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For: Case DA. Chemical shifts in biomolecules. Curr Opin Struct Biol 2013;23:172-6. [PMID: 23422068 DOI: 10.1016/j.sbi.2013.01.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/14/2013] [Accepted: 01/22/2013] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Fiorucci L, Schiavina M, Felli IC, Pierattelli R, Ravera E. Are Protein Conformational Ensembles in Agreement with Experimental Data? A Geometrical Interpretation of the Problem. J Chem Inf Model 2024. [PMID: 38959217 DOI: 10.1021/acs.jcim.4c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
2
Roy R, Geng A, Shi H, Merriman DK, Dethoff EA, Salmon L, Al-Hashimi HM. Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. J Am Chem Soc 2023;145:22964-22978. [PMID: 37831584 DOI: 10.1021/jacs.3c04614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
3
Kovács D, Bodor A. The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs. RSC Adv 2023;13:10182-10203. [PMID: 37006359 PMCID: PMC10065145 DOI: 10.1039/d3ra00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023]  Open
4
Sethio D, Poongavanam V, Xiong R, Tyagi M, Duy Vo D, Lindh R, Kihlberg J. Simulation Reveals the Chameleonic Behavior of Macrocycles. J Chem Inf Model 2023;63:138-146. [PMID: 36563083 PMCID: PMC9832480 DOI: 10.1021/acs.jcim.2c01093] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
5
Bakker MJ, Mládek A, Semrád H, Zapletal V, Pavlíková Přecechtělová J. Improving IDP theoretical chemical shift accuracy and efficiency through a combined MD/ADMA/DFT and machine learning approach. Phys Chem Chem Phys 2022;24:27678-27692. [PMID: 36373847 DOI: 10.1039/d2cp01638a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
6
Theillet FX. In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale. Chem Rev 2022;122:9497-9570. [PMID: 35357148 DOI: 10.1021/acs.chemrev.1c00937] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
7
Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nat Commun 2020;11:5531. [PMID: 33139729 PMCID: PMC7608651 DOI: 10.1038/s41467-020-19371-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/07/2020] [Indexed: 11/08/2022]  Open
8
Bernetti M, Bertazzo M, Masetti M. Data-Driven Molecular Dynamics: A Multifaceted Challenge. Pharmaceuticals (Basel) 2020;13:E253. [PMID: 32961909 PMCID: PMC7557855 DOI: 10.3390/ph13090253] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022]  Open
9
Li J, Bennett KC, Liu Y, Martin MV, Head-Gordon T. Accurate prediction of chemical shifts for aqueous protein structure on "Real World" data. Chem Sci 2020;11:3180-3191. [PMID: 34122823 PMCID: PMC8152569 DOI: 10.1039/c9sc06561j] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 03/02/2020] [Indexed: 02/04/2023]  Open
10
Pavlíková Přecechtělová J, Mládek A, Zapletal V, Hritz J. Quantum Chemical Calculations of NMR Chemical Shifts in Phosphorylated Intrinsically Disordered Proteins. J Chem Theory Comput 2019;15:5642-5658. [DOI: 10.1021/acs.jctc.8b00257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
11
Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM. Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA. Biochemistry 2019;58:1963-1974. [PMID: 30950607 DOI: 10.1021/acs.biochem.9b00027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
12
Kumari P, Frey L, Sobol A, Lakomek NA, Riek R. 15N transverse relaxation measurements for the characterization of µs-ms dynamics are deteriorated by the deuterium isotope effect on 15N resulting from solvent exchange. JOURNAL OF BIOMOLECULAR NMR 2018;72:125-137. [PMID: 30306288 DOI: 10.1007/s10858-018-0211-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
13
Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Struppe J, Case DA, Polenova T, Gronenborn AM. Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM. Phys Chem Chem Phys 2018;20:9543-9553. [PMID: 29577158 PMCID: PMC5892194 DOI: 10.1039/c8cp00647d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
14
Shi H, Clay MC, Rangadurai A, Sathyamoorthy B, Case DA, Al-Hashimi HM. Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. JOURNAL OF BIOMOLECULAR NMR 2018;70:229-244. [PMID: 29675775 PMCID: PMC6048961 DOI: 10.1007/s10858-018-0177-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/29/2018] [Indexed: 05/20/2023]
15
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments. COMPUTATION 2018. [DOI: 10.3390/computation6010015] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
16
Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017;1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
17
Jose KVJ, Raghavachari K. Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment. J Chem Theory Comput 2017;13:1147-1158. [DOI: 10.1021/acs.jctc.6b00922] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
18
Olsson S, Noé F. Mechanistic Models of Chemical Exchange Induced Relaxation in Protein NMR. J Am Chem Soc 2016;139:200-210. [DOI: 10.1021/jacs.6b09460] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
19
Nygaard M, Terkelsen T, Vidas Olsen A, Sora V, Salamanca Viloria J, Rizza F, Bergstrand-Poulsen S, Di Marco M, Vistesen M, Tiberti M, Lambrughi M, Jäättelä M, Kallunki T, Papaleo E. The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer. Front Mol Biosci 2016;3:78. [PMID: 28018905 PMCID: PMC5156680 DOI: 10.3389/fmolb.2016.00078] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/17/2016] [Indexed: 11/24/2022]  Open
20
Bratholm LA, Jensen JH. Protein structure refinement using a quantum mechanics-based chemical shielding predictor. Chem Sci 2016;8:2061-2072. [PMID: 28451325 PMCID: PMC5399634 DOI: 10.1039/c6sc04344e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/15/2016] [Indexed: 11/21/2022]  Open
21
van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ. Bestimmung von Strukturinformation aus experimentellen Messdaten für Biomoleküle. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601828] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
22
van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ. Deriving Structural Information from Experimentally Measured Data on Biomolecules. Angew Chem Int Ed Engl 2016;55:15990-16010. [PMID: 27862777 DOI: 10.1002/anie.201601828] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/08/2016] [Indexed: 12/27/2022]
23
Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. Finding Our Way in the Dark Proteome. J Am Chem Soc 2016;138:9730-42. [PMID: 27387657 PMCID: PMC5051545 DOI: 10.1021/jacs.6b06543] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
24
Shaghaghi H, Ebrahimi HP, Fathi F, Bahrami Panah N, Jalali-Heravi M, Tafazzoli M. A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory. J Comput Chem 2016;37:1296-305. [DOI: 10.1002/jcc.24323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/25/2015] [Accepted: 01/17/2016] [Indexed: 11/08/2022]
25
Vícha J, Babinský M, Demo G, Otrusinová O, Jansen S, Pekárová B, Žídek L, Munzarová ML. The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations. Proteins 2016;84:686-99. [PMID: 26879585 DOI: 10.1002/prot.25019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/29/2016] [Accepted: 02/10/2016] [Indexed: 11/09/2022]
26
Doyle CM, Rumfeldt JA, Broom HR, Sekhar A, Kay LE, Meiering EM. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts. Biochemistry 2016;55:1346-61. [PMID: 26849066 DOI: 10.1021/acs.biochem.5b01133] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
27
Fu I, Case DA, Baum J. Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide. Biochemistry 2016;54:6029-37. [PMID: 26339765 DOI: 10.1021/acs.biochem.5b00622] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
28
Swails J, Zhu T, He X, Case DA. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. JOURNAL OF BIOMOLECULAR NMR 2015;63:125-39. [PMID: 26232926 PMCID: PMC6556433 DOI: 10.1007/s10858-015-9970-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/20/2015] [Indexed: 05/08/2023]
29
Jee JG. Comparison of NMR structures refined under implicit and explicit solvents. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2015. [DOI: 10.6564/jkmrs.2015.19.1.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
30
Sturlese M, Bellanda M, Moro S. NMR-Assisted Molecular Docking Methodologies. Mol Inform 2015;34:513-25. [DOI: 10.1002/minf.201500012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/24/2015] [Indexed: 11/11/2022]
31
Pastor N, Amero C. Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations. FRONTIERS IN PLANT SCIENCE 2015;6:306. [PMID: 25999971 PMCID: PMC4419604 DOI: 10.3389/fpls.2015.00306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/17/2015] [Indexed: 06/04/2023]
32
He X, Zhu T, Wang X, Liu J, Zhang JZH. Fragment quantum mechanical calculation of proteins and its applications. Acc Chem Res 2014;47:2748-57. [PMID: 24851673 DOI: 10.1021/ar500077t] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
33
Camilloni C, Vendruscolo M. Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics. J Am Chem Soc 2014;136:8982-91. [PMID: 24884637 DOI: 10.1021/ja5027584] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
34
Jensen MR, Zweckstetter M, Huang JR, Blackledge M. Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy. Chem Rev 2014;114:6632-60. [PMID: 24725176 DOI: 10.1021/cr400688u] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
35
Christensen AS, Linnet TE, Borg M, Boomsma W, Lindorff-Larsen K, Hamelryck T, Jensen JH. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics. PLoS One 2013;8:e84123. [PMID: 24391900 PMCID: PMC3877219 DOI: 10.1371/journal.pone.0084123] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/11/2013] [Indexed: 11/18/2022]  Open
36
Frank AT, Bae SH, Stelzer AC. Prediction of RNA 1H and 13C chemical shifts: a structure based approach. J Phys Chem B 2013;117:13497-506. [PMID: 24033307 DOI: 10.1021/jp407254m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
37
Wang B, He X, Merz KM. Quantum Mechanical Study of Vicinal J Spin-Spin Coupling Constants for the Protein Backbone. J Chem Theory Comput 2013;9:4653-9. [PMID: 26589175 DOI: 10.1021/ct400631b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
38
Kragelj J, Ozenne V, Blackledge M, Jensen MR. Conformational Propensities of Intrinsically Disordered Proteins from NMR Chemical Shifts. Chemphyschem 2013;14:3034-45. [DOI: 10.1002/cphc.201300387] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Indexed: 12/22/2022]
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