Newsletter 527 (December 16, 2024) NIH Structural
Biology Methods SIG
NOVEMBER 2024 PUBLICATIONS BY MEMBERS OF THE GROUP
1: Reveiz M, Xu K, Lee M, Wang S, Olia AS, Harris DR, Liu
K, Liu T, Schaub AJ, Stephens T, Wang Y, Zhang B, Huang R, Tsybovsky
Y, Kwong PD, Rawi
R.
Front Immunol. 2024 Nov 14;15:1484029.
doi: 10.3389/fimmu.2024.1484029.
PMID: 39611147; PMCID: PMC11602501.
2: Becker W, Rebbani K, Duan
Z, Valkov E,
Bryant S, Ho M, Berzofsky JA, Olkhanud
PB.
Sci Rep. 2024 Nov 28;14(1):29609. doi:
10.1038/s41598-024-80636-3.
PMID: 39609527; PMCID: PMC11604653.
3: Han TH, Vicidomini R, Ramos
CI, Mayer ML,
Serpe M.
The
gating properties of Drosophila NMJ glutamate receptors and their dependence on
Neto.
J Physiol. 2024 Nov 27. doi:
10.1113/JP287331. Epub ahead of print.
PMID: 39602131.
4: Ishida M, Golding AE, Keren-Kaplan T, Li Y, Balla
T, Bonifacino JS.
ARMH3
is an ARL5 effector that promotes PI4KB-catalyzed PI4P synthesis at the
trans-Golgi network.
Nat Commun. 2024 Nov 23;15(1):10168. doi:
10.1038/s41467-024-54410-y.
PMID: 39580461; PMCID: PMC11585589.
5: Kaur M, Chen X, Lee SY, Weaver TM, Freudenthal BD, Walters KJ, Roelofs J.
bioRxiv
[Preprint]. 2024 Nov 5:2024.11.04.621988. doi:
10.1101/2024.11.04.621988.
PMID: 39574619; PMCID: PMC11580919.
6: Tripathi BK, Hirsh NH, Qian X, Durkin ME, Wang D,
Papageorge AG, Lake R, Evrard YA, Marcus AI,
Ramalingam SS, Dasso M, Vousden
KH, Doroshow JH, Walters KJ, Lowy DR.
Nat Cancer. 2024 Nov 11. doi:
10.1038/s43018-024-00847-5. Epub ahead of
print.
PMID: 39528835.
7: Loomis RJ, Lai YT, Sowers SB, Fisher B, Derrien-Colemyn A, Ambrozak DR, Tsybovsky Y, Crooke SN, Latner
DR, Kong WP, Ruckwardt TJ, Plotkin SA, Kwong PD, Mascola
JR, Graham BS, Hickman CJ, Stewart-Jones GBE.
Structure-based
design of glycoprotein subunit vaccines for mumps.
Proc Natl Acad Sci U S A. 2024
Nov 19;121(47):e2404053121. doi:
10.1073/pnas.2404053121. Epub 2024 Nov 11.
PMID: 39527740; PMCID: PMC11588112.
8: Wlodawer A, Dauter Z,
Rubach P, Minor W, Loch JI, Brzezinski D, Gilski M, Jaskolski M.
Waterless
structures in the Protein Data Bank.
IUCrJ. 2024
Nov 1;11(Pt 6):966-976. doi:
10.1107/S2052252524009928.
PMID: 39465564; PMCID: PMC11533996.
9: He S, Taher NM, Simard AR, Hvorecny
KL, Ragusa MJ, Bahl CD, Hickman AB, Dyda F,
Madden DR.
Nucleic Acids Res. 2024 Nov 11;52(20):12727-12747. doi: 10.1093/nar/gkae889.
PMID: 39413156.
10: Connacher RP, Roden RT, Huang
KL, Korte AJ, Yeruva S, Dittbenner
N, DesMarais AJ, Weidmann CA, Randall TA, Williams
J, Hall TMT, Wagner EJ, Goldstrohm
AC.
Nucleic Acids Res. 2024 Nov 11;52(20):12669-12688. doi: 10.1093/nar/gkae810.
PMID: 39351871; PMCID: PMC11551770.
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
Biophysical Society National Meeting, February
15-19, 2025
Los Angeles, CA
Early Registration Deadline: January 7, 2025
Cold Spring Harbor Laboratory Cryo-Electron Microscopy
Course, March 5-19, 2025
Cold Spring Harbor, NY
Application Deadline: January 6, 2025
2025 RNA Biology Symposium, April 3-4, 2025
Natcher, NIH
Campus, Bethesda, MD
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