Newsletter 529
(January 20, 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