2024 Publications (updated August 2024)
January 2024
1. Mendez D, Holton JM, Lyubimov AY, Hollatz S, Mathews II, Cichosz A, Martirosyan V, Zeng T, Stofer R, Liu R, Song J, McPhillips S, Soltis M, Cohen AE. Deep residual networks for crystallography trained on synthetic data. Acta Crystallogr D Struct Biol. 2024 Jan 1;80(Pt 1):26-43. doi: 10.1107/S2059798323010586. Epub 2024 Jan 1. PMID: 38164955; PMCID: PMC10833344. (BL 8.3.1)
2. Reddi R, Chatterjee S, Matulef K, Gustafson A, Gao L, Valiyaveetil FI. A facile approach for incorporating tyrosine esters to probe ion-binding sites and backbone hydrogen bonds. J Biol Chem. 2024 Jan;300(1):105517. doi: 10.1016/j.jbc.2023.105517. Epub 2023 Nov 30. PMID: 38042487; PMCID: PMC10790091. (BL 4.2.2 MBC)
3. Murray DT, Ge X, Schut GJ, Rosenberg DJ, Hammel M, Bierma JC, Hille R, Adams MWW, Hura GL. Correlating Conformational Equilibria with Catalysis in the Electron Bifurcating EtfABCX of Thermotoga maritima. Biochemistry. 2024 Jan 2;63(1):128-140. doi: 10.1021/acs.biochem.3c00472. Epub 2023 Nov 27. PMID: 38013433; PMCID: PMC10765413. (SIBYLS)
4. Sun Z, Lin H, Hu L, Neetu N, Sankaran B, Wang J, Prasad BVV, Palzkill T. Klebsiella pneumoniae carbapenemase variant 44 acquires ceftazidime-avibactam resistance by altering the conformation of active-site loops. J Biol Chem. 2024 Jan;300(1):105493. doi: 10.1016/j.jbc.2023.105493. Epub 2023 Nov 23. PMID: 38000656; PMCID: PMC10716778. (BCSB)
5. Ali BA, Judy RM, Chowdhury S, Jacobsen NK, Castanzo DT, Carr KL, Richardson CD, Lander GC, Martin A, Gardner BM. The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1. J Biol Chem. 2024 Jan;300(1):105504. doi: 10.1016/j.jbc.2023.105504. Epub 2023 Nov 29. PMID: 38036174; PMCID: PMC10777020. (BL 8.3.1)
6. Rosenberg DJ, Cunningham FJ, Hubbard JD, Goh NS, Wang JW, Nishitani S, Hayman EB, Hura GL, Landry MP, Pinals RL. Mapping the Morphology of DNA on Carbon Nanotubes in Solution Using X-ray Scattering Interferometry. J Am Chem Soc. 2024 Jan 10;146(1):386-398. doi: 10.1021/jacs.3c09549. Epub 2023 Dec 29. PMID: 38158616. (SIBYLS)
7. Ruocco V, Grünwald-Gruber C, Rad B, Tscheliessnig R, Hammel M, Strasser R. “Effects of N-glycans on the structure of human IgA2.” Frontiers in molecular biosciences 2024 ;11:1390659
8. Liu C, Powell MM, Rao G, Britt RD, Rittle J. “Bioinformatic Discovery of a Cambialistic Monooxygenase.” Journal of the American Chemical Society 2024 Jan 24 ;146(3):1783-1788
9. Luo Y, Hao H, Wang Z, Ong CY, Dutcher R, Xu Y, Liu J, Pedersen LC, Xu D. “Heparan sulfate promotes TRAIL-induced tumor cell apoptosis.” eLife 2024 Jan 24 ;12
10. Ali BA, Judy RM, Chowdhury S, Jacobsen NK, Castanzo DT, Carr KL, Richardson CD, Lander GC, Martin A, Gardner BM. “The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1.” The Journal of biological chemistry 2024 Jan ;300(1):105504
11. Lin DY, Kueffer LE, Juneja P, Wales TE, Engen JR, Andreotti AH. “Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states.” eLife 2024 Jan 08 ;12
Feb 2024
12. Bennett AL, Edwards R, Kosheleva I, Saunders C, Bililign Y, Williams A., Bubphamala P, Manosouri K, Anasti K, Saunders KO, Alam SM, Haynes BF, Acharya P, Henderson R. Microsecond dynamics control the HIV-1 Envelope conformation. Sci Adv. 2024 Feb 2;10(5):eadj0396. doi: 10.1126/sciadv.adj0396. Epub 2024 Feb 2. PMID: 38306419; PMCID: PMC10836732. (SIBYLS)
13. Hung LW, Terwilliger TC, Waldo GS, Nguyen HB. Engineering highly stable variants of Corynactis californica green fluorescent proteins. Protein Sci. 2024 Feb;33(2):e4886. doi: 10.1002/pro.4886. PMID: 38151801; PMCID: PMC10804665. (BCSB)
14. Kohlbrand AJ, Stokes RW, Sankaran B, Cohen SM. Structural Studies of Inhibitors with Clinically Relevant Influenza Endonuclease Variants. Biochemistry. 2024 Feb 6;63(3):264-272. doi: 10.1021/acs.biochem.3c00536. Epub 2024 Jan 8. PMID: 38190441; PMCID: PMC10851415. (BCSB)
15. Stanford SM, Nguyen TP, Chang J, Zhao Z, Hackman GL, Santelli E, Sanders CM, Katiki M, Dondossola E, Brauer BL, Diaz MA, Zhan Y, Ramsey SH, Watson PA, Sankaran B, Paindelli C, Parietti V, Mikos AG, Lodi A, Bagrodia A, Elliott A, McKay RR, Murali R, Tiziani S, Kettenbach AN, Bottini N. Targeting prostate tumor low-molecular weight tyrosine phosphatase for oxidation-sensitizing therapy. Sci Adv. 2024 Feb2;10(5):eadg7887. doi: 10.1126/sciadv.adg7887. Epub 2024 Jan 31. PMID: 38295166; PMCID: PMC10830117. (BCSB BL 8.2.1)
16. Xu X, Herdendorf TJ, Duan H, Rohlik DL, Roy S, Zhou H, Alkhateeb H, Khandelwal S, Zhou Q, Li P, Arepally GM, Walker JK, Garcia BL, Geisbrecht BV. Inhibition of the C1s Protease and the Classical Complement Pathway by 6-(4-Phenylpiperazin-1-yl) Pyridine-3-Carboximidamide and Chemical Analogs. J Immunol. 2024 Feb 15;212(4):689-701. doi: 10.4049/jimmunol.2300630. PMID: 38149922; PMCID: PMC10872613.
17. Schumacher MA, Cannistraci E, Salinas R, Lloyd D, Messner E, Gozzi K. Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site. Nucleic Acids Res. 2024 Feb 9;52(3):1435-1449. doi: 10.1093/nar/gkad1198. PMID: 38142455; PMCID:PMC10853764. (BCSB BL 5.0.2)
18. Ding D, Fang Z, Kim SC, O’Flaherty DK, Jia X, Stone TB, Zhou L, Szostak JW. Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying. J Am Chem Soc. 2024 Feb 14;146(6):3861-3871. doi: 10.1021/jacs.3c11158. Epub 2024 Jan 31. PMID: 38293747; PMCID: PMC10870715. (BL 2.0.1. BCSB)
19. Hung LW, Terwilliger TC, Waldo GS, Nguyen HB. Engineering highly stable variants of Corynactis californica green fluorescent proteins. Protein Sci. 2024 Feb;33(2):e4886. doi: 10.1002/pro.4886. PMID: 38151801; PMCID: PMC10804665. (BCSB)
20. Zhao W, Lin JS, Nielsen JE, Sørensen K, Wadurkar AS, Ji J, Barron AE, Nangia S, Libera MR. “Supramolecular Peptoid Structure Strengthens Complexation with Polyacrylic Acid Microgels.” Biomacromolecules 2024 Feb 12 ;25(2):1274-1281
21. Ghosh A, Delgado-Cunningham K, López T, Green K, Arias CF, DuBois RM. “Structure and antigenicity of the divergent human astrovirus VA1 capsid spike.” PLoS pathogens 2024 Feb ;20(2):e1012028
March 2024
22. Peng W, Garcia N, Servage KA, Kohler JJ, Ready JM, Tomchick DR, Fernandez J, Orth K. “Pseudomonas effector AvrB is a glycosyltransferase that rhamnosylates plant guardee protein RIN4.” Science advances 2024 Feb 16 ;10(7):eadd5108
March 2024
23. Milano CR, Ur SN, Gu Y, Zhang J, Allison R, Brown G, Neale MJ, Tromer EC, Corbett KD, Hochwagen A. “Chromatin binding by HORMAD proteins regulates meiotic recombination initiation.” The EMBO journal 2024 Mar ;43(5):836-867
24. Kim LJ, Shin D, Leite WC, O’Neill H, Ruebel O, Tritt A, Hura GL. “Simple Scattering: Lipid nanoparticle structural data repository.” Frontiers in molecular biosciences 2024 March ;11:1321364
25. Ruttenberg SM, Kreutzer AG, Truex NL, Nowick JS. “Correction to “β-Hairpin Alignment Alters Oligomer Formation in Aβ-Derived Peptides”.” Biochemistry 2024 Mar 05 ;63(5):723
26. Zhao B, Hu L, Kaundal S, Neetu N, Lee CH, Somoulay X, Sankaran B, Taylor GM, Dermody TS, Venkataram Prasad BV. “Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories.” Nature communications 2024 Mar 19 ;15(1):2460
27. Judge A, Sankaran B, Hu L, Palaniappan M, Birgy A, Prasad BVV, Palzkill T. “Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning.” Proceedings of the National Academy of Sciences of the United States of America 2024 Mar 19 ;121(12):e2313513121
April 2024
28. Gao S, Hou P, Oh J, Wang D, Greenberg MM. “Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG.” Journal of the American Chemical Society 2024 Mar 06 ;146(9):6274-6282
April 2024
29. Brosey CA, Link TM, Shen R, Moiani D, Burnett K, Hura GL, Jones DE, Tainer JA. “Chemical screening by time-resolved X-ray scattering to discover allosteric probes.” Nature chemical biology 2024 Apr 26
30. Lu J, Guo Y, Yin J, Chen J, Wang Y, Wang GG, Song J. “Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations.” Nature communications 2024 Apr 10 ;15(1):3111
May 2024
31. Rodríguez-Hernández D, Fenwick MK, Zigweid R, Sankaran B, Myler PJ, Sunnerhagen P, Kaushansky A, Staker BL, Grøtli M. “Exploring Subsite Selectivity within Plasmodium vivax N-Myristoyltransferase Using Pyrazole-Derived Inhibitors.” Journal of medicinal chemistry 2024 May 09 ;67(9):7312-7329
32. Korasick DA, Buckley DP, Palpacelli A, Cursio I, Cesaroni E, Cheng J, Tanner JJ. “Biochemical, structural, and computational analyses of two new clinically identified missense mutations of ALDH7A1.” Chemico-biological interactions 2024 May 01 ;394:110993
33. Phillips M, Malone KL, Boyle BW, Montgomery C, Kressy IA, Joseph FM, Bright KM, Boyson SP, Chang S, Nix JC, Young NL, Jeffers V, Frietze S, Glass KC. “Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains.” Journal of medicinal chemistry 2024 May 11
34. Jia X, Fang Z, Kim SC, Ding D, Zhou L, Szostak JW. Diaminopurine in Nonenzymatic RNA Template Copying. J Am Chem Soc. 2024 Jun 12;146(23):15897-15907. doi: 10.1021/jacs.4c02560. Epub 2024 May 31. PMID: 38818863; PMCID: PMC11177312.
35. Glenn SJ, Gentry-Lear Z, Shavlik M, Harms MJ, Asaki TJ, Baylink A. Bacterial vampirism mediated through taxis to serum. Elife. 2024 May 31;12:RP93178. doi: 10.7554/eLife.93178. PMID: 38820052; PMCID: PMC11142651.
36. Tipo J, Gottipati K, Choi KH. High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules. RNA. 2024 May 16;30(6):609-623. doi: 10.1261/rna.079796.123. PMID: 38383158; PMCID: PMC11098461.
June 2024
37. Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken S, Locksley RM, Fraser JS. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. Elife. 2024 Jun 17;12:RP89918. doi: 10.7554/eLife.89918. PMID:38884443; PMCID: PMC11182645.
38. Sampathkumar P, Jung H, Chen H, Zhang Z, Suen N, Yang Y, Huang Z, Lopez T, Benisch R, Lee SJ, Ye J, Yeh WC, Li Y. Targeted protein degradation systems to enhance Wnt signaling. Elife. 2024 Jun 7;13:RP93908. doi: 10.7554/eLife.93908. PMID: 38847394; PMCID: PMC11161174.
39. McElroy CA, Ihms EC, Kumar Yadav D, Holmquist ML, Wadhwa V, Wysocki VH, Gollnick P, Foster MP. “Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis.” Journal of structural biology: X 2024 Dec ;10:100103
40. Wacker JN, Woods JJ, Rupert PB, Peterson A, Allaire M, Lukens WW, Gaiser AN, Minasian SG, Strong RK, Abergel RJ. “Actinium chelation and crystallization in a macromolecular scaffold.” Nature communications 2024 Jul 15 ;15(1):5741
41. Edman NI, Phal A, Redler RL, Schlichthaerle T, Srivatsan SR, Ehnes DD, Etemadi A, An SJ, Favor A, Li Z, Praetorius F, Gordon M, Vincent T, Marchiano S, Blakely L, Lin C, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Zheng Y, Murry CE, Schweppe DK, Freedman BS, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. “Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.” Cell 2024 Jul 11 ;187(14):3726-3740.e43
42. Jia X, Fang Z, Kim SC, Ding D, Zhou L, Szostak JW. “Diaminopurine in Nonenzymatic RNA Template Copying.” Journal of the American Chemical Society 2024 Jun 12 ;146(23):15897-15907
43. He L, McAndrew R, Barbu R, Gifford G, Halacoglu C, Drouin-Allaire C, Weber L, Kristensen LG, Gupta S, Chen Y, Petzold CJ, Allaire M, Li KH, Ralston CY, Gochin M. “Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity.” Journal of molecular biology 2024 Jun 10 ;436(16):168650
44. Sampathkumar P, Jung H, Chen H, Zhang Z, Suen N, Yang Y, Huang Z, Lopez T, Benisch R, Lee SJ, Ye J, Yeh WC, Li Y. “Targeted protein degradation systems to enhance Wnt signaling.” eLife 2024 Jun 07 ;13
45. Chinnam NB, Thapar R, Arvai AS, Sarker AH, Soll JM, Paul T, Syed A, Rosenberg DJ, Hammel M, Bacolla A, Katsonis P, Asthana A, Tsai MS, Ivanov I, Lichtarge O, Silverman RH, Mosammaparast N, Tsutakawa SE, Tainer JA. “ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase.” The Journal of biological chemistry 2024 Jun ;300(6):107368
July 2024
46. Schumacher MA, Singh RR, Salinas R. “Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp.” Nucleic acids research 2024 Jul 08 ;52(12):7354-7366
47. Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. “De novo design of proteins housing excitonically coupled chlorophyll special pairs.” Nature chemical biology 2024 Jul ;20(7):906-915