Newsletter
520 (September
2, 2024) NIH X-ray Diffraction SIG
August
2024
PUBLICATIONS BY MEMBERS OF THE GROUP
1:
Folimonova
V, Chen X, Negi H, Schwieters CD, Li J, Byrd RA,
Taylor N, Youkharibache P, Walters KJ.
Commun
Biol.
2024 Aug 31;7(1):1072. doi: 10.1038/s42003-024-06770-w.
PMID:
39217198;
PMCID: PMC11365992.
2:
Ko
SH, Radecki P, Belinky F, Bhiman JN, Meiring S, Kleynhans J,
Amoako D,Guerra
Canedo V, Lucas M, Kekana D, Martinson N, Lebina L, Everatt J,
Tempia S, Bylund
T, Rawi R, Kwong PD,
Wolter N, von Gottberg A, Cohen C, Boritz EA.
Rapid
intra-host
diversification and evolution of SARS-CoV-2 in advanced
HIV infection.
Nat
Commun.
2024 Aug 22;15(1):7240. doi: 10.1038/s41467-024-51539-8.
PMID:
39174553;
PMCID: PMC11341811.
3:
Chao
FA, Byrd RA.
Existence
of
Singularities in NMR Relaxation Dispersion Profiles:
Implications for Hidden
Dynamics.
J
Am
Chem Soc. 2024 Aug 22. doi: 10.1021/jacs.4c06720. Epub ahead
of print.
PMID:
39172084.
4:
Bou-Nader
C, Gaikwad S, Bahmanjah S, Zhang F, Hinnebusch AG, Zhang J.
Proc
Natl
Acad Sci U S A. 2024 Aug 27;121(35):e2409628121. doi:
10.1073/pnas.2409628121. Epub 2024 Aug 20.
PMID:
39163341;
PMCID: PMC11363354.
5:
Senadeera
SPD, Wang D, Wilson BAP, Smith EA, Wamiru A, Martinez Fiesco
JA, Du L,
Zhang P,
O'Keefe BR, Beutler JA.
J
Nat
Prod. 2024 Aug 23;87(8):2014-2020. doi:
10.1021/acs.jnatprod.4c00477. Epub 2024
Aug 14.
PMID:
39142023.
6:
Gagne
M, Flynn BJ, Honeycutt CC, Flebbe DR, Andrew SF, Provost SJ,
McCormick L,
Van Ry A, McCarthy E, Todd JM, Bao S, Teng IT, Marciano S,
Rudich Y, Li C, Jain
S, Wali B, Pessaint L, Dodson A, Cook A, Lewis MG, Andersen H,
Zahradník J, Suthar
MS, Nason MC, Foulds KE, Kwong PD,
Roederer M, Schreiber G, Seder RA, Douek DC.
Variant-proof
high
affinity ACE2 antagonist limits SARS-CoV-2 replication
in upper and lower
airways. Nat Commun. 2024 Aug 12;15(1):6894. doi:
10.1038/s41467-024-51046-w.
PMID:
39134521;
PMCID: PMC11319446.
7:
Zhou
BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret
KS, Schlick T,
Landsman D, Wang Q, Bai Y.
Mol
Cell.
2024 Aug 22;84(16):3061-3079.e10. doi:
10.1016/j.molcel.2024.07.016. Epub
2024 Aug 8.
PMID:
39121853;
PMCID: PMC11344660.
8:
Li
W, Hu J, Song F, Yu J, Peng X, Zhang S, Wang L, Hu M, Liu JC,
Wei Y, Xiao X, Li
Y, Li D, Wang H, Zhou BR, Dai L, Mou Z, Zhou M, Zhang H, Zhou
Z, Zhang H, Bai Y,
Zhou
JQ, Li W, Li G, Zhu P.
Structural
basis for
linker histone H5-nucleosome binding and chromatin fiber
compaction.
Cell
Res.
2024 Aug 5. doi: 10.1038/s41422-024-01009-z. Epub ahead of
print.
PMID:
39103524.
9:
Dalal
K, Yang W, Tian E, Chernish A, McCluggage P, Lara AJ, Ten Hagen KG,
Tabak
LA.
In vivo
mapping
of the mouse Galnt3-specific O-glycoproteome.
J
Biol
Chem. 2024 Aug 2;300(9):107628. doi:
10.1016/j.jbc.2024.107628. Epub ahead of print.
PMID:
39098533.
10:
Cai
M, Agarwal N, Garrett DS, Baber J, Clore GM.
Biochemistry.
2024
Aug 20;63(16):2030-2039. doi: 10.1021/acs.biochem.4c00258.
Epub 2024 Aug
1.
PMID:
39088556;
PMCID: PMC11345854.
For timely listing, please send a heads-up
E-mail to
the Editor upon publication.
METHODS – Sample
Preparation
Tips
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 – 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
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.
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
E.
Nogales
& J. Mahamid, “Bridging structural and cell biology
with cryo-electron
microscopy” PMID: 38570716.
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,