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Newsletter No. 375
April 16, 2018

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2018, FEBS 2018, Protein Society 2018

MARCH 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Grabundzija I, Hickman AB, Dyda F. Helraiser intermediates provide insight
into the mechanism of eukaryotic replicative transposition
. Nat Commun. 2018 Mar
29;9(1):1278. doi: 10.1038/s41467-018-03688-w. PubMed PMID: 29599430.

2: Ruszkowska A, Ruszkowski M, Dauter Z, Brown JA. Structural insights into the
RNA methyltransferase domain of METTL16
. Sci Rep. 2018 Mar 28;8(1):5311. doi:
10.1038/s41598-018-23608-8. PubMed PMID: 29593291.

3: Schellenberg MJ, Petrovich RM, Malone CC, Williams RS. Selectable High-Yield
Recombinant Protein Production in Human Cells Using a GFP/YFP Nanobody Affinity
Support
. Protein Sci. 2018 Mar 25. doi: 10.1002/pro.3409. [Epub ahead of print]
PubMed PMID: 29577475.

4: Ma X, Lu M, Gorman J, Terry DS, Hong X, Zhou Z, Zhao H, Altman RB, Arthos J,
Blanchard SC,
Kwong PD, Munro JB, Mothes W. HIV-1 Env trimer opens through an
asymmetric intermediate in which individual protomers adopt distinct
conformations
. Elife. 2018 Mar 21;7. pii: e34271. doi: 10.7554/eLife.34271. [Epub
ahead of print] PubMed PMID: 29561264.

5: Ghequire MGK, Swings T, Michiels J,
Buchanan SK, De Mot R. Hitting with a BAM:
Selective Killing by Lectin-Like Bacteriocins
. MBio. 2018 Mar 20;9(2). pii:
e02138-17. doi: 10.1128/mBio.02138-17. PubMed PMID: 29559575; PubMed Central
PMCID: PMC5874912.

6: González N, McKee K, Lynch RM, Georgiev IS, Jimenez L, Grau E, Yuste E,
Kwong PD, Mascola JR, Alcamí J. Characterization of broadly neutralizing antibody
responses to HIV-1 in a cohort of long term non-progressors
. PLoS One. 2018 Mar
20;13(3):e0193773. doi: 10.1371/journal.pone.0193773. eCollection 2018. PubMed
PMID: 29558468; PubMed Central PMCID: PMC5860703.

7: Kisalu NK, Idris AH, Weidle C, Flores-Garcia Y, Flynn BJ, Sack BK, Murphy S,
Scho N A, Freire E, Francica JR, Miller AB, Gregory J, March S, Liao HX, Haynes
BF, Wiehe K, Trama AM, Saunders KO, Gladden MA, Monroe A, Bonsignori M, Kanekiyo
M, Wheatley AK, McDermott AB, Farney SK, Chuang GY, Zhang B, Kc N, Chakravarty S,
Kwong PD, Sinnis P, Bhatia SN, Kappe SHI, Sim BKL, Hoffman SL, Zavala F, Pancera
M, Seder RA. A human monoclonal antibody prevents malaria infection by targeting
a new site of vulnerability on the parasite
. Nat Med. 2018 Mar 19. doi:
10.1038/nm.4512. [Epub ahead of print] PubMed PMID: 29554083.

8: Zhou T, Zheng A, Baxa U, Chuang GY, Georgiev IS, Kong R, O'Dell S,
Shahzad-Ul-Hussan S, Shen CH, Tsybovsky Y, Bailer RT, Gift SK, Louder MK, McKee
K, Rawi R, Stevenson CH, Stewart-Jones GBE, Taft JD, Waltari E, Yang Y, Zhang B,
Shivatare SS, Shivatare VS, Lee CD, Wu CY; NISC Comparative Sequencing Program,
Mullikin JC, Bewley CA, Burton DR, Polonis VR, Shapiro L, Wong CH, Mascola JR,
Kwong PD, Wu X. A Neutralizing Antibody Recognizing Primarily N-Linked Glycan
Targets the Silent Face of the HIV Envelop
e. Immunity. 2018 Mar
20;48(3):500-513.e6. doi: 10.1016/j.immuni.2018.02.013. Epub 2018 Mar 13. PubMed
PMID: 29548671.

9: Wang L, Shi W, Chappell JD, Joyce MG, Zhang Y, Kanekiyo M, Becker MM, van
Doremalen N, Fischer R, Wang N, Corbett KS, Choe M, Mason RD, Van Galen JG, Zhou
T, Saunders KO, Tatti KM, Haynes LM,
Kwong PD, Modjarrad K, Kong WP, McLellan JS,
Denison MR, Munster VJ, Mascola JR, Graham BS. Importance of neutralizing
monoclonal antibodies targeting multiple antigenic sites on MERS-CoV Spike to
avoid neutralization escape
. J Virol. 2018 Mar 7. pii: JVI.02002-17. doi:
10.1128/JVI.02002-17. [Epub ahead of print] PubMed PMID: 29514901.

10: Margulies DH. How MHC molecules grab citrullinated peptides to foster
rheumatoid arthritis
. J Biol Chem. 2018 Mar 2;293(9):3252-3253. doi:
10.1074/jbc.H118.001829. PubMed PMID: 29500270; PubMed Central PMCID: PMC5836129.

11: Yang W, Gao Y. Translesion and Repair DNA Polymerases: Diverse Structure and
Mechanism
. Annu Rev Biochem. 2018 Mar 1. doi:
10.1146/annurev-biochem-062917-012405. [Epub ahead of print] PubMed PMID:
29494238.

12: Georgiev IS, Joyce MG, Chen RE, Leung K, McKee K, Druz A, Van Galen JG,
Kanekiyo M, Tsybovsky Y, Yang ES, Yang Y, Acharya P, Pancera M, Thomas PV,
Wanninger T, Yassine HM, Baxa U, Doria-Rose NA, Cheng C, Graham BS, Mascola JR,
Kwong PD. Two-Component Ferritin Nanoparticles for Multimerization of Diverse
Trimeric Antigens
. ACS Infect Dis. 2018 Mar 6. doi: 10.1021/acsinfecdis.7b00192.
[Epub ahead of print] PubMed PMID: 29451984.

13: Morellet N, Li X, Wieninger SA, Taylor JL, Bischerour J, Moriau S, Lescop E,
Bardiaux B, Mathy N, Assrir N, Bétermier M, Nilges M, Hickman AB, Dyda F, Craig
NL, Guittet E. Sequence-specific DNA binding activity of the cross-brace zinc
finger motif of the piggyBac transposase
. Nucleic Acids Res. 2018 Mar
16;46(5):2660-2677. doi: 10.1093/nar/gky044. PubMed PMID: 29385532; PubMed
Central PMCID: PMC5861402.

14: Fyodorov DV, Zhou BR, Skoultchi AI, Bai Y. Emerging roles of linker histones
in regulating chromatin structure and function
. Nat Rev Mol Cell Biol. 2018
Mar;19(3):192-206. doi: 10.1038/nrm.2017.94. Review. PubMed PMID: 29018282.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - A new MR-SAD algorithm

Recently, a  new MR-SAD algorithm was  reported  by Pavol Skubak, Navray Pannu, and co-workers in the IUCrJ (5:166-171, 2018), for automatic building of protein models from low-resolution X-ray diffraction data and a poor starting model. According to the authors, their algorithm uses a multivariate function to simultatnerously exploit informatino from both the initial partial model and low-resolution SAD data. Details of the algorithm and its application to six challenging structure determinations can be seen here.

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

TOPIC DISCUSSION - Protein Structure Prediction

According to Dr. Jason Stagno, the Protein Structure Prediction Center in UC Davis will have another round of CASP starting this coming May and ending in August. Last CASP (CASP12, 2016)  they secured more than 80 targets for prediction and hope that the structural biology community will help them to get as least as many for this CASP (CASP13, 2018). If you already have or will be having non-trivial for prediction structures (sequence identity < 50%), in the closest few months, please consider submitting them to CASP13 following the link here.

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.

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 (http://mcl1.ncifcrf.gov)