Newsletter 535 (July 21, 2025)
NIH Structural Biology Methods SIG
JUNE 2025 PUBLICATIONS BY MEMBERS OF THE GROUP
1:
Dharavath S, Song H, Ji X.
Biochem
Biophys Res Commun. 2025 Jun 13;777:152206. doi: 10.1016/j.bbrc.2025.152206.
Epub ahead of print.
PMID:
40578281.
2: Lu X,
Myint W, Muli CS, Larion M, Matsuo H, Walters KJ.
NMR in the age of modern biomedical research and drug discovery.
J Mol
Biol. 2025 Jun 23:169302. doi: 10.1016/j.jmb.2025.169302. Epub ahead of print.
PMID:
40562354.
3: Jones
CP, Ferré-D'Amaré AR.
RNA.
2025 Jun 16;31(7):949-960. doi: 10.1261/rna.080413.125.
PMID:
40527531; PMCID: PMC12170182.
4:
Morris DJ, Gorman J, Zhou T, Lora J, Connell AJ, Li H, Liu W, Roark RS, Campion
MS, Carey JW, Habib R, Li Y, Martella CL, Park Y, Singh A, Sowers KJ, Teng IT,
Wang S, Chohan N, Ding W, Lauer C, Lewis E, Mason RD, Rando JM, Peyton L,
Schramm CA, Wagh K, Korber B, Seaman MS, Douek DC, Haynes BF, Kulp DW, Roederer
M, Hahn BH, Kwong PD, Shaw
GM.
Cell
Rep. 2025 Jun 24;44(6):115848. doi: 10.1016/j.celrep.2025.115848. Epub 2025 Jun
13.
PMID:
40516049.
5: Simanshu DK, Xu R, Stice JP, Czyzyk
DJ, Feng S, Denson JP, Riegler E, Yang Y, Zhang C, Donovan S, Smith BP,
Abreu-Blanco M, Chen M, Feng C, Fu L, Rabara D, Young LC, Dyba M, Yan W, Lin K,
Ghorbanpoorvalukolaie S, Larsen EK, Malik W, Champagne A, Parker K, Ju JH, Jeknic
S, Esposito D, Turner DM, Lightstone FC, Wang B, Wehn PM, Wang K, Stephen AG,
Maciag AE, Hata AN, Sinkevicius KW, Nissley DV, Wallace EM, McCormick F,
Beltran PJ.
BBO-10203 inhibits tumor growth without inducing hyperglycemia
by blocking RAS-PI3Kα interaction.
Science. 2025 Jun
12:eadq2004. doi: 10.1126/science.adq2004. Epub ahead of print.
PMID: 40504949.
6: Witt KC, Dziulko A,
An J, Pekovic F, Cheng AX, Liu GY, Lee OV, Turner DJ, Lari A, Gaidt MM, Chavez
R, Fattinger SA, Abraham P, Dhaliwal H, Lee AY, Kotov DI, Coscoy L, Glaunsinger
BA, Valkov E, Chuong EB, Vance RE.
SP140-RESIST pathway regulates interferon mRNA stability and
antiviral immunity.
Nature. 2025 Jun 11.
doi: 10.1038/s41586-025-09152-2. Epub ahead of print.
PMID: 40500448.
7: Liu L, Li J,
Cisneros-Aguirre M, Merkell A, Stark JM, Gellert M, Yang W.
Dynamic assemblies and coordinated reactions of non-homologous
end joining.
Nature. 2025 Jun 11.
doi: 10.1038/s41586-025-09078-9. Epub ahead of print.
PMID: 40500445.
8: Tugarinov V,
Torricella F, Ghosh S, Clore GM.
Modeling Protein Aggregation Kinetics from NMR Data.
J Mol Biol. 2025 Jun
9:169269. doi: 10.1016/j.jmb.2025.169269. Epub ahead of print.
PMID: 40499748.
9: Du L, Wilson BAP,
Moore WJ, Dalilian M, Shenoy SR, Li N, Martinez Fiesco JA, Hwang JY, Smith EA,
Wamiru A, Goncharova EI, Alvarez de la Cruz A, Pagadala K, Piswa HK, Patteti V,
Jampana VP, Manepalli P, Nimmala R, Marri NR, Gunuguntla M, Reddy JJ, Schneekloth
JS Jr, Zhang P, O'Keefe BR.
Chemical Evolution of Aplithianine Class of Serine/Threonine
Kinase Inhibitors.
J Med Chem. 2025 Jun
26;68(12):12756-12785. doi: 10.1021/acs.jmedchem.5c00649. Epub 2025 Jun 6.
PMID: 40476486.
10: Alexander P, Chan
AH, Rabara D, Swain M, Larsen EK, Dyba M, Chertov O, Ashraf M, Champagne A, Lin
K, Maciag A, Gillette WK, Nissley DV, McCormick F, Simanshu DK, Stephen AG.
J Biol Chem. 2025 Jun
3:110331. doi: 10.1016/j.jbc.2025.110331. Epub ahead of print.
PMID: 40473215.
11: Cheng J, Krug PW,
Lei H, Moss DL, Lang ZC, Morton AJ, Shen CH, Pletnev S, Huang RK, Pierson TC,
Zhou T, Ruckwardt TJ, Kwong PD.
Structural insights from vaccine candidates for EV-D68.
Commun Biol. 2025 Jun
4;8(1):860. doi: 10.1038/s42003-025-08253-y.
PMID: 40467847; PMCID:
PMC12137623.
12: Matsuda K, Harrison
M, Wettstein E, Pederson J, Pullano AA, Bolkhovitinov L, Kim B, Steinberg I,
Griesman T, Stuccio S, Rogan D, Patamawenu A, Shofner T, Wright NE, Webber JD,
Van't Veer F, Roenicke R, Koory E,
Roeder PM, Ober E, Leach
B, Tsybovsky Y, Stephens T, Del Moral-Sanchez I, Bontjer I, McGinnes-Cullen LW,
Chu E, Liang J, Torres JL, Lin RN, Tran AS, Dziubla G, Serebryannyy L, Narpala
S, Lin B, Castro M, Ozorowski G, Ward AB, Sanders RW, Kwong PD, Guenaga J, Wyatt R,
Morrison T, Connors M.
Nat Commun. 2025 Jun
3;16(1):5162. doi: 10.1038/s41467-025-60481-2.
PMID: 40461490; PMCID:
PMC12134134.
For
timely listing, please send a heads-up E-mail to the Editor upon publication.
RECENT
TOPICS IN THE LITERATURE:
METHODS – Sample
Preparation Tips
N.
Gunkel et al., “Revisiting
sodium phosphotungstate and ammonium molybdate as nonradioactive
negative-staining agents for single-particle analysis” PMID:
39601624.
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:
“Pan-KRAS’ drug aiming at KRAS-related cancers lacking
targeted therapies now being tested in humans, 07/14/2025
Ruth Nussinov elected to the National
Academy of Sciences, 05/02/2025
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