Publications

41.

Replica exchange molecular dynamics with hydrogen mass repartitioning improves sampling of peptide binding to a lipid bilayer.

Bowers, S. R., Lockhart, C., & Klimov, D. K.

J. Chem. Theory Comput. (2026) (accepted)

40.

Discovery of actinator, actin-derived bioactive peptides that modulate cytoskeleton and actin-related cellular activities.

Yi, F., Guo, J., Vo, T. T., Hetrick, B., Haikerwal, A., Zhou, Z., Sealey, L., He, S., Han, Y., Chilin, L., Spear, M., Yu, D., Kim, Y., Kashanchi, F., Zhou, T., Xu, X., Lockhart, C., & Wu, Y.

Sci. Adv. (2026) 12(16): eaeb5548

39.

Accelerating replica exchange molecular dynamics: A comparison of hydrogen mass repartitioning and light water models.

Bowers, S. R., Jeffries, W., Lockhart, C., & Klimov, D. K.

J. Chem. Theory Comput. (2026) (accepted)

38.

Free energy perturbation simulations measure the change in binding affinity of the Aβ25–35 peptide to the zwitterionic bilayer caused by oxidation.

Luo, X., Khayat, E., Bowers, S. R., Delfing, B. M., Lockhart, C., & Klimov, D. K.

J. Chem. Inf. Model. (2025) 65(21): 12014-12026

37.

Ligands binding diffusively to protein target act as inhibitors of protein-protein interactions.

Jeffries, W., Delfing, B. M., Laracuente, X. E., Luo, X., Olson, A., Foreman, K. W., Lee, K. H., Petruncio, G., De Benedictis, V., Paige, M. Kehn-Hall, K., Lockhart, C., & Klimov, D. K.

PLoS Comput. Biol. (2025) 21(9): e1013495

36.

Combining molecular dynamics and machine learning to predict drug resistance causing variants of BRAF in colorectal cancer.

Xie, L., Lockhart, C., Klimov, D. K., & Jafri, M. S.

Molecules (2025) 30(17): 3556

35.

Binding of antimicrobial peptide indolicidin to DMPC bilayer using replica-exchange molecular dynamics.

Fitz, A. R., Klimov, D. K., & Lockhart, C.

J. Chem. Inf. Model. (2025) 65(17): 9251-9260

34.

The decameric repeat (DR) of PSGL-1 functions as a basic antiviral unit in restricting HIV-1 infectivity.

Han, Y., Sealey, L., Fu, Y., Delfing, B. M., Lockhart, C., Chilin, L., Tiwari, S., Jafri, M. S., Klimov, D. K., & Wu, Y.

bioRxiv (2025)(posted)

33.

Applying absolute free energy perturbation molecular dynamics to diffusively binding ligands.

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.

J. Chem. Theory Comput. (2025) 21(8): 4286-4298

32.

CD34 serves as an intrinsic innate immune guardrail protecting stem cells from replicating retroviruses.

He, S., Haikerwal, A., Tiwari, S., Dabbagh, D., Alam, M. Z., Yoon, J. L., Hetrick, B., Han, Y., Shan, L., Lockhart, C., & Wu, Y.

bioRxiv (2025)(posted)

31.

Structural analysis of amylin and amyloid β peptide signaling in Alzheimer’s disease.

Xie, L., Lockhart, C., Bowers, S. R., Klimov, D. K., & Jafri, M. S.

Biomolecules (2025) 15(1): 89

30.

PSGL-1 excludes HIV Env from virion surface through spatial hindrance involving structural folding of the decameric repeats.

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.

bioRxiv (2024)(posted)

29.

Proteomics in acute heart transplant rejection, on behalf of the GRAfT Investigators.

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.

Transplantation (2024)(in press)

28.

Binding of inhibitors to nuclear localization signal peptide from Venezuelan equine encephalitis virus capsid protein explored with all-atom replica exchange molecular dynamics.

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.

ACS Omega (2024) 9(38): 40259-40268

27.

Competitive binding of viral nuclear localization signal peptide and inhibitor ligands to importin-α nuclear transport protein.

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.

J. Chem. Inf. Model. (2024) 64(13): 5262-5272

26.

Binding and dimerization of PGLa peptides in anionic lipid bilayer studied by replica exchange molecular dynamics.

Bowers, S. R., Lockhart, C., & Klimov, D. K.

Sci. Rep. (2024) 14: 4972

25.

Replica exchange with hybrid tempering efficiently samples PGLa peptide binding to anionic bilayer.

Bowers, S. R., Lockhart, C., & Klimov, D. K.

J. Chem. Theory Comput. (2023) 19(18): 6532-6550

24.

Binding of viral nuclear localization signal peptides to importin-α nuclear transport protein.

Delfing, B. M., Laracuente, X. E., Olson, A., Foreman, K. W., Paige, M., Kehn-hall, K., Lockhart, C., & Klimov, D. K.

Biophys. J. (2023) 122(17): 3476-3488

23.

Can free energy perturbation simulations coupled with replica-exchange molecular dynamics study ligands with distributed binding sites?

Lockhart, C., Luo, X., Olson, A., Delfing, B. M., Laracuente, X. E., Foreman, K. W., Paige, M., Kehn-Hall, K., & Klimov, D. K.

J. Chem. Inf. Model. (2023) 63(15): 4791-4802

22.

Binding of Venezuelan equine encephalitis virus inhibitors to importin-α receptors explored with all-atom replica exchange molecular dynamics.

Delfing, B. M., Olson, A., Laracuente, X. E., Foreman, K. W., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K.

J. Phys. Chem. B (2023) 127(14): 3175-3186

21.

Lysine acetylation changes the mechanism of Aβ25-35 peptide binding and dimerization in the DMPC bilayer.

Khayat, E., Delfing, B. M., Laracuente, X. E., Olson, A., Lockhart, C., & Klimov, D. K.

ACS Chem. Neurosci. (2023) 14(3): 494-505

20.

De novo transmembrane aggregation of Aβ10-40 peptides in anionic lipid bilayer.

Vergilio, J., Lockhart, C., & Klimov, D. K.

J. Chem. Inf. Model. (2022) 62(23): 6228-6241

19.

Mechanisms of binding of antimicrobial peptide PGLa to DMPC/DMPG membrane.

Bowers, S. R., Klimov, D. K., & Lockhart, C.

J. Chem. Inf. Model. (2022) 62(6): 1525-1537

18.

Met35 oxidation hinders Aβ25-35 peptide aggregation within the dimyristoylphosphatidylcholine bilayer.

Khayat, E., Lockhart, C., Delfing, B. M., Smith, A. K., & Klimov, D. K.

ACS Chem. Neurosci. (2021) 12(17): 3225-3236

17.

Partitioning of Aβ peptide fragments into blood–brain barrier mimetic bilayer.

Siwy, C. M., Delfing, B. M., Lockhart, C., Smith, A. K., & Klimov, D. K.

J. Phys. Chem. B (2021) 125(10): 2658-2676

16.

Lockhart, C., Smith, A. K., & Klimov, D. K.

J. Chem. Inf. Model. (2020) 60(4): 2282-2293

15.

Do cholesterol and sphingomyelin change the mechanism of Aβ25-35 peptide binding to zwitterionic bilayer?

Smith, A. K., Khayat, E., Lockhart, C., & Klimov, D. K.

J. Chem. Inf. Model. (2019) 59(12): 5207-5217

14.

Methionine oxidation changes the mechanism of Aβ peptide binding to the DMPC bilayer.

Lockhart, C., Smith, A. K., & Klimov, D. K.

Sci. Rep. (2019) 9(5947): 1-12

13.

Cholesterol changes the mechanism of Aβ peptide binding to the DMPC bilayer.

Lockhart, C. & Klimov, D. K.

J. Chem. Inf. Model. (2017) 57(10): 2554-2565

12.

Is the conformational ensemble of Alzheimer's Aβ10-40 peptide force field dependent?

Siwy, C. M., Lockhart, C., & Klimov, D. K.

PLoS Comput. Biol. (2017) 13(1): e1005314

11.

Does replica exchange with solute tempering efficiently sample Aβ peptide conformational ensembles?

Smith, A. K., Lockhart, C., & Klimov, D. K.

J. Chem. Theory Comput. (2016) 12(10): 5201-5214

10.

The Alzheimer's disease Aβ peptide binds to the anionic DMPS lipid bilayer.

Lockhart, C. & Klimov, D. K.

Biochim. Biophys. Acta (2016) 1858(6): 1118-1128

Molecular dynamics simulations of peptides relevant to Alzheimer's disease

Lockhart, C.

PhD Dissertation, George Mason University (2015)

Greedy replica exchange algorithm for heterogeneous computing grids.

Lockhart, C., O'Connor, J., Armentrout, S., & Klimov, D. K.

J. Mol. Model. (2015) 21(9): 243

Calcium enhances binding of Aβ monomer to DMPC bilayer.

Lockhart, C. & Klimov, D. K.

Biophys. J. (2015) 108(7): 1807-1818

Binding of Aβ peptide creates lipid density depression in DMPC bilayer.

Lockhart, C. & Klimov, D. K.

Biochim. Biophys. Acta (2014) 1838(10): 2678-2688

Alzheimer's Aβ10-40 peptide binds and penetrates DMPC bilayer: an isobaric-isothermal replica exchange molecular dynamics study.

Lockhart, C. & Klimov, D. K.

J. Phys. Chem. B (2014) 118(10): 2638-2648

Revealing hidden helix propensity in Aβ peptide by molecular dynamics simulations.

Lockhart, C. & Klimov, D. K.

J. Phys. Chem. B (2013) 117(40): 12030-12038

Molecular interactions of Alzheimer's biomarker FDDNP with Aβ peptide.

Lockhart, C. & Klimov, D. K.

Biophys. J. (2012) 103(11): 2341-2351

Explicit solvent molecular dynamics simulations of Aβ peptide interacting with ibuprofen ligands.

Lockhart, C., Kim, S., & Klimov, D. K.

J. Phys. Chem. B (2012) 116(43): 12922-12932

Does amino acid sequence determine the properties of Aβ dimer?

Lockhart, C., Kim, S., Kumar, R., & Klimov, D. K.

J. Chem. Phys. (2011) 135: 35103