Newsletter 534 (July 7,
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. 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
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