scholarly journals PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities

2019 ◽  
Author(s):  
Thammakorn Saethang ◽  
Kenneth Hodge ◽  
Chin-Rang Yang ◽  
Yue Zhao ◽  
Ingorn Kimkong ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Regulatory Networks ◽  
Input Data ◽  
Mass Spectrometry Data ◽  
Supplementary Information ◽  
Post Translational Modifications ◽  
Specific Amino Acid ◽  
User Input ◽  
Sequence Logos

Abstract Summary Identification of the amino-acid motifs in proteins that are targeted for post-translational modifications (PTMs) is of great importance in understanding regulatory networks. Information about targeted motifs can be derived from mass spectrometry data that identify peptides containing specific PTMs such as phosphorylation, ubiquitylation and acetylation. Comparison of input data against a standardized ‘background’ set allows identification of over- and under-represented amino acids surrounding the modified site. Conventionally, calculation of targeted motifs assumes a random background distribution of amino acids surrounding the modified position. However, we show that probabilities of amino acids depend on (i) the type of the modification and (ii) their positions relative to the modified site. Thus, software that identifies such over- and under-represented amino acids should make appropriate adjustments for these effects. Here we present a new program, PTM-Logo, that generates representations of these amino acid preferences (‘logos’) based on position-specific amino-acid probability backgrounds calculated either from user-input data or curated databases. Availability and implementation PTM-Logo is freely available online at http://sysbio.chula.ac.th/PTMLogo/ or https://hpcwebapps.cit.nih.gov/PTMLogo/. Supplementary information Supplementary data are available at Bioinformatics online.

Transport of L-tyrosine by B16/F10 melanoma cells: the effect of the intracellular content of other amino acids

1990 ◽  
Vol 97 (3) ◽  
pp. 479-485
Author(s):  
J.R. Jara ◽  
J.H. Martinez-Liarte ◽  
F. Solano ◽  
R. Penafiel
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Initial Rate ◽  
Aromatic Amino Acids ◽  
Melanoma Cells ◽  
Transport Systems ◽  
Specific Amino Acid ◽  
Intracellular Content ◽  
Tyrosine Hydroxylation ◽  
In Cells

The uptake of L-Tyr by B16/F10 malignant melanocytes in culture has been studied. These melanoma cells can either be depleted of amino acids by 1 h preincubation in Hanks' isotonic medium or preloaded with a specific amino acid by 1 h preincubation in the same solution containing 2 mM of the amino acid to be preloaded. By means of these pretreatments, it is shown that the rate of L-Tyr uptake is greatly dependent on the content of other amino acids inside the cells. The L-Tyr uptake is higher in cells preloaded with amino acids transported by the L and ASC systems than in cells depleted of amino acids or preloaded with amino acids transported by the A system. It is concluded that L-Tyr is mainly taken up by an exchange mechanism with other amino acids mediated by the L1 system, although the ASC system can also participate in the process. In agreement with that, the homo-exchange performed by cells preloaded with unlabelled L-Tyr is more efficient than any other hetero-exchange, although L-Dopa, the product of tyrosine hydroxylation in melanin synthesis, is almost as efficient as L-Tyr. Apart from aromatic amino acids, melanoma cells preloaded with L-Met and L-His also yield a high initial rate of L-Tyr uptake. The results herein suggest that melanoma cells do not have transport systems specific for L-Tyr, even if this amino acid is needed to carry out the differential pathway of this type of cells, melanosynthesis.

scholarly journals ANALISIS ASAM AMINO PENSTIMULASI SEKRESI INSULIN DALAM BIJI KECIPIR, BIJI ASAM, DAN BIJI KELOR DENGAN HPLC

Jurnal Kimia ◽  
2016 ◽  
Author(s):  
Dita Rizkiyanti ◽  
Ni Made Suaniti ◽  
Ketut Ratnayani
Keyword(s):  
Amino Acids ◽  
Insulin Secretion ◽  
Amino Acid ◽  
Amino Acid Content ◽  
Total Content ◽  
Winged Bean ◽  
Specific Amino Acid ◽  
Treatment Of Diabetes ◽  
Limited Protein ◽  
Potential Content

Seeds are a source of high protein when compared with other parts of the plant. Compared to soy bean, the use of winged bean seeds, tamarind seeds, moringa seeds as protein sources are still very limited. Protein composed of several amino acids bond together to form a polypeptide. Some amino acids have been investigated to act as stimulating insulin secretion, namely, arginine, alanine, phenylalanine, isoleucine, and lysine. The aim of this study was to determine the potential content of amino acids stimulating the secretion of insulin in winged bean seeds, tamarind seeds, and moringa seeds. Based on the total content of amino acids in each seeds, the results showed that moringa seeds have the highest levels of total amino acids stimulating insulin secretion (16.4%), followed by winged bean seeds (16.2%), and tamarind seeds (12.1%). But if seen by the levels of each amino acid, the winged bean seeds on average had the highest amino acid content. The highest levels of arginine, alanine, phenylalanine, isoleucine, and leucine were found in winged bean seeds, while only one specific amino acid i.e. lysine was found to be the highest level on moringa seeds. It can be concluded that the most potential seeds as a source of amino acids stimulating insulin was the winged bean seeds, that will be useful in the prevention or treatment of diabetes mellitus.

QUALITATIVE STUDIES OF SOIL MICROORGANISMS: IX. AMINO ACID REQUIREMENTS OF RHIZOSPHERE BACTERIA

1950 ◽  
Vol 28c (1) ◽  
pp. 1-6 ◽  
Author(s):  
R. H. Wallace ◽  
A. G. Lochhead
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Soil Microorganisms ◽  
Maximum Growth ◽  
Defined Medium ◽  
Chemically Defined Medium ◽  
Special Significance ◽  
Specific Amino Acid ◽  
Pronounced Decrease ◽  
Amino Acid Requirements

A study was made of the more specific amino acid requirements of bacteria from the rhizospheres of clover, flax, and wheat plants for which a chemically defined medium containing 23 amino acids provided essentials for maximum growth. Of seven groups of amino acids, the sulphur-containing group (cysteine, methionine, and taurine) was found to be of special significance, the omission of this group resulting in a pronounced decrease in the percentage of organisms able to develop. Further study of organisms dependent upon this group of amino acids for growth showed methionine to be by far the most essential compound. While evident for bacteria from the rhizosphere of all three crops, the effect was more pronounced in the case of clover than with flax or wheat.

MAPRes: Mining association patterns among preferred amino acid residues in the vicinity of amino acids targeted for post-translational modifications

PROTEOMICS ◽  
2008 ◽  
Vol 8 (10) ◽  
pp. 1954-1958 ◽  
Author(s):  
Ishtiaq Ahmad ◽  
Wajahat M. Qazi ◽  
Ahmed Khurshid ◽  
Munir Ahmad ◽  
Daniel C. Hoessli ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Residues ◽  
Association Patterns ◽  
Post Translational Modifications

THE RELATIONSHIP BETWEEN SOIL BACTERIA WITH SIMPLE NUTRITIONAL REQUIREMENTS AND THOSE REQUIRING AMINO ACIDS

1957 ◽  
Vol 3 (1) ◽  
pp. 73-80 ◽  
Author(s):  
T. M. B. Payne ◽  
J. W. Rouatt ◽  
A. G. Lochhead
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Soil Bacteria ◽  
Single Case ◽  
The Other ◽  
Nutritional Requirements ◽  
Soil Organisms ◽  
Specific Amino Acid ◽  
The Relationship ◽  
Maximum Development

Twenty-two of 30 representative soil bacteria having simple nutritional requirements, in that they showed maximum development in a medium of inorganic salts and sugar, were found to be able to synthesize a variety of amino acids, though in no single case were more than four ninhydrin-positive substances found. The culture filtrates permitted the growth of amino-acid-requiring bacteria to the extent that they contained the specific amino acid or acids required by strains of the latter group. The findings point to an associative action between these nutritional groups of soil organisms and suggest that the preferential stimulation in the rhizosphere of bacteria requiring amino acids may be ascribed in part to the ability of the other group of bacteria, which are numerically increased in the rhizosphere, to synthesize amino acids.

scholarly journals Understanding the limit of open search in the identification of peptides with post-translational modifications — A simulation-based study

2018 ◽  
Author(s):  
Jiaan Dai ◽  
Fengchao Yu ◽  
Ning Li ◽  
Weichuan Yu
Keyword(s):  
Analytical Model ◽  
Mass Spectra ◽  
Mass Spectrometry Data ◽  
Supplementary Information ◽  
Necessary Condition ◽  
Tandem Mass ◽  
Search Methods ◽  
Post Translational Modifications ◽  
Tandem Mass Spectra ◽  
The Relationship

AbstractMotivationAnalyzing tandem mass spectrometry data to recognize peptides in a sample is the fundamental task in computational proteomics. Traditional peptide identification algorithms perform well when identifying unmodified peptides. However, when peptides have post-translational modifications (PTMs), these methods cannot provide satisfactory results. Recently, Chick et al., 2015 and Yu et al., 2016 proposed the spectrum-based and tag-based open search methods, respectively, to identify peptides with PTMs. While the performance of these two methods is promising, the identification results vary greatly with respect to the quality of tandem mass spectra and the number of PTMs in peptides. This motivates us to systematically study the relationship between the performance of open search methods and quality parameters of tandem mass spectrum data, as well as the number of PTMs in peptides.ResultsThrough large-scale simulations, we obtain the performance trend when simulated tandem mass spectra are of different quality. We propose an analytical model to describe the relationship between the probability of obtaining correct identifications and the spectrum quality as well as the number of PTMs. Based on the analytical model, we can quantitatively describe the necessary condition to effectively apply open search methods.AvailabilitySource codes of the simulation are available at http://bioinformatics.ust.hk/[email protected] or [email protected] informationSupplementary data are available at Bioinformatics online.

Changes in plasma amino acid patterns and wool growth in response to abomasal injections of amino acids during late pregnancy and early lactation

1993 ◽  
Vol 44 (5) ◽  
pp. 959 ◽  
Author(s):  
CA Stewart ◽  
DG Masters ◽  
IH Williams ◽  
PJ Connell
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Late Pregnancy ◽  
Early Lactation ◽  
Growth Responses ◽  
Specific Amino Acid ◽  
Protein Deposition ◽  
Wool Growth ◽  
Limiting Amino Acids ◽  
Sulfur Containing

Provision of sulfur-containing amino acids into the abomasum has increased wool production in non-reproducing sheep and, on the basis of such studies, they have generally been considered as the primary limiting nutrients for wool growth. The specific amino acid needs of reproducing ewes were investigated in the current study. Three groups of pregnant ewes were fitted with temporary abomasal fistulae. For the last 3-4 weeks of pregnancy and the first 3 weeks of lactation, solutions containing sodium hydroxide (as a carrier) or methionine or a mixture of valine, arginine, lysine and threonine (VALT) were injected into the abomasum twice per day. The injection of methionine did not increase protein deposition during pregnancy; this was indicated by the failure of the treatment to lower the concentration of other amino acids in plasma, or increase liveweight, lamb birth weight or wool growth. Responses in early lactation were different with the methionine injected sheep having a lower concentration of free lysine, valine, alanine and serine in plasma, indicating an increased rate of protein deposition, and a faster growth rate in the ewes. Injections of VALT caused a decrease in the concentration of cystine and methionine in plasma and depressed wool growth and tensile strength. Theresults indicate that a lack of methionine was not limiting protein deposition during late pregnancy, but may have been during early lactation. Valine, arginine, lysine and threonine were not the primary limiting amino acids in late pregnancy or early lactation.

Qualitative/chiral sensing of amino acids by naked-eye fluorescence change based on morphological transformation and hierarchizing in supramolecular assemblies of pyrene-conjugated glycolipids

2015 ◽  
Vol 51 (55) ◽  
pp. 11104-11107 ◽  
Author(s):  
Naohiro Kameta ◽  
Mitsutoshi Masuda ◽  
Toshimi Shimizu
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Supramolecular Assemblies ◽  
Morphological Transformation ◽  
Specific Amino Acid ◽  
Color Changes ◽  
Naked Eye ◽  
Fluorescence Color ◽  
Fluorescence Change ◽  
Chiral Sensing

Supramolecular assemblies exhibited fluorescence-color changes in response to not only a specific amino acid but also the chirality of the recognized amino acid.

CodonAdjust: a software for in silico design of a mutagenesis library with specific amino acid profiles

2019 ◽  
Vol 32 (11) ◽  
pp. 503-511
Author(s):  
Thuy Duong Nguyen ◽  
Yutaka Saito ◽  
Tomoshi Kameda
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Mathematical Optimization ◽  
Amino Acid Profile ◽  
Nucleotide Composition ◽  
Specific Amino Acid ◽  
Software Implementations ◽  
Amino Acid Profiles ◽  
Complementarity Determining Regions ◽  
Manual Tasks

Abstract In protein engineering, generation of mutagenesis libraries is a key step to study the functions of mutants. To generate mutants with a desired composition of amino acids (AAs), a codon consisting of a mixture of nucleotides is widely applied. Several computational methods have been proposed to calculate a codon nucleotide composition for generating a given amino acid profile based on mathematical optimization. However, these previous methods need to manually tune weights of amino acids in objective functions, which are time-consuming and, more importantly, lack publicly available software implementations. Here, we develop CodonAdjust, a software to adjust a codon nucleotide composition for mimicking a given amino acid profile. We propose different options of CodonAdjust, which provide various customizations in practical scenarios such as setting a guaranteeing threshold for the frequencies of amino acids without any manual tasks. We demonstrate the capability of CodonAdjust in the experiments on the complementarity-determining regions (CDRs) of antibodies and T-cell receptors (TCRs) as well as millions of amino acid profiles from Pfam. These results suggest that CodonAdjust is a productive software for codon design and may accelerate library generation. CodonAdjust is freely available at https://github.com/tiffany-nguyen/CodonAdjust. Paper edited by Dr. Jeffery Saven, Board Member for PEDS.

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