Publications

1. Laracuente, X. E., Delfing, B. M., Luo, X., Olson, A., Jeffries, W., Bowers, S. R., Foreman, K. W., Lee, K.-H., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2025) Applying absolute free energy perturbation molecular dynamics to diffusively binding ligands. J. Chem. Theory Comput. (accepted)

2. He, S., Haikerwal, A., Tiwari, S., Dabbagh, D., Alam, M. Z., Yoon, J. L., Hetrick, B., Han, Y., Shan, L., Lockhart, C., & Wu, Y. (2025) CD34 serves as an intrinsic innate immune guardrail protecting stem cells from replicating retroviruses. bioRxiv (posted), doi: 10.1101/2025.03.15.643450

3. Xie, L., Lockhart, C., Bowers, S. R., Klimov, D. K., & Jafri, M. S. (2025) Structural analysis of amylin and amyloid β peptide signaling in Alzheimer’s disease. Biomolecules 15(1): 89, doi: 10.3390/biom15010089

4. Tiwari, S., Delfing, B. M., Han, Y., Lockhart, C., Haikerwal, A., Waheed, A. A., Freed, E. O., Jafri, M. S., Klimov, D. K., & Wu, Y. (2024) PSGL-1 excludes HIV Env from virion surface through spatial hindrance involving structural folding of the decameric repeats. bioRxiv (posted), doi: 10.1101/2024.12.28.630612v1

5. Goldberg, J. F., de Filippi, C. R., Lockhart, C., McNair, E. R., Sinha, S., Kong, H., Najjar, S. S., Lohmar, B. J., Tchoukina, I., Shah, K., Feller, E., Hsu, S., Rodrigo, M. E., Jang, M., Marboe, C. C., Berry, G. J., Valantine, H. A., Agbor-Enoh, A., & Shah, P. (2024) Proteomics in acute heart transplant rejection, on behalf of the GRAfT Investigators. Transplantation (in press), doi: 10.1097/TP.0000000000005258

6. Delfing, B. M., Laracuente, X. E., Luo, X., Olson, A., Jeffries, W., Foreman, K. W., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2024) Binding of inhibitors to nuclear localization signal peptide from Venezuelan equine encephalitis virus capsid protein explored with all-atom replica exchange molecular dynamics. ACS Omega 9(38): 40259-40268, doi: 10.1021/acsomega.4c06981

7. Delfing, B. M., Laracuente, X. E., Jeffries, W., Luo, X., Olson, A., Foreman, K. W., Petruncio, G., Lee, K. H., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2024) Competitive binding of viral nuclear localization signal peptide and inhibitor ligands to importin-α nuclear transport protein. J. Chem. Inf. Model. 64(13): 5262-5272, doi: 10.1021/acs.jcim.4c00626

8. Bowers, S. R., Lockhart, C., & Klimov, D. K. (2024) Binding and dimerization of PGLa peptides in anionic lipid bilayer studied by replica exchange molecular dynamics. Sci. Rep. 14: 4972, doi: 10.1038/s41598-024-55270-8

9. Bowers, S. R., Lockhart, C., & Klimov, D. K. (2023) Replica exchange with hybrid tempering efficiently samples PGLa peptide binding to anionic bilayer. J. Chem. Theory Comput. 19(18): 6532-6550, doi: 10.1021/acs.jctc.3c00787

10. Delfing, B. M., Laracuente, X. E., Olson, A., Foreman, K. W., Paige, M., Kehn-hall, K., Lockhart, C., & Klimov, D. K. (2023) Binding of viral nuclear localization signal peptides to importin-α nuclear transport protein. Biophys. J. 122(17): 3476-3488, doi: 10.1016/j.bpj.2023.07.024

11. Lockhart, C., Luo, X., Olson, A., Delfing, B. M., Laracuente, X. E., Foreman, K. W., Paige, M., Kehn-Hall, K., & Klimov, D. K. (2023) Can free energy perturbation simulations coupled with replica-exchange molecular dynamics study ligands with distributed binding sites? J. Chem. Inf. Model. 63(15): 4791-4802, doi: 10.1021/acs.jcim.3c00631

12. Delfing, B. M., Olson, A., Laracuente, X. E., Foreman, K. W., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2023) Binding of Venezuelan equine encephalitis virus inhibitors to importin-α receptors explored with all-atom replica exchange molecular dynamics. J. Phys. Chem. B 127(14): 3175-3186, doi: 10.1021/acs.jpcb.3c00429

13. Khayat, E., Delfing, B. M., Laracuente, X. E., Olson, A., Lockhart, C., & Klimov, D. K. (2023) Lysine acetylation changes the mechanism of Aβ25-35 peptide binding and dimerization in the DMPC bilayer. ACS Chem. Neurosci. 14(3): 494-505, doi: 10.1021/acschemneuro.2c00722

14. Vergilio, J., Lockhart, C., & Klimov, D. K. (2022) De novo transmembrane aggregation of Aβ10-40 peptides in anionic lipid bilayer. J. Chem. Inf. Model. 62(23): 6228-6241, doi: 10.1021/acs.jcim.2c01192

15. Bowers, S. R., Klimov, D. K., & Lockhart, C. (2022) Mechanisms of binding of antimicrobial peptide PGLa to DMPC/DMPG membrane. J. Chem. Inf. Model. 62(6): 1525-1537, doi: 10.1021/acs.jcim.1c01518

16. Khayat, E., Lockhart, C., Delfing, B. M., Smith, A. K., & Klimov, D. K. (2021) Met35 oxidation hinders Aβ25-35 peptide aggregation within the dimyristoylphosphatidylcholine bilayer. ACS Chem. Neurosci. 12(17): 3225-3236, doi: 10.1021/acschemneuro.1c00407

17. Siwy, C. M., Delfing, B. M., Lockhart, C., Smith, A. K., & Klimov, D. K. (2021) Partitioning of Aβ peptide fragments into blood–brain barrier mimetic bilayer. J. Phys. Chem. B 125(10): 2658-2676, doi: 10.1021/acs.jpcb.0c11253

18. Lockhart, C., Smith, A. K., & Klimov, D. K. (2020) Three popular force fields predict consensus mechanism of Aβ peptide binding to the DMPC bilayer. J. Chem. Inf. Model. 60(4): 2282-2293, doi: 10.1021/acs.jcim.0c00096

19. Smith, A. K., Khayat, E., Lockhart, C., & Klimov, D. K. (2019) Do cholesterol and sphingomyelin change the mechanism of Aβ25-35 peptide binding to zwitterionic bilayer? J. Chem. Inf. Model. 59(12): 5207-5217, doi: 10.1021/acs.jcim.9b00763

20. Lockhart, C., Smith, A. K., & Klimov, D. K. (2019) Methionine oxidation changes the mechanism of Aβ peptide binding to the DMPC bilayer. Sci. Rep. 9(5947): 1-12, doi: 10.1038/s41598-019-42304-9

21. Lockhart, C. & Klimov, D. K. (2017) Cholesterol changes the mechanism of Aβ peptide binding to the DMPC bilayer. J. Chem. Inf. Model. 57(10): 2554-2565, doi: 10.1021/acs.jcim.7b00431

22. Siwy, C. M., Lockhart, C., & Klimov, D. K. (2017) Is the conformational ensemble of Alzheimer's Aβ10-40 peptide force field dependent? PLoS Comput. Biol. 13(1): e1005314, doi: 10.1371/journal.pcbi.1005314

23. Smith, A. K., Lockhart, C., & Klimov, D. K. (2016) Does replica exchange with solute tempering efficiently sample Aβ peptide conformational ensembles? J. Chem. Theory Comput. 12(10): 5201-5214, doi: 10.1021/acs.jctc.6b00660

24. Lockhart, C. & Klimov, D. K. (2016) The Alzheimer's disease Aβ peptide binds to the anionic DMPS lipid bilayer. Biochim. Biophys. Acta 1858(6): 1118-1128, doi: 10.1016/j.bbamem.2016.03.001

25. Lockhart, C. (2015) All-atom explicit-solvent replica-exchange molecular dynamics simulations of the Alzheimer's disease Aβ monomer. Dissertation. George Mason University.

26. Lockhart, C., O’Connor, J., Armentrout, S., & Klimov, D. K. (2015) Greedy replica exchange algorithm for heterogeneous computing grids. J. Mol. Model. 21(9): 243, doi: 10.1007/s00894-015-2763-5

27. Lockhart, C. & Klimov, D. K. (2015) Calcium enhances binding of Aβ monomer to DMPC bilayer. Biophys. J. 108(7): 1807-1818, doi: 10.1016/j.bpj.2015.03.001

28. Lockhart, C. & Klimov, D. K. (2014) Binding of Aβ peptide creates lipid density depression in DMPC bilayer. Biochim. Biophys. Acta 1838(10): 2678-2688, doi: 10.1016/j.bbamem.2014.07.010

29. Lockhart, C. & Klimov, D. K. (2014) Alzheimer's Aβ10-40 peptide binds and penetrates DMPC bilayer: an isobaric-isothermal replica exchange molecular dynamics study. J. Phys. Chem. B 118(10): 2638-2648, doi: 10.1021/jp412153s

30. Lockhart, C. & Klimov, D. K. (2013) Revealing hidden helix propensity in Aβ peptide by molecular dynamics simulations. J. Phys. Chem. B 117(40): 12030-12038, doi: 10.1021/jp407705j

31. Lockhart, C. & Klimov, D. K. (2012) Molecular interactions of Alzheimer's biomarker FDDNP with Aβ peptide. Biophys. J. 103(11): 2341-2351, doi: 10.1016/j.bpj.2012.10.003

32. Lockhart, C., Kim, S., & Klimov, D. K. (2012) Explicit solvent molecular dynamics simulations of Aβ peptide interacting with ibuprofen ligands. J. Phys. Chem. B 116(43): 12922-12932, doi: 10.1021/jp306208n

33. Lockhart, C., Kim, S., Kumar, R., & Klimov, D. K. (2011) Does amino acid sequence determine the properties of Aβ dimer? J. Chem. Phys. 135: 14915, doi: 10.1063/1.3610427