Publications
Research Articles and Reviews
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. J Am Chem Soc 2023 in press
37. . Conformational Plasticity of Parallel G-Quadruplex─Implications on Duplex-Quadruplex Motifs. J Am Chem Soc 2023 45:15370-15380
36.Elongated Bacterial Pili as a Versatile Alignment Medium for NMR Spectroscopy. Angew Chem Int Ed Engl 2023, 62:e202305120
35. Adenosine-Dependent Activation Mechanism of Prodrugs Targeting an Aminoacyl-tRNA Synthetase. J Am Chem Soc 2023 145:800-810.
34. J Phys Chem B 2020 124:11089-11097
33. J Am Chem Soc 2020 142:19660-19667
Highlighted in JACS Spotlights: Herman C. J Am Chem Soc 2020, 142:20271–20272
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. Acta Crystallogr D 2019 75:1084-1095.
31. Boudet 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. Cell 2019 176:154-166
Highlighted in Cell Previews: Walker JM, Varani G. Cell 2019 176:4–6
30. Salmon L*, Stull F, Sayle S, Cato C, Akgül Ş, Foit L, Ahlstrom LS, Eisenmesser EZ, Al-Hashimi HM, Bardwell JC*, Horowitz S*. The Mechanism of HdeA Unfolding and Chaperone Activation. J Mol Biol 2018, 430:33-40
29. Hofmann D, Salmon L, Wider G. Activity of Tumor Necrosis Factor α Is Modulated by Dynamic Conformational Rearrangements. J Am Chem Soc 2018, 140:167-175
Evaluated 2 in Faculty of F1000
28. Salvi N, Salmon L, Blackledge M. Dynamic Descriptions of Highly Flexible Molecules from NMR Dipolar Couplings: Physical Basis and Limitations. J Am Chem Soc 2017, 139 :5011-5014
27. Salmon L*, Ahlstrom LS, Horowitz S, Dickson A, Brooks CL*, Bardwell JC*. Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling. J Am Chem Soc 2016, 138:9826-9839
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. Nat Struct Mol Biol 2016, 23:691-697
Highlighted in News and Views: Clark PL, Elcock AH. Nat Struct Mol Biol 2016, 23:621-623
Evaluated 3 in Faculty of 1000
25. Swanson M, Boudreaux D, Salmon L, Chugh J, Winter H, Meagher J, André 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. Cell 2015, 163:746-758
24. Andrałojć 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. Phys Chem Chem Phys 2015, 18:5743-5752
23. Salmon L, Blackledge M. Investigating Protein Conformational Energy Landscapes and Atomic Resolution Dynamics from NMR Dipolar Couplings: A Review. Rep Prog Phys 2015, 78:126601
22. Salmon L, Giambaşu 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. J Am Chem Soc 2015, 137:12954-12965
21. Dahl JU, Koldewey P, Salmon L, Horowitz S, Bardwell JC, Jakob U. HdeB Functions as an Acid-Protective Chaperone in Bacteria. J Biol Chem 2015, 290:65-75
20. Dickson A, Mustoe A, Salmon L, Brooks CL. Efficient In-Silico Exploration of RNA Interhelical Conformations Using Euler Angles and WExplore. Nucleic Acids Res 2014, 42:12126-12137
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. Acc Chem Res 2014, 47:3118-3126
18. Yang S, Salmon L, Al-Hashimi HM. Measuring Similarity between Dynamic Ensembles of Biomolecules. Nat Methods 2014, 11:552-554
17. Salmon L, Yang S, Al-Hashimi HM. Advances in the Determination of Nucleic Acid Conformational Ensembles. Annu Rev Phys Chem 2014, 65:293-316
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. J Am Chem Soc 2013, 135:5457-5466
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. Angew Chem Int Ed 2013, 52:3181-3185
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. J Am Chem Soc 2012, 134:15138-15148
13. Ozenne V, Bauer F, Salmon L, Huang JR, Jensen MR, Segard S, Bernadó 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. Bioinformatics 2012, 28:1463-1470
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. Angew Chem Int Ed 2012, 51:6103-6106
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. Mol Biosyst 2012, 8:58-68
10. Jensen MR, Ortega-Roldan JL, Salmon L, van Nuland N, Blackledge M. Characterizing Weak Protein-Protein Complexes by NMR Residual Dipolar Couplings. Eur Biophys J 2011, 40:1371-1381
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. Proc Natl Acad Sci USA 2011, 108:9839-9844
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. Biochemistry 2011, 50:2735-2747
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. Angew Chem Int Ed 2011, 50:3755-3759
Evaluated 1 in Faculty of 1000
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. J Am Chem Soc 2010, 132:8407-8418
Evaluated 3 in Faculty of 1000
5. Jensen MR, Salmon L, Nodet G, Blackledge M. Defining Conformational Ensembles of Intrinsically Disordered and Partially Folded Proteins Directly from Chemical Shifts. J Am Chem Soc 2010, 132:1270-1271
Evaluated 3 in Faculty of 1000
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. J Am Chem Soc 2009, 131:17908-17918
3. Markwick P, Bouvignies G, Salmon L, McCammon J, Nilges M, Blackledge M. Toward a Unified Representation of Protein Structural Dynamics in Solution. J Am Chem Soc 2009, 131:16968-16975
2. Salmon L, Bouvignies G, Markwick P, Lakomek N, Showalter S, Li DW, Walter K, Griesinger C, Brüschweiler R, Blackledge M. Protein Conformational Flexibility from Structure-Free Analysis of NMR Dipolar Couplings: Quantitative and Absolute Determination of Backbone Motion in Ubiquitin. Angew Chem Int Ed 2009, 48:4154-4157
Highlighted in News and Views: Tolman JR. Nature 2009, 459:1063-1064
1. Hus JC, Salmon L, Bouvignies G, Lotze J, Blackledge M, Brüschweiler R. 16-Fold Degeneracy of Peptide Plane Orientations from Residual Dipolar Couplings: Analytical Treatment and Implications for Protein Structure Determination. J Am Chem Soc 2008, 130:15927-15937
Evaluated 2 in Faculty of 1000
Commentary
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’. Nat Struct Mol Biol 2018 25:990-991
Book Chapters
4. Salmon L*, Ahlstrom LS, Bardwell JC, Horowitz S*. Selecting Conformational Ensembles Using Residual Electron and Anomalous Density (READ). Methods in Molecular Biology 2018, 1764:491-504
3. Salmon L, Jensen MR, Bernado P, Blackledge M. Measurement and Analysis of NMR Residual Dipolar Couplings for the Study of Intrinsically Disordered Proteins. Intrinsically Disordered Protein Analysis: Volume 1, Methods and Experimental Tools, Humana Press 2012
2. Salmon L, Markwick P, Blackledge M. Residual Dipolar Couplings as a Tool for the Study of Protein Conformation and Conformational Flexibility. Recent Developments in Biomolecular NMR, The Royal Society of Chemistry 2012
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. Protein NMR Spectroscopy: Principal Techniques and Applications, Wiley-Blackwell 2011
Scientific Popularization
2. Salmon L, Blackledge M. La RMN Biomoléculaire ou la Révolution en Mouvement. L’Actualité Chimique 2012, 364-365: 56-58
1. Salmon L. La Biophysique des Protéines, un Domaine où Règne le Plus Grand des Ordres. Ordre et Désordre: Imbrication et Complémentarité des Notions d’Ordre et de Désordre, L’Harmattan 2009