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Newsletter No. 393
March 4, 2019

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

FEBRUARY 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Kotler SA, Tugarinov V, Schmidt T, Ceccon A, Libich DS, Ghirlando R,
Schwieters CD, Clore GM. Probing initial transient oligomerization events
facilitating Huntingtin fibril nucleation at atomic resolution by
relaxation-based NMR
. Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3562-3571.
doi: 10.1073/pnas.1821216116. Epub 2019 Feb 11. PubMed PMID: 30808748.

2: Muslinkina L, Roldán-Salgado A, Gaytán P, Juárez-González VR, Rudiño E,
Pletneva N, Pletnev V,
Dauter Z, Pletnev S. Structural Factors Enabling
Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming
Residue
. J Mol Biol. 2019 Feb 21. pii: S0022-2836(18)31051-9. doi:
10.1016/j.jmb.2019.02.013. [Epub ahead of print] PubMed PMID: 30797856.

3: Liu Q, Lai YT, Zhang P, Louder MK, Pegu A, Rawi R, Asokan M, Chen X, Shen CH,
Chuang GY, Yang ES, Miao H, Wang Y, Fauci AS,
Kwong PD, Mascola JR, Lusso P.
Improvement of antibody functionality by structure-guided paratope engraftment.
Nat Commun. 2019 Feb 13;10(1):721. doi: 10.1038/s41467-019-08658-4. PubMed PMID:
30760721; PubMed Central PMCID: PMC6374468.

4: Kanekiyo M, Joyce MG, Gillespie RA, Gallagher JR, Andrews SF, Yassine HM,
Wheatley AK, Fisher BE, Ambrozak DR, Creanga A, Leung K, Yang ES, Boyoglu-Barnum
S, Georgiev IS, Tsybovsky Y, Prabhakaran MS, Andersen H, Kong WP, Baxa U, Zephir
KL, Ledgerwood JE, Koup RA,
Kwong PD, Harris AK, McDermott AB, Mascola JR, Graham
BS. Mosaic nanoparticle display of diverse influenza virus hemagglutinins elicits
broad B cell responses
. Nat Immunol. 2019 Mar;20(3):362-372. doi:
10.1038/s41590-018-0305-x. Epub 2019 Feb 11. PubMed PMID: 30742080; PubMed
Central PMCID: PMC6380945.

5: Li Y, Soubias O, Li J, Sun S, Randazzo PA, Byrd RA. Functional Expression and
Characterization of Human Myristoylated-Arf1 in Nanodisc Membrane Mimetics
.
Biochemistry. 2019 Feb 20. doi: 10.1021/acs.biochem.8b01323. [Epub ahead of
print] PubMed PMID: 30735034.

6: Bibollet-Ruche F, Russell RM, Liu W, Stewart-Jones GBE, Sherrill-Mix S, Li Y,
Learn GH, Smith AG, Gondim MVP, Plenderleith LJ, Decker JM, Easlick JL, Wetzel
KS, Collman RG, Ding S, Finzi A, Ayouba A, Peeters M, Leendertz FH, van Schijndel
J, Goedmakers A, Ton E, Boesch C, Kuehl H, Arandjelovic M, Dieguez P, Murai M,
Colin C, Koops K, Speede S, Gonder MK, Muller MN, Sanz CM, Morgan DB, Atencia R,
Cox D, Piel AK, Stewart FA, Ndjango JN, Mjungu D, Lonsdorf EV, Pusey AE, Kwong
PD
, Sharp PM, Shaw GM, Hahn BH. CD4 receptor diversity in chimpanzees protects
against SIV infection
. Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3229-3238.
doi: 10.1073/pnas.1821197116. Epub 2019 Feb 4. PubMed PMID: 30718403; PubMed
Central PMCID: PMC6386711.

7: Jones HG, Wrapp D, Gilman MSA, Battles MB, Wang N, Sacerdote S, Chuang GY,
Kwong PD, McLellan JS. Iterative screen optimization maximizes the efficiency of
macromolecular crystallization
. Acta Crystallogr F Struct Biol Commun. 2019 Feb
1;75(Pt 2):123-131. doi: 10.1107/S2053230X18017338. Epub 2019 Jan 24. PubMed
PMID: 30713164; PubMed Central PMCID: PMC6360444.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS New Detergent-Free System for Membrane                                                                         Protein Structural Biology

Detergent-Free Membrane Protein System |  In a newly published paper in PNAS, a team led by Dr. Youzhong Guo of VCU's School of Pharmacy used a new detergent-free method that allowed them to examine the membrane of an Escherichia coli cell, with lipids still in place, providing the clearest view ever of cell membrane that yields unexpected structure. 

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

TOPIC DISCUSSIONSuggestions?

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.

LECTURES AND TUTORIALS CRYSTALLOGRAPHY


DR. ZBIGNIEW DAUTER'S LECTURES AT THE NIH (2005)
 

Part 1: "How to read international tables?"

Part 2: "Data collection strategy" and "Twinning"

           "Phasing methods - a general introduction to all methods"

Part 3: "SAD phasing, Quick halide soaking, and Radiation damage 

            with possible use of it for phasing"


RIGAKU WEBINAR SERIES (2009 - PRESENT)

LOW RESOLUTION PHASING AND REFINEMENT (2011)

CRYSTALLOGRAPHY: SEEING THINGS IN A DIFFERENT LIGHT (2013)

CRYSTALLOGRAPHY: FOR ASPIRING CRYSTALLOGRAPHERS (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

ACHESYM: AN ALGORITHM AND SERVER FOR STANDARDIZED PLACEMENT OF MACROMOLECULAR MODELS IN THE UNIT CELL (2014)

A GLIMPSE OF STRUCTURAL BIOLOGY THROUGH X-RAY CRYSTALLOGRAPHY (2014)

CRYSTAL CLEAR (2014)

NATIVE SAD IS MATURING (2015)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 LINKS - Suggestions?

Databases: BMCDDisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry, Scattering

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


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, Phyre, MolProbity, Protein, Robetta Fragment, HHpred,
 
            RestraintLib,


Facilities: 
APS SER-CAT, APS SAXS Capabilities

 
Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (https://mcl1.ncifcrf.gov)