Newsletter 524 (November 4, 2024) NIH Structural Biology Methods SIG

October 2024 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Wang H, Cheng C, Dal Santo JL, Shen CH, Bylund T, Henry AR, Howe CA, Hwang J, Morano NC, Morris DJ, Pletnev S, Roark RS, Zhou T, Hansen BT, Hoyt FH, Johnston TS, Wang S, Zhang B, Ambrozak DR, Becker JE, Bender MF, Changela A, Chaudhary R, Corcoran M, Corrigan AR, Foulds KE, Guo Y, Lee M, Li Y, Lin BC, Liu T, Louder MK, Mandolesi M, Mason RD, McKee K, Nair V, O'Dell S, Olia AS, Ou L, Pegu A, Raju N, Rawi R, Roberts-Torres J, Sarfo EK, Sastry M, Schaub AJ, Schmidt SD, Schramm CA, Schwartz CL, Smith SC, Stephens T, Stuckey J, Teng IT, Todd JP, Tsybovsky Y, Van Wazer DJ, Wang S, Doria-Rose NA, Fischer ER, Georgiev IS, Karlsson Hedestam GB, Sheng Z, Woodward RA, Douek DC, Koup RA, Pierson TC, Shapiro L, Shaw GM, Mascola JR, Kwong PD.

Potent and broad HIV-1 neutralization in fusion peptide-primed SHIV-infected macaques. Cell. 2024 Oct 23:S0092-8674(24)01151-6. doi: 10.1016/j.cell.2024.10.003. Epub ahead of print.

PMID: 39471811. 

2: Torricella F, Clore GM, Tugarinov V.

A Closed-Form Expression for Analysis of Dark State Exchange Saturation Transfer (DEST) NMR Experiments.

J Phys Chem Lett. 2024 Oct 28:11007-11014. doi: 10.1021/acs.jpclett.4c02509. Epub ahead of print.

PMID: 39465986.

3: He S, Taher NM, Simard AR, Hvorecny KL, Ragusa MJ, Bahl CD, Hickman AB, Dyda F, Madden DR.

Molecular basis for the transcriptional regulation of an epoxide- based virulence circuit in Pseudomonas aeruginosa.

Nucleic Acids Res. 2024 Oct 16:gkae889. doi: 10.1093/nar/gkae889. Epub ahead of print.

PMID: 39413156.

4: Stagno JR, Wang YX.

Riboswitch Mechanisms for Regulation of P1 Helix Stability.

Int J Mol Sci. 2024 Oct 4;25(19):10682. doi: 10.3390/ijms251910682.

PMID: 39409011; PMCID: PMC11477058.

5: Parker JL, Deme JC, Lichtinger SM, Kuteyi G, Biggin PC, Lea SM, Newstead S.

Structural basis for antibiotic transport and inhibition in PepT2.

Nat Commun. 2024 Oct 9;15(1):8755. doi: 10.1038/s41467-024-53096-6.

PMID: 39384780; PMCID: PMC11464717.

6: Misasi J, Wei RR, Wang L, Pegu A, Wei CJ, Oloniniyi OK, Zhou T, Moliva JI, Zhao B, Choe M, Yang ES, Zhang Y, Boruszczak M, Chen M, Leung K, Li J, Yang ZY, Andersen H, Carlton K, Godbole S, Harris DR, Henry AR, Ivleva VB, Lei QP, Liu C, Longobardi L, Merriam JS, Nase D, Olia AS, Pessaint L, Porto M, Shi W, Wallace SM, Wolff JJ, Douek DC, Suthar MS, Gall JG, Koup RA, Kwong PD, Mascola JR, Nabel GJ, Sullivan NJ.

A multispecific antibody against SARS-CoV-2 prevents immune escape in vitro and confers prophylactic protection in vivo.

Sci Transl Med. 2024 Oct 9;16(768):eado9026. doi: 10.1126/scitranslmed.ado9026. Epub 2024 Oct 9.

PMID: 39383243.

7: Lee HJ, Fenollar-Ferrer C, Isgrig K, Wang YX, Valente K, Eide J, Honda K, Chien WW, Petralia RS, Dong L, Friedman TB, Bonifacino JS, Griffith AJ, Roux I.

SLC26A4-AP-2 mu2 interaction regulates SLC26A4 plasma membrane abundance in the endolymphatic sac.

Sci Adv. 2024 Oct 11;10(41):eadm8663. doi: 10.1126/sciadv.adm8663. Epub 2024 Oct 9.

PMID: 39383236.

8: Williams JS, Lujan SA, Arana ME, Burkholder AB, Tumbale PP, Williams RS, Kunkel TA.

High fidelity DNA ligation prevents single base insertions in the yeast genome.

Nat Commun. 2024 Oct 9;15(1):8730. doi: 10.1038/s41467-024-53063-1.

PMID: 39379399; PMCID: PMC11461686.

9: Johnson D, Colijn S, Richee J, Yano J, Burns M, Davis AE, Pham VN, Saric A, Jain A, Yin Y, Castranova D, Melani M, Fujita M, Grainger S, Bonifacino JS, Weinstein BM, Stratman AN.

Angiogenesis is limited by LIC1-mediated lysosomal trafficking.

Angiogenesis. 2024 Oct 2. doi: 10.1007/s10456-024-09951-7. Epub ahead of print.

PMID: 39356418.

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.

The TRIM-NHL RNA-binding protein Brain Tumor coordinately regulates expression of the glycolytic pathway and vacuolar ATPase complex.

Nucleic Acids Res. 2024 Oct 1:gkae810. doi: 10.1093/nar/gkae810. Epub ahead of print.

PMID: 39351871.

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.

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

75^th ACA Annual Meeting, July 18-23, 2025

Lombard, IL

Microscopy Society of America Annual Meeting, July 27-31, 2025

Salt Lake City, UT