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1.
The carboxy-terminal pleckstrin homology (PH) domain recruits GRP1 to the plasma membrane through the specific binding to
phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3]. Here, we describe backbone and side chain assignments of the GRP1 PH domain determined by triple resonance experiments.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
2.
Jan Marchant Kovilen Sawmynaden Savvas Saouros Peter Simpson Stephen Matthews 《Biomolecular NMR assignments》2008,2(2):119-121
Microneme protein 4 is involved in cell binding by the important parasite Toxoplasma gondii. We present here the backbone and side-chain assignments of the first two apple domains together with a new graphical aid
for their assignment using NMRView.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
3.
NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR
chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of
a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness
of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol
was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated
by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta
approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing
or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment
selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift
assignments.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
4.
Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR
spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present
here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without
prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification
in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1Hα and 13C′ chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such
linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral
regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content
of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D
structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall
rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken
together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination,
monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
5.
Yina Gu Qiang Liu Peiyan Chen Chenyun Guo Yan Liu Yufen Zhao Yonglian Zhang Donghai Lin 《Biochimica et Biophysica Acta - Proteins and Proteomics》2013,1834(1):1-7
Lipocalin 11 (Lcn11), a recently identified member of the lipocalin family, potentially plays crucial physiological roles in male reproduction. In this present work, we cloned, expressed and purified the rat Lcn11 (rLcn11) protein in Escherichia coli. A C59A/C156A substitution was introduced to ameliorate the misfolding and aggregation problem associated with the wild-type protein. From circular dichroism and non-reducing SDS–PAGE, we characterized the conformational properties of rLcn11 as a typical lipocalin scaffold with the conserved disulfide bridge. The results obtained from size-exclusion chromatography, cross-linking experiment and dynamic light scattering analysis indicate that the recombinant rLcn11 protein forms dimer in neutral solution. By using fluorescent probe 8-anilino-1-naphtahlene sulfonic acid (ANS), we found rLcn11 might contain multiple hydrophobic binding sites for ligand binding. Similarly to the odorant-binding protein, rLcn11 processes a moderate affinity for binding 1-aminoanthracene (AMA), implying that Lcn11 might work as a dimeric chemoreception protein in male reproductive system. 相似文献
6.
Philippe S. Nadaud Jonathan J. Helmus Christopher P. Jaroniec 《Biomolecular NMR assignments》2007,1(1):117-120
Complete 13C and 15N assignments of the B3 IgG-binding domain of protein G (GB3) in the microcrystalline solid phase, obtained using 2D and 3D
MAS NMR, are presented. The chemical shifts are used to predict the protein backbone conformation and compared with solution-state
shifts.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
7.
Yu Peng Jiafu Liu Qiang Liu Yihe Yao Chenyun Guo Yonglian Zhang Donghai Lin 《Biochimica et Biophysica Acta - Proteins and Proteomics》2010,1804(11):2102-2110
Lipocalin 12 (Lcn12) is a recently identified epididymis-specific protein that might play a significant physiological role in male reproduction. However, the detailed structure and function of Lcn12 remain to be determined. In the present work, we cloned, expressed, and purified the rat Lcn12 (rLcn12) protein in Escherichia coli, introduced the Cys176Ala substitution to eliminate the aggregation problem associated with the wild-type protein. Homology modeling results demonstrated that rLcn12 adopted an eight-stranded, antiparallel β-barrel conformation containing a conserved disulfide bond between Cys98 and Cys203, which was in accordance with the physicochemical properties elucidated by a combination of mass, circular dichroism, and nuclear magnetic resonance spectrometry. The purified rLcn12 protein exhibited a high binding affinity for all-trans retinoic acid in fluorescence titration experiments, implying that rLcn12 could be involved in retinoic acid transport in the epididymis. 相似文献
8.
Outi Heikkinen Perttu Permi Harri Koskela Olli Carpén Jari Ylänne Ilkka Kilpeläinen 《Journal of biomolecular NMR》2009,44(2):107-112
Myotilin is a 57 kDa actin-binding and -bundling protein that consists of a unique serine-rich amino-terminus, two Ig-domains
and a short carboxy-terminus with a PDZ-binding motif. Myotilin localizes in sarcomeric Z-discs, where it interacts with several
sarcomeric proteins. Point mutations in myotilin cause muscle disorders morphologically highlighted by sarcomeric disarray
and aggregation. The actin-binding and dimerization propensity of myotilin has been mapped to the Ig-domains. Here we present
high-resolution structure of the first Ig-domain of myotilin (MyoIg1) determined with solution state NMR spectroscopy. Nearly
complete chemical shift assignments of MyoIg1 were achieved despite several missing backbone 1H-15N-HSQC signals. The structure derived from distance and dihedral angle restraints using torsion angle dynamics was further
refined using molecular dynamics. The structure of MyoIg1 exhibits I-type Ig-fold. The absence of several backbone 1H-15N-HSQC signals can be explained by conformational exchange taking place at the hydrophobic core of the protein.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
9.
Wang Yueling Jiang Yan Yang De Li Wanyi Gong Tianxiang Feng Yan Jiang Zhonghua Li Mingyuan 《World journal of microbiology & biotechnology》2009,25(5):917-920
Mouse beta defensin-1 (mBD-1) is a cationic peptide with broad antimicrobial activity. The mBD-1 gene was cloned and fused with TrxA to construct pET32-mBD1, which was transformed into E. coli BL21 (DE3). The optimal expression conditions of fusion protein TrxA–mBD1 were: cultivation at 32°C in 2 × YT medium, induction
with 0.2 mM isopropylthio-d-galactoside (IPTG), and post-induction expression for 8 h. The fusion protein was highly soluble (90.0%) and accounted for
65% of the total soluble protein; and its volumetric productivity reached 0.67 g/l, i.e., 0.14 g/l of recombinant mBD-1. At
5 μM, purified recombinant mBD-1 killed 50% of Candida albicans.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
10.
Geoffrey T. Gipson Kay S. Tatsuoka Bahrad A. Sokhansanj Rachel J. Ball Susan C. Connor 《Metabolomics : Official journal of the Metabolomic Society》2008,4(1):94-103
Assignment of physical meaning to mass spectrometry (MS) data peaks is an important scientific challenge for metabolomics
investigators. Improvements in instrumental mass accuracy reduce the number of spurious database matches, however, this alone
is insufficient for accurate, unique high-throughput assignment. We present a method for clustering MS instrumental artifacts
and a stochastic local search algorithm for the automated assignment of large, complex MS-based metabolomic datasets. Artifact
peaks and their associated source peaks are grouped into “instrumental clusters.” Instrumental clusters, peaks grouped together
by shared peak shape in the temporal domain, serve as a guide for the number of assignments necessary to completely explain
a given dataset. We refine mass only assignments through the intersection of peak correlation pairs with a database of biochemically
relevant interaction pairs. Further refinement is achieved through a stochastic local search optimization algorithm that selects
individual assignments for each instrumental cluster. The algorithm works by choosing the peak assignment that maximally explains
the connectivity of a given cluster. We demonstrate that this methodology provides a significant advantage over standard methods
for the assignment of metabolites in a UPLC-MS diabetes dataset.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
11.
Lei Shi Nathaniel J. Traaseth Raffaello Verardi Alessandro Cembran Jiali Gao Gianluigi Veglia 《Journal of biomolecular NMR》2009,44(4):195-205
To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine
the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid
objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously
defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane
proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy
and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based
potential, E
z (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a
virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software
for general use.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
12.
Liangfan Zhou Qingping Lin Baocun Li Nannan Li Shuangquan Zhang 《Biotechnology letters》2009,31(3):437-441
The antimicrobial peptide CM4 is a 35-residue cationic peptide. To explore a new approach for the expression and purification
of CM4 in Escherichia coli, the CM4 gene was cloned into the vector pET32a to construct an expression vector pET32a-CM4. The fusion protein Trx-CM4,
purified by Ni2+-chelating chromatography, was cleaved by hydroxylamine hydrochloride to release recombinant CM4. Purification of recombinant
CM4 was achieved by reverse HPLC chromatography, and about 1.4 mg/l active recombinant CM4 with the purity more than 98% was
obtained. The recombinant CM4 showed antimicrobial activities that were similar to synthetic one.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
An erratum to this article can be found at 相似文献
13.
Elena S. Kovaleva Kevin P. O’Connell Patricia Buckley Zhi Liu David C. Davis 《Biotechnology letters》2009,31(3):381-386
The expression of the fluorescent protein, DsRed, facilitates the optimization of protein production in orally-infected whole
larvae. Trichoplusia ni was shown to be a much better host for recombinant AcMNPV compared to four other noctuid Lepidopteran species achieving 100%
infectivity at the minimal tested dose. The highest density of marker protein was found in endothelial and tracheal cells,
fat body, and hemocytes. Trichoplusia ni larvae possessed visually detected color over sequential passages of oral infection until the sixth round. Western blot analysis
confirmed the progressive decrease of both tetramer and monomer forms of DsRed. The intact DsRed gene and promoter region
was present in late passages, but viral population carrying the heterologous gene had dropped more than 2-logs after the fifth
round while the amount of total viral DNA remained unchanged over sequential passages.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
14.
15.
Benoit Gorguet Danny Schipper André van Lammeren Richard G. F. Visser Adriaan W. van Heusden 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(6):1199-1209
The recessive mutation ps-2, which appeared spontaneously in tomato, confers functional male sterility due to non-dehiscent anthers. In this study, we
isolated and characterized the PS-2 gene. A single nucleotide mutation in a novel tomato polygalacturonase gene is responsible for the ps-2 phenotype. The mutation in ps-2 is responsible for an alternative splicing during maturation of the pre-mRNA, which leads to an aberrant mRNA. Differentiation
between ps-2 and wild type (PS-2) anthers only appears in the final developmental stage in which the stomium remains closed in the mutant. To our knowledge,
this is the first functional sterility gene isolated in the Solanaceae family. The specific expression of the Arabidopsis homolog of PS-2 in the anther dehiscence zone suggests a conserved mode of action over the plant kingdom, which means that the repression
of PS-2 homologs may be a potential way to introduce functional sterility in other species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
16.
Laura J. Rasmussen-Torvik James S. Pankow David R. JacobsJr Julia Steinberger Antoinette Moran Alan R. Sinaiko 《Human genetics》2009,125(1):21-28
Few studies have examined the association of SNPs in the adiponectin (ADIPOQ) and adiponectin receptor 1 and 2 (ADIPOR1, ADIPOR2)
genes with the euglycemic clamp, i.e. the gold standard measure of insulin sensitivity. The association of comprehensive tag
SNPs in these genes with insulin sensitivity was examined in a cohort of adolescents and their parents. Probands and siblings
(n = 441, mean age = 17.9 years) were recruited along with their parents (n = 262, mean age = 47.9 years). Typed SNPs included 21 SNPs in ADIPOQ, 7 SNPs in ADIPOR1, and 13 SNPs in ADIPOR2. Mixed model
linear regression was used to test the association of SNPs with euglycemic-clamp derived insulin sensitivity. All analyses
were stratified by race. After corrections to account for multiple testing and the linkage disequilibrium structure of the
genes, one SNP in the ADIPOQ gene (rs822393) was significantly associated with insulin sensitivity in white subjects. In whites,
six SNPs in ADIPOQ, one SNP in ADIPOR1 and one SNP in ADIPOR2 were associated with insulin sensitivity at the P < 0.05 level. In African Americans, two SNPs in ADIPOR1 were associated with insulin sensitivity at the P < 0.05 level. These results suggest that a variant in the ADIPOQ gene influences levels of insulin sensitivity and age may
modify the effects of this variant. There are several other variants in ADIPOQ, ADIPOR1, and ADIPOR2 that may influence insulin
sensitivity and these variants should be further investigated in other populations.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
17.
Liwen Sun Shichen Wang Jinghui Xi Shuo Yang Xiangguo Liu Xin Chai Hongbao Xin Baiyi An Dongyun Hao 《Biotechnology letters》2009,31(8):1289-1295
Extraction of plant proteins using typical extraction buffers leaves insoluble debris that cannot be investigated by conventional
2-DE technologies. In this paper, we present a scalable, off-line procedure for extraction of Arabidopsis thaliana homogenates that can be used in combination with both in-gel digestion and mass spectrometry. Based on sequential NaCl gradients
and strong detergent fractionation, this new strategy allowed detection of 11 novel proteins from Arabidopsis thaliana that were altered in response to chilling stress.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
18.
A framework physical map for peach, a model Rosaceae species 总被引:1,自引:0,他引:1
T. N. Zhebentyayeva G. Swire-Clark L. L. Georgi L. Garay S. Jung S. Forrest A. V. Blenda B. Blackmon J. Mook R. Horn W. Howad P. Arús D. Main J. P. Tomkins B. Sosinski W. V. Baird G. L. Reighard A. G. Abbott 《Tree Genetics & Genomes》2008,4(4):745-756
19.
Larry R. Masterson Lei Shi Marco Tonelli Alessandro Mascioni Michael M. Mueller Gianluigi Veglia 《Biomolecular NMR assignments》2009,3(1):115-117
The catalytic subunit of protein kinase A is involved with a number of signal transduction pathways and has been used as a
benchmark to study the structural biology and biochemistry for the entire kinase family of enzymes. Here, we report the backbone
assignment of the intact 41 kDa catalytic subunit bound to AMP-PNP.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
20.
Maxime Willems Mieke Boone Marjolein Couvreur Katrien De Mulder Jelka Van Ranst Tom Artois Gaëtan Borgonie 《Development genes and evolution》2009,219(5):273-279
A method for studying whole mount flatworm embryos based on freeze-cracking of the eggs is described. This method allows successful
immunohistological and immunocytological studies of whole mount embryos. It does not require the use of sharpened needles
or a microinjection system to puncture the eggshell. Moreover, this method is more practical and less time-consuming than
classical puncturing and much cheaper than the use of a microinjection system. The advantages of this method are illustrated
by results of several immunolocalisation experiments in the macrostomid flatworm Macrostomum lignano. The optimal procedure and crucial steps for this method are discussed.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献