D., and Bodenhausen G. Evidence of slow motions by cross-correlated chemical shift modulation in deuterated and protonated proteins. J. Biomol. NMR 28 (2004) 173-177
    • (2004) J. Biomol. NMR , vol.28 , pp. 173-177
    • Vugmeyster, L.1    Perazzolo, C.2    Wist, J.3    Frueh, D.4    Bodenhausen, G.5
  • 42
    • 0030990422 scopus 로고    scopus 로고
    • Are proteins even floppier than we thought?
    • Bax A., and Tjandra N. Are proteins even floppier than we thought?. Nature Struct. Biol. 4 (1997) 254-256
    • (1997) Nature Struct. Biol. , vol.4 , pp. 254-256
    • Bax, A.1    Tjandra, N.2
  • 43
    • 34250178787 scopus 로고    scopus 로고
    • A comparative NKR study of the polypeptide backbone dynamics of hemoglobin in the deoxy and carbonmoxy forms
    • Song X.-J., Yuan Y., Simplaceanu V., Sahu S.C., Ho N.T., and Ho C. A comparative NKR study of the polypeptide backbone dynamics of hemoglobin in the deoxy and carbonmoxy forms. Biochemistry 46 (2007) 6795-6803
    • (2007) Biochemistry , vol.46 , pp. 6795-6803
    • Song, X.-J.1    Yuan, Y.2    Simplaceanu, V.3    Sahu, S.C.4    Ho, N.T.5    Ho, C.6
  • 44
    • 0032311227 scopus 로고    scopus 로고
    • Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion
    • Minton A.P. Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. Methods Enzymol. 295 (1998) 127-149
    • (1998) Methods Enzymol. , vol.295 , pp. 127-149
    • Minton, A.P.1
  • 45
    • 2442595947 scopus 로고    scopus 로고
    • Dynamics of human serum albumin studied by acoustic relaxation spectroscopy
    • Hushcha T., Kaatze U., and Peytcheva A. Dynamics of human serum albumin studied by acoustic relaxation spectroscopy. Biopolymers 74 (2004) 32-36
    • (2004) Biopolymers , vol.74 , pp. 32-36
    • Hushcha, T.1    Kaatze, U.2    Peytcheva, A.3
  • 47
    • 19944427743 scopus 로고    scopus 로고
    • The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source
    • Fischetti R., Stepanov S., Rosenbaum G., Barrea R., Black E., Gore D., et al. The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source. J. Synchrotron Radiat. 11 (2004) 399-405
    • (2004) J. Synchrotron Radiat. , vol.11 , pp. 399-405
    • Fischetti, R.1    Stepanov, S.2    Rosenbaum, G.3    Barrea, R.4    Black, E.5    Gore, D.6
  • 48
    • 36549026975 scopus 로고    scopus 로고
    • Hammersley, A. P. (1997). FIT2D: an introduction and overview. ESRF Internal Report, ESRF97HA02.
  • 49
    • 36549045668 scopus 로고    scopus 로고
    • Hammersley, A. P. (1998). FIT2D V9.129 reference manual V3.1. ESRF Internal Report, ESRF98HA01.
  • 50
    • 0029695129 scopus 로고    scopus 로고
    • Two-dimensional detector software: from real detector to idealised image or two-theta scan
    • Hammersley A.P., Svensson S.O., Hanfland M., Fitch A.N., and Hausermann D. Two-dimensional detector software: from real detector to idealised image or two-theta scan. High Press. Res. 14 (1996) 235-248
    • (1996) High Press. Res. , vol.14 , pp. 235-248
    • Hammersley, A.P.1    Svensson, S.O.2    Hanfland, M.3    Fitch, A.N.4    Hausermann, D.5
  • 51
    • 0029185933 scopus 로고
    • CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
    • Svergun D., Barferato C., and Koch M.H.J. CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallog. 28 (1995) 768-773
    • (1995) J. Appl. Crystallog. , vol.28 , pp. 768-773
    • Svergun, D.1    Barferato, C.2    Koch, M.H.J.3
  • 52
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.