Newsletter 537 (September 3, 2025) NIH Structural Biology Methods SIG

AUGUST 2025 PUBLICATIONS BY MEMBERS OF THE GROUP

1: De Pace R, Ghosh S, Williamson CD, Bonifacino JS.
BLOC-1 and BORC: Complex regulators of endolysosomal dynamics.
Cell chemical biology 2025-09-02 doi: 10.1016/j.chembiol.2025.08.001 PMID: 40865516

2: Zhang H, Yang W, Zhou D, Wang Y, Zhu L, Jiang M, Zhang Q, Sirajuddin A, Arai AE, Zhao S, Lu M.
Prognostic Value of Myocardial T1 Mapping and Extracellular Volume Fraction in Heart Failure: A Meta-Analysis.
JACC. Cardiovascular imaging 2025-08-30 doi: 10.1016/j.jcmg.2025.06.017 PMID: 40884516

3: 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

4: Yang W, Jiang M, Zhang H, Zhou D, Wang Y, Zhu L, Tian Z, Yin G, Zhang Q, Sirajuddin A, Arai AE, Zhao S, Lu M.
Risk stratification and outcomes in diabetes mellitus patients with preserved ejection fraction: a cardiac MRI study.
BMC medicine 2025-08-29 doi: 10.1186/s12916-025-04354-x PMID: 40866930

5: 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

6: Lee J, Chin N, Zou J, Mazli WNAB, Jarnik M, Saidi L, Xu Y, Jeong E, Suh J, Replogle J, Ward ME, Bonifacino JS, Zheng W, Hao L, Ye Y.
CHIP protects lysosomes from CLN4 mutant-induced membrane damage.
Nature cell biology 2025-08-26 doi: 10.1038/s41556-025-01738-2 PMID: 40855364

7: Petrotchenko EV, Novy B, Nagy E, Popov KI, Cross JB, Thapar R, Borchers CH.
Characterization of the KRas G12D-inhibitor interactions by differential HDX-MS and molecular dynamics simulations.
Computational and structural biotechnology journal 2025-08-23 doi: 10.1016/j.csbj.2025.08.008 PMID: 40837237

8: Middleton SJ, Markússon 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

9: Banco MT, Paul T, Jiang J, Myong S, Ferré-D'Amaré AR.
Structural basis for dual DNA and RNA specificity of the G-quadruplex-resolving DEAH-box helicase DHX36.
Cell reports 2025-08-20 doi: 10.1016/j.celrep.2025.116136 PMID: 40833853

10: 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 mTORC1-catalyzed TFEB phosphorylation and cytoplasmic retention.
Molecular biology of the cell 2025-08-20 doi: 10.1091/mbc.E25-07-0346 PMID: 40833810

11: 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

12: 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

13: Rawi R, Morano NC, Cheung CS, Du H, Gorman J, Prabhakaran M, Becker JE, Bylund T, Charaf S, Chen X, Lee M, Harris DR, Olia AS, Ou L, Wang L, Wang S, Zhang B, Kanekiyo M, McDermott AB, Zhou T, Shapiro L, Kwong PD.
The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody.
Structure (London, England : 1993) 2025-08-16 doi: 10.1016/j.str.2025.07.015 PMID: 40816277

14: Sueyoshi T, Negishi M.
CAR: Discovery and development by the pharmacogenetics laboratory at NIEHS, NIH.
Pharmacological research 2025-08-14 doi: 10.1016/j.phrs.2025.107907 PMID: 40812694

15: Pekovic F, Lai WS, Corbo J, Hicks SN, Luke K, Blackshear PJ, Valkov E.
Multivalent interactions with CCR4-NOT and PABPC1 determine mRNA repression efficiency by tristetraprolin.
Nature communications 2025-08-14 doi: 10.1038/s41467-025-62741-7 PMID: 40804313

16: Parker JL, Deme JC, Feddersen B, Lea SM, Newstead S.
Structural basis for transport and inhibition of nucleotide sugar transport in pathogenic fungi.
Research square 2025-08-13 doi: 10.21203/rs.3.rs-7213965/v1 PMID: 40799752

17: Meana-Pañeda R, Ji C, Van CTS, Reboul CF, Kang S, Kim S, Rhee J, Lee Y, Ercius P, Czaja W, Park J, Elmlund H.
Time-resolved atomic-resolution Brownian tomography of single nanocrystals reveals size-dependent dynamics.
Science advances 2025-08-06 doi: 10.1126/sciadv.ady1413 PMID: 40768567

18: Lee K, Negi H, Chen X, Atallah-Yunes K, Truslow S, Castelino RE, Guest MR, Ciancone AM, Tarasov SG, Chari R, Walters KJ, O'Reilly FJ.
Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy.
bioRxiv : the preprint server for biology 2025-08-06 doi: 10.1101/2025.07.31.667872 PMID: 40766414

19: Martinez Fiesco JA, Beilina A, Alvarez de la Cruz A, Li N, Metcalfe RD, Cookson MR, Zhang P.
14-3-3 binding maintains the Parkinson's associated kinase LRRK2 in an inactive state.
Nature communications 2025-08-06 doi: 10.1038/s41467-025-62337-1 PMID: 40764514

20: Zhen T, Cao Y, Dou T, Chen Y, Lopez G, Menezes AC, Wu X, Hammer J, 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

21: Liu C, Wu K, Choi H, Han HL, Zhang X, Watson JL, Ahn G, Zhang JZ, Shijo S, Good LL, Fischer CM, Bera AK, Kang A, Brackenbrough E, Coventry B, Hick DR, Qamar S, Li X, Decarreau J, Gerben SR, Yang W, Goreshnik I, Vafeados D, Wang X, Lamb M, Murray A, Kenny S, Bauer MS, Hoofnagle AN, Zhu P, Knowles TPJ, Baker D.
Diffusing protein binders to intrinsically disordered proteins.
Nature 2025-07-31 doi: 10.1038/s41586-025-09248-9 PMID: 40739343

22: Chen X, Yao L, Li W, Ma S, Yuan X, Yang Y, Yuan Y, Liu Y, Liu L, Wang H, Gellert M, Yang W.
How RAG1/2 evolved from ancestral transposases to initiate V(D)J recombination without transposition.
Proceedings of the National Academy of Sciences of the United States of America 2025-07-29 doi: 10.1073/pnas.2512362122 PMID: 40729386

23: Van CTS, Reboul CF, Caesar JJE, Meana-Pañeda R, Lountos GT, Deme JC, Bryant OJ, Johnson S, Piczak CT, Valkov E, Lea SM, Elmlund H.
Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE.
Acta crystallographica. Section D, Structural biology 2025-07-07 doi: 10.1107/S2059798325005686 PMID: 40622679

24: Ciancone A, O'Reilly FJ.
Photo-crosslinkers boost structural information from crosslinking mass spectrometry.
Current opinion in structural biology 2025-07-06 doi: 10.1016/j.sbi.2025.103102 PMID: 40616977

25: Zare Jeddi M, Galea KS, Ashley-Martin J, Nassif J, Pollock T, Poddalgoda D, Kasiotis KM, Machera K, Koch HM, López ME, Chung MK, Kil J, Jones K, Covaci A, Ait Bamai Y, Fernandez MF, Kase RP, Louro H, Silva MJ, Santonen T, Katsonouri A, Castaño A, Quirós-Alcalá L, Lin EZ, Pollitt K, Virgolino A, Scheepers PTJ, Melnyk LJ, Mustieles V, Cañas Portilla AI, Viegas S, von Goetz N, Sepai O, Bird E, Göen T, Fustinoni S, Ghosh M, Dirven H, Kwon JH, Carignan C, Mizuno Y, Ito Y, Xia Y, Nakayama SF, Makris KC, Parsons PJ, Gonzales M, Bader M, Dusinska M, Menouni A, Duca RC, Chbihi K, Jaafari SE, Godderis L, van Nieuwenhuyse A, Qureshi A, Ali I, Trindade CC, Teixeira JP, Bartonova A, Tranfo G, Audouze K, Verpaele S, LaKind J, Mol H, Bessems J, Magagna B, Waras MN, Connolly A, Nascarella M, Yang W, Huang PC, Lee J, Heussen H, Goksel O, Yunesian M, Yeung LWY, Souza G, Vekic AM, Haynes EN, Hopf NB.
Guidance on minimum information requirements (MIR) from designing to reporting human biomonitoring (HBM).
Environment international 2025-07-04 doi: 10.1016/j.envint.2025.109601 PMID: 40609511

26: McCoy IE, Yang J, Go AS, Rincon-Choles H, Taliercio J, Rosas SE, Unruh M, Shah V, Cohen DL, He J, Chen J, Sondheimer J, Parsa A, Yang W, Rao PS, Hsu CY, None None.
Complex Etiologies of the Discordance Between Cystatin C- and Creatinine-Based Estimated GFR and Its Adverse Associations: Findings From the CRIC Study.
American journal of kidney diseases : the official journal of the National Kidney Foundation 2025-05-16 doi: 10.1053/j.ajkd.2025.03.018 PMID: 40373998


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