{"id":98,"date":"2018-05-14T11:31:00","date_gmt":"2018-05-14T09:31:00","guid":{"rendered":"http:\/\/perso.ens-lyon.fr\/loic.salmon\/?page_id=98"},"modified":"2025-01-31T10:34:30","modified_gmt":"2025-01-31T09:34:30","slug":"publications","status":"publish","type":"page","link":"https:\/\/perso.ens-lyon.fr\/loic.salmon\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

\"\"Research Articles and Reviews<\/h3>\n

40. Mitra R, Usher ET, Dedeo\u011flu S, Crotteau MJ, Fraser OA, Yennawar NH, Gadkari VV, Ruotolo BT, Holehouse AS, Salmon L, Showalter SA, Bardwell JCA. Molecular insights into the interaction between a disordered protein and a folded RNA. Proc Natl Acad Sci USA<\/em>. 2024<\/strong> 121(49):e2409139121.<\/p>\n

39. Wu P, Zehnder J, Schr\u00f6der N, Bl\u00fcmmel PEW, Salmon L, Damberger FF, Lipps G, Allain FH, Wiegand T.<\/span> J. <\/span>Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy.<\/a> J Am Chem Soc<\/em> 2024<\/strong> 146:9583-9596<\/span><\/p>\n

38. 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.<\/a> J Am Chem Soc<\/em> 2023<\/strong> 145(42):22964-22978.<\/span><\/p>\n

37. Sannapureddi RKR, Mohanty MK, Salmon L, Sathyamoorthy B<\/span>. Conformational Plasticity of Parallel G-Quadruplex\u2500Implications on Duplex-Quadruplex Motifs.\u00a0<\/a>J Am Chem Soc<\/em> 2023<\/strong> 145:15370-15380<\/span><\/p>\n

36.Nouri S, Boudet J, Dreher-Teo H, Allain FH, Glockshuber R, Salmon L, Giese C. <\/span>Elongated Bacterial Pili as a Versatile Alignment Medium for NMR Spectroscopy.\u00a0<\/a>Angew Chem Int Ed Engl<\/em> 2023,\u00a0<\/strong>62:e202305120
\n<\/span><\/p>\n

35.\u00a0Hoffmann G, Le Gorrec M, Mestdach E, Cusack S, Salmon L, Jensen MR, Palencia A.<\/span> Adenosine-Dependent Activation Mechanism of Prodrugs Targeting an Aminoacyl-tRNA Synthetase.<\/a> J Am Chem Soc<\/em> 2023<\/strong> 145:800-810.
\n<\/span><\/p>\n

34. Lacabanne D, Boudet J, Mal\u00e4r AA, Wu P, Cadalbert R, Salmon L, Allain FH, Meier BH, Wiegand T.\u00a0Protein Side-Chain-DNA Contacts Probed by Fast Magic-Angle Spinning NMR.<\/a><\/span>\u00a0J Phys Chem B<\/em> 2020<\/strong> 124:11089-11097<\/span><\/p>\n

33. Bonaccorsi M, Knight MJ, Le Marchand T, Dannatt HRW, Schubeis T, Salmon L, Felli IC, Emsley L, Pierattelli R, Pintacuda G. Multimodal Response to Copper Binding in Superoxide Dismutase Dynamics.<\/a><\/span> J Am Chem Soc<\/em> 2020<\/strong> 142:19660-19667<\/span>
\nHighlighted in JACS Spotlights: Herman C.<\/span> J Am Chem Soc<\/i><\/span> 2020<\/span><\/strong>, 142<\/span>:<\/span>20271\u201320272<\/span><\/p>\n

32. Rocchio S, Duman R, El Omari K, Mykhaylyk V, Orr C, Yan Z, Salmon L, Wagner A, Bardwell JCA, Horowitz S. Identifying dynamic, partially occupied residues using anomalous scattering.<\/a> Acta Crystallogr D 2019<\/strong> 75:1084-1095.<\/p>\n

31.\u00a0Boudet J, Devillier JC, Wiegand T, Salmon L, Meier BH, Lipps G, Allain FH. A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template.<\/a> Cell<\/em> 2019<\/strong> 176:154-166
\nHighlighted in Cell Previews: Walker JM, Varani G. Cell<\/em> 2019<\/strong> 176:4\u20136<\/p>\n

30. Salmon L*, Stull F, Sayle S, Cato C, Akgu\u0308l S\u0327, Foit L, Ahlstrom LS, Eisenmesser EZ, Al-Hashimi HM, Bardwell JC*, Horowitz S*. The Mechanism of HdeA Unfolding and Chaperone Activation<\/a>. J Mol Biol<\/em> 2018<\/strong>, 430:33-40<\/p>\n

29. Hofmann D, Salmon L, Wider G. Activity of Tumor Necrosis Factor \u03b1 Is Modulated by Dynamic Conformational Rearrangements.<\/a> J Am Chem Soc<\/em> 2018<\/strong>, 140:167-175
\nEvaluated 2 in Faculty of F1000<\/p>\n

28. Salvi N, Salmon L, Blackledge M. Dynamic Descriptions of Highly Flexible Molecules from NMR Dipolar Couplings: Physical Basis and Limitations.<\/a> J Am Chem Soc<\/em> 2017<\/strong>, 139 :5011-5014<\/p>\n

27. Salmon L*, Ahlstrom LS, Horowitz S, Dickson A, Brooks CL*, Bardwell JC*. Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling.<\/a> J Am Chem Soc<\/em> 2016<\/strong>, 138:9826-9839<\/p>\n

26. Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL, Bardwell JC. Visualizing chaperone-assisted protein folding.<\/a> Nat Struct Mol Biol<\/em> 2016<\/strong>, 23:691-697
\nHighlighted in News and Views: Clark PL, Elcock AH. Nat Struct Mol Biol<\/em> 2016<\/strong>, 23:621-623
\nEvaluated 3 in Faculty of 1000<\/p>\n

25. Swanson M, Boudreaux D, Salmon L, Chugh J, Winter H, Meagher J, Andr\u00e9 S, Murphy P, Oscarson S, Roy R, King S, Kaplan M, Goldstein I, Tarbet B, Hurst B, Smee D, de la Fuente C, Hoffmann HH, Xue Y, Rice C, Schols D, Garcia V, Stuckey J, Gabius HJ, Al-Hashimi HM, Markovitz DM. Engineering a Therapeutic Lectin: Uncoupling Mitogenicity from Antiviral Activity.<\/a> Cell<\/em> 2015<\/strong>, 163:746-758<\/p>\n

24. Andra\u0142oj\u0107 W, Ravera E, Salmon L, Parigi G, Al-Hashimi HM, Luchinat C. Inter-helical conformational preferences of HIV-1 TAR-RNA from Maximum Occurrence Analysis of NMR data and molecular dynamics simulations.<\/a> Phys Chem Chem Phys<\/em> 2015<\/strong>, 18:5743-5752<\/p>\n

23. Salmon L, Blackledge M. Investigating Protein Conformational Energy Landscapes and Atomic Resolution Dynamics from NMR Dipolar Couplings: A Review.<\/a> Rep Prog Phys<\/em> 2015<\/strong>, 78:126601<\/p>\n

22. Salmon L, Giamba\u015fu G, Nikolova E, Petzold K, Bhattacharya A, Case D, Al-Hashimi HM. Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.<\/a> J Am Chem Soc<\/em> 2015<\/strong>, 137:12954-12965<\/p>\n

21. Dahl JU, Koldewey P, Salmon L, Horowitz S, Bardwell JC, Jakob U. HdeB Functions as an Acid-Protective Chaperone in Bacteria.<\/a> J Biol Chem<\/em> 2015<\/strong>, 290:65-75<\/p>\n

20. Dickson A, Mustoe A, Salmon L, Brooks CL. Efficient In-Silico Exploration of RNA Interhelical Conformations Using Euler Angles and WExplore.<\/a> Nucleic Acids Res<\/em> 2014<\/strong>, 42:12126-12137<\/p>\n

19. Ravera E, Salmon L, Fragai M, Parigi G, Al-Hashimi HM, Luchinat C. Insights into Domain-Domain Motions in Proteins and RNA from Solution NMR.<\/a> Acc Chem Res<\/em> 2014<\/strong>, 47:3118-3126<\/p>\n

18. Yang S, Salmon L, Al-Hashimi HM. Measuring Similarity between Dynamic Ensembles of Biomolecules.<\/a> Nat Methods<\/em> 2014<\/strong>, 11:552-554<\/p>\n

17. Salmon L, Yang S, Al-Hashimi HM. Advances in the Determination of Nucleic Acid Conformational Ensembles.<\/a> Annu Rev Phys Chem<\/em> 2014<\/strong>, 65:293-316<\/p>\n

16. Salmon L, Bascom G, Andricioaei I, Al-Hashimi HM. A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Inter-helical Motions Revealed.<\/a> J Am Chem Soc<\/em> 2013<\/strong>, 135:5457-5466<\/p>\n

15. Guerry P, Salmon L, Mollica L, Ortega Roldan JL, Markwick PR, van Nuland N, McCammon JA, Blackledge M. Mapping the Population of Protein Conformational Energy Sub-States from NMR Dipolar Couplings.<\/a> Angew Chem Int Ed<\/em> 2013<\/strong>, 52:3181-3185<\/p>\n

14. Ozenne V, Schneider R, Yao M, Huang JR, Salmon L, Zweckstetter M, Jensen MR, Blackledge M. Mapping the Potential Energy Landscape of Intrinsically Disordered Proteins at Amino Acid Resolution.<\/a> J Am Chem Soc<\/em> 2012<\/strong>, 134:15138-15148<\/p>\n

13. Ozenne V, Bauer F, Salmon L, Huang JR, Jensen MR, Segard S, Bernad\u00f3 P, Charavay C, Blackledge M. Flexible-Meccano: a Tool for the Generation of Explicit Ensemble Descriptions of Intrinsically Disordered Proteins and their Associated Experimental Observables.<\/a> Bioinformatics<\/em> 2012<\/strong>, 28:1463-1470<\/p>\n

12. Salmon L, Pierce L, Grimm A, Ortega Roldan JL, Mollica L, Jensen MR, van Nuland N, Markwick PR, McCammon JA, Blackledge M. Multi-Timescale Conformational Dynamics of the SH3 Domain of CD2-Associated Protein using NMR Spectroscopy and Accelerated Molecular Dynamics.<\/a> Angew Chem Int Ed<\/em> 2012<\/strong>, 51:6103-6106<\/p>\n

11. Schneider R, Huang JR, Yao M, Communie G, Ozenne V, Mollica L, Salmon L, Jensen MR, Blackledge M. Towards A Robust Description of Intrinsic Protein Disorder using Nuclear Magnetic Resonance Spectroscopy.<\/a> Mol Biosyst<\/em> 2012<\/strong>, 8:58-68<\/p>\n

10. Jensen MR, Ortega-Roldan JL, Salmon L, van Nuland N, Blackledge M. Characterizing Weak Protein-Protein Complexes by NMR Residual Dipolar Couplings.<\/a> Eur Biophys J<\/em> 2011<\/strong>, 40:1371-1381<\/p>\n

9. Jensen MR, Communie G, Ribeiro EA, Martinez N, Desfosses A, Salmon L, Mollica L, Gabel F, Jamin M, Longhi S, Ruigrok R, Blackledge M. Intrinsic Disorder in Measles Virus Nucleocapsids.<\/a> Proc Natl Acad Sci USA<\/em> 2011<\/strong>, 108:9839-9844<\/p>\n

8. Salmon L, Bouvignies G, Markwick P, Blackledge M. Nuclear Magnetic Resonance Provides a Quantitative Description of Protein Conformational Flexibility on Physiologically Important Time Scales.<\/a> Biochemistry<\/em> 2011<\/strong>, 50:2735-2747<\/p>\n

7. Salmon L, Roldan JL, Lescop E, Licinio A, Van Nuland N, Jensen M, Blackledge M. Structure, Dynamics and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions.<\/a> Angew Chem Int Ed<\/em> 2011<\/strong>, 50:3755-3759
\nEvaluated 1 in Faculty of 1000<\/p>\n

6. Salmon L, Nodet G, Ozenne V, Yin G, Jensen MR, Zweckstetter M, Blackledge M. NMR Characterization of Long-Range Order in Intrinsically Disordered Proteins.<\/a> J Am Chem Soc<\/em> 2010<\/strong>, 132:8407-8418
\nEvaluated 3 in Faculty of 1000<\/p>\n

5. Jensen MR, Salmon L, Nodet G, Blackledge M. De\ufb01ning Conformational Ensembles of Intrinsically Disordered and Partially Folded Proteins Directly from Chemical Shifts.<\/a> J Am Chem Soc<\/em> 2010<\/strong>, 132:1270-1271
\nEvaluated 3 in Faculty of 1000<\/p>\n

4. Nodet G, Salmon L, Ozenne V, Meier S, Jensen MR, Blackledge M. Quantitative Description of Backbone Conformational Sampling of Unfolded Proteins at Amino Acid Resolution from NMR Residual Dipolar Couplings.<\/a> J Am Chem Soc<\/em> 2009<\/strong>, 131:17908-17918<\/p>\n

3. Markwick P, Bouvignies G, Salmon L, McCammon J, Nilges M, Blackledge M. Toward a Uni\ufb01ed Representation of Protein Structural Dynamics in Solution.<\/a> J Am Chem Soc<\/em> 2009<\/strong>, 131:16968-16975<\/p>\n

2. Salmon L, Bouvignies G, Markwick P, Lakomek N, Showalter S, Li DW, Walter K, Griesinger C, Br\u00fcschweiler R, Blackledge M. Protein Conformational Flexibility from Structure-Free Analysis of NMR Dipolar Couplings: Quantitative and Absolute Determination of Backbone Motion in Ubiquitin.<\/a> Angew Chem Int Ed<\/em> 2009<\/strong>, 48:4154-4157
\nHighlighted in News and Views: Tolman JR. Nature<\/em> 2009<\/strong>, 459:1063-1064<\/p>\n

1. Hus JC, Salmon L, Bouvignies G, Lotze J, Blackledge M, Br\u00fcschweiler R. 16-Fold Degeneracy of Peptide Plane Orientations from Residual Dipolar Couplings: Analytical Treatment and Implications for Protein Structure Determination.<\/a> J Am Chem Soc<\/em> 2008<\/strong>, 130:15927-15937
\nEvaluated 2 in Faculty of 1000<\/p>\n

Commentary<\/h3>\n
\n
\n
\n

2.\u00a0Bussi G, Bonomi M, Gkeka P, Sattler M, Al-Hashimi HM, Auffinger P, Duca M, Foricher Y, Incarnato D, Jones AN, Kirmizialtin S, Krepl M, Orozco M, Palermo G, Pasquali S, Salmon L, Schwalbe H, Westhof E, Zacharias M.<\/span> RNA dynamics from experimental and computational approaches.<\/a>\u00a0<\/span> Structure<\/em> 2024 <\/strong>32(9):1281-1287<\/span><\/p>\n

1. Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL 3rd, Bardwell JCA. Reply to ‘Misreading chaperone-substrate complexes from random noise’.<\/a> Nat Struct Mol Biol<\/em> 2018<\/strong> 25:990-991<\/p>\n<\/div>\n<\/div>\n<\/div>\n

Book Chapters<\/h3>\n

4. Salmon L*, Ahlstrom LS, Bardwell JC, Horowitz S*. Selecting Conformational Ensembles Using Residual Electron and Anomalous Density (READ).<\/a> Methods in Molecular Biology<\/em> 2018<\/strong>, 1764:491-504<\/p>\n

3. Salmon L, Jensen MR, Bernado P, Blackledge M. Measurement and Analysis of NMR Residual Dipolar Couplings for the Study of Intrinsically Disordered Proteins.<\/a> Intrinsically Disordered Protein Analysis: Volume 1, Methods and Experimental Tools, Humana Press<\/em> 2012<\/strong><\/p>\n

2. Salmon L, Markwick P, Blackledge M. Residual Dipolar Couplings as a Tool for the Study of Protein Conformation and Conformational Flexibility.<\/a> Recent Developments in Biomolecular NMR, The Royal Society of Chemistry<\/em> 2012<\/strong><\/p>\n

1. Jensen MR, Ozenne V, Salmon L, Nodet G, Markwick P, Bernado P, Blackledge M. Studying Partially Folded and Intrinsically Disordered Proteins using NMR Residual Dipolar Couplings.<\/a> Protein NMR Spectroscopy: Principal Techniques and Applications, Wiley-Blackwell<\/em> 2011<\/strong><\/p>\n

Scientific Popularization<\/h3>\n

2. Salmon L, Blackledge M. La RMN Biomol\u00e9culaire ou la R\u00e9volution en Mouvement.<\/a> L\u2019Actualit\u00e9 Chimique<\/em> 2012<\/strong>, 364-365: 56-58<\/p>\n

1. Salmon L. La Biophysique des Prot\u00e9ines, un Domaine o\u00f9 R\u00e8gne le Plus Grand des Ordres.<\/a> Ordre et D\u00e9sordre: Imbrication et Compl\u00e9mentarit\u00e9 des Notions d’Ordre et de D\u00e9sordre, L’Harmattan<\/em> 2009<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

Research Articles and Reviews 40. Mitra R, Usher ET, Dedeo\u011flu S, Crotteau MJ, Fraser OA,…<\/p>\n

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