Publications

Guzikowski NJ, Shin O, **Khan YA**, Esquivies L, Alten B, Brunger AT and Kavalali ET. Synaptobrevin-2 Disease Variants Reveal Spatial Constraints Within the Presynaptic Active Zone. Under text revision at PNAS.

Held RG, Liang J, Esquivies L, Khan YA, Wang C, Azubel M, Brunger AT. In-Situ Structure and Topography of AMPA Receptor Scaffolding Complexes Visualized by CryoET. Under review at Science (bioRxiv: https://doi.org/10.1101/2024.10.19.619226)

**Khan YA**, White KI, Pfuetzner RA, Singal B, Esquivis L, Mckenzie G, Liu F, DeLong K, Choi UB, Montabana E, Mclaughlin T, Wickner WT, **Brunger AT**. SNARE disassembly requires Sec18/NSF side loading. Nature Structural and Molecular Biology. 2025 Jul 2. doi: 10.1038/s41594-025-01590-w

Loughran G, De Pace R, Carancini G, Mudge MJ, Kellis M, Atkins JF, Baranov PV, Firth AE, Bonifacino JS, **Khan YA**. Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active mediator of kinesin-1-dependent lysosome transport. Under review at Science Advances (bioRxiv: https://doi.org/10.1101/2024.08.30.610563)

White KI, Khan YA, Qiu K, Couoh-Cardel S, Esquivies L, Pfuetzner R, Diao J, Brunger AT. NSF converts syntaxin nanodomains to a priming-ready state. Accepted and in press at Nature Communications. (bioRxiv: https://doi.org/10.1101/2024.10.11.617886)

Hayes T, …, Khan YA, … Rives A. Simulating 500 million years of evolution with a language model. Science. 2025 Jan 16:eads0018. doi: 10.1126/science.ads0018.

Abramson J, .., Khan YA, …, Hassabis D, Jumper JM. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature. 2024 Jun;630(8016):493-500. doi: 10.1038/s41586-024-07487-w.

**Khan YA**, Hokia C, Xu J, Ehlert B. covLLM: Large Language Models for COVID-19 Biomedical Literature. arXiv. 2023 https://doi.org/10.48550/arXiv.2306.04926.

**Gao Y**, **Khan YA**, Mo W, White KI, Perkins M, Pfuetzner RA, Trapani JG, Brunger AT, Nicolson T. Sensory deficit screen identifies nsf mutation that differentially affects SNARE recycling and quality control. Cell Rep. 2023 Apr 5;42(4):112345. doi: 10.1016/j.celrep.2023.112345.

Loughran G., Fedorova A. D., Khan YA, Atkins J. F., & Baranov P. V. Lack of evidence for ribosomal frameshifting in ATP7B mRNA decoding. Molecular cell, 82(19), 3745-3749.

**Khan YA**, **Loughran G**, Steckelberg AL, Brown K, Kiniry SJ, Stewart H, Baranov PV, Kieft JS, Firth AE, Atkins JF. Evaluating ribosomal frameshifting in CCR5 mRNA decoding. Nature. 2022 Apr;604(7906):E16-E23. doi: 10.1038/s41586-022-04627-y.

Zhang K, Horikoshi N, Li S, Powers AS, Hameedi MA, Pintilie GD, Chae HD, Khan YA, Suomivuori CM, Dror RO, Sakamoto KM, Chiu W, Wakatsuki S. Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia. ACS Cent Sci. 2022 Feb 23;8(2):214-222. doi: 10.1021/acscentsci.1c01090.

**Khan YA**, White KI, **Brunger AT**. The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines. Crit Rev Biochem Mol Biol. 2022 Apr;57(2):156-187. doi: 10.1080/10409238.2021.1979460.

**Khan YA**, **Jungreis I**, Wright JC, Mudge JM, Choudhary JS, Firth AE, Kellis M. Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. BMC Genetics. 2020;21(1):25. Published 2020 Mar 6. doi: 10.1186/s12863-020-0828-7

Rocco-Machado N, Cosentino-Gomes D, Nascimento M, L. Paes Vieriera, Khan YA, Mittra B, Andrews NW, Meyer-Fernandes JR. Leishmania amazonensis ferric iron reductase (LFR1) is a bifunctional enzyme: Unveiling a NADPH oxidase activity. Free Radical Biology and Medicine. 2019;143:341-353. doi: 10.1016/j.freeradbiomed.2019.08.026.

Khan YA, Andrews NW, Mittra B. ROS regulate differentiation of visceralizing Leishmania species into the virulent amastigote form. Parasitology Open. 2018;4:e19. doi: 10.1017/pao.2018.15

Sarkar A, Khan YA, Laranjeira-Silva MF, Andrews NW, Mittra B. Quantification of Intracellular Growth Inside Macrophages is a Fast and Reliable Method for Assessing the Virulence of Leishmania Parasites. Journal of Visualized Experiments. 2018;(133):57486. Published 2018 Mar 16. doi: 10.3791/57486

Briggs JW, Ren L, Chakrabarti KR, Tsai YC, Weissman AM, Hansen RJ, Gustafson DL, Khan YA, Dinman JD, Khanna C. Activation of the unfolded protein response in sarcoma cells treated with rapamycin or temsirolimus. PLoS One. 2017;12(9):e0185089. Published 2017 Sep 19. doi: 10.1371/journal.pone.0185089

Girardi T, Vereecke S, Sulima SO, Khan Y, Fancello L, Briggs JW, Schwab C, de Beeck JO, Verbeeck J, Royaert J, Geerdens E, Vicente C, Bornschein S, Harrison CJ, Meijerink JP, Cools J, Dinman JD, Kampen KR, De Keersmaecker K. The T-cell leukemia-associated ribosomal RPL10 R98S mutation enhances JAK-STAT signaling. Leukemia. 2018;32(3):809–819. doi: 10.1038/leu.2017.225

Meydan S, Klepacki D, Karthikeyan S, Margus T, Thomas P, Jones JE, Khan Y, Briggs J, Dinman JD, Vázquez-Laslop N, Mankin AS. Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene. Molecular Cell. 2017;65(2):207–219. doi: 10.1016/j.molcel.2016.12.008

Kendra JA, de la Fuente C, Brahms A, Woodson C, Bell TM, Chen B, Khan YA, Jacobs JL, Kehn-Hall K, Dinman JD. Ablation of Programmed -1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity. Journal of Virology. 2017;91(3):e01766-16. Published 2017 Jan 18. doi: 10.1128/JVI.01766-16

Moomau C, Musalgaonkar S, Khan YA, Jones JE, Dinman JD. Structural and Functional Characterization of Programmed Ribosomal Frameshift Signals in West Nile Virus Strains Reveals High Structural Plasticity Among cis-Acting RNA Elements. Journal of Biological Chemistry. 2016;291(30):15788–15795. doi: 10.1074/jbc.M116.735613