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Newsletter No. 486
March 20, 2023

ACA News, IUCr Newsletter, IUCr Meetings List


FEBRUARY 2023 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Segura J, Ireland J, Zou Z, Roth G, Buchwald J, Shen TJ, Fischer E, Moir S,
Chun TW, Sun PD. HIV-1 release requires Nef-induced caspase activation. PLoS
One. 2023 Feb 13;18(2):e0281087. doi: 10.1371/journal.pone.0281087. PMID:
36780482; PMCID: PMC9925082.

2: Kubatova N, Schmidt T, Schwieters CD, Clore GM. Quantitative analysis of
sterol-modulated monomer-dimer equilibrium of the β<sub>1</sub>-adrenergic
receptor by DEER spectroscopy
. Proc Natl Acad Sci U S A. 2023 Feb
14;120(7):e2221036120. doi: 10.1073/pnas.2221036120. Epub 2023 Feb 6. PMID:
36745787; PMCID: PMC9963004.

3: Cai M, Tugarinov V, Chiliveri SC, Huang Y, Schwieters CD, Mizuuchi K, Clore
GM
. Interaction of the bacterial division regulator MinE with lipid bicelles
studied by NMR spectroscopy
. J Biol Chem. 2023 Feb 16:103037. doi:
10.1016/j.jbc.2023.103037. Epub ahead of print. PMID: 36806683.

4: Samsel J, Boswell KL, Watkins TA, Ambrozak DR, Mason R, Yamamoto T, Ko S,
Yang Y, Zhou T, Doria-Rose NA, Foulds KE, Roederer M, Mascola JR, Kwong PD, Gama
L, Koup RA. Rhesus macaque Bcl-6/Bcl-xL B cell immortalization: Discovery of
HIV-1 neutralizing antibodies from lymph node
. J Immunol Methods. 2023 Feb
25:113445. doi: 10.1016/j.jim.2023.113445. Epub ahead of print. PMID: 36848985.

5: Ding J, Lee YT, Bhandari Y, Schwieters CD, Fan L, Yu P, Tarosov SG, Stagno
JR
, Ma B, Nussinov R, Rein A,
Zhang J, Wang YX. Visualizing RNA conformational
and architectural heterogeneity in solution
. Nat Commun. 2023 Feb 9;14(1):714.
doi: 10.1038/s41467-023-36184-x. PMID: 36759615; PMCID: PMC9911696.

6: Hoffka G, Lountos GT, Needle D,
Wlodawer A, Waugh DS, Tőzsér J, Mótyán JA.
Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2
Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis
. J Mol
Biol. 2023 Mar 15;435(6):168012. doi: 10.1016/j.jmb.2023.168012. Epub 2023 Feb
13. PMID: 36792007.

7: Buel GR, Chen X, Myint W, Kayode O, Folimonova V, Cruz A, Skorupka KA,
Matsuo H, Walters KJ. E6AP AZUL interaction with UBQLN1/2 in cells, condensates,
and an AlphaFold-NMR integrated structure
. Structure. 2023 Feb
14:S0969-2126(23)00033-3. doi: 10.1016/j.str.2023.01.012. Epub ahead of print.
PMID: 36827983.

8: Becht DC, Klein BJ, Kanai A, Jang SM, Cox KL, Zhou BR, Phanor SK, Zhang Y,
Chen RW, Ebmeier CC, Lachance C, Galloy M, Fradet-Turcotte A, Bulyk ML, Bai Y,
Poirier MG, Côté J, Yokoyama A, Kutateladze TG. MORF and MOZ acetyltransferases
target unmethylated CpG islands through the winged helix domain
. Nat Commun.
2023 Feb 8;14(1):697. doi: 10.1038/s41467-023-36368-5. PMID: 36754959; PMCID:
PMC9908889.

9: Rosenberg EM Jr, Jian X, Soubias O, Yoon HY, Yadav MP, Hammoudeh S,
Pallikkuth S, Akpan I, Chen PW, Maity TK, Jenkins LM, Yohe ME, Byrd RA, Randazzo
PA. The small molecule inhibitor NAV-2729 has a complex target profile including
multiple ADP-ribosylation factor regulatory proteins
. J Biol Chem. 2023 Feb
7:102992. doi: 10.1016/j.jbc.2023.102992. Epub ahead of print. PMID: 36758799.

10: Lu J, Spencer M, Zou Z, Traver M, Brzostowski J, Sun PD. FcγRI FG-loop
functions as a pH sensitive switch for IgG binding and release
. Front Immunol.
2023 Feb 6;14:1100499. doi: 10.3389/fimmu.2023.1100499. PMID: 36814926; PMCID:
PMC9940316.

11: Shaw GX, Fan L, Cherry S, Shi G, Tropea JE, Ji X. Structure of
<i>Helicobacter pylori</i> dihydroneopterin aldolase suggests a fragment-based
strategy for isozyme-specific inhibitor design
. Curr Res Struct Biol. 2023 Jan
30;5:100095. doi: 10.1016/j.crstbi.2023.100095. PMID: 36820301; PMCID:
PMC9937910.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS CryoEM: Grid Screening & Data Acquisition

 A. Cheng et al., "Fully automated multi-grid cryoEM screening using Smart Leginon"

 P.T. Kim et al., "Learning to automate cryo-electron microscopy data collection with Ptolemy"

ARCHIVE: Introduction, Sample Preparation, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation, Other Biophysical Methods, Integrative Structure Determination.

DISCUSSIONS - Suggestions?

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and PublicationValidation, Table 1,   Protein Data Bank & Protein Folding.

READINGS AND TUTORIALS - Alpha-helical coiled coils

D.N. Woolfson, "Understanding a protein fold: the physics, chemistry, and biology of alpha-helical coiled coils" (2023)

G. Huang, C. Zeng, Y. Shi, "Structure of the nuclear pore complex goes atomic" (2023)

Tom Blundell, "Structural Biology, Bioinformatics and Drug Discovery: Six Decades of Science & Its Applications" (2022)


ARCHIVE: Crystallography, Data AquisitionStructural BiologyStructure Prediction


 LINKS Suggestions?

Databases: DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe
, Protein Geometry
                  SARS-CoV-2 Related Structures, PDB SARS-CoV-2 Resources, AlphaFold DB,
                  virusMED, BioCyc, RaMP-DB,


Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, XDS


Servers: ACHESYM,
Anisotropy, C6@C3, DaliESPript, Grade, PDBePISA, Phyre2,
             MolProbity, RestraintLib, Robetta (RoseTTAFold),

Copyright © NIH X-Ray Diffraction Interest Group                       Maintained by Dr. Xinhua Ji