Newsletter 532 (June 2, 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
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
M. Schaefer et al., “Surface-mutagenesis strategies to enable structural biology
crystallization platforms” PMID: 39207897.
METHODS – Integrative Structural Biology
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: 38463967.
M. Bochtler, “X-rays, electrons, and neutrons as probes of atomic matter” PMID: 38412856.
METHODS – XFEL, 3D-printed liquid sheet jet technology
M. Trebbin, “Thinner than a knife’s edge: 3D-printed liquid sheet jet
technology for solution phase XFEL experiments” PMID: 37910141.
METHODS – Micro-ED, AlphaFold-Assisted
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
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
K. Lytje and J.S. Pederson, “Validation of electron-microscopy maps using solution
small-angle X-ray scattering” PMID: 38935344.
METHODS – NMR and Ligand Screening
M. Bütikofer et al., “Rapid Protein-Ligand Affinity Determination by Photoinduced
Hyperpolarized NMR” PMID: 38957136.
METHODS – AlphaFold
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.
READINGS
& TUTORIALS – General Structural Biology
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
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
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 – 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.
S. Subramaniam, “Structural biology in the age of AI” PMID:
38066345.
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