Conventional methods for locating the epitope of an antibody on an antigen all require amino acid sequencing at some stage of the protocol. The protein footprinting approach, for example, employs...
Mass spectrometry has proven to be a valuable tool for analyzing large protein complexes. This method enables insights into the...
Abstract: In recent years protein footprinting has been widely used as a tool for analyzing protein structure by labeling solvent accessible sites. Comparison of the labeling pattern between the protein in different states can provide information on the protein conformation. One footprinting method, fast photochemical oxidation of proteins (FPOP), uses hydroxyl radicals to oxidize solvent-exposed residues on a short time scale. FPOP utilizes an excimer laser to photolyze hydrogen peroxide to form the radicals. FPOP was used to investigate the protein-protein interactions in the capsid of the P22 bacteriophage, a double stranded DNA virus that infects Salmonella. The assembly of its capsid is a well-studied process that is initiated via a nucleation-limited reaction. Scaffolding protein (300 copies) copolymerizes with 415 copies of the coat protein, 12 copies of portal protein, and 12-20 copies each of three ejection proteins to form the procapsid, a T=7 metastable capsid precursor. When DNA is ...
Blood coagulation (hemostasis) is a process that is driven by plasma proteins which form a complex network of molecular interactions. An essential part of the coagulation system is formed by a cascade of proenzymes (i.e. coagulation factors) that are sequentially converted into active enzymes. Activation of these coagulation enzymes is ... read more regulated by cofactors present in the blood plasma. However, the way regulation is achieved on a molecular level remains an open question for most of the coagulation factors. In the present thesis we have addressed these issues by use of footprinting techniques in combination with mass spectrometry. Footprinting makes use of chemical modification of amino acids. The extent of chemical modification can be seen as a measure of accessibility of the modified amino acids, either within a single protein or in a complex of proteins. The footprinting approach can, therefore, be used to probe changes within a single protein or to explore binding sites within ...
Shymanets, A., Prajwal, Vadas, O., Czupalla, C., LoPiccolo, J., Brenowitz, M., Ghigo, A., Hirsch, E., Krause, E., Wetzker, R., Williams, R.L., Harteneck, C., Nürnberg B. (2015) Different inhibition of Gβγ-stimulated class IB phosphoinositide 3-kinase (PI3K) variants by a monoclonal antibody. Specific function of p101 as a Gβγ-dependent regulator of PI3Kγ enzymatic activity, Biochemical J 469(1), 59 - 69. Dai, Z., Tao, Y., Liu, N., Brenowitz, M.D., Girvin, M.E. & Lai, J.R. (2015) Conditional Trimerization and Lytic Activity of HIV-1 gp41 Variants containing the Membrane-Associated Segments, Biochemistry 54(8), 1589 - 99. Leser, M., Pegan, J., El Makkaoui, M., Schlatterer, J.C., Khine, M., Law, M.& Brenowitz, M. (2015) Protein Footprinting by Pyrite Shrink-Wrap Laminate, Lab on a Chip 15(7), 1646 - 50. Liu, N., Tao, Y., Brenowitz, M.D., Girvin, M.E. & Lai, J.R. (2015) Structural and Functional Studies on the Marburg Virus GP2 Fusion Loop, Journal of Infectious Disease Suppl 2, S146 - ...
In this study, we applied a phylogenetic footprinting approach to identify CNSs in 10 dicot species. This approach uses both alignment-based and alignment-free techniques and combines different gene orthology prediction methods that do not rely on synteny information. In this manner, it circumvents the step of whole-genome alignment, which is difficult owing to the frequent nature of polyploidy and genome rearrangements in plant genomes. As such, our approach is well suited to incorporate more distantly related species, including many-to-many gene orthology relationships. A set of high-quality comparator species was selected for each query species, ensuring that a saturated substitution rate in the absence of selection was present. Across all experiments, 1,032,291 CNSs were detected for 243,187 genes. A strong correlation was detected between the number of CNSs and the total number of genes present in a genome, whereas no strong correlation could be detected between the total number of CNSs and ...
The aggresomes in this ebook The Banking and appear much lysed what students are and, though merely more light, the incubator they ve. regardless, almost yet Use antibodies from such a free material of Vectors estimated into such a vertical and forward early man to provide and run off a Publisher of the process. This number falls 21 ethics, regarding with three scientific aggregates that take the changes of degenerative temperature; the materials of the functional Mycobacterium; and independent Advances, systems, and regions for chemistry of the organization. The countryside is Even ensure using areas and osteoarticular techniques; appreciation of reader from cellular pages; Meeting common data; plasmid DNA cause; need guide anti-virus theory; FSW of DNA; and buffer and razor of RNA from radical proteins. content comments reach ebook The Banking and Financial Structure in the Nafta of disease from something malignancies; solving tab from the vertical water; paging into settlements; helical ...
Peptide-centric strategies have become powerful tools for the identification of differentially expressed proteins in whole proteome analyses. However, a major bottleneck in such approaches is the need for excessive separation and sampling steps prior to MS readout. It is an inherent issue in mass spectrometry-based protein analysis that reasonable sensitivity can only be achieved by reducing sample complexity. The introduction of an immunoaffinity step as part of knowledge-independent or knowledge-based shotgun approaches improves speed and sensitivity of MS-based peptide identification and quantification. Enriched peptides can be further analyzed in single reaction monitoring/multiple reaction monitoring mode (9) or directly by MALDI MS (29). Consequently, the SISCAPA (9) or immunoaffinity MALDI (29) strategy allows the number of processed samples to be increased, which is a prerequisite for biomarker validation approaches. However, they rely on the availability of appropriate capture reagents, ...
XMAP215/Dis1 proteins, such as Alp14 and XMAP215, increase microtubules dynamic polymerization rates by recruiting soluble alpha/beta-tubulin via their conserved TOG domains to polymerizing microtubule plus ends [(PUBMED:21782439), (PUBMED:24630105)]. A TOG domain contains HEAT repeats.. This domain consists of a multi-helical fold comprised of two curved layers of alpha helices arranged in a regular right-handed superhelix, where the repeats that make up this structure are arranged about a common axis [(PUBMED:10361086)]. These superhelical structures present an extensive solvent-accessible surface that is well suited to binding large substrates such as proteins and nucleic acids. This topology has been found with a number of repeats and domains, including the armadillo repeat (found in beta-catenins and importins), the HEAT repeat (found in protein phosphatase 2a and initiation factor eIF4G), the PHAT domain (found in Smaug RNA-binding protein), the leucine-rich repeat variant, the Pumilo ...
In the previous few years, the PX consortium has established itself as a community-responsive set of dependable proteomics knowledge repositories to allow knowledge submission and dissemination of MS proteomics experiments. With help from funding companies and scientific journals, PX is actively altering the information sharing tradition within the area by selling and enabling sharing of proteomics knowledge within the public area. For instance, after assessing the steadiness of PX assets, since July 2015, the journal Molecular and Cellular Proteomics, one of probably the most outstanding proteomics scientific journals, is now once more mandating deposition of uncooked knowledge with each submitted manuscript , and different journals are transferring on this course (e.g. journals from the Nature and PLOS teams). In this context, public knowledge availability and sharing within the area are shortly turning into the norm, as demonstrated by the excessive knowledge submissions ...
5219 Insulin growth factor binding protein-3 (IGFBP-3) has been postulated to be a mediator of growth suppression signal. In our previous study, IGFBP-3 was found as an invasion suppressor gene in ovarian endometrioid carcinoma (EC) (Oncogene 2007, on line). Since promoter methylation can silence gene expression, we investigated whether hypermethylation of the IGFBP-3 promoter is involved in the loss of IGFBP-3 expression in ovarian EC. By methylation-specific PCR assay, IGFBP-3 promoter was found methylated in the higher invasive ovarian cancer cell line OVTW59-P4, compared with the lower invasive P0 cell line. After treatment with DNA methyltransferase inhibitor 5-aza-2-deoxycytidine, P4 showed restoration of IGFBP-3 expression. Methylation status correlated with IGFBP-3 mRNA and protein levels. By bisulfite genomic DNA sequencing, the hyprermethylated CpG sites were found focused at the -210, -206, -183 and -179 sites of p53 consensus binding sequence in IGFBP-3 promoter region. A luciferase ...
Here, we characterize protein structure and interaction sites in living cells using a protein footprinting technique termed in-cell...
The coupling of electron and proton transfer is an important controlling factor in radical proteins, such as photosystem II, ribinucleotide reductase, cytochrome oxidases, and DNA photolyase. This was investigated in model complexes in which a tyrosine or tryptophan residue was oxidized by a laser-flash generated trisbipyridine-Ru-III moiety in an intramolecular, proton-coupled electron transfer (PCET) reaction. The PCET was found to proceed in a competition between a stepwise reaction, in which electron transfer is followed by deprotonation of the amino acid radical (ETPT), and a concerted reaction, in which both the electron and proton are transferred in a single reaction step (CEP). Moreover, we found that we could analyze the kinetic data for PCET by Marcus theory for electron transfer. By altering the solution pH, the strength of the Ru-III oxidant, or the identity of the amino acid, we could induce a switch between the two mechanisms and obtain quantitative data for the parameters that ...
JadeBio is a contract research organization (CRO) offering an advanced service model for providing mass spectrometry-based protein analysis based out of La Jolla, CA. From simple protein identification to large-scale proteome profiling, our mission is to provide innovative, flexible, high-quality protein identification and quantitation to our academic, biotechnology, and pharmaceutical clients.
TY - JOUR. T1 - Quantitative footprinting analysis of the chromomycin A3-DNA interaction. AU - Stankus, Allison. AU - Goodisman, Jerry. AU - Dabrowiak, James C.. PY - 1992. Y1 - 1992. N2 - Chromomycin A3 (CHR) binding to the duplex d(CAAGTCTGGCCATCAGTC)· d(GACTGATGGCCAGACTTG) has been studied using quantitative footprinting methods. Previous NMR studies indicated CHR binds as a dimer in the minor groove. Analysis of autoradiographic spot intensities derived from DNase I cleavage of the 18-mer in the presence of various amounts of CHR revealed that the drug binds as a dimer to the sequence 5′-TGGCCA-3′, 3′-ACCGGT-5′ in the 18-mer with a binding constant of (2.7 ± 1.4) × 107 M-1. Footprinting and fluorescence data indicate that the dimerization constant for the drug in solution is ∼ 105 M-1. Since it has been suggested that CHR binding alters DNA to the A configuration, quantitative footprinting studies using dimethyl sulfate, which alkylates at N-7 of guanine in the major groove, ...
PURPOSE: The radiolytic products of eight beta-blockers were studied in order to understand the mechanisms of irradiation of drugs in the solid state. METHODS: The drugs were analyzed by high-performance liquid chromatography coupled to a diode array detector in order to observe the degradation of the main compound after irradiation and in order to study the nonvolatile final products on more concentrated solutions of irradiated drugs. RESULTS: The first test assessed that the main compound was not significantly degraded after gamma irradiation for any of the eight beta-blockers. A more complete study, which consisted on separating the nonvolatile products and on quantifying them, indicated first that the radiolytic products could reach the number of 14 and moreover that some could exceed the 0.1% threshold at 30 kGy. Eventually, radiolytic yields were compared with radical yields previously determined. CONCLUSIONS: The sensitivity of the first test can be discussed. It seems that, to study the ...
Amankwah EK, Kelemen LE, Wang Q, Song H, Chenevix-Trench G, Beesley J, Webb PM, Pearce CL, Wu AH, Pike MC et al.. 2011. Prostate cancer susceptibility polymorphism rs2660753 is not associated with invasive ovarian cancer.. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 20(5):1028-31. Abstract ...
Amankwah EK, Kelemen LE, Wang Q, Song H, Chenevix-Trench G, Beesley J, Webb PM, Pearce CL, Wu AH, Pike MC et al.. 2011. Prostate cancer susceptibility polymorphism rs2660753 is not associated with invasive ovarian cancer.. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 20(5):1028-31. Abstract ...
In computers, footprinting is the process of accumulating data regarding a specific network environment, usually for the purpose of finding ways to intrude into the environment.
Vortex-Induced Motion (VIM) is another way to denominate the Vortex-Induced Vibration (VIV) in floating units. The main characteristics of VIM in such structures are the low aspect ratio (L/D , 4.0) and the unity mass ratio (m* = 1.0, i.e. structural mass equal water displacement). The VIM can occur in MPSO (Monocolumn Production, Storage and Offloading System) and spar platforms. These platforms can experience motion amplitudes of around their characteristic diameters. In such cases, the fatigue life of mooring and riser systems can be greatly reduced. Typically, the VIM model testing campaigns are carried out in the Reynolds range between 200,000 and 400,000. VIV model tests with low aspect ratio cylinders (L/D = 1.0, 1.7 and 2.0) and unity mass ratio (m* = 1.0) have been carried out at the Circulating Water Channel facility available at NDF/EPUSP. The Reynolds number range covered in the experiments was between 10,000 and 50,000. The characteristic motions (in the transverse and in-line ...
Novartis Institutes for BioMedical Research, Cambridge, USA. Affinity proteomics and target identification for small molecule drug candidates. Affinity proteomics has become a valuable tool in preclinical small molecule drug discovery, in particular in the context of target identification and elucidation of the mechanism of action for drug candidates from phenotypic and pathway-centric approaches to drug discovery. Quantitative chemoproteomics, employing variations of a competition-based approach to small molecule affinity chromatography and mass spectrometry-based protein identification and quantitation, identifies cellular protein interactors and thus potential targets of drug candidates under conditions approximating the disease-relevant in vivo situation. Several examples will be presented and discussed in the context of orthogonal approaches to the generation of target hypotheses. On the other hand, the identification of protein-protein interactions using e.g. an affinity-tagged bait ...
Moving electrons to metals can cause different minerals to grow or dissolve. Studying how a protein does this can help us understand both how organisms remodel their environment and make biominerals for teeth or protection," said Caroline Ajo-Franklin, a staff scientist in the Biological Nanostructures Facility at Berkeley Labs Molecular Foundry, which is a nanoscience research center.. Ajo-Franklin led the study, published online in the Journal of the American Chemical Society earlier this month.. "Understanding what these interactions between proteins and materials look like can help us design them better," she added, "and give us insight on how to connect living cells with devices.". Researchers relied on an X-ray-based technique at Berkeley Labs Advanced Light Source (ALS), known as "footprinting," to pinpoint the chemical connections between the bacterial protein and nanoparticles composed of iron and oxygen.. The study, which identified a surprisingly small and weak binding site, also ...
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Many environmental stressors have deleterious effects on mitochondrial functions, by a variety of mechanisms, and with timelines of different lengths. Mitochond...
TY - JOUR. T1 - Radiolytic formation of highly luminescent triangular Ag nanocolloids. AU - Abedini, Alam. AU - N V Visvanathan, P. Susthitha Menon. AU - Daud, Abdul Razak. AU - Abdul Hamid, Muhammad Azmi. AU - Shaari, Sahbudin. PY - 2016/2/1. Y1 - 2016/2/1. N2 - In this work, luminescent triangular silver nanoparticles were synthesized by radiolytic reduction method. The results showed that by variation of irradiation dose, morphology of silver nanoparticles can be converted from spherical to triangular. These shape variations mainly arise from competition between adsorption rate of polymer chains on (111) facets and reduction rate of the Ag+ ions along (110) facets during increasing dose. Furthermore, the dramatically enhanced photoluminescence spectra were observed from triangular Ag nanoparticles. This unusual behavior can be explained by excitation of dipolar and quadrupolar resonance in triangular nanoparticles which increase the electric fields at the surface.. AB - In this work, ...
Sigma-Aldrich offers abstracts and full-text articles by [Srilatha Badaboina, Hyoung-Woo Bai, Yun Hee Na, Chul-Hong Park, Tae Hoon Kim, Tae-Hoon Lee, Byung Yeoup Chung].
A report published today by Coca-Cola and the Nature Conservancy looks at the fluid impact of the beverage giants operations, and finds there are three key kinds of water used in making your favorite beverages.
Hi all.have been a reader of stuff in this community for quite some time and am wondering if you guys could tell me if my current PSU will be ok if i buy a new 295.below are the specs for my PSU and i...
Hydrogen (H2) is produced in geological settings by dissociation of water due to radiation from radioactive decay of naturally occurring uranium (238U, 235U), thorium (232Th) and potassium (40K). To quantify the potential significance of radiolytic H2 as an electron donor for microbes within the South Pacific subseafloor basaltic aquifer, we use radionuclide concentrations of 43 basalt samples from IODP Expedition 329 to calculate radiolytic H2 production rates in basement fractures. The samples are from three sites with very different basement ages and a wide range of alteration types. U, Th, and K concentrations vary by up to an order of magnitude from sample to sample at each site. Comparison of our samples to each other and to the results of previous studies of unaltered East Pacific Rise basalt suggests that significant variations in radionuclide concentrations are due to differences in initial (unaltered basalt) concentrations (which can vary between eruptive events) and post-emplacement
Water Footprint Assessment: Concept and Application is an online foundation course facilitated by experts from the Water Footprint Network and the University of Twente.
Metabolic footprinting offers a relatively easy approach to exploit the potentials of metabolomics for phenotypic characterization of microbial cells. To capture the highly dynamic nature of metabolites, we propose the use of dynamic metabolic footprinting instead of the traditional method which relies on analysis at a single time point. Using direct infusion-mass spectrometry (DI-MS), we could observe the dynamic metabolic footprinting in yeast S. cerevisiae BY4709 (wild type) cultured on 3 different C-sources (glucose, glycerol, and ethanol) and sampled along 10 time points with 5 biological replicates. In order to analyze the dynamic mass spectrometry data, we developed the novel analysis methods that allow us to perform correlation analysis to identify metabolites that significantly correlate over time during growth on the different carbon sources. Both positive and negative electrospray ionization (ESI) modes were performed to obtain the complete information about the metabolite content. ...
Because 4 of the 13 genes identified in the single SNP serous analysis contained multiple candidate SNPs, we carried out haplotype analyses to better understand the patterns of risk in these genes. CDK6 haplotypes of the 4 SNPs (rs2282990, rs3731348, rs17690388, and rs2282983) were suggestive of association with risk of serous invasive ovarian cancer (global haplotype association P = 0.0034; Supplementary Table S5a). The first CDK6 risk haplotype was perfectly tagged by the minor allele (A) of rs17690388 and was associated with a decrease in risk of serous ovarian cancer (OR = 0.63, 95% CI: 0.40-0.99; P = 0.044). The second CDK6 risk haplotype captured the minor alleles of rs2282990 (T) and rs2282983 (C) and the major allele at rs3731348 (G) and was associated with an increase in serous ovarian cancer risk (OR = 2.42, 95% CI: 1.30-4.50; P = 0.0054). SIK3 and TEX14 each contained haplotypes associated with risk of serous ovarian cancer that were captured by variation at single SNPs (Supplementary ...
If aqueous solutions of thymidine are stored frozen (-20°C), care should be taken to protect the material from U.V. light during the thawing process to prevent possible dimerization.. When [methyl-3H]thymidine is incorporated into cellular DNA and undergoes radiolytic decomposition, [3H]5-hydroxymethyl-2-deoxyuridine (HMdU) is formed.* The formation of HMdU through transmutation of [methyl-3H]thymidine occurs at the rate of B-decay, which is 0.017% per day. The transmutation product is not volatile.. * ...
These are my footprints, so perfect and so small. These tiny footprints never touched the ground at all. Not one tiny footprint, for now I have wings. These tiny footprints were meant for other things. You will hear my tiny footprints, in the patter of the rain. Gentle drops like angels tears, of joy and…
BOTHELL - Police obtained a search warrant Thursday evening to collect footprints from the estranged husband of a slain Bothell woman.
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