Publications 2025

Highlights & Publications

FlbB forms a distinctive ring essential for periplasmic flagellar assembly and motility in Borrelia burgdorferi
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  1. AbdElwakil MM, Ni J, Ramsay-Burrough S, Hurst PJ, McClellan RL, Khasnavis SR, Jia Y, Masud SR, Blake TR, Sallets A, Haabeth OAW, Sagiv-Barfi I, Czerwinski DK, Herrera-Barrera M, Levy R, Wender PA, Kumar ME, Waymouth RM. “In Vivo mRNA Delivery to the Lung Vascular Endothelium by Dicationic Charge-Altering Releasable Transporters.” Journal of the American Chemical Society 2025 Nov 05 ;147(44):40146-40157 link
  2. Hurst PJ, Jia Y, Ramsay-Burrough S, McClellan RL, Arens JT, Khasnavis SR, Del Castillo TJ, AbdElwakil MM, Lueckheide MJ, Prabhu VM, Waymouth RM. “The Structure and Morphology of Single-Component Oligomeric RNA Delivery Vectors Derived from Amphiphilic Charge-Altering Releasable Transporters.” ACS nano 2025 Nov 18 ;19(45):38954-38969 link
  3. Nguyen K, Biswas S, Kc S, Walgren A, Nicholson V, Childs C, Medina-Rodriguez BX, Alvarado V, Sukenik S, Holehouse A, Boothby TC. “A phase transition modulates the protective function of a tardigrade disordered protein during desiccation.” Protein science : a publication of the Protein Society 2025 Oct ;34(10):e70300 link
  4. McBride AC, Yu F, Cheng EH, Mpouli A, Soe AC, Hammel M, Montelione GT, Oas TG, Tsutakawa SE, Donald BR. “Predicting Pose Distribution of Protein Domains Connected by Flexible Linkers Is an Unsolved Problem.” Proteins 2025 Oct 16 link
  5. Feinberg MA, Le MT, Carpio KL, Knyazhanskaya E, Barrett ADT, Choi KH. “Interaction of West Nile virus NS5 with orthoflavivirus SLA RNAs and their effects on viral replication and inhibition.” Journal of virology 2025 Sep 23 ;99(9):e0202324 link
  6. Berger S, Lee EF, Harris TJ, Tran S, Bera AK, Arguinchona L, Kang A, Sankaran B, Kasapgil S, Miller MS, Smyth S, Lutfi M, Uren RT, Kluck RM, Colman PM, Fairlie WD, Czabotar PE, Baker D, Birkinshaw RW. “Computational design of potent and selective binders of BAK and BAX.” Science advances 2025 Sep 05 ;11(36):eadt4170 link
  7. Nguyen BV, Özden C, Dong K, Koc OC, Torres-Ocampo AP, Dziedzic N, Flaherty D, Huang J, Sankara S, Abromson NL, Tomchick DR, Fissore RA, Chen J, Garman SC, Stratton MM. “A domain-swapped CaMKII conformation facilitates linker-mediated allosteric regulation.” Nature communications 2025 Sep 26 ;16(1):8461 link
  8. Shweta H, Gupta K, Zhou Y, Cui X, Li S, Lu Z, Goldman YE, Dantzig JA. “Characterization and structural basis for the brightness of mCLIFY: a novel monomeric and circularly permuted bright yellow fluorescent protein.” Research square 2024 Jul 19 link
  9. Driskill MM, Coates IA, Hurst PJ, Rajesh NU, Dulay MT, Waymouth RM, Akahata W, Matsuda K, Smith JF, Jacobson GB, Perry JL, Tian S, DeSimone JM. “Lyophilized SARS-CoV-2 self-amplifying RNA vaccines for microneedle array patch delivery.” Journal of controlled release : official journal of the Controlled Release Society 2025 Aug 10 ;384:113944 link
  10. Ralston CY, Gupta S, Del Mundo JT, Soe AC, Russell B, Rad B, Tyler J, Paul S, Kahan DN, Kristensen LG, Subramanian S, Kidd S, Burnett K, Sankaran B, Classen S, Prigozhin DM, Taylor JR, Dickert JM, Royal KB, Rozales A, Ortega SL, Allaire M, Nix JC, Hura GL, Holton JM, Hammel M, Adams PD. “ALS-ENABLE: creating synergy and opportunity at the Advanced Light Source synchrotron structural biology beamlines.” Journal of synchrotron radiation 2025 Jul 01 ;32(Pt 4):1059-1067 link
  11. Khmelinskaia A, Bethel NP, Fatehi F, Mallik BB, Antanasijevic A, Borst AJ, Lai SH, Chim HY, Wang JY’, Miranda MC, Watkins AM, Ogohara C, Caldwell S, Wu M, Heck AJR, Veesler D, Ward AB, Baker D, Twarock R, King NP. “Local structural flexibility drives oligomorphism in computationally designed protein assemblies.” Nature structural & molecular biology 2025 Jun ;32(6):1050-1060 link
  12. Rambo RP, Tainer JA. “Information Theory Optimization of Signals from Small Angle Scattering Measurements.” Biophysical journal 2025 Jun 27 link
  13. Longo MA, Ahmed SM, Chen Y, Tsai CL, Namjoshi S, Shen R, Ahmed Z, Wang X, Perera RL, Arvai A, Lee M, Kong LR, Engl W, Ng WS, Zhao ZW, Venkitaraman AR, Tainer JA, Schlacher K. “BRCA2 C-terminal clamp restructures RAD51 dimers to bind B-DNA for replication fork stability.” Molecular cell 2025 Jun 05 ;85(11):2080-2096.e6 link
  14. Gupta K, Sekulić N, Allu PK, Sapp N, Huang Q, Sarachan K, Christensen M, Lund R, Krueger S, Curtis JE, Gillilan RE, Van Duyne GD, Black BE. “Solution conformational differences between conventional and CENP-A nucleosomes are accentuated by reversible deformation under high pressure.” Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2025 Jun 12 ;33(1):11 link
  15. Eneli A, Wang K, Gan J, Diwan R, Lu Z, Yu M, Ackermann R, Shay B, Schwendeman A. “A Comparative Study on Physicochemical and Analytical Characterizations of Doxil® and its Generic Drug Products.” The AAPS journal 2025 Jun 02 ;27(4):100 link
  16. 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.” Proceedings of the National Academy of Sciences of the United States of America 2025 May 13 ;122(19):e2504757122 link
  17. Arkinson C, Dong KC, Gee CL, Costello SM, Soe AC, Hura GL, Marqusee S, Martin A. “NUB1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome.” Nature structural & molecular biology 2025 Apr 11 link
  18. Olp MD, Bursch KL, Wynia-Smith SL, Nuñez R, Goetz CJ, Jackson V, Smith BC. “Multivalent nucleosome scaffolding by bromodomain and extraterminal domain tandem bromodomains.” The Journal of biological chemistry 2025 Mar ;301(3):108289 link
  19. Roy S, Wang B, Roy K, Tian Y, Bhattacharya M, Williams S, Yin Q. “Crystal structures reveal nucleotide-induced conformational changes in G motifs and distal regions in human guanylate-binding protein 2.” Communications biology 2025 Feb 22 ;8(1):282 link
  20. Nicholson V, Nguyen K, Gollub E, McCoy M, Yu F, Holehouse AS, Sukenik S, Boothby TC. “LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation.” Protein science : a publication of the Protein Society 2025 Feb ;34(2):e70028 link
  21. 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 link
  22. Patt E, Classen S, Hammel M, Schneidman-Duhovny D. “Predicting RNA structure and dynamics with deep learning and solution scattering.” Biophysical journal 2025 Feb 04 ;124(3):549-564 link
  23. Brosey CA, Shen R, Tainer JA. “NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism.” The EMBO journal 2025 Feb ;44(4):1220-1248 link
  24. 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 link
  25. 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.” International journal of pharmaceutics 2025 Jan 25 ;669:125000 link
  26. 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 pathogens 2025 Jan 08 ;21(1):e1012812 link
  27. Berndsen CE, Storm AR, Sardelli AM, Hossain SR, Clermont KR, McFather LM, Connor MA, Monroe JD. “The Pseudoenzyme β-Amylase9 From Arabidopsis Activates α-Amylase3: A Possible Mechanism to Promote Stress-Induced Starch Degradation.” Proteins 2025 Jan 23 link

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