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Newsletter No. 381
July 16, 2018

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2018, FEBS 2018, Protein Society 2018

JUNE 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Mishra V, Rathore I, Arekar A, Sthanam LK, Xiao H, Kiso Y, Sen S, Patankar S, 
Gustchina A, Hidaka K, Wlodawer A, Yada RY, Bhaumik P. Deciphering the mechanism
of potent peptidomimetic inhibitors targeting Plasmepsins: Biochemical and
structural insights
. FEBS J. 2018 Jun 26. doi: 10.1111/febs.14598. [Epub ahead of
print] PubMed PMID: 29943906.

2: Maiti A, Myint W, Kanai T, Delviks-Frankenberry K, Sierra Rodriguez C, Pathak
VK, Schiffer CA, Matsuo H. Crystal structure of the catalytic domain of HIV-1
restriction factor APOBEC3G in complex with ssDNA
. Nat Commun. 2018 Jun
25;9(1):2460. doi: 10.1038/s41467-018-04872-8. PubMed PMID: 29941968; PubMed
Central PMCID: PMC6018426.

3: DeRose EF, Kirby TW, Mueller GA, Beard WA,
Wilson SH, London RE. Transitions
in DNA polymerase β μs-ms dynamics related to substrate binding and catalysis
.
Nucleic Acids Res. 2018 Jun 18. doi: 10.1093/nar/gky503. [Epub ahead of print]
PubMed PMID: 29917149.

4: Zhang P, Gorman J, Geng H, Liu Q, Lin Y, Tsybovsky Y, Go EP, Dey B, Andine T,
Kwon A, Patel M, Gururani D, Uddin F, Guzzo C, Cimbro R, Miao H, McKee K, Chuang
GY, Martin L, Sironi F, Malnati MS, Desaire H, Berger EA, Mascola JR, Dolan MA,
Kwong PD, Lusso P. Interdomain Stabilization Impairs CD4 Binding and Improves
Immunogenicity of the HIV-1 Envelope Trimer
. Cell Host Microbe. 2018 Jun
13;23(6):832-844.e6. doi: 10.1016/j.chom.2018.05.002. PubMed PMID: 29902444;
PubMed Central PMCID: PMC6007033.

5: Chen MC, Tippana R, Demeshkina NA, Murat P, Balasubramanian S, Myong S,
Ferré-D'Amaré AR. Structural basis of G-quadruplex unfolding by the DEAH/RHA
helicase DHX36
. Nature. 2018 Jun;558(7710):465-469. doi:
10.1038/s41586-018-0209-9. Epub 2018 Jun 13. PubMed PMID: 29899445.

6: Oertell K, Kashemirov BA, Negahbani A, Minard C, Haratipour P, Alnajjar KS,
Sweasy JB, Batra VK, Beard WA, Wilson SH, McKenna CE, Goodman MF. Probing DNA
Base-Dependent Leaving Group Kinetic Effects on the DNA Polymerase Transition
State
. Biochemistry. 2018 Jun 19. doi: 10.1021/acs.biochem.8b00417. [Epub ahead
of print] PubMed PMID: 29889506.

7: Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson
SH
. Mapping Functional Substrate-Enzyme Interactions in the pol β Active Site
through Chemical Biology: Structural Responses to Acidity Modification of
Incoming dNTPs
. Biochemistry. 2018 Jun 21. doi: 10.1021/acs.biochem.8b00418.
[Epub ahead of print] PubMed PMID: 29874056.

8: Yassine HM, McTamney PM, Boyington JC, Ruckwardt TJ, Crank MC, Smatti MK,
Ledgerwood JE, Graham BS. Use of Hemagglutinin Stem Probes Demonstrate Prevalence
of Broadly Reactive Group 1 Influenza Antibodies in Human Sera
. Sci Rep. 2018 Jun
5;8(1):8628. doi: 10.1038/s41598-018-26538-7. PubMed PMID: 29872070; PubMed
Central PMCID: PMC5988737.

9: Wälti MA, Libich DS,
Clore GM. Extensive Sampling of the Cavity of the GroEL
Nanomachine by Protein Substrates Probed by Paramagnetic Relaxation Enhancement
.
J Phys Chem Lett. 2018 Jun 21;9(12):3368-3371. doi: 10.1021/acs.jpclett.8b01586.
Epub 2018 Jun 7. PubMed PMID: 29869885.

10: Xu K, Acharya P, Kong R, Cheng C, Chuang GY, Liu K, Louder MK, O'Dell S, Rawi
R, Sastry M, Shen CH, Zhang B, Zhou T, Asokan M, Bailer RT, Chambers M, Chen X,
Choi CW, Dandey VP, Doria-Rose NA, Druz A, Eng ET, Farney SK, Foulds KE, Geng H,
Georgiev IS, Gorman J, Hill KR, Jafari AJ, Kwon YD, Lai YT, Lemmin T, McKee K,
Ohr TY, Ou L, Peng D, Rowshan AP, Sheng Z, Todd JP, Tsybovsky Y, Viox EG, Wang Y,
Wei H, Yang Y, Zhou AF, Chen R, Yang L, Scorpio DG, McDermott AB, Shapiro L,
Carragher B, Potter CS, Mascola JR,
Kwong PD. Epitope-based vaccine design yields
fusion peptide-directed antibodies that neutralize diverse strains of HIV-1
. Nat
Med. 2018 Jun;24(6):857-867. doi: 10.1038/s41591-018-0042-6. Epub 2018 Jun 4.
PubMed PMID: 29867235.

11: 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 Jun;27(6):1083-1092. doi: 10.1002/pro.3409. Epub 2018
Apr 17. PubMed PMID: 29577475; PubMed Central PMCID: PMC5980532.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS FSEARCH: cryo-EM Map Replacement

FSEARCH: cryo-EM Map Replacement |  Recently, a  hybrid method that integrates X-ray crystallography with cryo-EM for structure determination is presented by Lingxiao Zeng, Wei Ding, and Quan Hao in the IUCrJ (5:382-389, 2018). The starting point is a cryo-EM map  and the end point is a high-resolution crystal structure. The workflow of the method and four case study examples can be seen here.

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 DISCUSSIONTable 1

A perspective article "Against Method: Table 1--Cui Bono?" was  recently published in Structure by Bernhard Rupp, pointing out that "Information contained in 'Table 1' is insufficient to evaluate or repeat the experiment, is redundant with information extractable from deposited diffraction data, and includes data items whose meaning is under increased scruitiny in the crystallographic community," and suggesting that "Direct and consistent extraction and analysis of data quality metrics from prefereably unmerged intensity data with graphical presentation of reciprocal space features, including impact on map and model features, should replace 'Table 1'."

Do you agree with Bernhard? Please share your opionion and ideas with fellow crystallographers.

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)