Newsletter 526 (December 2, 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