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For: Walker O, Varadan R, Fushman D. Efficient and accurate determination of the overall rotational diffusion tensor of a molecule from (15)N relaxation data using computer program ROTDIF. J Magn Reson 2004;168:336-345. [PMID: 15140445 DOI: 10.1016/j.jmr.2004.03.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Revised: 02/19/2004] [Indexed: 05/24/2023]
Number Cited by Other Article(s)
1
Attionu SK, Dill R, Summers MF, Case DA, Marchant J, Dayie TK. Selective [9-15N] Guanosine for Nuclear Magnetic Resonance Studies of Large Ribonucleic Acids. Chembiochem 2025:e2500206. [PMID: 40320375 DOI: 10.1002/cbic.202500206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2025] [Revised: 05/01/2025] [Indexed: 05/24/2025]
2
Hologne M, Chen PC, Cantrelle FX, Walker O. Molecular dynamics as an efficient process to predict 15N chemical shift anisotropy at very high NMR magnetic fields. Phys Chem Chem Phys 2025;27:2320-2332. [PMID: 39688270 DOI: 10.1039/d4cp03821e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2024]
3
Lim LZ, Song J. NMR Dynamic View of the Stabilization of the WW4 Domain by Neutral NaCl and Kosmotropic Na2SO4 and NaH2PO4. Int J Mol Sci 2024;25:9091. [PMID: 39201778 PMCID: PMC11354479 DOI: 10.3390/ijms25169091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024]  Open
4
Cai M, Agarwal N, Garrett DS, Baber J, Clore GM. A Transient, Excited Species of the Autoinhibited α-State of the Bacterial Transcription Factor RfaH May Represent an Early Intermediate on the Fold-Switching Pathway. Biochemistry 2024;63:2030-2039. [PMID: 39088556 PMCID: PMC11345854 DOI: 10.1021/acs.biochem.4c00258] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
5
Wallerstein J, Han X, Levkovets M, Lesovoy D, Malmodin D, Mirabello C, Wallner B, Sun R, Sandalova T, Agback P, Karlsson G, Achour A, Agback T, Orekhov V. Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses. Commun Biol 2024;7:868. [PMID: 39014105 PMCID: PMC11252132 DOI: 10.1038/s42003-024-06558-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024]  Open
6
Lim LZ, Song J. NMR Dynamic View of the Destabilization of WW4 Domain by Chaotropic GdmCl and NaSCN. Int J Mol Sci 2024;25:7344. [PMID: 39000450 PMCID: PMC11242413 DOI: 10.3390/ijms25137344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024]  Open
7
Katikaridis P, Simon B, Jenne T, Moon S, Lee C, Hennig J, Mogk A. Structural basis of aggregate binding by the AAA+ disaggregase ClpG. J Biol Chem 2023;299:105336. [PMID: 37827289 PMCID: PMC10641755 DOI: 10.1016/j.jbc.2023.105336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/17/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]  Open
8
Cai M, Tugarinov V, Chaitanya Chiliveri S, Huang Y, Schwieters CD, Mizuuchi K, Clore GM. Interaction of the bacterial division regulator MinE with lipid bicelles studied by NMR spectroscopy. J Biol Chem 2023;299:103037. [PMID: 36806683 PMCID: PMC10031476 DOI: 10.1016/j.jbc.2023.103037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023]  Open
9
Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris. Int J Mol Sci 2023;24:ijms24043973. [PMID: 36835381 PMCID: PMC9961634 DOI: 10.3390/ijms24043973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023]  Open
10
Chen PC, Kutzki F, Mojzisch A, Simon B, Xu ER, Aponte-Santamaría C, Horny K, Jeffries C, Schneppenheim R, Wilmanns M, Brehm MA, Gräter F, Hennig J. Structure and dynamics of the von Willebrand Factor C6 domain. J Struct Biol 2022;214:107923. [PMID: 36410652 DOI: 10.1016/j.jsb.2022.107923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022]
11
Wernersson S, Bobby R, Flavell L, Milbradt AG, Holdgate GA, Embrey KJ, Akke M. Bromodomain Interactions with Acetylated Histone 4 Peptides in the BRD4 Tandem Domain: Effects on Domain Dynamics and Internal Flexibility. Biochemistry 2022;61:2303-2318. [PMID: 36215732 PMCID: PMC9631989 DOI: 10.1021/acs.biochem.2c00226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
12
Bolik-Coulon N, Ferrage F. Explicit models of motions to analyze NMR relaxation data in proteins. J Chem Phys 2022;157:125102. [DOI: 10.1063/5.0095910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
13
Namitz KEW, Zheng T, Canning AJ, Alicea-Velazquez NL, Castañeda CA, Cosgrove MS, Hanes SD. Structure analysis suggests Ess1 isomerizes the carboxy-terminal domain of RNA polymerase II via a bivalent anchoring mechanism. Commun Biol 2021;4:398. [PMID: 33767358 PMCID: PMC7994582 DOI: 10.1038/s42003-021-01906-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 01/07/2023]  Open
14
Huck V, Chen PC, Xu ER, Tischer A, Klemm U, Aponte-Santamaría C, Mess C, Obser T, Kutzki F, König G, Denis CV, Gräter F, Wilmanns M, Auton M, Schneider SW, Schneppenheim R, Hennig J, Brehm MA. Gain-of-Function Variant p.Pro2555Arg of von Willebrand Factor Increases Aggregate Size through Altering Stem Dynamics. Thromb Haemost 2020;122:226-239. [PMID: 33385180 PMCID: PMC8828397 DOI: 10.1055/a-1344-4405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
15
Marcellini M, Nguyen MH, Martin M, Hologne M, Walker O. Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion. J Phys Chem B 2020;124:5103-5112. [DOI: 10.1021/acs.jpcb.0c01922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
16
Molecular recognition of ubiquitin and Lys63-linked diubiquitin by STAM2 UIM-SH3 dual domain: the effect of its linker length and flexibility. Sci Rep 2019;9:14645. [PMID: 31601934 PMCID: PMC6787221 DOI: 10.1038/s41598-019-51182-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/25/2019] [Indexed: 11/09/2022]  Open
17
Smith AA, Ernst M, Meier BH, Ferrage F. Reducing bias in the analysis of solution-state NMR data with dynamics detectors. J Chem Phys 2019;151:034102. [PMID: 31325945 DOI: 10.1063/1.5111081] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
18
Xu ER, von Bülow S, Chen PC, Lenting PJ, Kolšek K, Aponte-Santamaría C, Simon B, Foot J, Obser T, Schneppenheim R, Gräter F, Denis CV, Wilmanns M, Hennig J. Structure and dynamics of the platelet integrin-binding C4 domain of von Willebrand factor. Blood 2019;133:366-376. [PMID: 30305279 PMCID: PMC6450055 DOI: 10.1182/blood-2018-04-843615] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/24/2018] [Indexed: 12/22/2022]  Open
19
Wallerstein J, Akke M. Minute Additions of DMSO Affect Protein Dynamics Measurements by NMR Relaxation Experiments through Significant Changes in Solvent Viscosity. Chemphyschem 2019;20:326-332. [PMID: 30102005 PMCID: PMC6391962 DOI: 10.1002/cphc.201800626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 11/07/2022]
20
Ubiquitin Modulates Liquid-Liquid Phase Separation of UBQLN2 via Disruption of Multivalent Interactions. Mol Cell 2018. [PMID: 29526694 DOI: 10.1016/j.molcel.2018.02.004] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
21
Chen PC, Hologne M, Walker O, Hennig J. Ab Initio Prediction of NMR Spin Relaxation Parameters from Molecular Dynamics Simulations. J Chem Theory Comput 2018;14:1009-1019. [PMID: 29294268 DOI: 10.1021/acs.jctc.7b00750] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
22
Hoffmann F, Xue M, Schäfer LV, Mulder FAA. Narrowing the gap between experimental and computational determination of methyl group dynamics in proteins. Phys Chem Chem Phys 2018;20:24577-24590. [DOI: 10.1039/c8cp03915a] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
23
Goodrich AC, Meyers DJ, Frueh DP. Molecular impact of covalent modifications on nonribosomal peptide synthetase carrier protein communication. J Biol Chem 2017;292:10002-10013. [PMID: 28455448 DOI: 10.1074/jbc.m116.766220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 04/27/2017] [Indexed: 11/06/2022]  Open
24
Munari F, Bortot A, Zanzoni S, D'Onofrio M, Fushman D, Assfalg M. Identification of primary and secondary UBA footprints on the surface of ubiquitin in cell-mimicking crowded solution. FEBS Lett 2017;591:979-990. [PMID: 28267209 DOI: 10.1002/1873-3468.12615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 02/24/2017] [Accepted: 02/24/2017] [Indexed: 01/09/2023]
25
Chen PC, Hologne M, Walker O. Computing the Rotational Diffusion of Biomolecules via Molecular Dynamics Simulation and Quaternion Orientations. J Phys Chem B 2017;121:1812-1823. [DOI: 10.1021/acs.jpcb.6b11703] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Ravera E, Sgheri L, Parigi G, Luchinat C. A critical assessment of methods to recover information from averaged data. Phys Chem Chem Phys 2017;18:5686-701. [PMID: 26565805 DOI: 10.1039/c5cp04077a] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
27
Characterizing Aciniform Silk Repetitive Domain Backbone Dynamics and Hydrodynamic Modularity. Int J Mol Sci 2016;17:ijms17081305. [PMID: 27517921 PMCID: PMC5000702 DOI: 10.3390/ijms17081305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/13/2023]  Open
28
Castañeda CA, Chaturvedi A, Camara CM, Curtis JE, Krueger S, Fushman D. Linkage-specific conformational ensembles of non-canonical polyubiquitin chains. Phys Chem Chem Phys 2016;18:5771-88. [PMID: 26422168 PMCID: PMC4758893 DOI: 10.1039/c5cp04601g] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
29
Goodrich AC, Harden BJ, Frueh DP. Solution Structure of a Nonribosomal Peptide Synthetase Carrier Protein Loaded with Its Substrate Reveals Transient, Well-Defined Contacts. J Am Chem Soc 2015;137:12100-9. [PMID: 26334259 DOI: 10.1021/jacs.5b07772] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
30
Brosey CA, Soss SE, Brooks S, Yan C, Ivanov I, Dorai K, Chazin WJ. Functional dynamics in replication protein A DNA binding and protein recruitment domains. Structure 2015;23:1028-38. [PMID: 26004442 DOI: 10.1016/j.str.2015.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/30/2015] [Accepted: 04/03/2015] [Indexed: 11/29/2022]
31
Schumann FH, Varadan R, Tayakuniyil PP, Grossman JH, Camarero JA, Fushman D. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain. Front Chem 2015;3:26. [PMID: 25905098 PMCID: PMC4389572 DOI: 10.3389/fchem.2015.00026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/23/2015] [Indexed: 12/02/2022]  Open
32
Rezaei-Ghaleh N, Klama F, Munari F, Zweckstetter M. HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins. Bioinformatics 2014;31:1319-21. [DOI: 10.1093/bioinformatics/btu824] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/08/2014] [Indexed: 11/14/2022]  Open
33
Richman DE, Majumdar A, García-Moreno E B. pH dependence of conformational fluctuations of the protein backbone. Proteins 2014;82:3132-43. [PMID: 25137073 DOI: 10.1002/prot.24673] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/25/2014] [Accepted: 08/04/2014] [Indexed: 01/08/2023]
34
Xu N, Tochio N, Wang J, Tamari Y, Uewaki JI, Utsunomiya-Tate N, Igarashi K, Shiraki T, Kobayashi N, Tate SI. The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif. Biochemistry 2014;53:5568-78. [PMID: 25100325 DOI: 10.1021/bi5007817] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
35
Gutte PGM, Jurt S, Grütter MG, Zerbe O. Unusual structural features revealed by the solution NMR structure of the NLRC5 caspase recruitment domain. Biochemistry 2014;53:3106-17. [PMID: 24815518 DOI: 10.1021/bi500177x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
36
Castañeda CA, Kashyap TR, Nakasone MA, Krueger S, Fushman D. Unique structural, dynamical, and functional properties of k11-linked polyubiquitin chains. Structure 2014;21:1168-81. [PMID: 23823328 DOI: 10.1016/j.str.2013.04.029] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 04/05/2013] [Accepted: 04/26/2013] [Indexed: 11/24/2022]
37
Lee SY, Pullen L, Virgil DJ, Castañeda CA, Abeykoon D, Bolon DNA, Fushman D. Alanine scan of core positions in ubiquitin reveals links between dynamics, stability, and function. J Mol Biol 2013;426:1377-89. [PMID: 24361330 DOI: 10.1016/j.jmb.2013.10.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/25/2013] [Accepted: 10/26/2013] [Indexed: 11/17/2022]
38
Berlin K, Longhini A, Dayie TK, Fushman D. Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface. JOURNAL OF BIOMOLECULAR NMR 2013;57:333-352. [PMID: 24170368 PMCID: PMC3939081 DOI: 10.1007/s10858-013-9791-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/11/2013] [Indexed: 05/28/2023]
39
Charlier C, Khan SN, Marquardsen T, Pelupessy P, Reiss V, Sakellariou D, Bodenhausen G, Engelke F, Ferrage F. Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry. J Am Chem Soc 2013;135:18665-72. [PMID: 24228712 PMCID: PMC3865798 DOI: 10.1021/ja409820g] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
40
Dosset P, Barthe P, Cohen-Gonsaud M, Roumestand C, Déméné H. Equivalence between Euler angle conventions for the description of tensorial interactions in liquid NMR: application to different software programs. JOURNAL OF BIOMOLECULAR NMR 2013;57:305-311. [PMID: 24132779 DOI: 10.1007/s10858-013-9790-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 10/09/2013] [Indexed: 06/02/2023]
41
Munari F, Rezaei-Ghaleh N, Xiang S, Fischle W, Zweckstetter M. Structural plasticity in human heterochromatin protein 1β. PLoS One 2013;8:e60887. [PMID: 23585859 PMCID: PMC3621757 DOI: 10.1371/journal.pone.0060887] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/04/2013] [Indexed: 01/12/2023]  Open
42
Zerbetto M, Anderson R, Bouguet-Bonnet S, Rech M, Zhang L, Meirovitch E, Polimeno A, Buck M. Analysis of 15N-1H NMR relaxation in proteins by a combined experimental and molecular dynamics simulation approach: picosecond-nanosecond dynamics of the Rho GTPase binding domain of plexin-B1 in the dimeric state indicates allosteric pathways. J Phys Chem B 2013;117:174-84. [PMID: 23214953 PMCID: PMC3556999 DOI: 10.1021/jp310142f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
43
Petty A, Myshkin E, Qin H, Guo H, Miao H, Tochtrop GP, Hsieh JT, Page P, Liu L, Lindner DJ, Acharya C, MacKerell AD, Ficker E, Song J, Wang B. A small molecule agonist of EphA2 receptor tyrosine kinase inhibits tumor cell migration in vitro and prostate cancer metastasis in vivo. PLoS One 2012;7:e42120. [PMID: 22916121 PMCID: PMC3419725 DOI: 10.1371/journal.pone.0042120] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 07/02/2012] [Indexed: 12/18/2022]  Open
44
D'Onofrio M, Gianolio E, Ceccon A, Arena F, Zanzoni S, Fushman D, Aime S, Molinari H, Assfalg M. High Relaxivity Supramolecular Adducts Between Human-Liver Fatty-Acid-Binding Protein and Amphiphilic GdIII Complexes: Structural Basis for the Design of Intracellular Targeting MRI Probes. Chemistry 2012;18:9919-28. [DOI: 10.1002/chem.201103778] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 05/08/2012] [Indexed: 01/14/2023]
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Lakomek NA, Ying J, Bax A. Measurement of ¹⁵N relaxation rates in perdeuterated proteins by TROSY-based methods. JOURNAL OF BIOMOLECULAR NMR 2012;53:209-21. [PMID: 22689066 PMCID: PMC3412688 DOI: 10.1007/s10858-012-9626-5] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 04/04/2012] [Indexed: 05/11/2023]
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Combining NMR and molecular dynamics studies for insights into the allostery of small GTPase-protein interactions. Methods Mol Biol 2012;796:235-59. [PMID: 22052494 DOI: 10.1007/978-1-61779-334-9_13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Fushman D. Determining protein dynamics from ¹⁵N relaxation data by using DYNAMICS. Methods Mol Biol 2012;831:485-511. [PMID: 22167688 DOI: 10.1007/978-1-61779-480-3_24] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Banerjee PR, Puttamadappa SS, Pande A, Shekhtman A, Pande J. Increased hydrophobicity and decreased backbone flexibility explain the lower solubility of a cataract-linked mutant of γD-crystallin. J Mol Biol 2011;412:647-59. [PMID: 21827768 DOI: 10.1016/j.jmb.2011.07.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 07/22/2011] [Accepted: 07/25/2011] [Indexed: 11/18/2022]
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Berlin K, O’Leary DP, Fushman D. Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes. Proteins 2011;79:2268-81. [PMID: 21604302 PMCID: PMC3115445 DOI: 10.1002/prot.23053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 03/14/2011] [Accepted: 03/21/2011] [Indexed: 11/11/2022]
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Lange A, Hoeller D, Wienk H, Marcillat O, Lancelin JM, Walker O. NMR reveals a different mode of binding of the Stam2 VHS domain to ubiquitin and diubiquitin. Biochemistry 2010;50:48-62. [PMID: 21121635 DOI: 10.1021/bi101594a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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