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Amino acid

About: Amino acid is a(n) research topic. Over the lifetime, 124999 publication(s) have been published within this topic receiving 4031370 citation(s).

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Open accessJournal ArticleDOI: 10.1016/1044-0305(94)80016-2
Abstract: A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (10–50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a mass tolerance of ±1 u of the precursor ion molecular weight A cross-correlation function is then used to provide a measurement of similarity between the mass-to-charge ratios for the fragment ions predicted from amino acid sequences obtained from the database and the fragment ions observed in the tandem mass spectrum. In general, a difference greater than 0.1 between the normalized cross-correlation functions of the first- and second-ranked search results indicates a successful match between sequence and spectrum. Searches of species-specific protein databases with tandem mass spectra acquired from peptides obtained from the enzymatically digested total proteins of E. coli and S. cerevisiae cells allowed matching of the spectra to amino acid sequences within proteins of these organisms. The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.

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Topics: Peptide sequence tag (62%), Bottom-up proteomics (61%), Isobaric labeling (58%) ...read more

5,948 Citations


Open accessJournal ArticleDOI: 10.1074/MCP.M200025-MCP200
Abstract: Quantitative proteomics has traditionally been performed by two-dimensional gel electrophoresis, but recently, mass spectrometric methods based on stable isotope quantitation have shown great promise for the simultaneous and automated identification and quantitation of complex protein mixtures. Here we describe a method, termed SILAC, for stable isotope labeling by amino acids in cell culture, for the in vivo incorporation of specific amino acids into all mammalian proteins. Mammalian cell lines are grown in media lacking a standard essential amino acid but supplemented with a non-radioactive, isotopically labeled form of that amino acid, in this case deuterated leucine (Leu-d3). We find that growth of cells maintained in these media is no different from growth in normal media as evidenced by cell morphology, doubling time, and ability to differentiate. Complete incorporation of Leu-d3 occurred after five doublings in the cell lines and proteins studied. Protein populations from experimental and control samples are mixed directly after harvesting, and mass spectrometric identification is straightforward as every leucine-containing peptide incorporates either all normal leucine or all Leu-d3. We have applied this technique to the relative quantitation of changes in protein expression during the process of muscle cell differentiation. Proteins that were found to be up-regulated during this process include glyceraldehyde-3-phosphate dehydrogenase, fibronectin, and pyruvate kinase M2. SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system.

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5,385 Citations



Open accessJournal ArticleDOI: 10.1093/NAR/GKG509
Pauline C. Ng1, Steven HenikoffInstitutions (1)
Abstract: Single nucleotide polymorphism (SNP) studies and random mutagenesis projects identify amino acid substitutions in protein-coding regions. Each substitution has the potential to affect protein function. SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study. We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html.

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Topics: Protein methods (51%), Amino acid (51%)

4,494 Citations


Open accessJournal ArticleDOI: 10.1073/PNAS.78.6.3824
Abstract: A method is presented for locating protein antigenic determinants by analyzing amino acid sequences in order to find the point of greatest local hydrophilicity. This is accomplished by assigning each amino acid a numerical value (hydrophilicity value) and then repetitively averaging these values along the peptide chain. The point of highest local average hydrophilicity is invariably located in, or immediately adjacent to, an antigenic determinant. It was found that the prediction success rate depended on averaging group length, with hexapeptide averages yielding optimal results. The method was developed using 12 proteins for which extensive immunochemical analysis has been carried out and subsequently was used to predict antigenic determinants for the following proteins: hepatitis B surface antigen, influenza hemagglutinins, fowl plague virus hemagglutinin, human histocompatibility antigen HLA-B7, human interferons, Escherichia coli and cholera enterotoxins, ragweed allergens Ra3 and Ra5, and streptococcal M protein. The hepatitis B surface antigen sequence was synthesized by chemical means and was shown to have antigenic activity by radioimmunoassay.

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Topics: Peptide sequence (54%), Epitope (53%), Hemagglutinin (influenza) (52%) ...read more

3,708 Citations


Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202230
20211,772
20202,208
20192,078
20182,092
20172,165

Top Attributes

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Topic's top 5 most impactful authors

Peter G. Schultz

167 papers, 21.5K citations

Hisashi Yamamoto

106 papers, 149 citations

Halvor N. Christensen

69 papers, 5.8K citations

Guoyao Wu

55 papers, 6.9K citations

Yoshikatsu Kanai

55 papers, 4.1K citations

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