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For: Pritchard RB, Hansen DF. Characterising side chains in large proteins by protonless 13C-detected NMR spectroscopy. Nat Commun 2019;10:1747. [PMID: 30988305 PMCID: PMC6465260 DOI: 10.1038/s41467-019-09743-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/28/2019] [Indexed: 11/24/2022]  Open
Number Cited by Other Article(s)
1
Shukla VK, Karunanithy G, Vallurupalli P, Hansen DF. A combined NMR and deep neural network approach for enhancing the spectral resolution of aromatic side chains in proteins. SCIENCE ADVANCES 2024;10:eadr2155. [PMID: 39705363 PMCID: PMC11801238 DOI: 10.1126/sciadv.adr2155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 11/15/2024] [Indexed: 12/22/2024]
2
Karunanithy G, Shukla VK, Hansen DF. Solution-state methyl NMR spectroscopy of large non-deuterated proteins enabled by deep neural networks. Nat Commun 2024;15:5073. [PMID: 38871714 PMCID: PMC11176362 DOI: 10.1038/s41467-024-49378-8] [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: 10/26/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024]  Open
3
Tiwari VP, De D, Thapliyal N, Kay LE, Vallurupalli P. Beyond slow two-state protein conformational exchange using CEST: applications to three-state protein interconversion on the millisecond timescale. JOURNAL OF BIOMOLECULAR NMR 2024;78:39-60. [PMID: 38169015 DOI: 10.1007/s10858-023-00431-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
4
Karamanos TK, Matthews S. Biomolecular NMR in the AI-assisted structural biology era: Old tricks and new opportunities. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024;1872:140949. [PMID: 37572958 DOI: 10.1016/j.bbapap.2023.140949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
5
Querci L, Grifagni D, Trindade IB, Silva JM, Louro RO, Cantini F, Piccioli M. Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center. JOURNAL OF BIOMOLECULAR NMR 2023;77:247-259. [PMID: 37853207 PMCID: PMC10687126 DOI: 10.1007/s10858-023-00425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023]
6
Shukla VK, Heller GT, Hansen DF. Biomolecular NMR spectroscopy in the era of artificial intelligence. Structure 2023;31:1360-1374. [PMID: 37848030 DOI: 10.1016/j.str.2023.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
7
Maksymenko K, Maurer A, Aghaallaei N, Barry C, Borbarán-Bravo N, Ullrich T, Dijkstra TM, Hernandez Alvarez B, Müller P, Lupas AN, Skokowa J, ElGamacy M. The design of functional proteins using tensorized energy calculations. CELL REPORTS METHODS 2023;3:100560. [PMID: 37671023 PMCID: PMC10475850 DOI: 10.1016/j.crmeth.2023.100560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/25/2023] [Accepted: 07/21/2023] [Indexed: 09/07/2023]
8
Khandave NP, Sekhar A, Vallurupalli P. Studying micro to millisecond protein dynamics using simple amide 15N CEST experiments supplemented with major-state R2 and visible peak-position constraints. JOURNAL OF BIOMOLECULAR NMR 2023;77:165-181. [PMID: 37300639 PMCID: PMC7615914 DOI: 10.1007/s10858-023-00419-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/10/2023] [Indexed: 06/12/2023]
9
Ghosh Biswas R, Soong R, Ning P, Lane D, Bastawrous M, Jenne A, Schmidig D, de Castro P, Graf S, Kuehn T, Kümmerle R, Bermel W, Busse F, Struppe J, Simpson MJ, Simpson AJ. Exploring the Applications of Carbon-Detected NMR in Living and Dead Organisms Using a 13C-Optimized Comprehensive Multiphase NMR Probe. Anal Chem 2022;94:8756-8765. [PMID: 35675504 DOI: 10.1021/acs.analchem.2c01356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
10
Felli IC, Pierattelli R. 13C Direct Detected NMR for Challenging Systems. Chem Rev 2022;122:9468-9496. [PMID: 35025504 PMCID: PMC9136920 DOI: 10.1021/acs.chemrev.1c00871] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Indexed: 12/14/2022]
11
Kabra A, Rumpa E, Li Y. Observation of Arginine Side-Chain Motions Coupled to the Global Conformational Exchange Process in Deubiquitinase A. ACS OMEGA 2022;7:9936-9943. [PMID: 35350351 PMCID: PMC8945143 DOI: 10.1021/acsomega.2c00492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
12
Karamanos TK, Clore GM. Large Chaperone Complexes Through the Lens of Nuclear Magnetic Resonance Spectroscopy. Annu Rev Biophys 2022;51:223-246. [PMID: 35044800 DOI: 10.1146/annurev-biophys-090921-120150] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
13
Fucci IJ, Byrd RA. nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological Magnetic Resonance Data Bank. Protein Sci 2022;31:63-74. [PMID: 34516045 PMCID: PMC8740831 DOI: 10.1002/pro.4181] [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: 08/18/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
14
Karunanithy G, Mackenzie HW, Hansen DF. Virtual Homonuclear Decoupling in Direct Detection Nuclear Magnetic Resonance Experiments Using Deep Neural Networks. J Am Chem Soc 2021;143:16935-16942. [PMID: 34633815 DOI: 10.1021/jacs.1c04010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
15
Xiang X, Hansen AL, Yu L, Jameson G, Bruschweiler-Li L, Yuan C, Brüschweiler R. Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation. J Am Chem Soc 2021;143:13593-13604. [PMID: 34428032 DOI: 10.1021/jacs.1c04687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
16
Karunanithy G, Shukla VK, Hansen DF. Methodological advancements for characterising protein side chains by NMR spectroscopy. Curr Opin Struct Biol 2021;70:61-69. [PMID: 33989947 DOI: 10.1016/j.sbi.2021.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/18/2022]
17
Singh A, Purslow JA, Venditti V. 15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale. J Vis Exp 2021. [PMID: 33938889 DOI: 10.3791/62395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
18
Alderson TR, Kay LE. NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function. Cell 2021;184:577-595. [PMID: 33545034 DOI: 10.1016/j.cell.2020.12.034] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 01/02/2023]
19
Nepravishta R, Pletka CC, Iwahara J. Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes. JOURNAL OF BIOMOLECULAR NMR 2020;74:421-429. [PMID: 32683519 PMCID: PMC7511421 DOI: 10.1007/s10858-020-00333-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/09/2020] [Indexed: 05/05/2023]
20
Tiwari VP, Vallurupalli P. A CEST NMR experiment to obtain glycine 1Hα chemical shifts in 'invisible' minor states of proteins. JOURNAL OF BIOMOLECULAR NMR 2020;74:443-455. [PMID: 32696193 DOI: 10.1007/s10858-020-00336-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
21
Karunanithy G, Reinstein J, Hansen DF. Multiquantum Chemical Exchange Saturation Transfer NMR to Quantify Symmetrical Exchange: Application to Rotational Dynamics of the Guanidinium Group in Arginine Side Chains. J Phys Chem Lett 2020;11:5649-5654. [PMID: 32543198 PMCID: PMC7370295 DOI: 10.1021/acs.jpclett.0c01322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
22
Alderson TR, Kay LE. Unveiling invisible protein states with NMR spectroscopy. Curr Opin Struct Biol 2020;60:39-49. [DOI: 10.1016/j.sbi.2019.10.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022]
23
Wong LE, Kim TH, Muhandiram DR, Forman-Kay JD, Kay LE. NMR Experiments for Studies of Dilute and Condensed Protein Phases: Application to the Phase-Separating Protein CAPRIN1. J Am Chem Soc 2020;142:2471-2489. [DOI: 10.1021/jacs.9b12208] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
24
Siemons L, Mackenzie HW, Shukla VK, Hansen DF. Intra-residue methyl-methyl correlations for valine and leucine residues in large proteins from a 3D-HMBC-HMQC experiment. JOURNAL OF BIOMOLECULAR NMR 2019;73:749-757. [PMID: 31720925 PMCID: PMC6875545 DOI: 10.1007/s10858-019-00287-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/03/2019] [Indexed: 05/21/2023]
25
Mateos B, Conrad-Billroth C, Schiavina M, Beier A, Kontaxis G, Konrat R, Felli IC, Pierattelli R. The Ambivalent Role of Proline Residues in an Intrinsically Disordered Protein: From Disorder Promoters to Compaction Facilitators. J Mol Biol 2019;432:3093-3111. [PMID: 31794728 DOI: 10.1016/j.jmb.2019.11.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/23/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022]
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