Newsletter 546 (May 1, 2026) NIH Structural Biology Methods SIG

APRIL 2026 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Tripathi P, Koo JH, Chen X, Silva Pereira LD, Dillon M, Zhang B, Lofgren M, Nguyen KT, Teng IT, Bonilla B, Kerscher S, Kong WP, Henry AR, Stephens T, Tsybovsky Y, Weldon SR, Douek DC, Pierson TC, Batista FD, Idris AH, Seder RA, Kwong PD, Zhou T.
Protective immunity against malaria by a nanoparticle CIS43-based junctional vaccine alone or in combination with R21.
NPJ vaccines 2026-04-28 doi: 10.1038/s41541-026-01455-3 PMID: 42045246

2: Soubias O, Heinrich F, Randazzo PA, Byrd RA.
Binding orientation of weakly associating membrane peripheral proteins via membrane paramagnetic relaxation enhancement NMR.
Communications chemistry 2026-04-24 doi: 10.1038/s42004-026-02037-z PMID: 42026204

3: Senadeera SPD, Wang D, Wilson BAP, Smith EA, Leal CV, Zhang P, O'Keefe BR, Carroll AR, Beutler JA.
Vosamidines A-C, Polycyclic 2-Aminoimidazole Alkaloids from a Marine Calcareous Sponge
Organic letters 2026-04-22 doi: 10.1021/acs.orglett.6c00476 PMID: 42018284

4: Stanley RE, Lowe TM, Ignatova Z.
The regulation, function and disease relevance of cytoplasmic tRNAs.
Nature reviews. Molecular cell biology 2026-04-22 doi: 10.1038/s41580-026-00963-3 PMID: 42014620

5: Yan W, Yang J, Tan S, Wang T, Xiao R, Li N, Chen M, Weinstein LS, He L, Ma C, Zhang J, Gao L, Liang X, Song X, Zhang W, Ma C.
Correction to: Gsα deficiency in macrophages promotes tumor progression via the MAPK signaling pathway.
Journal of molecular medicine (Berlin, Germany) 2026-04-22 doi: 10.1007/s00109-026-02673-x PMID: 42014531

6: Simko EAJ, Muthukumar S, Myers TM, Valkov AL, Valkov E.
Conserved and divergent features of human mRNA decapping revealed by biochemical reconstitution.
Nature communications 2026-04-22 doi: 10.1038/s41467-026-72177-2 PMID: 42014425

7: Mencacci NE, Minakaki G, Maroofian R, De Pace R, Paimboeuf A, Branco Fonseca T, Abramova T, Shannon P, Chitayat D, Magrinelli F, Peng WJ, Chatterjee D, Eldessouky SH, Baptista J, Marton T, Vogt J, Ortigoza-Escobar JD, Martorell L, Gómez-Chiari M, Wentzensen IM, Kamsteeg EJ, Zaki MS, Scardamaglia A, Zifarelli G, Al-Hassnan ZN, Miller E, Shinar S, Matsa LS, Appikonda SHC, Otaify GA, Al-Thihli K, Al-Maawali A, Schwake M, Severino M, Houlden H, Patten SA, Bonifacino JS, Bhatia KP, Krainc D.
Pathogenic variants in BORCS5 Cause a Spectrum of Neurodevelopmental and Neurodegenerative Disorders with Lysosomal Dysfunction.
The Journal of clinical investigation 2026-04-21 doi: 10.1172/JCI195336 PMID: 42012897

8: Lee YT, Degenhardt MFS, Skeparnias I, Chen SY, Bhoge BA, Tarasov SG, Dyba MA, Zhang J, Stagno JR, Wang YX.
Structural basis for protein-free catalysis by ribonuclease P ribozyme.
Nature communications 2026-04-16 doi: 10.1038/s41467-026-71597-4 PMID: 41986363

9: Nataletti S, Okita S, Sindorf J, O'Brien MK, Maronati R, McGuire M, Hoppe-Ludwig S, Banerjee A, Wacek A, Cave J, Looft JM, Hendershot BD, Jayaraman A.
Predicting prosthesis use and mobility needs in lower limb amputees: a machine learning approach using clinical and actigraphy data.
Journal of neuroengineering and rehabilitation 2026-04-10 doi: 10.1186/s12984-026-01954-3 PMID: 41957611

10: Andricioaei I, Best RB, Birge RR, Boresch S, Brunger A, Brooks BR, Buck M, Brüschweiler R, Caflisch A, Case DA, Cui Q, Dejaegere A, Dinner AR, Elber R, Evanseck JD, Gao J, Guo H, Hubbard RE, Kuriyan J, Joseph-McCarthy D, Levy RM, Nilsson L, Mattos C, MacKerell AD, McCammon JA, Michnick SW, Mulholland A, Meuwly M, Pastor RW, Reuter N, Roux B, Sali A, Schlick T, Smith JC, Stote RH, Straub JE, Taly A, van der Vaart A, Wan S, Weiss MA, Yang W, York DM, Zhou Y.
The scientific legacy of Martin Karplus from the perspective of his collaborators.
Biophysical journal 2026-04-03 doi: 10.1016/j.bpj.2026.03.050 PMID: 41928473

11: De Pace R, Dominguez Gonzalez CA, Williamson CD, Helman G, Sanderson LE, Disanza B, Hsiao-Sánchez N, Pizzino A, Muirhead K, Bonkowsky JL, Taft RJ, Sannaa NA, Dias P, Quintas AS, Mutlu MB, Bas H, Oztürk H, Mojarrad M, Alerasool M, Sheikhani S, Jabbar HK, Issa AH, Houlden H, Zonic E, Barakat TS, Tripolski K, Romito A, Teferedegn E, Vossough A, Whitehead MT, Bhoj E, Ahrens-Nicklas RC, Simons C, Wolvetang E, van Ham TJ, Bertoli-Avella AM, Maroofian R, Bonifacino JS, Vanderver A.
BLOC1S1 variants cause lysosomal and autophagic defects resulting in a hypomyelinating leukodystrophy with epileptic encephalopathy.
American journal of human genetics 2026-03-27 doi: 10.1016/j.ajhg.2026.02.024 PMID: 41887224

12: De Rosa SC, Gravett RM, Hahn WO, Villaran M, Huang Y, Schmitzberger L, Montefiori D, Domin E, Tomaras GD, Heptinstall J, Seaton KE, Ferrari G, Ozorowski G, Ward AB, Lee WH, van der Maas L, Polakowski L, Frank I, Tieu HV, Kalams SA, Garcia NMG, Huang J, Ghosh S, Purwar M, Kulp D, Humeau L, Kwong PD, McElrath MJ, Corey L, Weiner D, None None.
DNA electroporation of HIV Env elicits robust T cell responses and memory B cell responses with muted serum antibody levels that can be boosted with recombinant protein.
Vaccine 2026-03-23 doi: 10.1016/j.vaccine.2026.128487 PMID: 41865485

13: Stahlhut C, Maciag AE, Sullivan KA, Singh K, Gitego N, Zhang Z, Chan AH, Sharma AK, Alexander PA, Shu J, Yang Y, Rigby M, Ma R, Setoodeh S, Smith BP, Pei J, Rabara D, Larsen EK, Turner DM, Zhang C, Feng C, Feng S, Stice JP, Xu R, Lin K, Stephen AG, Lightstone FC, Ji C, Wang K, Simanshu DK, Nissley DV, Wallace E, Wang B, Sinkevicius KW, McCormick F, Beltran PJ.
Discovery of BBO-11818, a Potent and Selective Noncovalent Inhibitor of (ON) and (OFF) KRAS with Activity against Multiple Oncogenic Mutants.
Cancer discovery 2026-03-06 doi: 10.1158/2159-8290.CD-25-1280 PMID: 41790032

14: 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

15: 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

16: 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

17: 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


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