Newsletter 528 (January 6, 2025) NIH Structural
Biology Methods SIG
HAPPY NEW YEAR!!
DECEMBER 2024 PUBLICATIONS BY MEMBERS OF THE GROUP
1: Bregnard T, Fairchild D, Chen X, Erlandsen H, Tarasov
SG, Walters KJ, Korzhnev DM, Bezsonova I.
J Biol Chem. 2024 Dec 30:108149. doi:
10.1016/j.jbc.2024.108149. Epub ahead of print.
PMID: 39742997.
2: Das M, Hile SE, Brewster J, Boer JL, Bezalel-Buch R, Guo
Q, Yang W, Burgers PM, Eckert KA, Freudenreich
CH.
Nucleic Acids Res. 2024 Dec 27:gkae1254.
doi: 10.1093/nar/gkae1254. Epub ahead of print.
PMID: 39727171.
3: Degenhardt MFS, Degenhardt HF, Bhandari YR, Lee YT, Ding
J, Yu P, Heinz WF, Stagno JR, Schwieters CD, Watts NR, Wingfield
PT, Rein A,Zhang J, Wang YX.
Determining
structures of RNA conformers using AFM and deep neural networks.
Nature. 2024 Dec 18. doi: 10.1038/s41586-024-07559-x. Epub
ahead of print.
PMID: 39695231.
4: Lee YT, Degenhardt MFS, Skeparnias I, Degenhardt HF,
Bhandari YR, Yu P, Stagno JR, Fan L, Zhang J, Wang YX.
The
conformational space of RNase P RNA in solution.
Nature. 2024 Dec 18. doi: 10.1038/s41586-024-08336-6. Epub
ahead of print.
PMID: 39695229.
5: Ghosh S, Clore GM.
Decoding
chaperone complexes: Insights from NMR spectroscopy.
Biophys Rev (Melville). 2024 Dec 10;5(4):041308. doi:
10.1063/5.0233299.
PMID: 39679202; PMCID:
PMC11637561.
6: Cale EM, Shen CH, Olia AS, Radakovich NA, Rawi R, Yang
Y, Ambrozak DR,
Bennici AK, Chuang GY, Crooks ED, Driscoll JI, Lin BC,
Louder MK, Madden PJ,
Messina MA, Osawa K, Stewart-Jones GBE, Verardi R, Vrakas
Z, Xie D, Zhang B,
Binley JM, Connors M, Koup RA, Pierson TC, Doria-Rose NA, Kwong PD, Mascola JR, Gorman J.
Cell Rep. 2024 Dec 24;43(12):115010. doi:
10.1016/j.celrep.2024.115010. Epub 2024 Dec 14.
PMID: 39675002.
7: Reimund M, Dearborn AD, Graziano G, Lei H, Ciancone AM,
Kumar A, Holewinski R, Neufeld EB, O'Reilly FJ, Remaley AT, Marcotrigiano J.
Structure
of apolipoprotein B100 bound to the low-density lipoprotein receptor.
Nature. 2024 Dec 11. doi: 10.1038/s41586-024-08223-0. Epub
ahead of print.
PMID: 39663455.
8: Wlodawer A, Hmeljak J.
In
conversation with Alexander Wlodawer.
FEBS J. 2024 Dec 6. doi: 10.1111/febs.17322. Epub ahead of
print.
PMID: 39642095.
9: Lee M, Lu M, Zhang B, Zhou T, Katte R, Han Y, Rawi R, Kwong PD.
Comput Struct Biotechnol J. 2024 Nov 12;23:4192-4204.
doi: 10.1016/j.csbj.2024.11.020.
PMID: 39640534; PMCID:
PMC11617889.
10: Temme JS, Tan Z, Li M, Yang M, Wlodawer A, Huang X, Schneekloth JS Jr,
Gildersleeve JC.
Cell Chem Biol. 2024 Dec 19;31(12):2096-2111.e7. doi:
10.1016/j.chembiol.2024.11.005. Epub 2024 Dec 4.
PMID: 39637855.
11: Bu F, Adam Y, Adamiak RW, Antczak M, de Aquino BRH,
Badepally NG, Batey RT, Baulin EF, Boinski P, Boniecki MJ,
Bujnicki JM, Carpenter KA, Chacon J, Chen SJ, Chiu
W, Cordero P, Das NK, Das R, Dawson WK, DiMaio F, Ding F, Dock Bregeon AC,
Dokholyan NV, Dror RO, Dunin-Horkawicz S, Eismann S, Ennifar E, Esmaeeli R,
Farsani MA, Ferré-D'Amaré AR, Geniesse C, Ghanim GE,
Guzman HV, Hood IV, Huang L, Jain DS, Jaryani F, Jin L, Joshi A, Karelina M,
Kieft JS, Kladwang W, Kmiecik S, Koirala D, Kollmann M, Kretsch RC,
Kurciński M, Li J, Li S, Magnus M, Masquida B, Moafinejad SN, Mondal A,
Mukherjee S, Nguyen THD, Nikolaev G, Nithin C, Nye G, Pandaranadar Jeyeram IPN,
Perez A, Pham P, Piccirilli JA, Pilla SP, Pluta R, Poblete S, Ponce-Salvatierra
A, Popenda M, Popenda L, Pucci F, Rangan R, Ray A, Ren A, Sarzynska J, Sha
CM, Stefaniak F, Su Z, Suddala KC, Szachniuk M, Townshend R, Trachman RJ 3rd,
Wang J, Wang W, Watkins A, Wirecki TK, Xiao Y, Xiong P, Xiong Y, Yang J,
Yesselman JD, Zhang J, Zhang Y, Zhang Z, Zhou Y, Zok T,
Zhang D, Zhang S, Żyła A, Westhof E, Miao Z.
RNA-Puzzles
Round V: blind predictions of 23 RNA structures.
Nat Methods. 2024 Dec 2. doi:0.1038/s41592-024-02543-9.
Epub ahead of print.
PMID: 39623050.
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