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)
Large-scale evaluation of protein reductive methylation for improving protein crystallization
  • References (16)
  • Citations (65)
📖 Papers frequently viewed together
203 Citations
69 Authors (Aiping Dong, ..., H. Zhu)
166 Citations
18.7k Citations
78% of Scinapse members use related papers. After signing in, all features are FREE.
#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
view all 11 authors...
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
10 CitationsSource
#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
view all 4 authors...
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...
21 CitationsSource
#1Thomas S. Walter (University of Oxford)H-Index: 25
#2C. Meier (University of Oxford)H-Index: 8
Last. Jonathan M. Grimes (University of Oxford)H-Index: 46
view all 10 authors...
203 CitationsSource
#1Jaume M. Canaves (UCSD: University of California, San Diego)H-Index: 19
#2Rebecca Page (Scripps Research Institute)H-Index: 34
Last. Raymond C. Stevens (Scripps Research Institute)H-Index: 100
view all 4 authors...
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 ...
79 CitationsSource
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...
29 CitationsSource
#1Youngchang Kim (Argonne National Laboratory)H-Index: 37
#2I. Dementieva (Argonne National Laboratory)H-Index: 17
Last. Andrzej Joachimiak (Argonne National Laboratory)H-Index: 67
view all 10 authors...
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...
94 CitationsSource
#1Douglas H. Juers (HHMI: Howard Hughes Medical Institute)H-Index: 17
#2Brian W. Matthews (HHMI: Howard Hughes Medical Institute)H-Index: 95
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...
79 CitationsSource
#1Fabian Glaser (TAU: Tel Aviv University)H-Index: 32
#2David M. Steinberg (TAU: Tel Aviv University)H-Index: 40
Last. Nir Ben-Tal (TAU: Tel Aviv University)H-Index: 49
view all 4 authors...
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...
338 CitationsSource
#1Allan D'Arcy (Hoffmann-La Roche)H-Index: 31
#2Martine Stihle (Hoffmann-La Roche)H-Index: 20
Last. Glenn E. Dale (Hoffmann-La Roche)H-Index: 23
view all 4 authors...
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...
28 CitationsSource
#1Masanori Kobayashi (Osaka University)H-Index: 2
#2Michio KubotaH-Index: 27
Last. Yoshiki Matsuura (Osaka University)H-Index: 27
view all 3 authors...
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,...
28 CitationsSource
Cited By65
#1M.A. Jarva (University of Melbourne)H-Index: 1
#2James P. Lingford (University of Melbourne)H-Index: 2
Last. Ethan D. Goddard-Borger (University of Melbourne)H-Index: 15
view all 6 authors...
The mucosal epithelium secretes a host of protective disulfide-rich peptides, including the trefoil factors (TFFs). The TFFs increase the viscoelasticity of the mucosa and promote cell migration, though the molecular mechanisms underlying these functions have remained poorly defined. Here, we demonstrate that all TFFs are divalent lectins that recognise the GlcNAc-α-1,4-Gal disaccharide, which terminates some mucin-like O-glycans. Degradation of this disaccharide by a glycoside hydrolase abrogat...
#1M.A. Jarva (University of Melbourne)
#1M.A. Jarva (University of Melbourne)H-Index: 1
Last. Ethan D. Goddard-Borger (University of Melbourne)H-Index: 15
view all 5 authors...
The trefoil factors (TFFs) are disulfide-rich mucosal peptides that protect the epithelium by promoting cell migration and increasing the viscoelasticity of the mucosa. Here we show that all TFFs are divalent lectins that recognise the GlcNAc-α-1,4-Gal disaccharide, which term-inates type-III mucin-like O-glycans. Structural, mutagenic and biophysical data support a model of mucus viscoelasticity that features non-covalent cross-linking of glycoproteins by TFFs.
#1Hwa Jin Cho (UPR-RP: UPRRP College of Natural Sciences)
#2Hyunjun Yoon (UPR-RP: UPRRP College of Natural Sciences)H-Index: 1
Last. Hyung Ho Lee (UPR-RP: UPRRP College of Natural Sciences)H-Index: 15
view all 3 authors...
Abstract Most phospholipids—essential building blocks of cellular membranes—are synthesized in the endoplasmic reticulum (ER) and distributed to the intracellular membranes. Yeast phosphatidylserine (PtdSer) is produced in the ER and is transported to the mitochondria, Golgi, or vacuoles; it is subsequently converted into phosphatidylethanolamine by phosphatidylserine decarboxylase. In yeast, PstB2p (Sec14p homolog) and Pbi1p are known to be involved in non-vesicular lipid transport from the ER ...
#1Wei QinH-Index: 1
#2Si-Xiao Xie (NPU: Northwestern Polytechnical University)H-Index: 3
Last. Hui-Ling CaoH-Index: 1
view all 11 authors...
#1Kanika Arora (UCSD: University of California, San Diego)H-Index: 1
#2Kevin D. Corbett (UCSD: University of California, San Diego)H-Index: 26
Author(s): Arora, Kanika; Corbett, Kevin D | Abstract: In eukaryotic meiosis, generation of haploid gametes depends on the formation of inter-homolog crossovers, which enable the pairing, physical linkage, and eventual segregation of homologs in the meiosis I division. A class of conserved meiosis-specific proteins, collectively termed ZMMs, are required for formation and spatial control of crossovers throughout eukaryotes. Here, we show that three Saccharomyces cerevisiae ZMM proteins-Zip2, Zip...
6 CitationsSource
#1David Burnand (University of Fribourg)H-Index: 4
#2Ana Milosevic (University of Fribourg)H-Index: 6
Last. Alke Petri-Fink (University of Fribourg)H-Index: 35
view all 9 authors...
: Amino groups presented on the surface of nanoparticles are well-known to be a predominant factor in the formation of the protein corona and subsequent cellular uptake. However, the molecular mechanism underpinning this relationship is poorly defined. This study investigates how amine type and density affect the protein corona and cellular association of gold nanoparticles with cells in vitro. Four specific poly(vinyl alcohol-co-N-vinylamine) copolymers are synthesized containing primary, secon...
3 CitationsSource
#1K. Arora (Ludwig Institute for Cancer Research)
#2Kevin D. Corbett (Ludwig Institute for Cancer Research)H-Index: 26
In eukaryotic meiosis, generation of haploid gametes depends on the formation of inter-homolog crossovers, which enable homolog segregation to reduce ploidy in the meiosis I division. A class of conserved meiosis-specific proteins, collectively termed ZMMs, are required for formation and spatial control of crossovers throughout eukaryotes. Here, we show that three S. cerevisiae ZMM proteins - Zip2, Zip4, and Spo16 - interact with one another to form a complex critical for crossover formation and...
#1Jennifer Neumann (University of Mainz)H-Index: 5
#2Dania Rose-Sperling (University of Mainz)H-Index: 2
Last. Ute A. Hellmich (University of Mainz)H-Index: 1
view all 3 authors...
It was first discovered in 1992 that P-glycoprotein (Pgp, ABCB1), an ATP binding cassette (ABC) transporter, can transport phospholipids such as phosphatidylcholine, − ethanolamine and -serine as well as glucosylceramide and glycosphingolipids. Subsequently, many other ABC transporters were identified to act as lipid transporters. For substrate transport by ABC transporters, typically a classic, alternating access model with an ATP-dependent conformational switch between a high and a low affinit...
27 CitationsSource
#1Guochen QinH-Index: 2
#2Jun MaH-Index: 2
Last. Yi-Min SheH-Index: 2
view all 5 authors...
Methylated-antibody affinity purification to improve proteomic identification of plant RNA polymerase Pol V complex and the interacting proteins
2 CitationsSource
#1Lothar EsserH-Index: 18
#2Fei ZhouH-Index: 6
Last. Di XiaH-Index: 32
view all 15 authors...
Abstract P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancer; it plays important roles in determining the pharmacokinetics of many drugs. Understanding the structural basis of P-gp substrate polyspecificity has been hampered by its intrinsic flexibility, which is facilitated by a 75-residue linker that connects the two halves of P-gp. Here we constructed a mutant murine P-gp with a shortened linker to facilitate structure determination. Desp...
51 CitationsSource