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For: Schuler B, Lipman EA, Steinbach PJ, Kumke M, Eaton WA. Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence. Proc Natl Acad Sci U S A 2005;102:2754-9. [PMID: 15699337 PMCID: PMC549440 DOI: 10.1073/pnas.0408164102] [Citation(s) in RCA: 366] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Zenker S, Lohmann J, Chiorescu I, Krüger S, Kumke MU, Reich T, Schmeide K, Kretzschmar J. Complexation of Ln(III) Ions by Gluconate: Joint Investigation Applying TRLFS, CE-ICP-MS, NMR, and DF Calculations. Inorg Chem 2025;64:7970-7987. [PMID: 40214153 PMCID: PMC12042262 DOI: 10.1021/acs.inorgchem.4c05476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 03/14/2025] [Accepted: 03/31/2025] [Indexed: 04/29/2025]
2
Dhiman M, Escobar L, Smith JT, Hunter CA. Cooperativity in the assembly of H-bonded duplexes of synthetic recognition-encoded melamine oligomers. Chem Sci 2025;16:5995-6002. [PMID: 40060096 PMCID: PMC11886990 DOI: 10.1039/d4sc08591d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Accepted: 03/02/2025] [Indexed: 04/04/2025]  Open
3
Girvan P, Ying L, Dodson CA. Tetramethylrhodamine self-quenching is a probe of conformational change on the scale of 15-25 Å. Chem Commun (Camb) 2025;61:5353-5356. [PMID: 40084975 PMCID: PMC11908412 DOI: 10.1039/d4cc04524f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 02/27/2025] [Indexed: 03/16/2025]
4
Nüesch M, Ivanović MT, Nettels D, Best RB, Schuler B. Accuracy of distance distributions and dynamics from single-molecule FRET. Biophys J 2025:S0006-3495(25)00202-4. [PMID: 40165371 DOI: 10.1016/j.bpj.2025.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Revised: 02/12/2025] [Accepted: 03/26/2025] [Indexed: 04/02/2025]  Open
5
Gonzalo D, Cupellini L, Curutchet C. On the breakdown of Förster energy transfer theory due to solvent effects: atomistic simulations unveil distance-dependent dielectric screening in calmodulin. Chem Sci 2025;16:3693-3704. [PMID: 39886442 PMCID: PMC11775579 DOI: 10.1039/d4sc07679f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 01/21/2025] [Indexed: 02/01/2025]  Open
6
Peulen TO, Hemmen K, Greife A, Webb BM, Felekyan S, Sali A, Seidel CAM, Sanabria H, Heinze KG. tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling. Bioinformatics 2025;41:btaf025. [PMID: 39836627 PMCID: PMC11796090 DOI: 10.1093/bioinformatics/btaf025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 01/04/2025] [Accepted: 01/17/2025] [Indexed: 01/23/2025]  Open
7
Lam AYW, Tsuboyama K, Tadakuma H, Tomari Y. DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43. RNA (NEW YORK, N.Y.) 2024;30:1422-1436. [PMID: 39117455 PMCID: PMC11482610 DOI: 10.1261/rna.080165.124] [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: 06/26/2024] [Accepted: 07/27/2024] [Indexed: 08/10/2024]
8
Sahl SJ, Matthias J, Inamdar K, Weber M, Khan TA, Brüser C, Jakobs S, Becker S, Griesinger C, Broichhagen J, Hell SW. Direct optical measurement of intramolecular distances with angstrom precision. Science 2024;386:180-187. [PMID: 39388556 DOI: 10.1126/science.adj7368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/03/2024] [Indexed: 10/12/2024]
9
Venturelli A, Guaitoli G, Vanossi D, Saitta F, Fessas D, Vitiello S, Malpezzi G, Aiello D, Ferrari S, Tondi D, Ponterini G, Paola Costi M. Intersite communication in dimeric enzymes highlighted by structural and thermodynamic analysis of didansyltyrosine binding to thymidylate synthases. Bioorg Chem 2024;151:107663. [PMID: 39088977 DOI: 10.1016/j.bioorg.2024.107663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 08/03/2024]
10
Pati AK, Kilic Z, Martin MI, Terry DS, Borgia A, Bar S, Jockusch S, Kiselev R, Altman RB, Blanchard SC. Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation. Nat Methods 2024;21:1222-1230. [PMID: 38877317 PMCID: PMC11239528 DOI: 10.1038/s41592-024-02293-8] [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: 03/29/2023] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
11
Jacobi R, González L. Resonance energy transfer in orthogonally arranged chromophores: a question of molecular representation. Phys Chem Chem Phys 2024;26:12299-12305. [PMID: 38602332 DOI: 10.1039/d4cp00420e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
12
Pietrek LM, Stelzl LS, Hummer G. Hierarchical Assembly of Single-Stranded RNA. J Chem Theory Comput 2024;20:2246-2260. [PMID: 38361440 PMCID: PMC10938505 DOI: 10.1021/acs.jctc.3c01049] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/09/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024]
13
Montepietra D, Tesei G, Martins JM, Kunze MBA, Best RB, Lindorff-Larsen K. FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries. Commun Biol 2024;7:298. [PMID: 38461354 PMCID: PMC10925062 DOI: 10.1038/s42003-024-05910-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/12/2024] [Indexed: 03/11/2024]  Open
14
Waly SMA, Benniston AC, Harriman A. Deducing the conformational space for an octa-proline helix. Chem Sci 2024;15:1657-1671. [PMID: 38303943 PMCID: PMC10829019 DOI: 10.1039/d3sc05287g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]  Open
15
Tsai CL, Chang JW, Cheng KY, Lan YJ, Hsu YC, Lin QD, Chen TY, Shih O, Lin CH, Chiang PH, Simenas M, Kalendra V, Chiang YW, Chen CH, Jeng US, Wang SK. Comprehensive characterization of polyproline tri-helix macrocyclic nanoscaffolds for predictive ligand positioning. NANOSCALE ADVANCES 2024;6:947-959. [PMID: 38298598 PMCID: PMC10825903 DOI: 10.1039/d3na00945a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
16
Oltrogge LM, Chen AW, Chaijarasphong T, Turnšek JB, Savage DF. α-Carboxysome Size Is Controlled by the Disordered Scaffold Protein CsoS2. Biochemistry 2024;63:219-229. [PMID: 38085650 PMCID: PMC10795168 DOI: 10.1021/acs.biochem.3c00403] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
17
Elena-Real CA, Mier P, Sibille N, Andrade-Navarro MA, Bernadó P. Structure-function relationships in protein homorepeats. Curr Opin Struct Biol 2023;83:102726. [PMID: 37924569 DOI: 10.1016/j.sbi.2023.102726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/06/2023]
18
Wu X, Barner-Kowollik C. Fluorescence-readout as a powerful macromolecular characterisation tool. Chem Sci 2023;14:12815-12849. [PMID: 38023522 PMCID: PMC10664555 DOI: 10.1039/d3sc04052f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023]  Open
19
Nepal S, Holmstrom ED. Single-molecule-binding studies of antivirals targeting the hepatitis C virus core protein. J Virol 2023;97:e0089223. [PMID: 37772835 PMCID: PMC10617558 DOI: 10.1128/jvi.00892-23] [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: 06/14/2023] [Accepted: 08/10/2023] [Indexed: 09/30/2023]  Open
20
Detwiler R, McPartlon TJ, Coffey CS, Kramer JR. Clickable Polyprolines from Azido-proline N-Carboxyanhydride. ACS POLYMERS AU 2023;3:383-393. [PMID: 37841952 PMCID: PMC10571246 DOI: 10.1021/acspolymersau.3c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 10/17/2023]
21
Mapes JH, Stover J, Stout HD, Folsom TM, Babcock E, Loudwig S, Martin C, Austin MJ, Tu F, Howdieshell CJ, Simpson ZB, Blom T, Weaver D, Winkler D, Vander Velden K, Ossareh PM, Beierle JM, Somekh T, Bardo AM, Anslyn EV, Marcotte EM, Swaminathan J. Robust and scalable single-molecule protein sequencing with fluorosequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.558007. [PMID: 37745461 PMCID: PMC10516020 DOI: 10.1101/2023.09.15.558007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
22
Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023;435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
23
Heesink G, Marseille MJ, Fakhree MAA, Driver MD, van Leijenhorst-Groener KA, Onck PR, Blum C, Claessens MM. Exploring Intra- and Inter-Regional Interactions in the IDP α-Synuclein Using smFRET and MD Simulations. Biomacromolecules 2023;24:3680-3688. [PMID: 37407505 PMCID: PMC10428166 DOI: 10.1021/acs.biomac.3c00404] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/23/2023] [Indexed: 07/07/2023]
24
Jacob MH, D’Souza RN, Lazar AI, Nau WM. Diffusion-Enhanced Förster Resonance Energy Transfer in Flexible Peptides: From the Haas-Steinberg Partial Differential Equation to a Closed Analytical Expression. Polymers (Basel) 2023;15:polym15030705. [PMID: 36772006 PMCID: PMC9919848 DOI: 10.3390/polym15030705] [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: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023]  Open
25
Montepietra D, Tesei G, Martins JM, Kunze MBA, Best RB, Lindorff-Larsen K. FRETpredict: A Python package for FRET efficiency predictions using rotamer libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525885. [PMID: 36789411 PMCID: PMC9928041 DOI: 10.1101/2023.01.27.525885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
26
Jin Z, Ling C, Li Y, Zhou J, Li K, Yim W, Yeung J, Chang YC, He T, Cheng Y, Fajtová P, Retout M, O'Donoghue AJ, Jokerst JV. Spacer Matters: All-Peptide-Based Ligand for Promoting Interfacial Proteolysis and Plasmonic Coupling. NANO LETTERS 2022;22:8932-8940. [PMID: 36346642 DOI: 10.1021/acs.nanolett.2c03052] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
27
Jacobi R, Hernández-Castillo D, Sinambela N, Bösking J, Pannwitz A, González L. Computation of Förster Resonance Energy Transfer in Lipid Bilayer Membranes. J Phys Chem A 2022;126:8070-8081. [PMID: 36260519 PMCID: PMC9639162 DOI: 10.1021/acs.jpca.2c04524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
28
Rowling PJE, Murton BL, Du Z, Itzhaki LS. Multivalent Interaction of Beta-Catenin With its Intrinsically Disordered Binding Partner Adenomatous Polyposis Coli. Front Mol Biosci 2022;9:896493. [PMID: 35755812 PMCID: PMC9214244 DOI: 10.3389/fmolb.2022.896493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022]  Open
29
Barth A, Opanasyuk O, Peulen TO, Felekyan S, Kalinin S, Sanabria H, Seidel CAM. Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines. J Chem Phys 2022;156:141501. [PMID: 35428384 PMCID: PMC9014241 DOI: 10.1063/5.0089134] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/31/2023]  Open
30
Yokomine M, Morimoto J, Fukuda Y, Shiratori Y, Kuroda D, Ueda T, Takeuchi K, Tsumoto K, Sando S. Oligo(N-methylalanine) as a Peptide-Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites. Angew Chem Int Ed Engl 2022;61:e202200119. [PMID: 35088931 DOI: 10.1002/anie.202200119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Indexed: 12/26/2022]
31
Hu Y, Tian ZY, Xiong W, Wang D, Zhao R, Xie Y, Song YQ, Zhu J, Lu H. Water-Assisted and Protein-Initiated Fast and Controlled Ring-Opening Polymerization of Proline N-Carboxyanhydride. Natl Sci Rev 2022;9:nwac033. [PMID: 36072505 PMCID: PMC9438472 DOI: 10.1093/nsr/nwac033] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/29/2021] [Accepted: 02/15/2022] [Indexed: 12/04/2022]  Open
32
He W, Henning-Knechtel A, Kirmizialtin S. Visualizing RNA Structures by SAXS-Driven MD Simulations. FRONTIERS IN BIOINFORMATICS 2022;2:781949. [PMID: 36304317 PMCID: PMC9580860 DOI: 10.3389/fbinf.2022.781949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022]  Open
33
Yokomine M, Morimoto J, Fukuda Y, Shiratori Y, Kuroda D, Ueda T, Takeuchi K, Tsumoto K, Sando S. Oligo(N‐methylalanine) as a Peptide‐Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
34
Gopich IV, Chung HS. Theory and Analysis of Single-Molecule FRET Experiments. Methods Mol Biol 2022;2376:247-282. [PMID: 34845614 DOI: 10.1007/978-1-0716-1716-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
35
Naudi-Fabra S, Tengo M, Jensen MR, Blackledge M, Milles S. Quantitative Description of Intrinsically Disordered Proteins Using Single-Molecule FRET, NMR, and SAXS. J Am Chem Soc 2021;143:20109-20121. [PMID: 34817999 PMCID: PMC8662727 DOI: 10.1021/jacs.1c06264] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 12/18/2022]
36
Klose D, Holla A, Gmeiner C, Nettels D, Ritsch I, Bross N, Yulikov M, Allain FHT, Schuler B, Jeschke G. Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries. Biophys J 2021;120:4842-4858. [PMID: 34536387 PMCID: PMC8595751 DOI: 10.1016/j.bpj.2021.09.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/09/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023]  Open
37
Das D, Arora L, Mukhopadhyay S. Fluorescence Depolarization Kinetics Captures Short-Range Backbone Dihedral Rotations and Long-Range Correlated Dynamics of an Intrinsically Disordered Protein. J Phys Chem B 2021;125:9708-9718. [PMID: 34415768 DOI: 10.1021/acs.jpcb.1c04426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
38
Alston JJ, Soranno A, Holehouse AS. Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins. Methods 2021;193:116-135. [PMID: 33831596 PMCID: PMC8713295 DOI: 10.1016/j.ymeth.2021.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/21/2022]  Open
39
Li RS, Liu J, Yan Y, Su C, Lai T, Liao Y, Li YF, Li N, Huang CZ. Aggregation-Enhanced Energy Transfer for Mitochondria-Targeted ATP Ratiometric Imaging in Living Cells. Anal Chem 2021;93:11878-11886. [PMID: 34403238 DOI: 10.1021/acs.analchem.1c02833] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
40
Felli IC, Bermel W, Pierattelli R. Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021;2:511-522. [PMID: 37904768 PMCID: PMC10539766 DOI: 10.5194/mr-2-511-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 11/01/2023]
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Mondal S, Mondal S, Seki K, Bagchi B. An exact solution in the theory of fluorescence resonance energy transfer with vibrational relaxation. J Chem Phys 2021;154:134104. [PMID: 33832249 DOI: 10.1063/5.0045008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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Angevine CE, Robertson JWF, Dass A, Reiner JE. Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions. SCIENCE ADVANCES 2021;7:eabf5462. [PMID: 33883140 PMCID: PMC8059931 DOI: 10.1126/sciadv.abf5462] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/04/2021] [Indexed: 05/05/2023]
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021;10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022]  Open
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Panniello A, Trapani M, Cordaro M, Dibenedetto CN, Tommasi R, Ingrosso C, Fanizza E, Grisorio R, Collini E, Agostiano A, Curri ML, Castriciano MA, Striccoli M. High-Efficiency FRET Processes in BODIPY-Functionalized Quantum Dot Architectures. Chemistry 2021;27:2371-2380. [PMID: 32896940 DOI: 10.1002/chem.202003574] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Indexed: 01/24/2023]
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Schepers B, Gohlke H. AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools. J Chem Phys 2021;152:221103. [PMID: 32534525 DOI: 10.1063/5.0007630] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
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Li D, Ren J, Ji F, Peng Q, Teng H, Jia L. Peptide Linker Affecting the Activity Retention Rate of VHH in Immunosorbents. Biomolecules 2020;10:biom10121610. [PMID: 33261088 PMCID: PMC7760621 DOI: 10.3390/biom10121610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/21/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022]  Open
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Sherck N, Webber T, Brown DR, Keller T, Barry M, DeStefano A, Jiao S, Segalman RA, Fredrickson GH, Shell MS, Han S. End-to-End Distance Probability Distributions of Dilute Poly(ethylene oxide) in Aqueous Solution. J Am Chem Soc 2020;142:19631-19641. [DOI: 10.1021/jacs.0c08709] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Morató A, Elena-Real CA, Popovic M, Fournet A, Zhang K, Allemand F, Sibille N, Urbanek A, Bernadó P. Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins. Biomolecules 2020;10:E1458. [PMID: 33086646 PMCID: PMC7603387 DOI: 10.3390/biom10101458] [Citation(s) in RCA: 6] [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: 09/16/2020] [Revised: 10/07/2020] [Accepted: 10/16/2020] [Indexed: 12/23/2022]  Open
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Yang L, Jang SJ. Theoretical investigation of non-Förster exciton transfer mechanisms in perylene diimide donor, phenylene bridge, and terrylene diimide acceptor systems. J Chem Phys 2020;153:144305. [PMID: 33086841 DOI: 10.1063/5.0023709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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Chavali S, Singh AK, Santhanam B, Babu MM. Amino acid homorepeats in proteins. Nat Rev Chem 2020;4:420-434. [PMID: 37127972 DOI: 10.1038/s41570-020-0204-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/16/2022]
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