Newsletter 533 (June 16, 2025) NIH Structural Biology
Methods SIG
MAY 2025 PUBLICATIONS BY MEMBERS OF THE GROUP
1:
Shaukat AN, Zhang J.
Conduits,
Doppelgängers, and Chimeras: RNA Structures at the Virus-Host Interface.
Annu Rev Virol. 2025 May 30. doi:
10.1146/annurev-virology-100422-031237. Epub ahead
of print.
PMID:
40446307.
2:
Maloney SM, Shaw TM, Nennig KM, Larsen MS, Shah A, Kumar A, Marcotrigiano J, Grove J, Snijder EJ, Kirchdoerfer RN, Bailey AL.
CD81
is a receptor for equine arteritis virus (family: Arteriviridae).
mBio.
2025 May 27:e0062325. doi:
10.1128/mbio.00623-25. Epub ahead of print.
PMID:
40422661.
3: Demeshkina NA, Ferré-D'Amaré AR.
Cell
Rep. 2025 May 23;44(6):115738. doi:
10.1016/j.celrep.2025.115738. Epub ahead of
print.
PMID:
40413746.
4: Tugarinov V, Clore GM.
J Biomol NMR. 2025 May 25. doi:
10.1007/s10858-025-00469-8. Epub ahead of
print.
PMID:
40413664.
5: Wu
RL, Houser KV, Gaudinski MR, Widge AT, Awan SF, Carter CA, Holman LA, Saunders J,
Hendel CS, Eshun A, Whalen WR, Wang X, Arthur A, Cunningham JE, Beck A, Casazza
JP, Yamshchikov GV, Rothwell RS, Strom L, Dittakavi T, Happe M, Hickman SP, Conan-Cibotti M,
Carlton K, Zhang L, Huang Y, Capparelli EV, Castro M, Lin
BC, O'Connell S, Flach BS, Bailer RT, Narpala SR, Serebryannyy L, McDermott AB, Arnold FJ, Gall JG,
Vazquez S, Berkowitz NM, Gordon IJ, Chen GL, Kwong PD, Huang J, Pierson TC, Connors M,
Mascola JR, Zhou T, Doria-Rose NA, Koup RA, Dropulic LK; VRC 609 study team.
Lancet
HIV. 2025 May 20:S2352-3018(25)00041-4. doi: 10.1016/S2352 3018(25)00041-4. Epub ahead of print.
PMID:
40409326.
6: Mencacci NE, Minakaki G, Maroofian R, De Pace R, Paimboeuf A,
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,
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.
medRxiv [Preprint]. 2025 May
7:2025.04.30.25326597. doi:
0.1101/2025.04.30.25326597.
PMID:
40385417; PMCID: PMC12083638.
7:
Thakur B, Katte RH, Xu W, Janowska K, Sammour S, Henderson R, Lu M, Kwong PD, Acharya P.
Conformational
trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening.
Nat
Commun. 2025 May 17;16(1):4595. doi:
10.1038/s41467-025-59721-2.
PMID:
40382314; PMCID: PMC12085566.
8: Cai
M, Ying J, Lopez JM, Huang Y, Clore GM.
Proc
Natl Acad Sci U S A. 2025 May 20;122(20):e2506441122. doi:
10.1073/pnas.2506441122. Epub 2025 May 14.
PMID:
40366684; PMCID: PMC12107155.
9:
Maciag AE, Yang Y, Sharma AK, Turner DM, DeHart CJ, Abdelkarim H, Fan L, Smith
BP, Kumari V, Dyba M, Rigby M, Castillo Badillo JA, Adams L, Fornelli L, Fox S, Brafman
A, Turbyville T, Gillette W, Messing S, Agamasu C, Wolfe AL, Gysin S, Chan AH, Simanshu DK, Esposito D, Chertov O, Stephen AG, Arkin M, Renslo A, Kelleher NL, Gaponenko V, Lightstone FC,
Nissley DV, McCormick F.
Blocking
C-terminal processing of KRAS4b via a direct covalent attack on the CaaX-box cysteine.
Proc
Natl Acad Sci U S A. 2025 May 13;122(19):e2410766122. doi:
10.1073/pnas.2410766122. Epub 2025 May 9.
PMID:
40343987; PMCID: PMC12088381.
10: Slyvka A, Rathore I, Yang R, Gewartowska O,
Kanai T, Lountos GT, Skowronek K, Czarnocki-Cieciura M, Wlodawer A, Bochtler M.
Activity
and structure of human (d)CTP deaminase CDADC1.
Proc
Natl Acad Sci U S A. 2025 May 13;122(19):e2424245122. doi:
10.1073/pnas.2424245122. Epub 2025 May 5.
PMID:
40324085; PMCID: PMC12088426.
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