메뉴 건너뛰기




Volumn 330, Issue 1, 2003, Pages 129-135

Conformational flexibility of pyruvate dehydrogenase complexes: A computational analysis by quantized elastic deformational model

Author keywords

Conformational flexibility; Elastic deformation; Elastic network; Large conformational change; Normal mode analysis

Indexed keywords

PYRUVATE DEHYDROGENASE; ACYLTRANSFERASE; DIHYDROLIPOAMIDE ACETYLTRANSFERASE; PYRUVATE DEHYDROGENASE COMPLEX;

EID: 0037666985     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00555-2     Document Type: Article
Times cited : (33)

References (32)
  • 1
    • 0035914303 scopus 로고    scopus 로고
    • A trial of research from lipoic acid to alpha-keto acid dehydrogenase complexes
    • Reed L.J. A trial of research from lipoic acid to alpha-keto acid dehydrogenase complexes. J. Biol. Chem. 276:2001;38329-38336.
    • (2001) J. Biol. Chem. , vol.276 , pp. 38329-38336
    • Reed, L.J.1
  • 2
    • 0025370816 scopus 로고
    • Structure-function relationships in dihydrolipoamide acyltransferases
    • Reed L.J., Hackert M.L. Structure-function relationships in dihydrolipoamide acyltransferases. J. Biol. Chem. 265:1990;8971-8974.
    • (1990) J. Biol. Chem. , vol.265 , pp. 8971-8974
    • Reed, L.J.1    Hackert, M.L.2
  • 3
    • 0033790516 scopus 로고    scopus 로고
    • Swinging arms and swinging domains in multifunctional enzymes: Catalytic machines for multistep reactions
    • Perham R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69:2000;961-1004.
    • (2000) Annu. Rev. Biochem. , vol.69 , pp. 961-1004
    • Perham, R.N.1
  • 4
    • 0025221771 scopus 로고
    • Molecular biology and biochemistry of pyruvate dehydrogenase complexes
    • Patel M.S., Roche T.E. Molecular biology and biochemistry of pyruvate dehydrogenase complexes. FASEB J. 4:1990;3224-3233.
    • (1990) FASEB J. , vol.4 , pp. 3224-3233
    • Patel, M.S.1    Roche, T.E.2
  • 5
    • 0024954386 scopus 로고
    • Structure, expression, and protein engineering of the pyruvate dehydrogenase complex of Escherichia coli
    • Guest J.R., Angier S.J., Russell G.C. Structure, expression, and protein engineering of the pyruvate dehydrogenase complex of Escherichia coli. Ann. N.Y. Acad. Sci. 573:1989;76-99.
    • (1989) Ann. N.Y. Acad. Sci. , vol.573 , pp. 76-99
    • Guest, J.R.1    Angier, S.J.2    Russell, G.C.3
  • 7
    • 0032563138 scopus 로고    scopus 로고
    • Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex
    • Knapp J.E., Mitchell D.T., Yazdi M.A., Ernst S.R., Reed L.J., Hackert M.L. Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex. J. Mol. Biol. 280:1998;655-668.
    • (1998) J. Mol. Biol. , vol.280 , pp. 655-668
    • Knapp, J.E.1    Mitchell, D.T.2    Yazdi, M.A.3    Ernst, S.R.4    Reed, L.J.5    Hackert, M.L.6
  • 8
    • 0033573917 scopus 로고    scopus 로고
    • Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes
    • Izard T., Aevarsson A., Allen M.D., Westphal A.H., Perham R.N., de Kok A., Hol W.G. Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes. Proc. Natl Acad. Sci. USA. 96:1999;1240-1245.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 1240-1245
    • Izard, T.1    Aevarsson, A.2    Allen, M.D.3    Westphal, A.H.4    Perham, R.N.5    De Kok, A.6    Hol, W.G.7
  • 9
    • 0026476564 scopus 로고
    • Three-dimensional structure of the truncated core of the Saccharomyces cerevisiae pyruvate dehydrogenase complex determined from negative stain and cryoelectron microscopy images
    • Stoops J.K., Baker T.S., Schroeter J.P., Kolodziej S.J., Niu X.D., Reed L.J. Three-dimensional structure of the truncated core of the Saccharomyces cerevisiae pyruvate dehydrogenase complex determined from negative stain and cryoelectron microscopy images. J. Biol. Chem. 267:1992;24769-24775.
    • (1992) J. Biol. Chem. , vol.267 , pp. 24769-24775
    • Stoops, J.K.1    Baker, T.S.2    Schroeter, J.P.3    Kolodziej, S.J.4    Niu, X.D.5    Reed, L.J.6
  • 10
    • 0031041382 scopus 로고    scopus 로고
    • On the unique structural organization of the Saccharomyces cerevisiae pyruvate dehydrogenase complex
    • Stoops J.K., Cheng R.H., Yazdi M.A., Maeng C.Y., Schroeter J.P., Klueppelberg U., et al. On the unique structural organization of the Saccharomyces cerevisiae pyruvate dehydrogenase complex. J. Biol. Chem. 272:1997;5757-5764.
    • (1997) J. Biol. Chem. , vol.272 , pp. 5757-5764
    • Stoops, J.K.1    Cheng, R.H.2    Yazdi, M.A.3    Maeng, C.Y.4    Schroeter, J.P.5    Klueppelberg, U.6
  • 11
    • 0035877764 scopus 로고    scopus 로고
    • Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy. The "breathing" core and its functional relationship to protein dynamics
    • Zhou Z.H., Liao W., Cheng R.H., Lawson J.E., McCarthy D.B., Reed L.J., Stoops J.K. Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy. The "breathing" core and its functional relationship to protein dynamics. J. Biol. Chem. 276:2001;21704-21713.
    • (2001) J. Biol. Chem. , vol.276 , pp. 21704-21713
    • Zhou, Z.H.1    Liao, W.2    Cheng, R.H.3    Lawson, J.E.4    McCarthy, D.B.5    Reed, L.J.6    Stoops, J.K.7
  • 12
    • 0035909958 scopus 로고    scopus 로고
    • The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes
    • Zhou Z.H., McCarthy D.B., O'Connor C.M., Reed L.J., Stoops J.K. The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes. Proc. Natl Acad. Sci. USA. 98:2001;14802-14807.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 14802-14807
    • Zhou, Z.H.1    McCarthy, D.B.2    O'Connor, C.M.3    Reed, L.J.4    Stoops, J.K.5
  • 13
    • 0001031179 scopus 로고
    • Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
    • Brooks C.L. III, Karplus M., Pettitt B.M. Proteins: a theoretical perspective of dynamics, structure, and thermodynamics. Advan. Chem. Phys. 71:1988;1-249.
    • (1988) Advan. Chem. Phys. , vol.71 , pp. 1-249
    • Brooks C.L. III1    Karplus, M.2    Pettitt, B.M.3
  • 15
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino-acid sequence and atomic coordinates
    • Ming D., Kong Y., Lambert M., Huang Z., Ma J. How to describe protein motion without amino-acid sequence and atomic coordinates. Proc. Natl Acad. Sci. USA. 99:2002;8620-8625.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 8620-8625
    • Ming, D.1    Kong, Y.2    Lambert, M.3    Huang, Z.4    Ma, J.5
  • 16
    • 0036382958 scopus 로고    scopus 로고
    • Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
    • Tama F., Wriggers W., Brooks C.L. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 321:2002;297-305.
    • (2002) J. Mol. Biol. , vol.321 , pp. 297-305
    • Tama, F.1    Wriggers, W.2    Brooks, C.L.3
  • 17
    • 0037062479 scopus 로고    scopus 로고
    • Domain movements in human fatty acid synthase by quantized elastic deformational model
    • Ming D., Kong Y., Wakil S.J., Brink J., Ma J. Domain movements in human fatty acid synthase by quantized elastic deformational model. Proc. Natl Acad. Sci. USA. 99:2002;7895-7899.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 7895-7899
    • Ming, D.1    Kong, Y.2    Wakil, S.J.3    Brink, J.4    Ma, J.5
  • 18
    • 0037436340 scopus 로고    scopus 로고
    • Mega-dalton biomolecular motion captured from electron microscopy reconstructions
    • Chacon P., Tama F., Wriggers W. Mega-dalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol. 326:2003;485-492.
    • (2003) J. Mol. Biol. , vol.326 , pp. 485-492
    • Chacon, P.1    Tama, F.2    Wriggers, W.3
  • 19
    • 0344091553 scopus 로고    scopus 로고
    • Motions and negative cooperativity between p97 domains revealed by cryoelectron microscopy and quantized elastic deformational model
    • Beuron F., Flynn T.C., Ma J., Kondo H., Zhang X., Freemont P.S. Motions and negative cooperativity between p97 domains revealed by cryoelectron microscopy and quantized elastic deformational model. J. Mol. Biol. 327:2003;619-629.
    • (2003) J. Mol. Biol. , vol.327 , pp. 619-629
    • Beuron, F.1    Flynn, T.C.2    Ma, J.3    Kondo, H.4    Zhang, X.5    Freemont, P.S.6
  • 22
    • 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
  • 23
    • 0036307741 scopus 로고    scopus 로고
    • The mechanism and pathway of ph induced swelling in cowpea chlorotic mottle virus
    • Tama F., Brooks C.L. III. The mechanism and pathway of ph induced swelling in cowpea chlorotic mottle virus. J. Mol. Biol. 318:2002;733-747.
    • (2002) J. Mol. Biol. , vol.318 , pp. 733-747
    • Tama, F.1    Brooks C.L. III2
  • 24
    • 0027632248 scopus 로고
    • "Neural-gas" network for vector quantization and its application to time-series prediction
    • Martinetz T.M., Berkovich S.G., Schulten K.J. "Neural-gas" network for vector quantization and its application to time-series prediction. IEEE Trans. Neural Networks. 4:1993;558-569.
    • (1993) IEEE Trans. Neural Networks , vol.4 , pp. 558-569
    • Martinetz, T.M.1    Berkovich, S.G.2    Schulten, K.J.3
  • 25
    • 0032545184 scopus 로고    scopus 로고
    • Self-organizing neural networks bridge the biomolecular resolution gap
    • Wriggers W., Milligan R.A., Schulten K., McCammon J.A. Self-organizing neural networks bridge the biomolecular resolution gap. J. Mol. Biol. 284:1998;1247-1254.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1247-1254
    • Wriggers, W.1    Milligan, R.A.2    Schulten, K.3    McCammon, J.A.4
  • 26
    • 0037079578 scopus 로고    scopus 로고
    • Dynamic of large proteins through hierarchical levels of coarse-grained structures
    • Doruker P., Jernigan R.L., Bahar I. Dynamic of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23:2002;119-127.
    • (2002) J. Comput. Chem. , vol.23 , pp. 119-127
    • Doruker, P.1    Jernigan, R.L.2    Bahar, I.3
  • 27
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1996;1905-1908.
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 28
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I., Atilgan A.R., Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:1997;173-181.
    • (1997) Fold. Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 29
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks B.R., Janezic D., Karplus M. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 16:1995;1522-1542.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 30
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F., Sanejouand Y.H. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:2001;1-6.
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 31
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins: Struct. Funct. Genet. 33:1998;417-429.
    • (1998) Proteins: Struct. Funct. Genet. , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 32
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.