Newsletter 514 (May 20, 2024) NIH X-ray Diffraction SIG

APRIL 2024 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Kaiser JA, Nelson CE, Liu X, Park HS, Matsuoka Y, Luongo C, Santos C, Ahlers LRH, Herbert R, Moore IN, Wilder-Kofie T, Moore R, Walker A, Yang L, Munir S, Teng IT, Kwong PD, Dowdell K, Nguyen H, Kim J, Cohen JI, Johnson RF, Garza NL, Via LE, Barber DL, Buchholz UJ, Le Nouën C. 

Mucosal prime-boost immunization with live murine pneumonia virus-vectored SARS-CoV-2 vaccine is protective inmacaques.

Nat Commun. 2024 Apr 26;15(1):3553. doi: 10.1038/s41467-024-47784-6.

PMID: 38670948; PMCID: PMC11053155.

2: Golda M, Hoffka G, Cherry S, Tropea JE, Lountos GT, Waugh DS, Wlodawer A, Tőzsér J, Mótyán JA. 

P1' specificity of the S219V/R203G mutant tobacco etch virus protease. 

Proteins. 2024 Apr 26. doi: 10.1002/prot.26693. Epub ahead of print.

PMID: 38666764.

3: Elder JJH, Papadopoulos R, Hayne CK, Stanley RE.

The making and breaking of tRNAs by ribonucleases. 

Trends Genet. 2024 Apr 18:S0168-9525(24)00069-6. doi: 10.1016/j.tig.2024.03.007. Epub ahead of print. 

PMID: 38641471.

4: Bicknell AA, Reid DW, Licata MC, Jones AK, Cheng YM, Li M, Hsiao CJ, Pepin CS, Metkar M, Levdansky Y, Fritz BR, Andrianova EA, Jain R, Valkov E, Köhrer C, Moore MJ. 

Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay.

Cell Rep. 2024 Apr 23;43(4):114098. doi: 10.1016/j.celrep.2024.114098. Epub 2024 Apr 15. 

PMID: 38625793.

5: Shah K, He S, Turner DJ, Corbo J, Rebbani K, Dominguez D, Bateman JM, Cheloufi S, Igreja C, Valkov E, Murn J. 

Regulation by the RNA-binding protein Unkempt at its effector interface.

Nat Commun. 2024 Apr 11;15(1):3159. doi: 10.1038/s41467-024-47449-4. 

PMID: 38605040; PMCID: PMC11009413.

6: Du G, Healy LB, David L, Walker C, El-Baba TJ, Lutomski CA, Goh B, Gu B, Pi X, Devant P, Fontana P, Dong Y, Ma X, Miao R, Balasubramanian A, Puthenveetil R, Banerjee A, Luo HR, Kagan JC, Oh SF, Robinson CV, Lieberman J, Wu H. 

ROS-dependent S-palmitoylation activates cleaved and intact gasdermin D.

Nature. 2024 Apr 10. doi: 10.1038/s41586-024-07373-5. Epub ahead of print. 

PMID:38599239.

7: Schotte F, Cho HS, Dyda F, Anfinrud P. 

Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein.

Struct Dyn. 2024 Apr 8;11(2):021303. doi: 10.1063/4.0000241.

PMID: 38595979; PMCID: PMC11003764.

8: Awan SF, Pegu A, Strom L, Carter CA, Hendel CS, Holman LA, Costner PJ, Trofymenko O, Dyer R, Gordon IJ, Rothwell RSS, Hickman SP, Conan-Cibotti M, Doria-Rose NA, Lin BC, O'Connell S, Narpala SR, Almasri CG, Liu C, Ko S, Kwon YD, Namboodiri AM, Pandey JP, Arnold FJ, Carlton K, Gall JG, Kwong PD,

Capparelli EV, Bailer RT, McDermott AB, Chen GL, Koup RA, Mascola JR, Coates EE, Ledgerwood JE, Gaudinski MR; VRC 610 study team. 

Phase 1 trial evaluating safety and pharmacokinetics of HIV-1 broadly neutralizing mAbs 10E8VLS and VRC07-523LS.

JCI Insight. 2024 Apr 8;9(7):e175375. doi: 10.1172/jci.insight.175375.

PMID: 38587079.

9: Rosenberg EM Jr, Jian X, Soubias O, Jackson RA, Gladu E, Andersen E, Esser L, Sodt AJ, Xia D, Byrd RA, Randazzo PA. 

Point mutations in Arf1 reveal cooperative effects of the N-terminal extension and myristate for GTPase-activating protein catalytic activity.

PLoS One. 2024 Apr 4;19(4):e0295103. doi: 10.1371/journal.pone.0295103. 

PMID: 38574162; PMCID: PMC10994351.

10: Lauber F, Deme JC, Liu X, Kjær A, Miller HL, Alcock F, Lea SM, Berks BC.

Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon.

Nat Microbiol. 2024 Apr;9(4):1089-1102. doi: 10.1038/s41564-024-01644-7. Epub 2024 Mar 27. 

PMID: 38538833; PMCID: PMC10994853.

11: Bermejo GA, Tjandra N, Clore GM, Schwieters CD. 

Xplor-NIH: Better parameters and protocols for NMR protein structure determination.

Protein Sci. 2024 Apr;33(4):e4922. doi: 10.1002/pro.4922. 

PMID: 38501482; PMCID: PMC10962493.

12: Zhang D, Czapinska H, Bochtler M, Wlodawer A, Lubkowski J. 

RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases.

Protein Sci. 2024 Apr;33(4):e4920. doi: 10.1002/pro.4920. 

PMID: 38501449; PMCID: PMC10949315.

13: Boyd LF, Jiang J, Ahmad J, Natarajan K, Margulies DH. 

Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by

Computational Prediction.

J Immunol. 2024 Apr 15;212(8):1366-1380. doi: 10.4049/jimmunol.2300839. 

PMID: 38456672; PMCID: PMC10982845. 

14: Jiang J, Natarajan K, Margulies DH.

Chaperone-mediated MHC-I peptide exchange in antigen presentation.

IUCrJ. 2024 May 1;11(Pt 3):287-298. doi: 10.1107/S2052252524002768. 

PMID: 38656309.

For timely listing, please send a heads-up E-mail to the Editor upon publication.

METHODS – Integrative Structural Biology

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, in Rational Design of Hybrid Inhibitors

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.

READINGS & TUTORIALS – Macromolecular Crystallography

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.

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,