-
1
-
-
0032530836
-
A database of macromolecular motions
-
Gerstein M., Krebs W. A database of macromolecular motions. Nucleic Acids Res. 26:1998;4280-4290.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 4280-4290
-
-
Gerstein, M.1
Krebs, W.2
-
2
-
-
0037246863
-
MolMovDB: Analysis and visualization of conformational change and structural flexibility
-
Echols N., Milburn D., Gerstein M. MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 31:2003;478-482.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 478-482
-
-
Echols, N.1
Milburn, D.2
Gerstein, M.3
-
3
-
-
0034655949
-
The morph server: A standardized system for analyzing and visualizing macromolecular motions in a database framework
-
Krebs W.G., Gerstein M. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 28:2000;1665-1675.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1665-1675
-
-
Krebs, W.G.1
Gerstein, M.2
-
4
-
-
0021604916
-
Mechanisms of domain closure in proteins
-
Lesk A.M., Chothia C. Mechanisms of domain closure in proteins. J. Mol. Biol. 174:1984;175-191.
-
(1984)
J. Mol. Biol.
, vol.174
, pp. 175-191
-
-
Lesk, A.M.1
Chothia, C.2
-
5
-
-
0036073866
-
A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase
-
Ma J., Flynn T.C., Cui Q., Leslie A.G., Walker J.E., Karplus M. A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure. 10:2002;921-931.
-
(2002)
Structure
, vol.10
, pp. 921-931
-
-
Ma, J.1
Flynn, T.C.2
Cui, Q.3
Leslie, A.G.4
Walker, J.E.5
Karplus, M.6
-
6
-
-
0034665864
-
A dynamic model for the allosteric mechanism of GroEL
-
Ma J., Sigler P.B., Xu Z., Karplus M. A dynamic model for the allosteric mechanism of GroEL. J. Mol. Biol. 302:2000;303-313.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 303-313
-
-
Ma, J.1
Sigler, P.B.2
Xu, Z.3
Karplus, M.4
-
7
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama F., Valle M., Frank J., Brooks C.L. III Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. USA. 100:2003;9319-9323.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks III, C.L.4
-
9
-
-
0033579380
-
Structure of a transcribing T7 RNA polymerase initiation complex
-
Cheetham G.M., Steitz T.A. Structure of a transcribing T7 RNA polymerase initiation complex. Science. 286:1999;2305-2309.
-
(1999)
Science
, vol.286
, pp. 2305-2309
-
-
Cheetham, G.M.1
Steitz, T.A.2
-
11
-
-
0037112082
-
Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase
-
Crystal structure of the elongation phase reveals a massive conformational change, involving extensive remodeling of the N-terminal domains. This is one of the most drastic structural transitions observed.
-
Yin Y.W., Steitz T.A. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science. 298:2002;1387-1395 Crystal structure of the elongation phase reveals a massive conformational change, involving extensive remodeling of the N-terminal domains. This is one of the most drastic structural transitions observed.
-
(2002)
Science
, vol.298
, pp. 1387-1395
-
-
Yin, Y.W.1
Steitz, T.A.2
-
12
-
-
0343986407
-
Structure of the Mad2 spindle assembly checkpoint protein and its interaction with Cdc20
-
Luo X., Fang G., Coldiron M., Lin Y., Yu H., Kirschner M.W., Wagner G. Structure of the Mad2 spindle assembly checkpoint protein and its interaction with Cdc20. Nat. Struct. Biol. 7:2000;224-229.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 224-229
-
-
Luo, X.1
Fang, G.2
Coldiron, M.3
Lin, Y.4
Yu, H.5
Kirschner, M.W.6
Wagner, G.7
-
13
-
-
0036161468
-
The Mad2 spindle checkpoint protein undergoes similar major conformational changes upon binding to either Mad1 or Cdc20
-
Rearrangement of a beta sheet seen in structure, bound to small signaling peptide; NMR shows that other binding partners induce a similar change.
-
Luo X., Tang Z., Rizo J., Yu H. The Mad2 spindle checkpoint protein undergoes similar major conformational changes upon binding to either Mad1 or Cdc20. Mol. Cell. 9:2002;59-71 Rearrangement of a beta sheet seen in structure, bound to small signaling peptide; NMR shows that other binding partners induce a similar change.
-
(2002)
Mol. Cell.
, vol.9
, pp. 59-71
-
-
Luo, X.1
Tang, Z.2
Rizo, J.3
Yu, H.4
-
14
-
-
0035932465
-
Covalent inhibition revealed by the crystal structure of the caspase-8/p35 complex
-
Xu G., Cirilli M., Huang Y., Rich R.L., Myszka D.G., Wu H. Covalent inhibition revealed by the crystal structure of the caspase-8/p35 complex. Nature. 410:2001;494-497.
-
(2001)
Nature
, vol.410
, pp. 494-497
-
-
Xu, G.1
Cirilli, M.2
Huang, Y.3
Rich, R.L.4
Myszka, D.G.5
Wu, H.6
-
15
-
-
0025742788
-
Serpin tertiary structure transformation
-
Stein P., Chothia C. Serpin tertiary structure transformation. J. Mol. Biol. 221:1991;615-621.
-
(1991)
J. Mol. Biol.
, vol.221
, pp. 615-621
-
-
Stein, P.1
Chothia, C.2
-
16
-
-
0242516080
-
Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase
-
These structures, with and without the translocation inhibitor sordarin, indicate a domain movement that is associated with the ribosome-bound state, previously suggested by structures of the prokaryotic homolog EF-G.
-
Jorgensen R., Ortiz P.A., Carr-Schmid A., Nissen P., Kinzy T.G., Andersen G.R. Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase. Nat. Struct. Biol. 10:2003;379-385 These structures, with and without the translocation inhibitor sordarin, indicate a domain movement that is associated with the ribosome-bound state, previously suggested by structures of the prokaryotic homolog EF-G.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 379-385
-
-
Jorgensen, R.1
Ortiz, P.A.2
Carr-Schmid, A.3
Nissen, P.4
Kinzy, T.G.5
Andersen, G.R.6
-
17
-
-
0035697089
-
Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1
-
Vestergaard B., Van L.B., Andersen G.R., Nyborg J., Buckingham R.H., Kjeldgaard M. Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Mol. Cell. 8:2001;1375-1382.
-
(2001)
Mol. Cell.
, vol.8
, pp. 1375-1382
-
-
Vestergaard, B.1
Van, L.B.2
Andersen, G.R.3
Nyborg, J.4
Buckingham, R.H.5
Kjeldgaard, M.6
-
18
-
-
0037413610
-
Structure of the Escherichia coli ribosomal termination complex with release factor 2
-
Klaholz B.P., Pape T., Zavialov A.V., Myasnikov A.G., Orlova E.V., Vestergaard B., Ehrenberg M., van Heel M. Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature. 421:2003;90-94.
-
(2003)
Nature
, vol.421
, pp. 90-94
-
-
Klaholz, B.P.1
Pape, T.2
Zavialov, A.V.3
Myasnikov, A.G.4
Orlova, E.V.5
Vestergaard, B.6
Ehrenberg, M.7
Van Heel, M.8
-
19
-
-
0347721768
-
A cryo-electron microscopic study of ribosome-bound termination factor RF2
-
••], demonstrates large domain movements in RF2, by docking the crystal structure into a low-resolution EM map.
-
••], demonstrates large domain movements in RF2, by docking the crystal structure into a low-resolution EM map.
-
(2003)
Nature
, vol.421
, pp. 87-90
-
-
Rawat, U.B.1
Zavialov, A.V.2
Sengupta, J.3
Valle, M.4
Grassucci, R.A.5
Linde, J.6
Vestergaard, B.7
Ehrenberg, M.8
Frank, J.9
-
20
-
-
0036500658
-
Structural basis of gating by the outer membrane transporter FecA
-
Ferguson A.D., Chakraborty R., Smith B.S., Esser L., van der Helm D., Deisenhofer J. Structural basis of gating by the outer membrane transporter FecA. Science. 295:2002;1715-1719.
-
(2002)
Science
, vol.295
, pp. 1715-1719
-
-
Ferguson, A.D.1
Chakraborty, R.2
Smith, B.S.3
Esser, L.4
Van Der Helm, D.5
Deisenhofer, J.6
-
21
-
-
0037387189
-
Potassium channel gating observed with site-directed mass tagging
-
Kelly B.L., Gross A. Potassium channel gating observed with site-directed mass tagging. Nat. Struct. Biol. 10:2003;280-284.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 280-284
-
-
Kelly, B.L.1
Gross, A.2
-
23
-
-
0037198625
-
The open pore conformation of potassium channels
-
Comparison of crystal structures of structurally related MthK and KcsA channels indicates that bending of transmembrane helices controls gating.
-
Jiang Y., Lee A., Chen J., Cadene M., Chait B.T., MacKinnon R. The open pore conformation of potassium channels. Nature. 417:2002;523-526 Comparison of crystal structures of structurally related MthK and KcsA channels indicates that bending of transmembrane helices controls gating.
-
(2002)
Nature
, vol.417
, pp. 523-526
-
-
Jiang, Y.1
Lee, A.2
Chen, J.3
Cadene, M.4
Chait, B.T.5
MacKinnon, R.6
-
24
-
-
0038752614
-
The principle of gating charge movement in a voltage-dependent K+ channel
-
Electrophysiological data, coupled with structural information, is used to elucidate a model involving large translations of the voltage-sensing domain within the membrane.
-
Jiang Y., Ruta V., Chen J., Lee A., MacKinnon R. The principle of gating charge movement in a voltage-dependent K+ channel. Nature. 423:2003;42-48 Electrophysiological data, coupled with structural information, is used to elucidate a model involving large translations of the voltage-sensing domain within the membrane.
-
(2003)
Nature
, vol.423
, pp. 42-48
-
-
Jiang, Y.1
Ruta, V.2
Chen, J.3
Lee, A.4
MacKinnon, R.5
-
25
-
-
0034621834
-
Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 a resolution
-
Toyoshima C., Nakasako M., Nomura H., Ogawa H. Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution. Nature. 405:2000;647-655.
-
(2000)
Nature
, vol.405
, pp. 647-655
-
-
Toyoshima, C.1
Nakasako, M.2
Nomura, H.3
Ogawa, H.4
-
26
-
-
0036300446
-
A structural model for the catalytic cycle of Ca(2+)-ATPase
-
Xu C., Rice W.J., He W., Stokes D.L. A structural model for the catalytic cycle of Ca(2+)-ATPase. J. Mol. Biol. 316:2002;201-211.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 201-211
-
-
Xu, C.1
Rice, W.J.2
He, W.3
Stokes, D.L.4
-
27
-
-
0037043709
-
Structural changes in the calcium pump accompanying the dissociation of calcium
-
A high-resolution strucure of the E1 state of Ca2+-ATPase, demonstrating considerable reorientation of the cytoplasmic domains, accompanied by significant changes in the transmembrane region. Together with the T7 polymerase and haemagluttinin, this is one of the largest changes observed in a single polypeptide chain.
-
Toyoshima C., Nomura H. Structural changes in the calcium pump accompanying the dissociation of calcium. Nature. 418:2002;605-611 A high-resolution strucure of the E1 state of Ca2+-ATPase, demonstrating considerable reorientation of the cytoplasmic domains, accompanied by significant changes in the transmembrane region. Together with the T7 polymerase and haemagluttinin, this is one of the largest changes observed in a single polypeptide chain.
-
(2002)
Nature
, vol.418
, pp. 605-611
-
-
Toyoshima, C.1
Nomura, H.2
-
28
-
-
0037058922
-
Homology modeling of the cation binding sites of Na+K+-ATPase
-
Ogawa H., Toyoshima C. Homology modeling of the cation binding sites of Na+K+-ATPase. Proc. Natl. Acad. Sci. USA. 99:2002;15977-15982.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 15977-15982
-
-
Ogawa, H.1
Toyoshima, C.2
-
29
-
-
0035035788
-
Structure of Na+, K+-ATPase at 11-A resolution: Comparison with Ca2+-ATPase in E1 and E2 states
-
Rice W.J., Young H.S., Martin D.W., Sachs J.R., Stokes D.L. Structure of Na+, K+-ATPase at 11-A resolution: comparison with Ca2+-ATPase in E1 and E2 states. Biophys. J. 80:2001;2187-2197.
-
(2001)
Biophys. J.
, vol.80
, pp. 2187-2197
-
-
Rice, W.J.1
Young, H.S.2
Martin, D.W.3
Sachs, J.R.4
Stokes, D.L.5
-
30
-
-
0035849582
-
Crystal structure of ATP sulfurylase from Penicillium chrysogenum: Insights into the allosteric regulation of sulfate assimilation
-
MacRae I.J., Segel I.H., Fisher A.J. Crystal structure of ATP sulfurylase from Penicillium chrysogenum: insights into the allosteric regulation of sulfate assimilation. Biochemistry. 40:2001;6795-6804.
-
(2001)
Biochemistry
, vol.40
, pp. 6795-6804
-
-
MacRae, I.J.1
Segel, I.H.2
Fisher, A.J.3
-
31
-
-
0036897415
-
Allosteric inhibition via R-state destabilization in ATP sulfurylase from Penicillium chrysogenum
-
MacRae I.J., Segel I.H., Fisher A.J. Allosteric inhibition via R-state destabilization in ATP sulfurylase from Penicillium chrysogenum. Nat. Struct. Biol. 9:2002;945-949.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 945-949
-
-
MacRae, I.J.1
Segel, I.H.2
Fisher, A.J.3
-
32
-
-
0038414540
-
VirB11 ATPases are dynamic hexameric assemblies: New insights into bacterial type IV secretion
-
Good example of domain movements in the absence of ligand/substrate; also demonstrates the role of ATP binding, rather than hydrolysis for stabilizing a closed structure.
-
Savvides S.N., Yeo H.-J., Beck M.R., Blaesing F., Lurz R., Lanka E., Buhrdorf R., Fischer W., Haas R., Waksman G. VirB11 ATPases are dynamic hexameric assemblies: new insights into bacterial type IV secretion. EMBO J. 22:2003;1969-1980 Good example of domain movements in the absence of ligand/substrate; also demonstrates the role of ATP binding, rather than hydrolysis for stabilizing a closed structure.
-
(2003)
EMBO J.
, vol.22
, pp. 1969-1980
-
-
Savvides, S.N.1
Yeo, H.-J.2
Beck, M.R.3
Blaesing, F.4
Lurz, R.5
Lanka, E.6
Buhrdorf, R.7
Fischer, W.8
Haas, R.9
Waksman, G.10
-
33
-
-
0141507032
-
Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains
-
DeLaBarre B., Brunger A.T. Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nat. Struct. Biol. 10:2003;856-863.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 856-863
-
-
Delabarre, B.1
Brunger, A.T.2
-
34
-
-
18744414494
-
Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle
-
Rouiller I., DeLaBarre B., May A.P., Weis W.I., Brunger A.T., Milligan R.A., Wilson-Kubalek E.M. Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle. Nat. Struct. Biol. 9:2002;950-957.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 950-957
-
-
Rouiller, I.1
Delabarre, B.2
May, A.P.3
Weis, W.I.4
Brunger, A.T.5
Milligan, R.A.6
Wilson-Kubalek, E.M.7
-
35
-
-
0037374820
-
Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase
-
Darnault C., Volbeda A., Kim E.J., Legrand P., Vernade X., Lindahl P.A., Fontecilla-Camps J.C. Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase. Nat. Struct. Biol. 10:2003;271-279.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 271-279
-
-
Darnault, C.1
Volbeda, A.2
Kim, E.J.3
Legrand, P.4
Vernade, X.5
Lindahl, P.A.6
Fontecilla-Camps, J.C.7
-
36
-
-
0037224131
-
Structure of Escherichia coli ribose-5-phosphate isomerase. a ubiquitous enzyme of the pentose phosphate pathway and the calvin cycle
-
Zhang R., Andersson C.E., Savchenko A., Skarina T., Evdokimova E., Beasley S., Arrowsmith C.H., Edwards A.M., Joachimiak A., Mowbray S.L. Structure of Escherichia coli ribose-5-phosphate isomerase. A ubiquitous enzyme of the pentose phosphate pathway and the calvin cycle. Structure. 11:2003;31-42.
-
(2003)
Structure
, vol.11
, pp. 31-42
-
-
Zhang, R.1
Andersson, C.E.2
Savchenko, A.3
Skarina, T.4
Evdokimova, E.5
Beasley, S.6
Arrowsmith, C.H.7
Edwards, A.M.8
Joachimiak, A.9
Mowbray, S.L.10
-
37
-
-
0035829518
-
Crystal structure of the anthrax lethal factor
-
Pannifer A.D., Wong T.Y., Schwarzenbacher R., Renatus M., Petosa C., Bienkowska J., Lacy D.B., Collier R.J., Park S., Leppla S.H. et al. Crystal structure of the anthrax lethal factor. Nature. 414:2001;229-233.
-
(2001)
Nature
, vol.414
, pp. 229-233
-
-
Pannifer, A.D.1
Wong, T.Y.2
Schwarzenbacher, R.3
Renatus, M.4
Petosa, C.5
Bienkowska, J.6
Lacy, D.B.7
Collier, R.J.8
Park, S.9
Leppla, S.H.10
-
38
-
-
0037165139
-
Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin
-
Crystal structures show extension of a domain to allow calmodulin binding, which enables catalytic activity.
-
Drum C.L., Yan S.-Z., Bard J., Shen Y.-Q., Lu D., Soelaiman S., Grabarek Z., Bohm A., Tang W.-J. Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin. Nature. 415:2002;396-402 Crystal structures show extension of a domain to allow calmodulin binding, which enables catalytic activity.
-
(2002)
Nature
, vol.415
, pp. 396-402
-
-
Drum, C.L.1
Yan, S.-Z.2
Bard, J.3
Shen, Y.-Q.4
Lu, D.5
Soelaiman, S.6
Grabarek, Z.7
Bohm, A.8
Tang, W.-J.9
-
39
-
-
0027438949
-
Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces
-
Gerstein M., Anderson B.F., Norris G.E., Baker E.N., Lesk A.M., Chothia C. Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces. J. Mol. Biol. 234:1993;357-372.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 357-372
-
-
Gerstein, M.1
Anderson, B.F.2
Norris, G.E.3
Baker, E.N.4
Lesk, A.M.5
Chothia, C.6
-
40
-
-
3543012707
-
Crystallography and NMR system (CNS): A new software system for macromolecular structure determination
-
Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.-S., Kuszewski J., Nilges N., Pannu N.S. et al. Crystallography and NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921.
-
(1998)
Acta Crystallogr. D Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.-S.7
Kuszewski, J.8
Nilges, N.9
Pannu, N.S.10
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