Complete publication list

23. Goncalves, M. M.; Uday, A. B.; Forrester, T. J. B.; Currie, S. Q. W.; Kim, A. S.; Feng, Y.; Jitkova, Y.; Velyvis, A.; Harkness, R. W.; Kimber, M. S.; Schimmer, A. D.; Zeytuni, N.; Vahidi, S. Mechanism of allosteric activation in human mitochondrial ClpP protease. bioRxiv 2024. https://doi.org/10.1101/2024.09.27.615468.

22. Harkness, R. W.; Zhao, H.; Toyama, Y.; Schuck, P.; Kay, L. E. Exploring Host–Guest Interactions within a 600 kDa DegP Protease Cage Complex Using Hydrodynamics Measurements and Methyl-TROSY NMR. J. Am. Chem. Soc. 2024, 146 (12), 8242–8259. https://doi.org/10.1021/jacs.3c13247. 

21. Nosella, M. L.; Kim, T. H.; Huang, S. K.; Harkness, R. W.; Goncalves, M.; Pan, A.; Tereshchenko, M.; Vahidi, S.; Rubinstein, J. L.; Lee, H. O.; Forman-Kay, J. D.; Kay, L. E. Poly(ADP-Ribosyl)ation Enhances Nucleosome Dynamics and Organizes DNA Damage Repair Components within Biomolecular Condensates. Molecular Cell 2024, S1097276523010389. https://doi.org/10.1016/j.molcel.2023.12.019. 

20. Irwin, R.; Harkness, R. W.; Forman-Kay, J. D. A FRET-Based Assay and Computational Tools to Quantify Enzymatic Rates and Explore the Mechanisms of RNA Deadenylases in Heterogeneous Environments. In: Deadenylation: Methods and Protocols; Valkov, E., Goldstrohm, A. C., Eds.; Methods in Molecular Biology; Springer US: New York, NY, 2024; Vol. 2723. https://doi.org/10.1007/978-1-0716-3481-3.

19. Sever, A. I. M.; Alderson, T. R.; Rennella, E.; Aramini, J. M.; Liu, Z. H.; Harkness, R. W.; Kay, L. E. Activation of Caspase-9 on the Apoptosome as Studied by Methyl-TROSY NMR. Proc. Natl. Acad. Sci. U.S.A. 2023, 120 (51), e2310944120. https://doi.org/10.1073/pnas.2310944120. 

18. Harkness, R. W.; Ripstein, Z. A.; Di Trani, J. M.; Kay, L. E. Flexible Client-Dependent Cages in the Assembly Landscape of the Periplasmic Protease-Chaperone DegP. J. Am. Chem. Soc. 2023, 145 (24), 13015–13026. https://doi.org/10.1021/jacs.2c11849. 

17. Kim, T. H.; Nosella, M. L.; Bolik-Coulon, N.; Harkness, R. W.; Huang, S. K.; Kay, L. E. Correlating Histone Acetylation with Nucleosome Core Particle Dynamics and Function. Proc. Natl. Acad. Sci. U.S.A. 2023, 120 (15), e2301063120. https://doi.org/10.1073/pnas.2301063120. 

16. Bolik-Coulon, N.; Sever, A. I. M.; Harkness, R. W.; Aramini, J. M.; Toyama, Y.; Hansen, D. F.; Kay, L. E. Less Is More: A Simple Methyl-TROSY Based Pulse Scheme Offers Improved Sensitivity in Applications to High Molecular Weight Complexes. Journal of Magnetic Resonance 2023, 346, 107326. https://doi.org/10.1016/j.jmr.2022.107326. 

15. Toyama, Y.; Harkness, R. W.; Kay, L. E. Structural Basis of Protein Substrate Processing by Human Mitochondrial High-Temperature Requirement A2 Protease. Proc. Natl. Acad. Sci. U.S.A. 2022, 119 (17), e2203172119. https://doi.org/10.1073/pnas.2203172119. 

14. Toyama, Y.; Harkness, R. W.; Kay, L. E. Dissecting the Role of Interprotomer Cooperativity in the Activation of Oligomeric High-Temperature Requirement A2 Protein. Proc. Natl. Acad. Sci. U.S.A. 2021, 118 (35), e2111257118. https://doi.org/10.1073/pnas.2111257118. 

13. Harkness, R. W.; Toyama, Y.; Ripstein, Z. A.; Zhao, H.; Sever, A. I. M.; Luan, Q.; Brady, J. P.; Clark, P. L.; Schuck, P.; Kay, L. E. Competing Stress-Dependent Oligomerization Pathways Regulate Self-Assembly of the Periplasmic Protease-Chaperone DegP. Proc. Natl. Acad. Sci. U.S.A. 2021, 118 (32), e2109732118. https://doi.org/10.1073/pnas.2109732118. 

12. Toyama, Y.; Harkness, R. W.; Lee, T. Y. T.; Maynes, J. T.; Kay, L. E. Oligomeric Assembly Regulating Mitochondrial HtrA2 Function as Examined by Methyl-TROSY NMR. Proc. Natl. Acad. Sci. U.S.A. 2021, 118 (11), e2025022118. https://doi.org/10.1073/pnas.2025022118. 

11. Parupudi, A.; Chaturvedi, S. K.; Adão, R.; Harkness, R. W.; Dragulin-Otto, S.; Kay, L. E.; Esfandiary, R.; Zhao, H.; Schuck, P. Global Multi-Method Analysis of Interaction Parameters for Reversibly Self-Associating Macromolecules at High Concentrations. Sci Rep 2021, 11 (1), 5741. https://doi.org/10.1038/s41598-021-84946-8. 

10. Harkness, R. W.; Hennecker, C.; Grün, J. T.; Blümler, A.; Heckel, A.; Schwalbe, H.; Mittermaier, A. K. Parallel Reaction Pathways Accelerate Folding of a Guanine Quadruplex. Nucleic Acids Research 2021, 49 (3), 1247–1262. https://doi.org/10.1093/nar/gkaa1286. 

9. Harkness, R. W.; Toyama, Y.; Kay, L. E. Analyzing Multi-Step Ligand Binding Reactions for Oligomeric Proteins by NMR: Theoretical and Computational Considerations. Journal of Magnetic Resonance 2020, 318, 106802. https://doi.org/10.1016/j.jmr.2020.106802.  

8. Grün, J. T.; Hennecker, C.; Klötzner, D.-P.; Harkness, R. W.; Bessi, I.; Heckel, A.; Mittermaier, A. K.; Schwalbe, H. Conformational Dynamics of Strand Register Shifts in DNA G-Quadruplexes. J. Am. Chem. Soc. 2020, 142 (1), 264–273. https://doi.org/10.1021/jacs.9b10367. 

7. Harkness V, R. W.; Avakyan, N.; Sleiman, H. F.; Mittermaier, A. K. Mapping the Energy Landscapes of Supramolecular Assembly by Thermal Hysteresis. Nat Commun 2018, 9 (1), 3152. https://doi.org/10.1038/s41467-018-05502-z. 

6. Harkness V, R. W.; Johnson, P. E.; Mittermaier, A. K. Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions. JoVE 2017, No. 129, 55959. https://doi.org/10.3791/55959. 

5. Harkness, R. W.; Mittermaier, A. K. G-Quadruplex Dynamics. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2017, 1865 (11), 1544–1554. https://doi.org/10.1016/j.bbapap.2017.06.012. 

4. Assi, H. A.; Harkness, R. W.; Martin-Pintado, N.; Wilds, C. J.; Campos-Olivas, R.; Mittermaier, A. K.; González, C.; Damha, M. J. Stabilization of I-Motif Structures by 2′-β-Fluorination of DNA. Nucleic Acids Res 2016, 44 (11), 4998–5009. https://doi.org/10.1093/nar/gkw402. 

3. Harkness, R. W.; Mittermaier, A. K. G-Register Exchange Dynamics in Guanine Quadruplexes. Nucleic Acids Res 2016, 44 (8), 3481–3494. https://doi.org/10.1093/nar/gkw190. 

2. Harkness, R. W.; Slavkovic, S.; Johnson, P. E.; Mittermaier, A. K. Rapid Characterization of Folding and Binding Interactions with Thermolabile Ligands by DSC. Chem. Commun. 2016, 52 (92), 13471–13474. https://doi.org/10.1039/C6CC05576A. 

1. Edwards, D. R.; Maxwell, C. I.; Harkness, R. W.; Neverov, A. A.; Mosey, N. J.; Stan Brown, R. Experimental and Computational Determination of Brønsted Coefficients for Equilibrium Transfer of the O , O ‐dimethyl Phosphorothioyl Group between Oxyanion Nucleophiles. J of Physical Organic Chem 2012, 25 (3), 258–266. https://doi.org/10.1002/poc.1903.