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Newsletter No. 483
February 6, 2023

ACA News, IUCr Newsletter, IUCr Meetings List


JANUART 2023 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Oda K, Wlodawer A. Overview of the Properties of Glutamic Peptidases That Are
Present in Plant and Bacterial Pathogens and Play a Role in Celiac Disease and
Cancer
. Biochemistry. 2023 Jan 27. doi: 10.1021/acs.biochem.2c00622. Epub ahead
of print. PMID: 36705990.

2: Trachman RJ 3rd, Link KA, Knutson JR, Ferré-D'Amaré AR. Characterizing
Fluorescence Properties of Turn-on RNA Aptamers
. Methods Mol Biol.
2023;2568:25-36. doi: 10.1007/978-1-0716-2687-0_3. PMID: 36227560; PMCID:
PMC9812286.

3: Stagno JR, Knoska J, Chapman HN, Wang YX. Mix-and-Inject Serial Femtosecond
Crystallography to Capture RNA Riboswitch Intermediates
. Methods Mol Biol.
2023;2568:243-249. doi: 10.1007/978-1-0716-2687-0_16. PMID: 36227573.

4: Kumar A, Rohe TC, Elrod EJ, Khan AG, Dearborn AD, Kissinger R, Grakoui A,
Marcotrigiano J. Regions of hepatitis C virus E2 required for membrane
association
. Nat Commun. 2023 Jan 26;14(1):433. doi: 10.1038/s41467-023-36183-y.
PMID: 36702826; PMCID: PMC9879980.

5: Sapkota KP, Li S, Zhang J. Cotranscriptional Assembly and Native Purification
of Large RNA-RNA Complexes for Structural Analyses
. Methods Mol Biol.
2023;2568:1-12. doi: 10.1007/978-1-0716-2687-0_1. PMID: 36227558.

6: Zhang J. Probing RNA Structures and Interactions Using Fluorescence Lifetime
Analyses
. Methods Mol Biol. 2023;2568:13-23. doi: 10.1007/978-1-0716-2687-0_2.
PMID: 36227559.

7: Lee YT, Fan L, Ding J,
Wang YX. Combining Biophysical Methods for Structure-
Function Analyses of RNA in Solution
. Methods Mol Biol. 2023;2568:165-177. doi:
10.1007/978-1-0716-2687-0_11. PMID: 36227568.

8: Bibollet-Ruche F, Russell RM, Ding W, Liu W, Li Y, Wagh K, Wrapp D, Habib R,
Skelly AN, Roark RS, Sherrill-Mix S, Wang S, Rando J, Lindemuth E, Cruickshank
K, Park Y, Baum R, Carey JW, Connell AJ, Li H, Giorgi EE, Song GS, Ding S, Finzi
A, Newman A, Hernandez GE, Machiele E, Cain DW, Mansouri K, Lewis MG, Montefiori
DC, Wiehe KJ, Alam SM, Teng IT,
Kwong PD, Andrabi R, Verkoczy L, Burton DR,
Korber BT, Saunders KO, Haynes BF, Edwards RJ, Shaw GM, Hahn BH. A Germline-
Targeting Chimpanzee SIV Envelope Glycoprotein Elicits a New Class of V2-Apex
Directed Cross-Neutralizing Antibodies
. mBio. 2023 Jan 11:e0337022. doi:
10.1128/mbio.03370-22. Epub ahead of print. PMID: 36629414.

9: Sahu S, Gordon J, Gu C, Sobhany M, Fiedler D, Stanley RE, Shears SB.
Nucleolar Architecture Is Modulated by a Small Molecule, the Inositol
Pyrophosphate 5-InsP<sub>7</sub>
. Biomolecules. 2023 Jan 12;13(1):153. doi:
10.3390/biom13010153. PMID: 36671538; PMCID: PMC9855682.

10: Zhang B, Gorman J, Kwon YD, Pegu A, Chao CW, Liu T, Asokan M, Bender MF,
Bylund T, Damron L, Gollapudi D, Lei P, Li Y, Liu C, Louder MK, McKee K, Olia
AS, Rawi R, Schön A, Wang S, Yang ES, Yang Y, Carlton K, Doria-Rose NA, Shapiro
L, Seaman MS, Mascola JR,
Kwong PD. Bispecific antibody CAP256.J3LS targets
V2-apex and CD4-binding sites with high breadth and potency
. MAbs. 2023 Jan-
Dec;15(1):2165390. doi: 10.1080/19420862.2023.2165390. PMID: 36729903.

11: Wojtaszek JL, Williams RS. The ends in sight: Mre11-Rad50-Nbs1 complex
structures come into focus
. Mol Cell. 2023 Jan 19;83(2):160-162. doi:
10.1016/j.molcel.2022.12.016. PMID: 36669476.

12: Buehl CJ, Goff NJ, Hardwick SW, Gellert M, Blundell TL, Yang W, Chaplin AK,
Meek K. Two distinct long-range synaptic complexes promote different aspects of
end processing prior to repair of DNA breaks by non-homologous end joining
. Mol
Cell. 2023 Jan 24:S1097-2765(23)00032-1. doi: 10.1016/j.molcel.2023.01.012. Epub
ahead of print. PMID: 36724784.

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.

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