Newsletter 522 (October 7, 2024) NIH X-ray Diffraction SIG

 

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SEPTEMBER 2024 PUBLICATIONS BY MEMBERS OF THE GROUP

 

1: Shi G, Shaw GX, Ji X.

Bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydroptein pyrophosphokinase: Toward cell permeability.

Bioorg Med Chem Lett. 2024 Sep 25:129977. doi: 10.1016/j.bmcl.2024.129977. Epub ahead of print.

PMID: 39332646. 

 

2: Fullenkamp CR, Mehdi S, Jones CP, Tenney L, Pichling P, Prestwood PR, Ferré-D'Amaré AR, Tiwary P, Schneekloth JS Jr.

Machine learning-augmented molecular dynamics simulations (MD) reveal insights into the disconnect between affinity and activation of ZTP riboswitch ligands.

bioRxiv [Preprint]. 2024 Sep 14:2024.09.13.612887. doi: 10.1101/2024.09.13.612887.

PMID: 39314358; PMCID: PMC11419147.

 

3: Pala ZR, Alves E Silva TL, Minai M, Crews B, Patino-Martinez E, Carmona-Rivera C, Valenzuela Leon PC, Martin-Martin I, Flores-Garcia Y, Cachau RE,

Muslinkina L, Gittis AG, Srivastava N, Garboczi DN, Alves DA, Kaplan MJ, Fischer E, Calvo E, Vega-Rodriguez J.

Mosquito salivary apyrase regulates blood meal hemostasis and facilitates malaria parasite transmission.

Nat Commun. 2024 Sep 18;15(1):8194. doi: 10.1038/s41467-024-52502-3.

PMID: 39294191; PMCID: PMC11410810.

 

4: Zhao XZ, Barakat IA, Lountos GT, Wang W, Agama K, Mahmud MRA, Suazo KF, Andresson T, Pommier Y, Burke TR Jr.

Targeted sulfur(VI) fluoride exchange-mediated covalent modification of a tyrosine residue in the catalytic pocket of tyrosyl-DNA phosphodiesterase 1.

Commun Chem. 2024 Sep 16;7(1):208. doi:10.1038/s42004-024-01298-w.

PMID: 39284936; PMCID: PMC11405833.

 

5: Hedger AK, Myint W, Lee JM, Suchenski-Loustaunau D, Balachandran V, Shaqra AM, Kurt-Yilmaz N, Watts JK, Matsuo H, Schiffer CA.

Next generation APOBEC3 inhibitors: Optimally designed for potency and nuclease stability.

bioRxiv [Preprint]. 2024 Sep 6:2024.09.05.611238. doi: 10.1101/2024.09.05.611238.

PMID: 39282427; PMCID: PMC11398451.

 

6: Rackova M, Mattera R, Svaton M, Fencl F, Kanderova V, Spicakova K, Park SY, Fabian O, Koblizek M, Fronkova E, Bonifacino JS, Skvarova Kramarzova K.

Revising pathogenesis of AP1S1-related MEDNIK syndrome: a missense variant in the AP1S1 gene as a causal genetic lesion.

J Mol Med (Berl). 2024 Sep 13. doi:10.1007/s00109-024-02482-0. Epub ahead of print.

PMID: 39269494.

 

7: Hattori SI, Bulut H, Hayashi H, Kishimoto N, Takamune N, Hasegawa K, Furusawa Y, Yamayoshi S, Murayama K, Tamamura H, Li M, Wlodawer A, Kawaoka Y, Misumi S, Mitsuya H.

Structural and virologic mechanism of the emergence of resistance to Mpro inhibitors in SARS-CoV-2.

Proc Natl Acad Sci U S A. 2024 Sep 10;121(37):e2404175121. doi: 10.1073/pnas.2404175121. Epub 2024 Sep 5.

PMID: 39236245; PMCID: PMC11406233.

 

8: Gagne M, Flynn BJ, Andrew SF, Marquez J, Flebbe DR, Mychalowych A, Lamb E, Davis-Gardner ME, Burnett MR, Serebryannyy LA, Lin BC, Ziff ZE, Maule E, Carroll R, Naisan M, Jethmalani Y, Pessaint L,

Todd JM, Doria-Rose NA, Case JB, Dmitriev IP, Kashentseva EA, Ying B, Dodson A, Kouneski K, O'Dell S, Wali B, Ellis M, Godbole S, Laboune F, Henry AR, Teng IT, Wang D, Wang L, Zhou Q, Zouantchangadou S, Van Ry A, Lewis MG, Andersen H, Kwong PD, Curiel DT, Roederer M, Nason MC, Foulds KE, Suthar MS, Diamond MS,  Douek DC, Seder RA.

Mucosal adenovirus vaccine boosting elicits IgA and durably prevents XBB.1.16 infection in nonhuman primates.

Nat Immunol. 2024 Oct;25(10):1913-1927. doi: 10.1038/s41590-024-01951-5. Epub 2024 Sep 3.

PMID: 39227514; PMCID: PMC11436372.

 

9: Chen JCH, Gilski M, Chang C, Borek D, Rosenbaum G, Lavens A, Otwinowski Z, Kubicki M, Dauter Z, Jaskolski M, Joachimiak A.

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature.

IUCrJ. 2024 Sep 1;11(Pt 5):649-663. doi: 10.1107/S2052252524007784.

PMID: 39190507; PMCID: PMC11364037.

 

10: Walters KJ.

Virus-host warfare by PROTACs.

Nat Rev Mol Cell Biol. 2024 Sep;25(9):675. doi: 10.1038/s41580-024-00761-9.

PMID: 38982303.

 

 

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, 

 

 

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