2025 Publications

Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV

Biswas A, Choudhuri I, Huang K, Sun Q, Sali A, Echeverria I, Haldane A, Levy RM, Lyumkis D. bioRxiv [Preprint]. 2025 May 2:2025.04.30.651576. doi: 10.1101/2025.04.30.651576.

PMID: 40364913

PMCID: PMC12073831

Structural and mechanistic bases for resistance of the M66I capsid variant to lenacapavir

Briganti L, Annamalai AS, Bester SM, Wei G, Andino-Moncada JR, Singh SP, Kleinpeter AB, Tripathi M, Nguyen B, Radhakrishnan R, Singh PK, Greenwood J, Schope LI, Haney R, Huang S-W, Freed EO, Engelman AN, Francis AC, Kvaratskhelia M. mBio. 2025 May 14;16(5):e0361324. doi: 10.1128/mbio.03613-24. Epub 2025 Apr 15.

PMID: 40231850

PMCID: PMC12077090

In vivo detection of HIV-1 antisense transcripts in untreated and ART-treated individuals

Capoferri AA, Sklutuis R, Famuyiwa TO, Pathak S, Li R, Rausch JW, Luke BT, Hoh R, Deeks SG, Mellors JW, Coffin JM, Groebner JL, Romerio F, Kearney MF. bioRxiv [Preprint]. 2025 Feb 25:2024.12.06.627170. doi: 10.1101/2024.12.06.627170.

PMID: 40093179

PMCID: PMC11908204

Elements in the 5′ Untranslated Region of Viral RNA Important for HIV Gag Recognition and Cross-Packaging

Cheng Z, Nikolaitchik OA, Duchon A, Rawson JMO, Pathak VK, Hu WS. Viruses. 2025 Apr 10;17(4):551. doi: 10.3390/v17040551.

PMID: 40284994

PMCID: PMC12031250

A monomeric envelope glycoprotein cytoplasmic tail is sufficient for HIV-1 Gag lattice trapping and incorporation

Groves NS, Clark AR, Aguilar RS, Hikichi Y, Kostenko A, Bruns MM, Aron AT, Freed EO, van Engelenburg SB. J Virol. 2025 May 20;99(5):e0210524. doi: 10.1128/jvi.02105-24. Epub 2025 Apr 15.

PMID: 40231821

PMCID: PMC12090761

Differential HIV-1 Proviral Defects in Children vs. Adults on Antiretroviral Therapy

Hasson JM, Katusiime MG, Capoferri AA, Bale MJ, Luke BT, Shao W, Cotton MF, van Zyl G, Patro SC, Kearney MF. bioRxiv [Preprint]. 2025 May 27:2025.05.23.655786. doi: 10.1101/2025.05.23.655786. Update in: Viruses. 2025 Jul 09;17(7):961. doi: 10.3390/v17070961.

PMID: 40501537

PMCID: PMC12154797

The primary mechanism for highly potent inhibition of HIV-1 maturation by lenacapavir

Huang SW, Briganti L, Annamalai AS, Greenwood J, Shkriabai N, Haney R, Armstrong ML, Wempe MF, Singh SP, Francis AC, Engelman AN, Kvaratskhelia M.  PLoS Pathog. 2025 Jan 27;21(1):e1012862. doi: 10.1371/journal.ppat.1012862.

PMID: 39869652

PMCID: PMC11892807

HIV-1 transcription start sites usage and its impact on unspliced RNA functions in people living with HIV

Islam S, Maldarelli F, Nikolaitchik OA, Cheng Z, Gorelick R, Nikolaitchik MA, Pathak VK, Hu W-S. mBio. 2025 Feb 5;16(2):e0357624. doi: 10.1128/mbio.03576-24. Epub 2024 Dec 27.

PMID: 39727416

PMCID: PMC11796365

Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding

Jing T, Shan Z, Dinh T, Biswas A, Jang S, Greenwood J, Li M, Zhang Z, Gray G, Shin HJ, Zhou B, Passos D, Strutzenberg TS, Aiyer S, Andrade L, Zhang Y, Li Z, Craigie R, Engelman AN, Kvaratskhelia M, Lyumkis D.. bioRxiv [Preprint]. 2025 May 21:2024.01.26.577436. doi: 10.1101/2024.01.26.577436.

PMID: 38328132

PMCID: PMC10849644

Divergent populations of HIV-infected naive and memory CD4+ T cell clones in children on antiretroviral therapy

Katusiime MG, Neer V, Guo S, Patro SC, Wang W, Luke B, Capoferri AA, Wu X, Horner AM, Rausch JW, Chahroudi A, Mavigner M, Kearney MF. J Clin Invest. 2025 Mar 6;135(9):e188533. doi: 10.1172/JCI188533.

PMID: 40048262

PMCID: PMC12043081

The central pore of HIV-1 capsomers promotes sustained stability of the viral capsid

Kleinpeter AB, Mallery DL, Albecka A, Burdick RC, Renner N, Klarhof JO, Vamos B, Pathak VK, James LC, Freed EO. bioRxiv [Preprint]. 2025 May 19:2025.05.19.654868. doi: 10.1101/2025.05.19.654868.

PMID: 40475674

PMCID: PMC12139970

Lenacapavir disrupts HIV-1 core integrity while stabilizing the capsid lattice

Li C, Burdick RC, Siddiqui R, Janaka SK, Hsia RC, Hu WS, Pathak VK. Proc Natl Acad Sci U S A. 2025 Apr 8;122(14):e2420497122. doi: 10.1073/pnas.2420497122. Epub 2025 Apr 1.

PMID: 40168125

PMCID: PMC12002175

A Hybrid Bottom-Up and Data-Driven Machine Learning Approach for Accurate Coarse-Graining of Large Molecular Complexes

Liebl K, Voth GA. J Chem Theory Comput. 2025 May 13;21(9):4846-4854. doi: 10.1021/acs.jctc.5c00063. Epub 2025 Apr 16.

PMID: 40241350

PMCID: PMC12268871

Considerations for capsid-targeting antiretrovirals in pre-exposure prophylaxis

McFadden WM, Faerch M, Kirby KA, Dick RA, Torbett BE, Sarafianos SG. Trends Mol Med. 2025 Feb 27:S1471-4914(25)00013-9. doi: 10.1016/j.molmed.2025.01.013. Epub ahead of print.

PMID: 40021388

PMCID: PMC12270248

How to recover from a bad start: adaptation of HIV-1 transcription start site mutants during serial passaging in culture

Nikolaitchik OA, Chameettachal A, Islam S, Cheng Z, Delviks-Frankenberry K, Keele BF, Pathak VK, Hu W-S. J Virol. 2025 Jun 17;99(6):e0015925. doi: 10.1128/jvi.00159-25. Epub 2025 May 7.

PMID: 40331822

PMCID: PMC12172438

Anti-sense oligonucleotide probing as a structural platform for studying ribonucleoprotein complex assembly

Sheng K, Dong X, Aiyer S, Lee J, Đorđević-Marquardt S, Lyumkis D, Williamson JR. Nat Commun. 2025 Jul 18;16(1):6642. doi: 10.1038/s41467-025-61640-1.

PMID: 40681486

PMCID: PMC12274283

Nucleosome Engagement Regulates RORγt Structure and Dynamics

Strutzenberg TS, Mann MD, Li X, Shin H, Kelsey J, Aiyer S, Yu J, Gray G, Zhang Z, Shan Z, Zhou B, Zheng Y, Griffin PR, Lyumkis D. bioRxiv [Preprint]. 2025 Mar 12:2025.03.10.642251. doi: 10.1101/2025.03.10.642251

PMID: 40161694

PMCID: PMC11952427

MSBack: Multiscale Backmapping of Highly Coarse-Grained Proteins Using Constrained Diffusion

Waltmann C, Wang Y, Yang C, Kim S, Voth GA. J Chem Theory Comput. 2025 Jun 24;21(12):6184-6193. doi: 10.1021/acs.jctc.5c00459. Epub 2025 Jun 1.

PMID: 40452189

PMCID: PMC12199737