Newsletter 543 (March 13, 2026) NIH Structural Biology Methods SIG

FEBRUARY 2026 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Quintero-Barbosa JS, Song Y, Mehl F, Mathur S, Livingston L, Kwong PD, Shen X, Montefiori DC, Zeichner SL.
HIV Membrane-Proximal External Region Scaffolded Immunogen as Killed Whole-Cell Genome-Reduced Vaccines.
Viruses 2026-02-27 doi: 10.3390/v18020209 PMID: 41754552

2: Lima NS, McCormick L, Li S, Wake CG, Subramanian R, Spangler A, Pinto Y, Catalano W, Henry AR, Laboune F, Teng IT, Lyke KE, Atmar RL, Deming ME, Jackson LA, Branche AR, Rostad CA, Martin JM, Johnston CM, Rupp RE, Kottkamp AC, Brady RC, Backer M, Edupuganti S, None None, Posavad CM, Roberts PC, Kwong PD, Andrews S, Schramm CA, Douek DC, None None.
The vaccine platform used for COVID-19 primary immunization shapes the quality of the human B cell response to a vaccine boost.
Science translational medicine 2026-02-25 doi: 10.1126/scitranslmed.aeb9837 PMID: 41739906

3: McCaffrey EF, Delmastro AC, Fitzhugh I, Ranek JS, Douglas S, Peters JM, Fullaway CC, Bosse M, Liu CC, Gillen C, Greenwald NF, Anzick S, Martens C, Winfree S, Bai Y, Sowers C, Goldston M, Kong A, Boonrat P, Bigbee CL, Venugopalan R, Maiello P, Klein E, Rodgers MA, Scanga CA, Lin PL, Bendall SC, Kirschner DE, Fortune SM, Bryson BD, Butler JR, Mattila JT, Flynn JL, Angelo M.
The immunometabolic topography of cellular organization and bacterial control in tuberculosis granulomas.
Nature immunology 2026-02-24 doi: 10.1038/s41590-026-02431-8 PMID: 41731147

4: He X, Yang W, Zeng Z, Wei Y, Gao J, Zhang B, Li L, Liu L, Wan Y, Zeng Q, Gong Z, Liu L, Zhang H, Li Y, Yang S, Hu T, Wu L, Masliah E, Huang S, Cao H.
Author Correction: NLRP3-dependent pyroptosis is required for HIV-1 gp120-induced neuropathology.
Cellular & molecular immunology 2026-02-24 doi: 10.1038/s41423-026-01394-y PMID: 41731130

5: Brugger-Muli CS, Gaikwad SM, du Bois W, Sabbasani VR, Swenson RE, Heinz WF, Peat TJ, Mock BA, Walters KJ.
SCaN: A Screening and Characterization Platform for Nanosuspensions Enables In Vivo Delivery of a Crystalline hRpn13
ACS pharmacology & translational science 2026-02-19 doi: 10.1021/acsptsci.5c00644 PMID: 41710746

6: Cox JB, Nair V, Mandal P, Reyna N, Tran T, Mustachio LM, Bardenhagen J, Fawver J, Shepard H, Hickey AM, Wu Q, Rodriguez C, Yu F, Phan P, Mendiola AJ, Johnson R, Thapar R, Johnson T, Jiang Y, Cross JB, Do MKG, Jones P, Marsalek J, Heffernan T, Soth MJ, Nagy E.
Structure-Guided Development of NRAS G12D Inhibitors Based on a 5‑Azaindole Core.
ACS medicinal chemistry letters 2026-02-18 doi: 10.1021/acsmedchemlett.5c00647 PMID: 41704364

7: Dearborn AD, Remaley AT, Marcotrigiano J.
Structural heterogeneity of apolipoprotein B-100.
The FEBS journal 2026-02-17 doi: 10.1111/febs.70451 PMID: 41700118

8: Fan W, Lu N, Shen Z, Tang W, Shen B, Cui Z, Shan L, Yang Z, Wang Z, Jacobson O, Zhou Z, Liu Y, Hu P, Yang W, Song J, Zhang Y, Zhang L, Khashab NM, Aronova MA, Lu G, Chen X.
Author Correction: Generic synthesis of small-sized hollow mesoporous organosilica nanoparticles for oxygen-independent X-ray-activated synergistic therapy.
Nature communications 2026-02-17 doi: 10.1038/s41467-026-69291-6 PMID: 41698903

9: He T, Wang J, Tumba MC, Wang S, Luo Y, Chen J, Li G, Shu Z, Zhang S, Stone DL, Huang Y, Lv Q, Xiong W, Wang J, Yu Z, Cuff CV, Kairis E, Kethri A, Towheed A, Goyette K, Karri U, Wang J, Liu C, Romeo T, Manrique De Lara LA, Rosenberg DL, Clemente D, Lopez Robledillo JC, Rong Z, Zhao X, Jiang L, Aldave-Becerra JC, Muñoz-Urribarri AB, Oommen PT, Campbell-Stokes P, Zhu M, Liu P, Guo L, Xu Y, Yu Z, Tong H, Qiu X, Zhang Y, Chen H, Zhang C, Ou J, Liu C, Liu J, Shen Y, Cao J, Zhang X, Yang K, Bao Y, Li Z, Cao J, Duan Y, Liu F, Shi B, Sun M, Ma L, Chen Y, Yang W, Han X, Ma S, Luo J, Gu W, Yu G, Shi W, Zhao R, Sun L, Li W, An Y, Tang X, Zhao X, Han T, Ma J, Li Y, Piao Y, Sun F, Zhang D, Yin M, Zheng S, Li T, Niu H, Lin L, Mei S, Zhou F, Yang S, Li D, Yan M, Zeng H, Zeng P, Zheng W, Li X, Li X, Liu Y, Huang L, Yu H, Fan Z, Shen M, Lu M, Fang Z, Rimland CA, Song H, Peterson LW, Yousuf Al-Nesf MA, Aqel S, Mudawi DS, Raje N, Slowik V, Harris JG, Snyder B, Scheffler-Mendoza S, Yamazaki-Nakashimada M, Cooper MA, Lau YL, Gedik KC, Wang W, Ying W, Hou J, Zhou Q, Sun B, Sun J, Wang X, Ombrello AK, Huang Y, Wu HL, Sun L, Mao H, Yu X, Liu Z, Aksentijevich I, Kastner DL, Schwartz DM, Yang J, Zhou Q.
Multicenter international cohort study of HA20 reveals novel genetic architecture and phenotypic evolution.
The Journal of allergy and clinical immunology 2026-02-16 doi: 10.1016/j.jaci.2026.02.002 PMID: 41692116

10: Dunshee EB, Saladin BA, Turner DJ, Qiu C, Dutcher RC, Williams JG, Corbo J, Wolcott OR, Korte AJ, Haugen RJ, Tanaka Hall TM, Valkov E, Goldstrohm AC.
Human pumilio proteins use fuzzy multivalent hydrophobic interactions to recruit the CCR4-NOT deadenylase complex to repress mRNAs.
The Journal of biological chemistry 2026-02-15 doi: 10.1016/j.jbc.2026.111281 PMID: 41690588

11: Lu X, Osei-Amponsa V, Michelis G, Castelino RE, Negi H, Das S, Turner JL, King JC, Martin D, Wang Y, Andresson T, Chari R, Werner A, Walters KJ.
Proteasome activity maintains cell-type-specific gene expression.
Cell reports 2026-02-14 doi: 10.1016/j.celrep.2026.116973 PMID: 41689797

12: Li ECL, Kim J, Brussee SJ, Sugasawa K, Luijsterburg MS, Yang W.
Pre-incision structures reveal principles of DNA nucleotide excision repair.
Nature 2026-02-12 doi: 10.1038/s41586-026-10122-5 PMID: 41673165

13: Georgouli K, Tempkin JOB, Stanton LG, Oppelstrup T, Shrestha R, Carpenter TS, Aydin F, Zhang X, Bhatia H, Yang Y, Van QN, Bonilla PA, Gulten G, Goswami D, Di Natale F, Chavez JR, Moon JY, Dharuman G, Hengartner NW, Simanshu DK, Tran TH, Nguyen K, Stanley CB, Van Essen B, Bremer PT, Lightstone FC, Stephen AG, Glosli JN, Gnanakaran S, Turbyville TJ, McCormick F, Nissley DV, Streitz FH, Ingólfsson HI.
KRAS4a and KRAS4b show distinct lipid-dependent regulation of RAS-RAF membrane dynamics.
The Journal of biological chemistry 2026-02-07 doi: 10.1016/j.jbc.2026.111237 PMID: 41651414

14: Schmidt T, Torricella F, Clore GM.
Direct observation and measurement of the average quantum methyl-tunneling frequency in a protein using
Chemical communications (Cambridge, England) 2026-02-04 doi: 10.1039/d5cc06305a PMID: 41635961

15: Jiang J, Panda AK, Natarajan K, Lei H, Sharma S, Boyd LF, Towler RR, Chempati S, Ahmad J, Morton AJ, Lang ZC, Sun Y, Sgourakis N, Meier-Schellersheim M, Huang RK, Shevach EM, Margulies DH.
Structural mechanism of anti-MHC-I antibody blocking of inhibitory NK cell receptors in tumor immunity.
Communications biology 2026-02-03 doi: 10.1038/s42003-026-09641-8 PMID: 41629525

16: Duan H, Nkolola JP, Wang S, Chaudhari J, Teng IT, Lavine C, Parchment DK, Sellers GS, McKee K, O'Dell S, Choe M, Du H, Zhang B, Perez AAE, Rossler A, Lasrado N, Biju A, Becker JE, Carroll R, Carson AS, Henry AR, Morano NC, Mughal M, Rawi R, Roark RS, Schramm CA, Shen CH, Smith SC, Stephens T, Tsybovsky Y, Van Wazer DJ, Wang H, Yang Y, Rutten L, Langedijk JPM, Cheng C, Wang L, Douek DC, Koup RA, Mascola JR, Shapiro L, Zhou T, Doria-Rose NA, Korber B, Seaman MS, Pierson TC, Kwong PD, Barouch DH.
Vaccine elicitation of HIV-1 neutralizing antibodies against both V2 apex and fusion peptide in rhesus macaques.
Cell reports 2026-01-30 doi: 10.1016/j.celrep.2025.116905 PMID: 41615799

17: Nam H, Deme JC, Sim S, Boccitto M, Lea SM, Wolin SL.
Mechanistic insights into RNA chaperoning by Ro60 and La autoantigens.
Cell 2026-01-30 doi: 10.1016/j.cell.2025.12.030 PMID: 41610850

18: Mills MN, Pacheo G, Tong AY, Tong EL, Hannani MA, Heganovic L, Fleary K, Shaffer SN, Vairavan MS, Ferré-D'Amaré AR, Passalacqua LFM, Abdelsayed MM.
The RNA thermometer motif ROSE-G regulates ABC transporter gene expression in bacteria.
The Journal of biological chemistry 2026-01-02 doi: 10.1016/j.jbc.2025.111119 PMID: 41478572


RECENT TOPICS IN THE LITERATURE:


METHODS — Sample Preparation Tips


N. Premaraj et al., "Advancing cryo-EM and cryo-ET through innovation in sample carriers: a perspective" PMID: 40476672.
I.J. Hirst et al., "Untangling the effects of flexibility and the AWI in cryoEM sample preparation: A case study using KtrA" PMID: 40324569.
Y. Huang et al., "Recent Advances in Expression Screening and Sample Evaluation for Structural Studies of Membrane Proteins" PMID: 39362625.
K. McGuire et al., "Tuning ice thickness using the chameleon for high-quality cryoEM data collection" PMID: 38746094.
B. Cook et al., "Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using (an)aerobic blot-free vitrification" PMID: 39091810.
R. Warmack et al., "Anaerobic cryoEM protocols for air- sensitive nitrogenase proteins" PMID: 38575747.
I.J. Hirst et al., "CryoEM grid preparation: a closer look at advancements and impact of preparation mode and new approaches" PMID: 38864435.
S. Yadav and K.R. Vinothkumar, "Factors affecting macromolecule orientations in thin films formed in cryo-EM" PMID: 38935342.
S.E.J. Bowman et al., "Preparing research samples for safe arrival at centers and facilities: recipes for successful experiments" PMID: 38990054.

METHODS — Macromolecular Crystallography


N. L. Inniss et al., "Structural genomics of bacterial drug targets: application of a high-throughput pipeline to solve 59 protein structures from pathogenic and related bacteria" PMID: 40391899.
.J. Simpkin et al. "Slice'N'Dice: maximizing the value of predicted models for structural biologists" PMID: 39976565.
G. Budziszewski et al. "Preparing for successful protein crystallization experiments" PMID: 40454464.
M. Schaefer et al., "Surface-mutagenesis strategies to enable structural biology crystallization platforms" PMID: 39207897.

METHODS — Integrative Structural Biology


S. Bazzi and S. Sayyed, "Revealing arginine-cysteine and glycine-cysteine NOS linkages by a systematic re-evaluation of protein structures" PMID: 40360719.
R. Mitra et al. "RNAproDB: a webserver and interactive database for analyzing protein-RNA interactions" PMID: 40126909.
H. McCann et al., "R2DT: a comprehensive platform for visualizing RNA secondary structure" PMID: 39921562.
B. Vallat et al., "PDB-IHM: a system for deposition, curation, validation, and dissemination of integrative structures" PMID: 40110969.
D. A. Erlanson et al., "Where and how to house big data on small fragments" PMID: 40325009.
M. Bazayeva et al., "A database overview of metal-coordination distances in metalloproteins" PMID: 38682667.
H. Zheng et al., "PinMyMetal: a hybrid learning system to accurately model metal binding sites in macromolecules" PMID: 40155596.
M. Bochtler, "X-rays, electrons, and neutrons as probes of atomic matter" PMID: 38412856.

METHODS — XFEL, Serial Crystallography


L. Sauthof et al. "Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes" PMID: 40435264.
M. Maestre-Reyna et al., "Capturing structural intermediates in an animal-like cryptochrome photoreceptor by time-resolved crystallography" PMID: 40378212.
M. Sonawal et al. "Functional implications of hexameric dynamics in SARS-CoV-2 Nsp15" PMID: 40411374.

METHODS — Micro-ED


M.T.B. Clabbers and T. Gonen, "Recovering high-resolution information using energy filtering in MicroED" PMID: 40370641.
J. Lin et al., "Ligand screening and discovery using cocktail soaking and automated MicroED" PMID: 40027750.
W. J. Nicolas et al., "Structure of the lens MP20 mediated adhesive junction" PMID: 40140346.
J.E. Miller et al., "AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography" PMID: 38451205.

METHODS — Cryo-EM


R.C. Kretsch et al., "Complex water networks visualized by cryogenic electron microscopy of RNA" PMID: 40068818.
R.C. Kretsch et al., "Naturally ornate RNA-only complexes revealed by cryo-EM" PMID: 40328315.
G. Pintilie et al., "Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps" PMID: 39868161.
R. Read et al., "Likelihood-based interactive local docking into cryo-EM maps in ChimeraX" PMID: 39058381.
R. Karimi et al., "Vesicle Picker: a tool for efficient identification of membrane protein complexes in vesicles" PMID: 39481498.
D. Bobe et al., "Multi-species cryoEM calibration and workflow verification standard" PMID: 39494502.
C.L. Lawson et al., "Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge" PMID: 38343795.
B. Greber et al., "High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design" PMID: 38480681.
G.J. Kleywegt, "Community recommendations on cryoEM data archiving and validation" PMID: 38358351.
M. Kschonsak et al., "Cryo-EM reveals an unprecedented binding site for Nav1.7 inhibitors enabling rational design of potent hybrid inhibitors" PMID: 36975198.

METHODS — SAXS


E. Brookes et al., "SAXS-A-Fold: a website for fast ensemble modeling optimizing the fit of AlphaFold or user-supplied protein structures with flexible regions to SAXS data" PMID: 40475948.
K. Lytje and J.S. Pederson, "Validation of electron-microscopy maps using solution small-angle X-ray scattering" PMID: 38935344.

METHODS — NMR Spectroscopy


L. S. Pidgu et al., "Observing nucleotide flipping in DNA using indirect 2’-F nucleotide probes and 19F NMR" PMID: 40488280.
M. Bütikofer et al., "Rapid Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR" PMID: 38957136.

METHODS — AlphaFold


A. Fadini et al., "AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network" PMID: 40027838.
R.M. Keegan et al., "The success rate of processed predicted models in molecular replacement: implication for experimental phasing in the AlphaFold era" PMID: 39360967.
B.K. Poon et al., "The Phenix-AlphaFold webservice: enabling AlphaFold predictions for use in Phenix" PMID: 3864706.
A.M. Lau et al., "Exploring structural diversity across the protein universe with The Encyclopedia of Domains" PMID: 39480926.
J. Abramson et al., "Accurate structure prediction of biomolecular interactions with AlphaFold 3" PMID: 38718835.

METHODS — Mass Spectrometry


M.A. Gonzalez-Lozano et al., "EndoMAP.v1 charts the structural landscape of human early endosome complexes" PMID: 40437099.
R.A. D'Ippoito et al., "Determining KRAS4B-Targeting Compound Specificity by Top-Down Mass Spectrometry" PMID: 39052227.
A. Vetrano et al., "Protein secondary structure patterns in short-range cross-link atlas" PMID: 4043759.
M.D. Mann et al., "Structural proteomics defines a sequential priming mechanism for the progesterone receptor" PMID: 403555435.

READINGS & TUTORIALS — General Structural Biology


R. Nussinov et al., "Allostery in disease: anticancer drugs, pockets, and the tumor heterogeneity challenge" PMID: 40021049.
K. Matange et al., "Biological polymers: evolution, function, and significance" PMID: 39905926.
L.C. Schofield et al., "Post-translational modifications in the Protein Data Bank" PMID: 39207896.

READINGS & TUTORIALS — Macromolecular Crystallography


K.L. Shelley and E.F. Garman, "Identifying and avoiding radiation damage in macromolecular crystallography" PMID: 38700059.
G. Khusainov et al., "The time revolution in macromolecular crystallography" PMID: 38616866.
J.R. Helliwell et al., "The evolution of raw data archiving and the growth of its importance in crystallography" PMID: 38864497.
D.J. Haas, "Fifty years on: why macromolecular cryocrystallography has been so successful" IUCr Newsletter (2023) 31(3).
W.A. Hendrickson, "Facing the phase problem" PMID: 37668214.

READINGS & TUTORIALS — Cryo-EM


C.T. Chien et al., "Single-particle cryogenic electron microscopy structure determination for membrane proteins" PMID: 40228430.
G.C. Lander, "Single particle cryo-EM map and model validation: It's not crystal clear" PMID: 39293191.
E. Nogales & J. Mahamid, "Bridging structural and cell biology with cryo-electron microscopy" PMID: 38570716.

READINGS & TUTORIALS — Serial Crystallography


C. J. Tremlett et al., "Small but mighty: the power of microcrystals in structural biology" PMID: 40080159.
A. Henkel and D. Oberthur, "A snapshot love story: what serial crystallography has done for us" PMID: 38984902.

READINGS & TUTORIALS — MicroED


A. Haymaker & B.L. Nannenga, "Advances and applications of microcrystal electron diffraction (MicroED)" PMID: 10882645.

READINGS & TUTORIALS — NMR Spectroscopy


O. A. Alimowska et al., "Advances in the application of NMR to the study of GPCRs and ligand-GPCR interactions" PMID: 40485639.
G. Platzer et al., "NMR-driven structure-based drug discovery by unveiling molecular interactions" PMID: 40450181.

READINGS & TUTORIALS — Atomic Force Microscopy (AFM)


Y. Jiang et al., "A structural biology compatible file format for atomic force microscopy" PMID: 39955301.
A.C. Dumitru et al., "Recent advances in the application of atomic force microscopy to structural biology" PMID: 37044358.

READINGS & TUTORIALS — AlphaFold/AI


E. Callaway, "Chemistry Nobel goes to developers of AlphaFold AI that predicts protein structures" PMID: 39384918.
E. Callaway, "The huge protein database that spawned AlphaFold and biology's AI revolution" PMID: 39424937.
T.C. Terwilliger et al., "AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination" PMID: 38036854.
S. Subramaniam, "Structural biology in the age of AI" PMID: 38066345.

READINGS & TUTORIALS — Protein Data Bank/Data Archiving


H. Berman and S.K. Burley, "Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society" PMID: 39973356.
S.K. Burley et al., "Updated resources for exploring experimentally-determined PDB structures and computed structure models at the RCSB Protein Data Bank" PMID: 39607707.

IN THE NEWS:


Ruth Nussinov elected to the National Academy of Sciences, 05/02/2025
Simulations implicate structural changes as a culprit in mutant protein’s cancer role and point to possible treatments, 03/25/2025
Lipoprotein structure gives insights into "bad" cholesterol, 01/14/2025

DATABASES — Structural Biology


AlphaFold DB
BioCyc
DisProt
ExPASy
HAD
HIC-Up
NDB
PDB
PDBe
PDB SARS-CoV-2 Resources
SARS-CoV-2 Related Structures
RaMP-DB
virusMED

UPCOMING MEETINGS, CONFERENCES, & WORKSHOPS


75th ACA Annual Meeting, July 18-23, 2025 Lombard, IL
Microscopy Society of America Annual Meeting, July 27-31, 2025 Salt Lake City, UT
Cold Spring Harbor Laboratory Macromolecular Crystallography Course, October 12-28, 2025 Cold Spring Harbor, NY Application Deadline: July 15, 2025