Newsletter 547 (June 1, 2026) NIH Structural Biology Methods SIG

MAY 2026 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Zhan J, Hsieh CM, Esser L, Lang ZC, Morton AJ, Robey R, Zhou F, Ambudkar SV, Huang RK, Gottesman MM, Xia D.
Functional implications of the conformational landscape of a multidrug transporter revealed by Zebrafish Abcb4 structures.
Nature communications 2026-05-31 doi: 10.1038/s41467-026-73751-4 PMID: 42218127

2: Gordon K, Wright ZM, Stephens CR, Frazier MN, Clark BS, Wilson IM, Silvernail I, Stanley RE, LeBlanc SJ.
A combined PIE-FRET and FCS assay to monitor RNA dynamics and cleavage by SARS-CoV-2 Nsp15.
Scientific reports 2026-05-30 doi: 10.1038/s41598-026-52571-y PMID: 42215555

3: López-Silva P, Martínez-Valdebenito C, Jiang J, Abarca K, López J, Richards AL, Weitzel T, Acosta-Jamett G.
Surveillance of vector-borne infections: Dogs as sentinel animals for
One health (Amsterdam, Netherlands) 2026-05-22 doi: 10.1016/j.onehlt.2026.101437 PMID: 42170635

4: Rana MS, Banerjee A.
Engineering NRas palmitoylation to hook zDHHC inhibitors.
Cell chemical biology 2026-05-22 doi: 10.1016/j.chembiol.2026.04.002 PMID: 42167141

5: Chen T, Alexander KK, Martinez Fiesco JA, Naaldijk Y, Fasiczka R, Brahmia B, de la Cruz AA, LeClair TJ, Steude EG, Zhang P, Hilfiker S, Kennedy EJ.
Constrained peptide mimics of the LRRK2 C-terminal Helix inhibits its kinase activity.
Bioorganic chemistry 2026-05-18 doi: 10.1016/j.bioorg.2026.109994 PMID: 42143840

6: Zhu L, Xu J, Cui C, Sun P, Wu X, Duan X, Zhang H, Zheng T, Jiang M, Zhou D, Yang W, Wang Y, Yin G, Zhou W, Lian X, Sirajuddin A, Arai AE, Zhang Q, Li L, Zhao S, Lu M.
Impact of formalin fixation on biventricular parameters in cardiac diffusion tensor imaging: A pilot study in a miniature swine model.
The international journal of cardiovascular imaging 2026-05-16 doi: 10.1007/s10554-026-03730-9 PMID: 42141274

7: Sikkema AP, Klemm BP, Perera L, Hall TMT.
Enzyme structure and kinetics produce tRNA and nucleotide specificity of Schizosaccharomyces pombe CC- and A-adding enzymes.
Nucleic acids research 2026-05-14 doi: 10.1093/nar/gkag475 PMID: 42130072

8: Wang HC, Chen R, Yang W, Muthukumar R, Hu T, Patel RM, Casey EB, Denby ED, Zhang R, Xie G, Ge K, Challen G, Bednarski JJ, Magee JA.
MLL3 and MLL4 sustain hematopoietic stem cell multipotency by opposing a B-cell default state.
Blood 2026-05-12 doi: 10.1182/blood.2025032969 PMID: 42118696

9: Zhang L, Tisserand G, Shen Y, Salehi M, Amar L, Cui Y, Świątkowska-Stodulska R, Moog S, Liu J, Gubbi S, Falhammar H, Kocjan T, Igaz P, Hadoux J, Young WF, Remde H, Babińska A, Miguel V, Beuschlein F, Liu L, Palmieri S, Jiang J, Fischer A, Varghese J, Carreira A, Parasiliti-Caprino M, Nölting S, Zhou Y, Prodanov T, Bancos I, Fassnacht M, Jimenez C, Alkaissi H, Tong A, Pacak K, Crona J.
Safety of biopsy in phaeochromocytoma and paraganglioma: an international, multicentre, retrospective cohort study.
The lancet. Diabetes & endocrinology 2026-05-12 doi: 10.1016/S2213-8587(26)00033-1 PMID: 42114537

10: Parker JL, Deme JC, Feddersen B, Lea SM, Newstead S.
Structural basis for transport and inhibition of nucleotide sugar transport in pathogenic fungi.
Nature communications 2026-05-03 doi: 10.1038/s41467-026-72729-6 PMID: 42069710

11: 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

12: Simanshu DK, McCormick F.
Revisiting RAS family GTPase signaling: effector selectivity and oncogenic bypass.
The Biochemical journal 2026-04-22 doi: 10.1042/BCJ20250142 PMID: 42017331

13: Andorsky D, Lopez AT, Vaidya R, Madueno FV, Ibrahimi S, Naik S, Gandhi M, Haydu JE, Lash B, Fesler M, Hrom J, Lee EH, Sundaram S, Conte K, Osei-Bonsu K, Doerr T, Bai Y, Dixit N, Eskelund CW, Boardman AP, Boccia R, Lee CY, Sharman JP.
Epcoritamab Monotherapy as Outpatient Treatment for Patients With Relapsed/Refractory Diffuse Large B-Cell Lymphoma: Interim Results From EPCORE NHL-6.
Clinical lymphoma, myeloma & leukemia 2026-03-26 doi: 10.1016/j.clml.2026.02.006 PMID: 41881714

14: Geng A, Roy R, Ken M, Li L, Chime A, Abou Assi H, Liu B, Bou-Nader C, Lee Y, Zhang J, Herschlag D, Goff SP, Al-Hashimi HM.
Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.
Cell 2026-03-20 doi: 10.1016/j.cell.2026.02.021 PMID: 41856113

15: Greenhalgh R, Brady SW, Yang W, Flasch DA, Edmonson MN, Terekhanova NV, Liu Y, Wang J, Szlachta KA, Tian L, Putnam DK, Rahbarinia D, Kolekar P, Zhou X, Gerhard DS, Ma X, Zhang J.
The landscape of structural variation in pediatric cancer.
Cancer cell 2026-03-14 doi: 10.1016/j.ccell.2026.02.012 PMID: 41825442

16: 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, Lochmüller 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

17: Suger AH, Chen H, Haas CB, Fan S, Scott CG, Bolla MK, Dennis J, Dunning AM, Michailidou K, Wang Q, Fasching PA, Haeberle L, Stone J, Gago-Dominguez M, Castelao JE, Murphy RA, Aronson K, Couch FJ, Yadav S, Milne RL, Hopper JL, Norman A, Eliassen AH, Tapper WJ, Eccles DM, Evans DG, Astley S, Hall P, Czene K, Pharoah PDP, Antoniou AC, García-Closas M, Berrington A, Easton DF, Gierach GL, Tamimi RM, Vachon CM, Lindström S, Harrison TA.
Interactions between genetic and epidemiological factors influencing mammographic density.
American journal of epidemiology 2025-03-28 doi: 10.1093/aje/kwaf067 PMID: 40153356


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