2025 publications (updated June 16, 2025)
1. Pham S, Zhao B, Neetu N, Sankaran B, Patil K, Ramani S, Song Y, Estes MK, Palzkill T, Prasad BVV. Conformational flexibility is a critical factor in designing broad-spectrum human norovirus protease inhibitors. J Virol. 2025 Feb 25;99(2):e0175724. doi: 10.1128/jvi.01757-24. Epub 2025 Jan 28.PMID: 39873493 (5.0.1, 5.0.2, 8.2.1, 8.2.2)
2. Gupta S, Russell B, Kristensen LG, Tyler J, Costello SM, Marqusee S, Rad B, Ralston CY. Enabling simultaneous photoluminescence spectroscopy and X-ray footprinting mass spectrometry to study protein conformation and interactions. Anal Methods. 2025 Feb 6;17(6):1214-1225. Doi: 10.1039/d4ay01670j. PMID: 39749913 (3.3.1)
3. Patt E, Classen S, Hammel M, Schneidman-Duhovny D. Predicting RNA structure and dynamics with deep learning and solution scattering. Biophys J. 2025 Feb 4;124(3):549-564. doi: 10.1016/j.bpj.2024.12.024. PMID: 39722452 (12.3.1)
4. Surendra Bikram Silwal, Bode Wamsley, Zongyao Wang, Benjamin W Gung, Jay C Nix, Richard C Page. Mutation of an active site-adjacent residue in VIM indirectly dictates interactions with and blunts inhibition by D-captopril. J Inorg Biochem. 2025 Jun 10:271:112975. doi: 10.1016/j.jinorgbio.2025.112975. PMID: 40513263
5. Kiera Malone, Margaret Phillips, Ajit Singh, Isabelle Kressy, Brian Boyle, James Lignos, Jay Nix, Karen Glass. High conservation doesn’t always translate: A comparison of ATAD2 and ATAD2B structure and function. Struct. Dyn. 12, A67 (2025). https://doi.org/10.1063/4.0000376
6. Karen Glass, Ajit Singh, Mirabella Vulikh, Margaret Phillips, Marco Tonelli, Trushar Patel, Borries Demeler, Jay Nix. Plasmodium falciparum Bromodomain Protein 1 (PfBDP1): A master regulator of red blood cell invasion genes. Struct. Dyn. 12, A399 (2025), https://doi.org/10.1063/4.0000705
7. Sayler RI, Thomas WC, Rose AJ, Marletta MA. Electron transfer in polysaccharide monooxygenase catalysis. Proc Natl Acad Sci U S A. 2025 Jan 7;122(1):e2411229121. doi: 10.1073/pnas.2411229121. Epub 2024 Dec 30.PMID: 39793048 (5.0.1, 5.0.2, 5.0.3., 2.0.1)
8. Stadnicki EJ, Ludewig H, Kumar RP, Wang X, Qiao Y, Kern D, Bradshaw N. Dual-Action Kinase Inhibitors Influence p38α MAP Kinase Dephosphorylation. Proc Natl Acad Sci U S A. 2025 Jan 7;122(1):e2415150122. doi: 10.1073/pnas.2415150122.PMID: 39149408 (2.0.1)
9. Gan J, Juang V, Wang K, Xia Z, Ackermann R, Yu M, Dorsey KH, Lin W, Wang X, Wang Y, Liang J, Zheng J, Xu X, Park JH, Schwendeman A. Reverse engineering of Onivyde® – Irinotecan liposome injection. Int J Pharm. 2025 Jan 25;669:125000. doi: 10.1016/j.ijpharm.2024.125000. Epub 2024 Nov 27.PMID: 39608586 (12.3.1)
10. Liu F, Mailhot O, Glenn IS, Vigneron SF, Bassim V, Xu X, Fonseca-Valencia K, Smith MS, Radchenko DS, Fraser JS, Moroz YS, Irwin JJ, Shoichet BK. The impact of Library Size and Scale of Testing on Virtual Screening. Nat Chem Biol. 2025 Jan 3. doi: 10.1038/s41589-024-01797-w.PMID: 39026784 (8.3.1)
11. Liu C, Rao G, Nguyen J, Britt RD, Rittle J. O2 Activation and Enzymatic C-H Bond Activation Mediated by a Dimanganese Cofactor. J Am Chem Soc. 2025 Jan 15;147(2):2148-2157. doi: 10.1021/jacs.4c16271. Epub 2025 Jan 1.PMID: 39741465 (5.0.1, 5.0.2)
12. Craven, G.B., H. Chu, J.D. Sun, J.D. Carelli, B. Coyne, H. Chen, Y. Chen, X. Ma, S. Das, W. Kong, A.D. Zajdlik, K.S. Yang, S.H. Reisberg, P.A. Thompson, J.R. Lipford, and J. Taunton, “Mutant-selective AKT inhibition through lysine targeting and neo-zinc chelation,” Nature 2025 Jan 637(8044), 205-214 (2025). (doi:10.1038/s41586-024-08176-4) (2.0.1, 8.3.1)
13. Samuels ER, Sevrioukova IF. Evaluation of Larger Side-Group Functionalities and the Side/End-Group Interplay in Ritonavir-Like Inhibitors of CYP3A4. Chem Biol Drug Des. 2025 Jan;105(1):e70043. doi: 10.1111/cbdd.70043.PMID: 39792691 (8.2.1, 8.2.2)
14. Botting JM, Rahman MK, Xu H, Yue J, Guo W, Del Mundo JT, Hammel M, Motaleb MA, Liu J. FlbB forms a distinctive ring essential for periplasmic flagellar assembly and motility in Borrelia burgdorferi. PLoS Pathog. 2025 Jan 8;21(1):e1012812. doi: 10.1371/journal.ppat.1012812. eCollection 2025 Jan.PMID: 39777417 (12.3.1)
15. Lee S, Kibler RD, Ahn G, Hsia Y, Borst AJ, Philomin A, Kennedy MA, Huang B, Stoddard B, Baker D. Four-component protein nanocages designed by programmed symmetry breaking. Nature. 2025 Feb;638(8050):546-552. doi: 10.1038/s41586-024-07814-1. Epub 2024 Dec 18.PMID: 39695226 (5.0.1)
16. Cory SA, Lin CW, Patra S, Havens SM, Putnam CD, Shirzadeh M, Russell DH, Barondeau DP. Frataxin Traps Low Abundance Quaternary Structure to Stimulate Human Fe-S Cluster Biosynthesis. Biochemistry. 2025 Feb 18;64(4):903-916. doi: 10.1021/acs.biochem.4c00733. Epub 2025 Feb 5.PMID: 39909887 (12.3.1)
17. Li B, Usai R, Campbell J, Wang Y. Elucidating ligand interactions and small-molecule activation in the pyrrolnitrin biosynthetic enzyme PrnB. J Biol Chem. 2025 Feb;301(2):108123. doi: 10.1016/j.jbc.2024.108123. Epub 2024 Dec 25.PMID: 39725034 (5.0.3)
18. Brosey CA, Shen R, Tainer JA. NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism. EMBO J. 2025 Feb;44(4):1220-1248. doi: 10.1038/s44318-024-00360-6. Epub 2025 Jan 13.PMID: 39806100 (8.3.1,12.3.1)
19. Rodriguez Carrero RJ, Lloyd CT, Borkar J, Nath S, Mirica LM, Nair S, Booker SJ, Metcalf W. Genetic and biochemical characterization of a radical SAM enzyme required for post-translational glutamine methylation of methyl-coenzyme M reductase. mBio. 2025 Feb 5;16(2):e0354624. doi: 10.1128/mbio.03546-24. Epub 2025 Jan 8.PMID: 39772843 (BCSB)
20. Williford EE, Xue YP, Tang WK, Li R, Jones KV, Blake KS, Blaine HC, Lian X, Stallings CL, Tolia NH, Dantas G, Wencewicz TA. C10-Benzoate Esters of Anhydrotetracycline Inhibit Tetracycline Destructases and Recover Tetracycline Antibacterial Activity. ACS Infect Dis. 2025 Mar 14;11(3):738-749. doi: 10.1021/acsinfecdis.4c00912. Epub 2025 Feb 6.PMID: 39912785 (5.0.2)
21. Ireland KA, Kayrouz CM, Abbott ML, Seyedsayamdost MR, Davis KM. Structural and functional analysis of SAM-dependent N-methyltransferases involved in ovoselenol and ovothiol biosynthesis. Structure. 2025 Mar 6;33(3):528-538.e5. doi: 10.1016/j.str.2024.12.020. Epub 2025 Jan 24.PMID: 39862859 (8.2.2, 8.2.1)
22. Meeks KR, Ji J, Scott GK, Campbell AC, Nix JC, Tadeo A, Ellerby LM, Benz CC, Tanner JJ. Biochemical, structural, and cellular characterization of S-but-3-yn-2-ylglycine as a mechanism-based covalent inactivator of the flavoenzyme proline dehydrogenase. Arch Biochem Biophys. 2025 Mar;765:110319. doi: 10.1016/j.abb.2025.110319. Epub 2025 Jan 25.PMID: 39870289 (4.2.2, 8.2.1)
23. Gong M, Ye Q, Gu Y, Chambers LR, Bobkov AA, Arakawa NK, Matyszewski M, Corbett KD. Structural diversity and oligomerization of bacterial ubiquitin-like proteins. Structure. 2025 Apr 8:S0969-2126(25)00108-X. doi: 10.1016/j.str.2025.03.011.PMID: 39605667 (5.0.1)
24. Cannistraci E, Srinivasu BY, Chavez Orozco J Jr, Gozzi K, Wales TE, Schumacher MA. Allosteric activation mechanism of DriD, a WYL-domain containing transcription regulator. Commun Biol. 2025 Apr 29;8(1):679. doi: 10.1038/s42003-025-08111-x.PMID: 40301632 (5.0.2)
25. Srisantitham S, Walker AL, Markel U, Tezcan FA. De Novo Design of Proteins for Autocatalytic Isopeptide Bond Formation. J Am Chem Soc. 2025 Apr 9;147(14):12338-12346. doi: 10.1021/jacs.5c03319. Epub 2025 Mar 26.PMID: 40138671 (8.3.1, 5.0.1)
26. Jones CP, Ferré-D’Amaré AR. Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus-programmed ribosomal frameshifting element. Proc Natl Acad Sci U S A. 2025 Apr 8;122(14):e2418418122. doi: 10.1073/pnas.2418418122. Epub 2025 Apr 2.PMID: 40172966 (5.0.1)
27. Trasviña-Arenas CH, Dissanayake UC, Tamayo N, Hashemian M, Lin WJ, Demir M, Hoyos-Gonzalez N, Fisher AJ, Cisneros GA, Horvath MP, David SS. Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair. Nat Commun. 2025 Apr 16;16(1):3596. doi: 10.1038/s41467-025-58361-w.PMID: 40234396 (5.0.1, 8.3.1)
28. Basanta B, Nugroho K, Yan NL, Kline GM, Powers ET, Tsai FJ, Wu M, Hansel-Harris A, Chen JS, Forli S, Kelly JW, Lander GC. The conformational landscape of human transthyretin revealed by cryo-EM. Nat Struct Mol Biol. 2025 May;32(5):876-883. doi: 10.1038/s41594-024-01472-7.PMID: 38328110 (5.0.1)
29. Correy GJ, Rachman MM, Togo T, Gahbauer S, Doruk YU, Stevens MGV, Jaishankar P, Kelley B, Goldman B, Schmidt M, Kramer T, Radchenko DS, Moroz YS, Ashworth A, Riley P, Shoichet BK, Renslo AR, Walters WP, Fraser JS. Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning. Sci Adv. 2025 May 30;11(22):eads7187. doi: 10.1126/sciadv.ads7187. Epub 2025 May 28.PMID: 40435250 (8.3.1)
30. Fenwick MK, Mayclin SJ, Seibold S, DeRocher AE, Subramanian S, Phan IQ, Dranow DM, Lorimer DD, Abramov AB, Choi R, Hewitt SN, Edwards TE, Bullard JM, Battaile KP, Wower IK, Soe AC, Tsutakawa SE, Lovell S, Myler PJ, Wower J, Staker BL. Architecture of Pseudomonas aeruginosa glutamyl-tRNA synthetase defines a subfamily of dimeric class Ib aminoacyl-tRNA synthetases. Proc Natl Acad Sci U S A. 2025 May 13;122(19):e2504757122. doi: 10.1073/pnas.2504757122. Epub 2025 May 9.PMID: 40343997 (12.3.1)
31. Berndsen CE, Storm AR, Sardelli AM, Hossain SR, Clermont KR, McFather LM, Connor MA, Monroe JD. The pseudoenzyme β-amylase9 from Arabidopsis binds to and enhances the activity of α-amylase3: A possible mechanism to promote stress-induced starch degradation. Proteins. 2025 Jun;93(6):1189-1201. doi: 10.1002/prot.26803.PMID: 39149391 (12.3.1)
32. Cheung YWS, Nam SE, Fairlie GMJ, Scheu K, Bui JM, Shariati HR, Gsponer J, Yip CK. Structure of the human autophagy factor EPG5 and the molecular basis of its conserved mode of interaction with Atg8-family proteins. Autophagy. 2025 Jun;21(6):1173-1191. doi: 10.1080/15548627.2024.2447213. Epub 2025 Jan 14.PMID: 39809444 (5.0.2)