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Newsletter No. 481
January 2, 2023

Happy New Year!


Special: Career Overview by Prof Sir Tom Blundell



DECEMBER 2022 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Wang P, Casner RG, Nair MS, Yu J, Guo Y, Wang M, Chan JF, Cerutti G, Iketani
S, Liu L, Sheng Z, Chen Z, Yuen KY,
Kwong PD, Huang Y, Shapiro L, Ho DD. A
monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other
sarbecoviruses
. Emerg Microbes Infect. 2022 Dec;11(1):147-157. doi:
10.1080/22221751.2021.2011623. PMID: 34836485; PMCID: PMC8725896.

2: Strzelczyk P, Zhang D,
Wlodawer A, Lubkowski J. The E. coli L-asparaginase
V27T mutant: structural and functional characterization and comparison with
theoretical predictions
. FEBS Lett. 2022 Dec;596(23):3060-3068. doi:
10.1002/1873-3468.14526. Epub 2022 Nov 7. PMID: 36310372.

3: Curreli F, Kwon YD, Nicolau I, Burgos G, Altieri A, Kurkin AV, Verardi R,
Kwong PD, Debnath AK. Antiviral Activity and Crystal Structures of HIV-1 gp120
Antagonists
. Int J Mol Sci. 2022 Dec 15;23(24):15999. doi:
10.3390/ijms232415999. PMID: 36555641; PMCID: PMC9784924.

4: Luo W, Hickman AB, Genzor P, Ghirlando R, Furman CM, Menshikh A, Haase A,
Dyda F, Wilson MH. Transposase N-terminal phosphorylation and asymmetric
transposon ends inhibit piggyBac transposition in mammalian cells
. Nucleic Acids
Res. 2022 Dec 20:gkac1191. doi: 10.1093/nar/gkac1191. Epub ahead of print. PMID:
36537219.

5: Weber R, Kleemann L, Hirschberg I, Chung MY,
Valkov E, Igreja C. DAP5 enables
main ORF translation on mRNAs with structured and uORF-containing 5' leaders
.
Nat Commun. 2022 Dec 6;13(1):7510. doi: 10.1038/s41467-022-35019-5. PMID:
36473845; PMCID: PMC9726905.

6: Chen Y, Prévost J, Ullah I, Romero H, Lisi V, Tolbert WD, Grover JR, Ding S,
Gong SY, Beaudoin-Bussières G, Gasser R, Benlarbi M, Vézina D, Anand SP,
Chatterjee D, Goyette G, Grunst MW, Yang Z, Bo Y, Zhou F, Béland K, Bai X, Zeher
AR, Huang RK, Nguyen DN, Sherburn R, Wu D, Piszczek G, Paré B, Matthies D, Xia
D
, Richard J, Kumar P, Mothes W, Côté M, Uchil PD, Lavallée VP, Smith MA,
Pazgier M, Haddad E, Finzi A. Molecular basis for antiviral activity of two
pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD
. iScience. 2023
Jan 20;26(1):105783. doi: 10.1016/j.isci.2022.105783. Epub 2022 Dec 9. PMID:
36514310; PMCID: PMC9733284.

7: Lima NS, Musayev M, Johnston TS, Wagner DA, Henry AR, Wang L, Yang ES, Zhang
Y, Birungi K, Black WP, O'Dell S, Schmidt SD, Moon D, Lorang CG, Zhao B, Chen M,
Boswell KL, Roberts-Torres J, Davis RL, Peyton L, Narpala SR, O'Connell S,
Serebryannyy L, Wang J, Schrager A, Talana CA, Shimberg G, Leung K, Shi W,
Khashab R, Biber A, Zilberman T, Rhein J, Vetter S, Ahmed A, Novik L, Widge A,
Gordon I, Guech M, Teng IT, Phung E, Ruckwardt TJ, Pegu A, Misasi J, Doria-Rose
NA, Gaudinski M, Koup RA,
Kwong PD, McDermott AB, Amit S, Schacker TW, Levy I,
Mascola JR, Sullivan NJ, Schramm CA, Douek DC. Primary exposure to SARS-CoV-2
variants elicits convergent epitope specificities, immunoglobulin V gene usage
and public B cell clones
. Nat Commun. 2022 Dec 14;13(1):7733. doi:
10.1038/s41467-022-35456-2. PMID: 36517467; PMCID: PMC9748393.

8: Boswell KL, Watkins TA, Cale EM, Samsel J, Andrews SF, Ambrozak DR, Driscoll
JI, Messina MA, Narpala S, Hopp CS, Cagigi A, Casazza JP, Yamamoto T, Zhou T,
Schief WR, Crompton PD, Ledgerwood JE, Connors M, Gama L,
Kwong PD, McDermott A,
Mascola JR, Koup RA. Application of B cell immortalization for the isolation of
antibodies and B cell clones from vaccine and infection settings
. Front Immunol.
2022 Dec 13;13:1087018. doi: 10.3389/fimmu.2022.1087018. PMID: 36582240; PMCID:
PMC9794141.

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

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.

DISCUSSIONSThe Protein Folding Problem
J. Dauparas et al., "Robust deep learning-based protein sequence design using ProteinMPNN"

B. I. M. Wicky et al., "Hallucinating symmetric protein assemblies"

P. B. Moore et al., "The protein-folding problem: Not yet solved"

K. A Dill et al., "The protein folding problem"

The Protein Data Bank                          

Mariusz Jaskolski et al., "Group depositiions to the Protein Data Bank need adequate presentation and different archiving protocol"

Stephen Burley, "Looking ahead to the next 50 years of the Protein Data Bank"

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.

READINGS AND TUTORIALS - Career Overview of Prof Sir Tom Blundell

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


ARCHIVE: Integrative Structural Biology, 2005-2021


 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 Group                       Maintained by Dr. Xinhua Ji