Newsletter 521 (September 16, 2024) NIH X-ray Diffraction SIG

AUGUST 2024 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Folimonova V, Chen X, Negi H, Schwieters CD, Li J, Byrd RA, Taylor N, Youkharibache P, Walters KJ.

CD28 hinge used in chimeric antigen receptor (CAR) T-cells exhibits local structure and conformational exchange amidst global disorder.

Commun Biol. 2024 Aug 31;7(1):1072. doi: 10.1038/s42003-024-06770-w.

PMID: 39217198; PMCID: PMC11365992. 

2: Ko SH, Radecki P, Belinky F, Bhiman JN, Meiring S, Kleynhans J, Amoako D,Guerra Canedo V, Lucas M, Kekana D, Martinson N, Lebina L, Everatt J, Tempia S, Bylund T, Rawi R, Kwong PD, Wolter N, von Gottberg A, Cohen C, Boritz EA.

Rapid intra-host diversification and evolution of SARS-CoV-2 in advanced HIV infection.

Nat Commun. 2024 Aug 22;15(1):7240. doi: 10.1038/s41467-024-51539-8.

PMID: 39174553; PMCID: PMC11341811.

3: Chao FA, Byrd RA.

Existence of Singularities in NMR Relaxation Dispersion Profiles: Implications for Hidden Dynamics.

J Am Chem Soc. 2024 Aug 22. doi: 10.1021/jacs.4c06720. Epub ahead of print.

PMID: 39172084.

4: Bou-Nader C, Gaikwad S, Bahmanjah S, Zhang F, Hinnebusch AG, Zhang J.

Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response.

Proc Natl Acad Sci U S A. 2024 Aug 27;121(35):e2409628121. doi: 10.1073/pnas.2409628121. Epub 2024 Aug 20.

PMID: 39163341; PMCID: PMC11363354.

5: Senadeera SPD, Wang D, Wilson BAP, Smith EA, Wamiru A, Martinez Fiesco JA, Du L, Zhang P, O'Keefe BR, Beutler JA.

Acroamine A, a 2-Amino Adenine Alkaloid from the Marine Soft Coral Acrozoanthus australiae and Its Semisynthetic Derivatives That Inhibit cAMP-Dependent Protein Kinase A Catalytic Subunit Alpha.

J Nat Prod. 2024 Aug 23;87(8):2014-2020. doi: 10.1021/acs.jnatprod.4c00477. Epub 2024 Aug 14.

PMID: 39142023.

6: Gagne M, Flynn BJ, Honeycutt CC, Flebbe DR, Andrew SF, Provost SJ, McCormick L, Van Ry A, McCarthy E, Todd JM, Bao S, Teng IT, Marciano S, Rudich Y, Li C, Jain S, Wali B, Pessaint L, Dodson A, Cook A, Lewis MG, Andersen H, Zahradník J, Suthar MS, Nason MC, Foulds KE, Kwong PD, Roederer M, Schreiber G, Seder RA, Douek DC.

Variant-proof high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways. Nat Commun. 2024 Aug 12;15(1):6894. doi: 10.1038/s41467-024-51046-w.

PMID: 39134521; PMCID: PMC11319446.

7: Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y.

Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4.

Mol Cell. 2024 Aug 22;84(16):3061-3079.e10. doi: 10.1016/j.molcel.2024.07.016. Epub 2024 Aug 8.

PMID: 39121853; PMCID: PMC11344660.

8: Li W, Hu J, Song F, Yu J, Peng X, Zhang S, Wang L, Hu M, Liu JC, Wei Y, Xiao X, Li Y, Li D, Wang H, Zhou BR, Dai L, Mou Z, Zhou M, Zhang H, Zhou Z, Zhang H, Bai Y, Zhou JQ, Li W, Li G, Zhu P.

Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction.

Cell Res. 2024 Aug 5. doi: 10.1038/s41422-024-01009-z. Epub ahead of print.

PMID: 39103524.

9: Dalal K, Yang W, Tian E, Chernish A, McCluggage P, Lara AJ, Ten Hagen KG, Tabak LA.

In vivo mapping of the mouse Galnt3-specific O-glycoproteome.

J Biol Chem. 2024 Aug 2;300(9):107628. doi: 10.1016/j.jbc.2024.107628. Epub ahead of print.

PMID: 39098533.

10: Cai M, Agarwal N, Garrett DS, Baber J, Clore GM.

A Transient, Excited Species of the Autoinhibited α-State of the Bacterial Transcription Factor RfaH May Represent an Early Intermediate on the Fold-Switching Pathway.

Biochemistry. 2024 Aug 20;63(16):2030-2039. doi: 10.1021/acs.biochem.4c00258. Epub 2024 Aug 1.

PMID: 39088556; PMCID: PMC11345854.

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 – 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

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 – 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

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

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,