Newsletter 542 (February 6, 2026) NIH Structural Biology Methods SIG

JANUARY 2026 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Bulut H, Higashi-Kuwata N, Ogata-Aoki H, Hayashi H, Takamune N, Kishimoto N, Das D, Li M, Wlodawer A, Misumi S, Tamamura H, Mitsuya H.
Impact of Single Halogen Atom Substitutions on Antiviral Profile of Inhibitors Targeting SARS-CoV‑2 Main Protease.
ACS omega 2026-02-02 doi: 10.1021/acsomega.5c10895 PMID: 41626465

2: 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

3: Celia H, Buchanan SK, Botos I.
Advances in understanding Ton and Tol system motor proteins.
Biochemical Society transactions 2026-01-30 doi: 10.1042/BST20253128 PMID: 41615764

4: 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

5: Mondal T, Banerjee A.
In vitro reconstitution in membrane environment reveals critical lipid dependence of substrate S-acylation by protein palmitoyltransferase enzymes.
The Journal of biological chemistry 2026-01-26 doi: 10.1016/j.jbc.2026.111194 PMID: 41581876

6: Mann DL, Chirinos JA, Yu J, Yang W, McNamara DM, Richards B, Taddei-Peters WC, Jeffries N, Stewart GC, Qian C, Cappola TP, Aaronson KD, None None.
Circulating Proteomic Profiles in Ambulatory Patients With Advanced Stage C2D Heart Failure: Insights From the REVIVAL Registry.
Journal of cardiac failure 2026-01-25 doi: 10.1016/j.cardfail.2026.01.006 PMID: 41580271

7: Foote MK, Huffman WC, Santos EN, Lee PR, Jarnik M, Li W, Bonifacino JS, Fields RD.
Non-Synaptic Mechanism of Ocular Dominance Plasticity.
ASN neuro 2026-01-20 doi: 10.1080/17590914.2026.2616376 PMID: 41556652

8: Onda M, Liu X, Liu W, Zhan J, Maslanka CA, Xia D, Ho M, Pastan I.
RO4, a high-affinity humanized antibody against the juxtamembrane region of mesothelin for targeted cancer therapy.
Antibody therapeutics 2026-01-19 doi: 10.1093/abt/tbaf022 PMID: 41550974

9: Zhan J, Ho M, Esser L, Maslanka CA, Pastan I, Xia D.
Recent advances in structural investigations of cancer antigen mesothelin and its interactions with therapeutic antibodies.
Antibody therapeutics 2026-01-19 doi: 10.1093/abt/tbaf028 PMID: 41550972

10: Bonsor DA, Finci LI, Potter JR, Young LC, Wall VE, Goldstein de Salazar R, Geis KR, Stephens T, Finney J, Nissley DV, McCormick F, Simanshu DK.
Structure of SHOC2-KRAS-PP1C complex reveals RAS isoform-specific determinants and insights into targeting complex assembly by RAS inhibitors.
Nature communications 2026-01-11 doi: 10.1038/s41467-026-68319-1 PMID: 41519889

11: Thakur K, Fucci I, Pandian J, Suazo KF, Monteiro DCF, Yoo E.
Structure-Guided Optimization of 4-Chloro-Pyrazolopyridine Analogs for Covalent PREP Inhibition.
Journal of medicinal chemistry 2026-01-09 doi: 10.1021/acs.jmedchem.5c02680 PMID: 41512187

12: Zhang Y, Kennedy FD, Hall TMT.
Crystal structures of Caenorhabditis elegans PUF-3 depict plasticity of RNA recognition that enables germline gene regulation.
Nucleic acids research 2026-01-07 doi: 10.1093/nar/gkaf1431 PMID: 41495898

13: 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

14: 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 in vivo efficacy, cryo-EM-epitope identification, and breadth of two anti-alphavirus bispecific single domain antibodies
Journal of virology 2025-12-16 doi: 10.1128/jvi.01875-25 PMID: 41400357

15: 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

16: 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

17: Jiang M, Zhou W, Qiao HY, Zheng T, Lian X, Wang Y, Yang W, Zhu L, Xu J, Zhou D, Zhang H, Arai AE, Sirajuddin A, Zhao S, Lu M.
Phenotypic stratification and prognostic value of cardiac magnetic resonance in non-dilated left ventricular cardiomyopathy.
Heart (British Cardiac Society) 2025-08-18 doi: 10.1136/heartjnl-2025-326192 PMID: 40819904


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