Newsletter 541 (January 2, 2026) NIH Structural Biology Methods SIG

2026 PUBLICATIONS BY MEMBERS OF THE GROUP

1: 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

2: Behera AK, Kim JJ, Kordale S, Pekovic F, Damodaran AP, Kumari B, Vidak S, Dickson E, Xiao MS, Duncan G, Andresson T, Misteli T, Valkov E, Gonatopoulos-Pournatzis T.
RNA-coupled CRISPR screens reveal ZNF207 as a regulator of LMNA aberrant splicing in progeria.
Molecular cell 2026-01-01 doi: 10.1016/j.molcel.2025.12.003 PMID: 41475346

3: Kim H, Issara-Amphorn J, Yoon SH, Banerjee A, Nita-Lazar A.
Proteome-Wide Analysis of Palmitoylated Proteins in Macrophages Reveals Novel Insights Into Early Immune Signaling.
Proteomics 2025-12-29 doi: 10.1002/pmic.70100 PMID: 41457686

4: 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.
bioRxiv : the preprint server for biology 2025-12-25 doi: 10.64898/2025.12.18.695197 PMID: 41446148

5: Gardner CL, Pletnev S, Liu JL, Anderson GP, Shriver-Lake LC, Bylund T, Green C, Stephens T, Sutton MS, Tsybovsky Y, Roederer M, Kwong PD, Zhou T, Goldman ER, Burke CW.
Demonstration of
Journal of virology 2025-12-16 doi: 10.1128/jvi.01875-25 PMID: 41400357

6: Bou-Nader C, Juma KM, Bothra A, Brasington AJ, Ghirlando R, Suzuki M, Garboczi DN, Leppla SH, Zhang J.
Structural basis of double-stranded RNA recognition by the J2 monoclonal antibody.
Nature communications 2025-12-14 doi: 10.1038/s41467-025-67414-z PMID: 41390480

7: Trang KB, Sharma P, Cook L, Mount Z, Thomas RM, Kulkarni NN, Cabrera EC, Rachimi S, Pahl MC, Pippin JA, Su C, Kaestner KH, O'Brien JM, Wagley Y, Hankenson KD, Jermusyk A, Hoskins JW, Amundadottir LT, Xu M, Brown KM, Anderson SA, Yang W, Titchenell PM, Seale P, Zemel BS, Chesi A, Romberg N, Levings MK, Grant SFA, Wells AD.
3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility.
Genome biology 2025-12-09 doi: 10.1186/s13059-025-03880-4 PMID: 41361473

8: Kim H, Issara-Amphorn J, Yoon S, Banerjee A, Nita-Lazar A.
Enhanced S-Palmitoylated Protein Detection by Mild Nonionic Detergent in Proteomic Workflow.
Journal of the American Society for Mass Spectrometry 2025-12-02 doi: 10.1021/jasms.5c00186 PMID: 41328681

9: Newman CE, Gygi MA, Alimohamadi H, DeAngelo TM, Camara CM, Mintseris J, Yu E, Harvey EP, Hauseman ZJ, Fan L, Wang YX, Luo EW, Godes M, Gehtman J, Cathcart AM, Gygi SP, Engen JR, Bird GH, Wong GCL, Wales TE, Walensky LD.
Inhibition of oligomeric BAX by an anti-apoptotic dimer.
Cell 2025-11-23 doi: 10.1016/j.cell.2025.10.037 PMID: 41274283

10: Pan Y, Zhan J, Wang Z, Jiang Y, Xia D, Scheuring S.
Single-Molecule Structures and Kinetics of the AAA-ATPase Bcs1 Translocating Folded ISP.
Journal of molecular biology 2025-11-04 doi: 10.1016/j.jmb.2025.169531 PMID: 41183768

11: 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

12: 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

13: 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

14: Zhou BR, Orris B, Guan R, Lian T, Bai Y, Bai Y.
Erratum to "Structural insights into the recognition of native nucleosomes by pioneer transcription factors" [Current Opinion in structural Biology 92 (June 2025) 1-1, article number: 103,024].
Current opinion in structural biology 2025-09-25 doi: 10.1016/j.sbi.2025.103161 PMID: 40992137

15: Lu X, Myint W, Muli CS, Larion M, Matsuo H, Walters KJ.
NMR in the Age of Modern Biomedical Research and Drug Discovery.
Journal of molecular biology 2025-06-26 doi: 10.1016/j.jmb.2025.169302 PMID: 40562354

16: Tugarinov V, Torricella F, Ghosh S, Clore GM.
Modeling Protein Aggregation Kinetics from NMR Data.
Journal of molecular biology 2025-06-12 doi: 10.1016/j.jmb.2025.169269 PMID: 40499748

17: Tugarinov V, Clore GM.
Estimating cross-relaxation rates between methyl and neighboring labile proton spins in high molecular weight proteins.
Journal of biomolecular NMR 2025-05-25 doi: 10.1007/s10858-025-00469-8 PMID: 40413664


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