메뉴 건너뛰기




Volumn 36, Issue 4, 1999, Pages 425-435

Structural principles governing domain motions in proteins

Author keywords

Dynamic domains; Hinge axis; Hinge bending; X ray conformers

Indexed keywords

ADENYLATE KINASE; ALCOHOL DEHYDROGENASE; ASPARTATE AMINOTRANSFERASE; CALMODULIN; CITRATE SYNTHASE; CYCLIC AMP DEPENDENT PROTEIN KINASE; DIPHTHERIA TOXIN; DNA POLYMERASE; ENDOTHIAPEPSIN; FORMATE DEHYDROGENASE; GLUTAMATE DEHYDROGENASE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HEXOKINASE; IMMUNOGLOBULIN; INITIATION FACTOR; LACTOFERRIN; LYSOZYME; MALTODEXTRIN;

EID: 0032769661     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990901)36:4<425::AID-PROT6>3.0.CO;2-S     Document Type: Article
Times cited : (130)

References (51)
  • 1
    • 0018802524 scopus 로고
    • Space-filling models of kinase clefts and conformational change
    • Anderson CM, Zucker FH, Steitz T. Space-filling models of kinase clefts and conformational change. Science 1979;204:375-380.
    • (1979) Science , vol.204 , pp. 375-380
    • Anderson, C.M.1    Zucker, F.H.2    Steitz, T.3
  • 2
    • 0029150760 scopus 로고
    • Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme
    • Zhang X, Wozniak JA, Matthews BW. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J Mol Biol 1995;250:527-552.
    • (1995) J Mol Biol , vol.250 , pp. 527-552
    • Zhang, X.1    Wozniak, J.A.2    Matthews, B.W.3
  • 3
    • 0025047629 scopus 로고
    • A mutant T4 lysozyme displays five different crystal conformations
    • Faber HR, Matthews BW. A mutant T4 lysozyme displays five different crystal conformations. Nature 1990;348:263-266.
    • (1990) Nature , vol.348 , pp. 263-266
    • Faber, H.R.1    Matthews, B.W.2
  • 4
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein M, Lesk AM, Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry 1994;33:6739-6749.
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 5
    • 0030883755 scopus 로고    scopus 로고
    • Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
    • Wriggers W, Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 1997;29:1-14.
    • (1997) Proteins , vol.29 , pp. 1-14
    • Wriggers, W.1    Schulten, K.2
  • 6
  • 7
    • 0032006209 scopus 로고    scopus 로고
    • Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
    • Hayward S, Berendsen HJC. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 1998;30:144-154.
    • (1998) Proteins , vol.30 , pp. 144-154
    • Hayward, S.1    Berendsen, H.J.C.2
  • 9
    • 0032080528 scopus 로고    scopus 로고
    • Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data
    • de Groot BL, Hayward S, van Aalten DMF, Berendsen HJC. Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data. Proteins 1998;31:116-127.
    • (1998) Proteins , vol.31 , pp. 116-127
    • De Groot, B.L.1    Hayward, S.2    Van Aalten, D.M.F.3    Berendsen, H.J.C.4
  • 10
    • 0026679890 scopus 로고
    • The three-dimensional structure of an intact monoclonal antibody for canine lymphoma
    • Harris LJ, Larson SB, Hasel KW, Day J, Greenwood A, McPherson A. The three-dimensional structure of an intact monoclonal antibody for canine lymphoma. Nature 1992;360:369-372.
    • (1992) Nature , vol.360 , pp. 369-372
    • Harris, L.J.1    Larson, S.B.2    Hasel, K.W.3    Day, J.4    Greenwood, A.5    McPherson, A.6
  • 11
    • 0027769953 scopus 로고
    • Conformational flexibility in glutamate dehydrogenase: Role of water in substrate recognition and catalysis
    • Stillman TJ, Baker BJ, Britton KL, Rice DW. Conformational flexibility in glutamate dehydrogenase: role of water in substrate recognition and catalysis. J Mol Biol 1993;234:1131-1139.
    • (1993) J Mol Biol , vol.234 , pp. 1131-1139
    • Stillman, T.J.1    Baker, B.J.2    Britton, K.L.3    Rice, D.W.4
  • 13
    • 0026575572 scopus 로고
    • Crystal and molecular structure of human annexin V after refinement: Implications for structure, membrane binding and ion channel formation of the annexin family of proteins
    • Huber R, Berendes R, Burger A, et al. Crystal and molecular structure of human annexin V after refinement: implications for structure, membrane binding and ion channel formation of the annexin family of proteins. J Mol Biol 1992;223:683-704.
    • (1992) J Mol Biol , vol.223 , pp. 683-704
    • Huber, R.1    Berendes, R.2    Burger, A.3
  • 14
    • 0030888546 scopus 로고    scopus 로고
    • Model free methods to analyze domain motions in proteins from simulation. A comparison of a normal mode analysis and a molecular dynamics simulation of lysozyme
    • Hayward S, Kitao A, Berendsen HJC. Model free methods to analyze domain motions in proteins from simulation. A comparison of a normal mode analysis and a molecular dynamics simulation of lysozyme. Proteins 1997;27:425-437.
    • (1997) Proteins , vol.27 , pp. 425-437
    • Hayward, S.1    Kitao, A.2    Berendsen, H.J.C.3
  • 16
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 17
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990;8:52-56.
    • (1990) J Mol Graph , vol.8 , pp. 52-56
    • Vriend, G.1
  • 18
    • 0023661228 scopus 로고
    • Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 resolution
    • Weber IT, Steitz TA. Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 resolution. J Mol Biol 1987;198:311-326.
    • (1987) J Mol Biol , vol.198 , pp. 311-326
    • Weber, I.T.1    Steitz, T.A.2
  • 19
    • 0026751404 scopus 로고
    • X-ray structure refinement and comparison of three forms of mitochondrial aspartate-aminotransferase
    • McPhalen CA, Vincent MG, Jansonius JN. X-ray structure refinement and comparison of three forms of mitochondrial aspartate-aminotransferase. J Mol Biol 1992;225:495-517.
    • (1992) J Mol Biol , vol.225 , pp. 495-517
    • McPhalen, C.A.1    Vincent, M.G.2    Jansonius, J.N.3
  • 20
    • 0023717499 scopus 로고
    • Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from bacillus stearothermophilus
    • Skarzynski T, Wonacott AJ. Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from bacillus stearothermophilus. J Mol Biol 1988;203:1097-1118.
    • (1988) J Mol Biol , vol.203 , pp. 1097-1118
    • Skarzynski, T.1    Wonacott, A.J.2
  • 21
    • 0030729838 scopus 로고    scopus 로고
    • An extensively modified versiton of MOLSCRIPT that includes greatly enhanced coloring capabilities
    • Esnoug RM. An extensively modified versiton of MOLSCRIPT that includes greatly enhanced coloring capabilities. J Mol Graph 1997;15:132-134.
    • (1997) J Mol Graph , vol.15 , pp. 132-134
    • Esnoug, R.M.1
  • 22
    • 0028057108 scopus 로고
    • Raster3D Version 2.0. A program for photorealistic molecular graphics
    • Merrit EA, Murphy MEP. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D 1994;50:869-873.
    • (1994) Acta Crystallogr D , vol.50 , pp. 869-873
    • Merrit, E.A.1    Murphy, M.E.P.2
  • 23
    • 0028338283 scopus 로고
    • The closed conformation of a highly flexible protein: The structure of E. Coli adenylate kinase with bound AMP and AMPNP
    • Berry MB, Meador B, Bilderback T, Liang P, Glaser M, Phillips JGN. The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPNP. Proteins 1994;19:183-198.
    • (1994) Proteins , vol.19 , pp. 183-198
    • Berry, M.B.1    Meador, B.2    Bilderback, T.3    Liang, P.4    Glaser, M.5    Phillips, J.G.N.6
  • 24
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
    • Mueller CW, Schlauderer GJ, Reinstein J, Schulz GE. Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure 1996;4:147-156.
    • (1996) Structure , vol.4 , pp. 147-156
    • Mueller, C.W.1    Schlauderer, G.J.2    Reinstein, J.3    Schulz, G.E.4
  • 25
    • 0019880506 scopus 로고
    • Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 A resolution
    • Eklund J, Samaha JP, Wallen L, Branden CI, Akeson A, Jones TA. Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 A resolution. J Mol Biol 1981;146:561-587.
    • (1981) J Mol Biol , vol.146 , pp. 561-587
    • Eklund, J.1    Samaha, J.P.2    Wallen, L.3    Branden, C.I.4    Akeson, A.5    Jones, T.A.6
  • 26
    • 0021099424 scopus 로고
    • Three-dimensional structure of isonicotinimidylated liver alcohol dehydrogenase
    • Plapp BV, Eklund H, Jones TA, Branden C. Three-dimensional structure of isonicotinimidylated liver alcohol dehydrogenase. J Biol Chem 1983;258:5537-5547.
    • (1983) J Biol Chem , vol.258 , pp. 5537-5547
    • Plapp, B.V.1    Eklund, H.2    Jones, T.A.3    Branden, C.4
  • 28
    • 0000127673 scopus 로고
    • Sowadski JM. 2.2Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor
    • Zheng J, Trafney EA, Knighton DR, Nguyen HX, Taylor SS, Ten Eyck LF, Sowadski JM. 2.2Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor. Acta Crystallogr D 1993;49: 362-364.
    • (1993) Acta Crystallogr D , vol.49 , pp. 362-364
    • Zheng, J.1    Trafney, E.A.2    Knighton, D.R.3    Nguyen, H.X.4    Taylor, S.S.5    Ten Eyck, L.F.6
  • 29
    • 0001328416 scopus 로고
    • Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and inhibitor peptide displays an open conformation
    • Karlsson R, Zheng JH, Xuong NH, Taylor SS, Sowadski JM. Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and inhibitor peptide displays an open conformation. Acta Crystallogr D 1993;49:381-388.
    • (1993) Acta Crystallogr D , vol.49 , pp. 381-388
    • Karlsson, R.1    Zheng, J.H.2    Xuong, N.H.3    Taylor, S.S.4    Sowadski, J.M.5
  • 31
    • 0026794065 scopus 로고
    • Target enzyme recognition by calmodulin: 2.4Å structure of a calmodulin-peptide complex
    • Meador WE, Means AR, Quiocho FA. Target enzyme recognition by calmodulin: 2.4Å structure of a calmodulin-peptide complex. Science 1992;257:1251-1255.
    • (1992) Science , vol.257 , pp. 1251-1255
    • Meador, W.E.1    Means, A.R.2    Quiocho, F.A.3
  • 32
    • 0020483375 scopus 로고
    • Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 angstroms resolution
    • Remington S, Wiegand G, Huber R. Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 angstroms resolution. J Mol Biol 1982;158:111-152.
    • (1982) J Mol Biol , vol.158 , pp. 111-152
    • Remington, S.1    Wiegand, G.2    Huber, R.3
  • 33
    • 0028077637 scopus 로고
    • Refined structure of dimeric diptheria toxin at 2.0Å resolution
    • Bennett MR, Choe S, Eisenberg D. Refined structure of dimeric diptheria toxin at 2.0Å resolution. Prot Sci 1994;3:1444-1463.
    • (1994) Prot Sci , vol.3 , pp. 1444-1463
    • Bennett, M.R.1    Choe, S.2    Eisenberg, D.3
  • 34
    • 0028077639 scopus 로고
    • Refined structure of monomeric diptheria toxin at 2.3Å resolution
    • Bennett MR, Eisenberg D. Refined structure of monomeric diptheria toxin at 2.3Å resolution. Prot Sci 1994;3:1464-1475.
    • (1994) Prot Sci , vol.3 , pp. 1464-1475
    • Bennett, M.R.1    Eisenberg, D.2
  • 35
    • 0024438910 scopus 로고
    • High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: Analysis of the inhibitor binding and description of the rigid-body shift in the enzyme
    • Sali A, Veerapandian B, Cooper JB, Foundling SI, Hoover DJ, Blundell TL. High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: analysis of the inhibitor binding and description of the rigid-body shift in the enzyme. EMBO J 1989;8:2179-2188.
    • (1989) EMBO J , vol.8 , pp. 2179-2188
    • Sali, A.1    Veerapandian, B.2    Cooper, J.B.3    Foundling, S.I.4    Hoover, D.J.5    Blundell, T.L.6
  • 36
    • 0021767550 scopus 로고
    • The active site of aspartic proteinases
    • Pearl L, Blundell T. The active site of aspartic proteinases. FEBS Lett 1984;174:96-101.
    • (1984) FEBS Lett , vol.174 , pp. 96-101
    • Pearl, L.1    Blundell, T.2
  • 38
    • 0023644310 scopus 로고
    • Structure of hologlyceraldehyde-3-phosphate dehydrogenase from bacillus stearothermophilus at 1.8Å resolution
    • Skarzynski T, Moody PCE, Wonacott AJ. Structure of hologlyceraldehyde-3-phosphate dehydrogenase from bacillus stearothermophilus at 1.8Å resolution. J Mol Biol 1987;193:171-187.
    • (1987) J Mol Biol , vol.193 , pp. 171-187
    • Skarzynski, T.1    Moody, P.C.E.2    Wonacott, A.J.3
  • 39
    • 13244249836 scopus 로고
    • The structure of pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion pair networks in maintaining enzyme stability at extreme temperatures
    • Yip KSP, Stillman TJ, Britton KL, et al. The structure of pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion pair networks in maintaining enzyme stability at extreme temperatures. Structure 1995;3:1147-1158.
    • (1995) Structure , vol.3 , pp. 1147-1158
    • Yip, K.S.P.1    Stillman, T.J.2    Britton, K.L.3
  • 40
    • 0017807668 scopus 로고
    • Sequencing a protein by X-ray crystallography. II. Refinement of yeast hexokinase B coordinates and sequence at 2.1Å resolution
    • Anderson CM, Stenkamp RE, Steitz TA. Sequencing a protein by X-ray crystallography. II. Refinement of yeast hexokinase B coordinates and sequence at 2.1Å resolution. J Mol Biol 1978;123: 15-33.
    • (1978) J Mol Biol , vol.123 , pp. 15-33
    • Anderson, C.M.1    Stenkamp, R.E.2    Steitz, T.A.3
  • 41
    • 0000539364 scopus 로고
    • Glucose induced conformational change in yeast hexokinase
    • Benett WS Jr, Steitz TA. Glucose induced conformational change in yeast hexokinase. Proc Natl Acad Sci USA 1978;75:4848-4852.
    • (1978) Proc Natl Acad Sci USA , vol.75 , pp. 4848-4852
    • Benett W.S., Jr.1    Steitz, T.A.2
  • 42
    • 0025273624 scopus 로고
    • Apolactoferrin structure demonstrates ligand-induced conformational change in transferrins
    • Anderson BF, Baker HM, Norris GE, Rumball SV, Baker EN. Apolactoferrin structure demonstrates ligand-induced conformational change in transferrins. Nature 1990;344:784-787.
    • (1990) Nature , vol.344 , pp. 784-787
    • Anderson, B.F.1    Baker, H.M.2    Norris, G.E.3    Rumball, S.V.4    Baker, E.N.5
  • 43
    • 0027235488 scopus 로고
    • Three-dimensional structures of the periplasmic lysine/ arginine/ornithine-binding protein with and without a ligand
    • Oh B-H, Pandit J, Kang C-H, Nikaido K, Gokcen S, Ames GF-L, Kim S-H. Three-dimensional structures of the periplasmic lysine/ arginine/ornithine-binding protein with and without a ligand. J Biol Chem 1993;268:11348-11355.
    • (1993) J Biol Chem , vol.268 , pp. 11348-11355
    • Oh, B.-H.1    Pandit, J.2    Kang, C.-H.3    Nikaido, K.4    Gokcen, S.5    Ames, G.F.-L.6    Kim, S.-H.7
  • 44
    • 0026493924 scopus 로고
    • Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis
    • Sharff AJ, Rodseth LE, Spurlino JC, Quiocho FA. Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. Biochemistry 1992;31:10657-10663.
    • (1992) Biochemistry , vol.31 , pp. 10657-10663
    • Sharff, A.J.1    Rodseth, L.E.2    Spurlino, J.C.3    Quiocho, F.A.4
  • 45
    • 0025754301 scopus 로고
    • The 23Å resolution structure of the maltose-or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis
    • Spurlino JC, Lu G-Y, Quiocho FA. The 23Å resolution structure of the maltose-or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. J Biol Chem 1991;266: 5202-5219.
    • (1991) J Biol Chem , vol.266 , pp. 5202-5219
    • Spurlino, J.C.1    Lu, G.-Y.2    Quiocho, F.A.3
  • 46
    • 0024215739 scopus 로고
    • Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products
    • Shirakihara Y, Evans PR. Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products. J Mol Biol 1988;204:973-994.
    • (1988) J Mol Biol , vol.204 , pp. 973-994
    • Shirakihara, Y.1    Evans, P.R.2
  • 47
    • 0028049441 scopus 로고
    • Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP
    • Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J. Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science 1994;264:1891-1903.
    • (1994) Science , vol.264 , pp. 1891-1903
    • Pelletier, H.1    Sawaya, M.R.2    Kumar, A.3    Wilson, S.H.4    Kraut, J.5
  • 48
    • 0028136070 scopus 로고
    • Crystal structure of rat DNA polymerase beta: Evidence for a common polymerase mechanism
    • Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J. Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Science 1994;264:1930-1935.
    • (1994) Science , vol.264 , pp. 1930-1935
    • Sawaya, M.R.1    Pelletier, H.2    Kumar, A.3    Wilson, S.H.4    Kraut, J.5
  • 49
    • 0027250617 scopus 로고
    • Crystal structure of yeast TATA-binding protein and model for interaction with DNA
    • Chasman DI, Flaherty KM, Sharp PA, Kornberg RD. Crystal structure of yeast TATA-binding protein and model for interaction with DNA. Proc Natl Acad Sci USA 1993;90:8174-8178.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 8174-8178
    • Chasman, D.I.1    Flaherty, K.M.2    Sharp, P.A.3    Kornberg, R.D.4
  • 50
    • 0021112807 scopus 로고
    • Structure of tomato bushy stunt virus: The virus particle at 2.9 A resolution
    • Olson AJ, Bricogne G, Harrison SC. Structure of tomato bushy stunt virus: the virus particle at 2.9 A resolution. J Mol Biol 1983;171:61-93.
    • (1983) J Mol Biol , vol.171 , pp. 61-93
    • Olson, A.J.1    Bricogne, G.2    Harrison, S.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.