Newsletter 518 (July 15, 2024) NIH X-ray Diffraction SIG
June
2024 PUBLICATIONS BY MEMBERS OF THE GROUP
1: Elghondakly A, Jermain MD,
Winkler WC, Ferré-D'Amaré AR.
Structure. 2024 Jun 28:S0969-2126(24)00219-3.
doi: 10.1016/j.str.2024.06.001. Epub
ahead of print.
PMID: 38959899.
2: Schmidt T, Kubatova N, Clore GM.
J Am Chem Soc. 2024 Jun 18. doi:
10.1021/jacs.4c03916. Epub ahead of print.
PMID: 38888555.
3: Torricella F, Tugarinov V, Clore GM.
J PhysChem Lett. 2024 Jun
20;15(24):6375-6382. doi:
10.1021/acs.jpclett.4c01410. Epub 2024 Jun 10.
PMID: 38857530.
4: Avila YI, Rebolledo LP, Skelly
E, de Freitas Saito R, Wei H, Lilley D, Stanley RE, Hou YM, Yang H, Sztuba-Solinska J, Chen SJ, Dokholyan
NV, Tan C, Li SK, He X, Zhang X, Miles W, Franco E, Binzel
DW, Guo P, Afonin KA.
Cracking the Code: Enhancing Molecular
Tools for Progress in Nanobiotechnology.
ACS Appl Bio Mater. 2024 Jun 17;7(6):3587-3604. doi: 10.1021/acsabm.4c00432. Epub
2024 Jun 4.
PMID: 38833534; PMCID: PMC11190997.
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,