Newsletter 539 (November 7, 2025) NIH Structural Biology Methods SIG

OCTOBER 2025 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Roark RS, Schaub AJ, Shi W, Wang M, Bahna FA, Becker JE, Biju A, Chong S, Du H, Guo Y, Hong H, Katsamba PS, Mannepalli SM, Olia AS, Ou L, Rubin SK, Sabo Y, Suleiman M, Wells ML, Zhang B, Cheng C, Glasgow A, Ho DD, Huang Y, Pierson TC, Rawi R, Zhou T, Shapiro L, Kwong PD.
Prefusion structure, evasion and neutralization of HSV-1 glycoprotein B.
Nature microbiology 2025-11-01 doi: 10.1038/s41564-025-02153-x PMID: 41174178

2: Fortin A, Huot S, Caron E, Laflamme C, Pagliuzza A, Chomont N, Gilbert C, Zhang B, Kwong PD, Pouliot M, Grandvaux N.
No evidence of direct activation of human neutrophil responses by multivalent prefusion trimeric SARS-CoV-2 Spike protein ex vivo.
PloS one 2025-10-29 doi: 10.1371/journal.pone.0332261 PMID: 41160626

3: Gillet JP, Gerard L, Vieira W, Fourrez M, Gaudray F, Rathkolb B, Rozman J, Klein-Rodewald T, Becker L, Aguilar-Pimentel A, Horsch M, Spielmann N, Prehn C, Bihin B, Beckers J, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, Southon E, Tessarollo L, Xia D, Gottesman MM.
Abcb5-deficient mice show a subtle, pleiotropic phenotype indicating a role for this transporter in intermediary metabolism.
iScience 2025-10-27 doi: 10.1016/j.isci.2025.113617 PMID: 41142997

4: Torricella F, Clore GM, Tugarinov V.
Triple-Resonance NMR Experiments for Assignment of Asparagine and Glutamine Side-Chain NH
Chemphyschem : a European journal of chemical physics and physical chemistry 2025-10-27 doi: 10.1002/cphc.202500630 PMID: 41139430

5: Loughran G, De Pace R, Ding N, Zhang J, Jungreis I, Carancini G, Mudge JM, Wang J, Kellis M, Atkins JF, Baranov PV, Firth AE, Li X, Bonifacino JS, Khan YA.
Programmed ribosomal frameshifting during
Science advances 2025-10-24 doi: 10.1126/sciadv.ady1742 PMID: 41134891

6: Ciancone A, Wu H, Atallah-Yunes K, Lee K, Sibley C, Spivey J, Swenson RE, Schneekloth JS, O'Reilly FJ.
Expanding the crosslinking mass spectrometry toolbox with vinyl sulfone crosslinkers.
Molecular & cellular proteomics : MCP 2025-10-24 doi: 10.1016/j.mcpro.2025.101315 PMID: 41130296

7: Alcock F, Yang Y, Deme J, Casabona G, Mendonca C, Ulhuq F, Lea S, Palmer T.
Distinct immunity protein families mediate compartment-specific neutralization of a bacterial toxin.
Cell reports 2025-10-23 doi: 10.1016/j.celrep.2025.116459 PMID: 41129315

8: Maurakis SA, O'Donnell AC, Botos I, Ghirlando R, Davies BW, Buchanan SK.
Structural insights into Cir-mediated killing by the antimicrobial protein Microcin V.
Communications biology 2025-10-10 doi: 10.1038/s42003-025-08846-7 PMID: 41068465

9: Alexander LT, Follonier OM, Kryshtafovych A, Abesamis K, Bibi-Triki S, Box HG, Breyton C, Bringel F, Carrique L, d'Acapito A, Dong G, DuBois R, Fass D, Fiesco JM, Fox DR, Grimes JM, Grinter R, Jenkins M, Kamyshinsky R, Keown JR, Lackner G, Lammers M, Liu S, Lovering AL, Malinauskas T, Masquida B, Palm GJ, Siebold C, Su T, Zhang P, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T.
Protein Target Highlights in CASP16: Insights From the Structure Providers.
Proteins 2025-10-09 doi: 10.1002/prot.70025 PMID: 41065010

10: Ghosh S, Singh J, Damseh NS, Severino M, De Pace R, Golding AE, Jarnik M, Thakran P, Faivre L, Heitz J, Denommé-Pichon AS, Vitobello A, AlAbdi L, Abdulwahab F, Sumayli S, Alqahtani M, Cheema HA, Javed I, Kim J, Lochmuller H, Mor-Shaked H, Neil JE, Mochida GH, Zifarelli G, Bauer P, Barkhordari E, Ghayoor Karimiani E, Houlden H, Abu-Libdeh B, Edvardson S, Elpeleg O, Maroofian R, Patten SA, Bonifacino JS.
EIPR1 variants cause a neurodevelopmental disorder with endolysosomal and dense core vesicle defects.
Brain : a journal of neurology 2025-10-08 doi: 10.1093/brain/awaf371 PMID: 41058046

11: De Souza Degenhardt MF, Wang YX.
Challenges and opportunities in technologies and methods for lncRNA structure determination.
Cell & bioscience 2025-10-03 doi: 10.1186/s13578-025-01470-2 PMID: 41039493

12: Liu X, Orenday Tapia L, Deme JC, Lea SM, Berks BC.
A new paradigm for outer membrane protein biogenesis in the Bacteroidota.
Nature 2025-10-02 doi: 10.1038/s41586-025-09532-8 PMID: 41034578

13: Mulder CV, Yang X, Jee YH, Scott CG, Gao C, Cao Y, Hurson AN, Eriksson M, Vachon CM, Hall P, Antoniou AC, Kraft P, Gierach GL, Garcia-Closas M, Pal Choudhury P.
Evaluating mammographic density's contribution to improve a breast cancer risk model with questionnaire-based and polygenic factors.
NPJ breast cancer 2025-10-02 doi: 10.1038/s41523-025-00813-z PMID: 41034228

14: Panda AK, Natarajan K, Sinha S, Jiang J, Chempati S, Boyd LF, Desai PP, Buszko M, Kim YH, Kazmi S, Fisk B, Teke ME, Larrain CM, Remmert K, Blakely AM, Douagi I, Hernandez JM, Margulies DH, Shevach EM.
Antibody Mediated Inhibition of HLA/LILR Interactions Breaks Innate Immune Tolerance and Induces Antitumor Immunity.
Cancer immunology research 2025-10-01 doi: 10.1158/2326-6066.CIR-25-0343 PMID: 41032026

15: Dussupt V, Jensen JL, Thomas PV, Mendez-Rivera L, Lal KG, Zemil McCrea M, Swafford I, Hernandez J, Sankhala RS, Rao M, Arora J, Hajduczki A, Jian N, Rees PA, Showell-De Leon I, Smith G, Smith L, Wasson D, Schmid A, Teng I-T, Zhou T, Kwong PD, Currier JR, Reiley WW, Paquin-Proulx D, Polonis VR, Collins ND, Michael NL, Joyce MG, Krebs SJ.
First-generation N-terminal domain supersite public antibodies retain activity against Omicron-derived lineages and protect mice against Omicron BA.5 challenge.
mBio 2025-08-29 doi: 10.1128/mbio.01036-25 PMID: 40882161

16: Lai Y-T, Dingens AS, DeMouth M, Helmold Hait S, O'Dell S, Schon A, Olia AS, Wang T, Shrader HR, Lovelace SE, Pegu A, Doria-Rose NA, Mascola JR, Bloom JD, Kwong PD.
Fostemsavir analog BMS-818251 has enhanced viral neutralization potency and similar escape mutation profile.
Antimicrobial agents and chemotherapy 2025-08-27 doi: 10.1128/aac.01910-24 PMID: 40863730

17: Middleton SJ, Markósson S, Åkerlund M, Deme JC, Tseng M, Li W, Zuberi SR, Kuteyi G, Sarkies P, Baskozos G, Perez-Sanchez J, Farah A, Hébert HL, Toikumo S, Yu Z, Maxwell S, Dong YY, Kessler BM, Kranzler HR, Linley JE, Smith BH, Lea SM, Parker JL, Lyssenko V, Newstead S, Bennett DL.
SLC45A4 is a pain gene encoding a neuronal polyamine transporter.
Nature 2025-08-21 doi: 10.1038/s41586-025-09326-y PMID: 40836097

18: Kunselman JM, Williamson CD, Golding AE, Jia R, Sohn M, Dale RK, Bonifacino JS.
The hereditary spastic paraplegia type 21 (SPG21) protein is a RAB7A effector that promotes noncanonical mTORC1-catalyzed TFEB phosphorylation and cytoplasmic retention.
Molecular biology of the cell 2025-08-20 doi: 10.1091/mbc.E25-07-0346 PMID: 40833810

19: Roark RS, Habib R, Gorman J, Li H, Connell AJ, Bonsignori M, Guo Y, Hogarty MP, Olia AS, Sowers KJ, Zhang B, Bibollet-Ruche F, Bylund T, Callaghan S, Carey JW, Cerutti G, Harris DR, He W, Lewis E, Liu T, Mason RD, Qiao Y, Park Y, Rando JM, Singh A, Wolff JJ, Lei QP, Louder MK, Andrabi R, Doria-Rose NA, Saunders KO, Seaman MS, Haynes BF, Kulp DW, Mascola JR, Roederer M, Pierson TC, Sheng Z, Hahn BH, Shaw GM, Kwong PD, Shapiro L.
Structural and genetic basis of HIV-1 envelope V2 apex recognition by rhesus broadly neutralizing antibodies.
The Journal of experimental medicine 2025-08-18 doi: 10.1084/jem.20250638 PMID: 40824240

20: Zhen T, Cao Y, Dou T, Chen Y, Lopez G, Menezes AC, Wu X, Hammer JA, Cheng J, Garrett L, Anderson S, Kirby M, Wincovitch S, Sisay B, Elkahloun AG, Wu D, Castilla LH, Yang W, Jiang J, Zhao K, Liu PP.
CBFΒ-SMMHC-driven leukemogenesis requires enhanced RUNX1-DNA binding affinity in mice.
The Journal of clinical investigation 2025-08-05 doi: 10.1172/JCI192923 PMID: 40763310


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