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Large-scale evaluation of protein reductive methylation for improving protein crystallization

Published on Oct 1, 2008in Nature Methods28.467
· DOI :10.1038/nmeth1008-853
Youngchang Kim37
Estimated H-index: 37
(Argonne National Laboratory),
P. Quartey5
Estimated H-index: 5
(Argonne National Laboratory)
+ 17 AuthorsAndrzej Joachimiak67
Estimated H-index: 67
(Argonne National Laboratory)
Abstract
Large-scale evaluation of protein reductive methylation for improving protein crystallization
  • References (16)
  • Citations (65)
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References16
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#1Neil Shaw (CAS: Chinese Academy of Sciences)H-Index: 19
#2Chongyun Cheng (CAS: Chinese Academy of Sciences)H-Index: 6
Last. Zhi-Jie Liu (CAS: Chinese Academy of Sciences)H-Index: 37
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Background The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization
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#1Anastasya Anashkina (EIMB: Engelhardt Institute of Molecular Biology)H-Index: 1
#2E. N. Kuznetsov (RAS: Russian Academy of Sciences)H-Index: 4
Last. Vladimir G. Tumanyan (EIMB: Engelhardt Institute of Molecular Biology)H-Index: 15
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We calculated interchain contacts on the atomic level for nonredundant set of 4602 pro- tein-protein interfaces using an unbiased Voronoi- Delaune tessellation method, and made 20320 resi- due contact matrixes both for homodimers and heterocomplexes. The area of contacts and the dis- tance distribution for these contacts were calculated on both the residue and the atomic levels. We ana- lyzed residue area distribution and showed the exis- tence of two types of interresidue contacts: stochas- tic...
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#2C. Meier (University of Oxford)H-Index: 8
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Cost and time reduction are two of the driving forces in the development of new strategies for protein crystallization and subsequent structure determination. Here, we report the analysis of the Thermotoga maritima proteome, in which we compare the proteins that were successfully expressed, purified and crystallized versus the rest of the proteome. This set of almost 500 proteins represents one of the largest, internally consistent, protein expression and crystallization datasets available. The ...
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Structural studies of a ternary complex composed of the Yersina pestis virulence factors YopN, SycN and YscB were initially hampered by poor solubility of the individual proteins. Co-expression of all three proteins in Escherichia coli yielded a well behaved complex, but this sample proved to be recalcitrant to crystallization. As crystallization efforts remained fruitless, even after the proteolysis-guided engineering of a truncated YopN polypeptide, reductive methylation of lysine residues was...
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A critical issue in structural genomics, and in structural biology in general, is the availability of high-quality samples. The additional challenge in structural genomics is the need to produce high numbers of proteins with low sequence similarities and poorly characterized or unknown properties. ‘Structural-biology-grade’ proteins must be generated in a quantity and quality suitable for structure determination experiments using X-ray crystallography or nuclear magnetic resonance (NMR). The cho...
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Flash-freezing, which has become routine in macromolecular X-ray crystallography, causes the crystal to contract substantially. In the case of Escherichia coli β-galactosidase the changes are reversible and are shown to be due to lattice repacking. On cooling, the area of the protein surface involved in lattice contacts increases by 50%. There are substantial alterations in intermolecular contacts, these changes being dominated by the long, polar side-chains. For entropic reasons such side-chain...
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We used a nonredundant set of 621 protein–protein interfaces of known high-resolution structure to derive residue composition and residue–residue contact preferences. The residue composition at the interfaces, in entire proteins and in whole genomes correlates well, indicating the statistical strength of the data set. Differences between amino acid distributions were observed for interfaces with buried surface area of less than 1,000 A versus interfaces with area of more than 5,000 A. Hydrophobi...
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Site-directed mutagenesis was used to determine the efficacy of changing surface residues to improve crystal quality. Nine mutants of the 24 kDa fragment of the Escherichia coli DNA gyrase B subunit were produced, changing residues on the protein's surface. The mutations changed either the charge or the polarity of the wild-type amino acid. It was found that single amino-acid changes on the surface could have a dramatic effect on the crystallization properties of the protein and generally result...
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Maltooligosyl trehalose synthase, one of the two enzymes in the coupled trehalose biosynthesis system in Sulfolobus acidocaldarius, has been purified and crystallized. The chemical modification of this enzyme by reductive methylation of lysine residues significantly improved the crystal quality for X-ray diffraction experiments. The crystals of the modified enzyme belong to orthorhombic space group P212121, with unit-cell parameters a = 56.70, b = 140.1, c = 205.2 A measured at cryo-temperature,...
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