scholarly journals Leri: a web-server for identifying protein functional networks from evolutionary couplings

2020 ◽  
Author(s):  
Ngaam J. Cheung ◽  
Arun T. John Peter ◽  
Benoit Kornmann
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Function ◽  
Structure Prediction ◽  
High Performance ◽  
Web Server ◽  
Functional Networks ◽  
Computational Results ◽  
High Quality ◽  
Recent Developments

ABSTRACTInformation on the co-evolution of amino acid pairs in a protein can be used for endeavors such as protein engineering, mutation design, and structure prediction. Here we report a method that captures significant determinants of proteins using estimated co-evolution information to identify networks of residues, termed “residue communities”, relevant to protein function. By taking advantage of recent developments in high-performance and parallel computing, we constructed a web-server, Leri, that identifies relevant residue communities to allow researchers to investigate how a protein evolves and folds for function(s). All the data of the computational results including high-quality images can be downloaded and presented for publication. This web-server, written in C++, is sufficiently rapid to enable the studies on proteins of up to 400 amino acids.

scholarly journals Avoided motifs: short amino acid strings missing from protein datasets

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Function ◽  
Large Protein ◽  
New Approach ◽  
Cellular Context ◽  
Human Proteins ◽  
Context Specific ◽  
Protein Datasets

Abstract According to the amino acid composition of natural proteins, it could be expected that all possible sequences of three or four amino acids will occur at least once in large protein datasets purely by chance. However, in some species or cellular context, specific short amino acid motifs are missing due to unknown reasons. We describe these as Avoided Motifs, short amino acid combinations missing from biological sequences. Here we identify 209 human and 154 bacterial Avoided Motifs of length four amino acids, and discuss their possible functionality according to their presence in other species. Furthermore, we determine two Avoided Motifs of length three amino acids in human proteins specifically located in the cytoplasm, and two more in secreted proteins. Our results support the hypothesis that the characterization of Avoided Motifs in particular contexts can provide us with information about functional motifs, pointing to a new approach in the use of molecular sequences for the discovery of protein function.

scholarly journals Determination of amino acids in human biological fluids by high-performance liquid chromatography: critical review

Amino Acids ◽  
2021 ◽  
Author(s):  
Grażyna Gałęzowska ◽  
Joanna Ratajczyk ◽  
Lidia Wolska
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
High Performance ◽  
Hplc Analysis ◽  
Limit Of Detection ◽  
Biological Fluids ◽  
Analytical Techniques ◽  
Epidemiological Studies ◽  
Preparation Conditions

AbstractThe quantitation and qualification of amino acids are most commonly used in clinical and epidemiological studies, and provide an excellent way of monitoring compounds in human fluids which have not been monitored previously, to prevent some diseases. Because of this, it is not surprising that scientific interest in evaluating these compounds has resurfaced in recent years and has precipitated the development of a multitude of new analytical techniques. This review considers recent developments in HPLC analytics on the basis of publications from the last few years. It helps to update and systematize knowledge in this area. Particular attention is paid to the progress of analytical methods, pointing out the advantages and drawbacks of the various techniques used for the preparation, separation and determination of amino acids. Depending on the type of sample, the preparation conditions for HPLC analysis change. For this reason, the review has focused on three types of samples, namely urine, blood and cerebrospinal fluid. Despite time-consuming sample preparation before HPLC analysis, an additional derivatization technique should be used, depending on the detection technique used. There are proposals for columns that are specially modified for amino acid separation without derivatization, but the limit of detection of the substance is less beneficial. In view of the fact that amino acid analyses have been performed for years and new solutions may generate increased costs, it may turn out that older proposals are much more advantageous.

scholarly journals Phylogenetic analysis and predicted functional effect of protein mutations of E6 and E7 HPV16 strains isolated in Indonesia

2015 ◽  
Vol 24 (4) ◽  
pp. 197-205
Author(s):  
Dwi Wulandari ◽  
Lisnawati Rachmadi ◽  
Tjahjani M. Sudiro
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Asian American ◽  
Protein Function ◽  
Single Amino Acid ◽  
Hpv16 E6 ◽  
E6 And E7 ◽  
Neutral Mutations

Background: E6 and E7 are oncoproteins of HPV16. Natural amino acid variation in HPV16 E6 can alter its carcinogenic potential. The aim of this study was to analyze phylogenetically E6 and E7 genes and proteins of HPV16 from Indonesia and predict the effects of single amino acid substitution on protein function. This analysis could be used to reduce time, effort, and research cost as initial screening in selection of protein or isolates to be tested in vitro or in vivo.Methods: In this study, E6 and E7 gene sequences were obtained from 12 samples of  Indonesian isolates, which  were compared with HPV16R (prototype) and 6 standard isolates in the category of European (E), Asian (As), Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and North American (NA) branch from Genbank. Bioedit v.7.0.0 was used to analyze the composition and substitution of single amino acids. Phylogenetic analysis of E6 and E7 genes and proteins was performed using Clustal X (1.81) and NJPLOT softwares. Effects of single amino acid substitutions on protein function of E6 and E7 were analysed by SNAP.Results: Java variants and isolate ui66* belonged to European branch, while the others belonged to Asian and African branches. Twelve changes of amino acids were found in E6 and one in E7 proteins. SNAP analysis showed two non neutral mutations, i.e. R10I and C63G in E6 proteins. R10I mutations were found in Af-2 genotype (AF472509) and Indonesian isolates (Af2*), while C63G mutation was found only in Af2*.Conclusion: E6 proteins of HPV16 variants were more variable than E7. SNAP analysis showed that only E6 protein of African-2 branch had functional differences compared to HPV16R.

scholarly journals Features of сalibration еequations for IR scanners in determining the amino acid composition of soy proteins

2020 ◽  
Author(s):  
С.Е. НИЗКИЙ ◽  
Г.А. КОДИРОВА ◽  
Г.В. КУБАНКОВА
Keyword(s):  
Amino Acids ◽  
Liquid Chromatography ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
High Performance ◽  
Near Infrared ◽  
Soybean Proteins ◽  
Calibration Equation ◽  
Calibration Equations

Из 20 аминокислот, входящих в состав растительных белков, 17 лучше всего определяются с помощью высокоэффективной жидкостной хроматографии. Но эта технология затратна по времени, в том числе из-за подготовки проб, что делает ее малопригодной при проведении массовых анализов, например при оценке селекционного материала. В этом случае наиболее приемлемы технологии, основанные на сканировании в ближнем инфракрасном диапазоне излучения. Несмотря на то что ИК-сканеры способны по одному калибровочному уравнению выявлять большое количество компонентов, необходима постоянная коррекция при определении состава аминокислот и приведении его в процентное соотношение. В статье рассматриваются варианты создания калибровочных уравнений для расчета аминокислотного состава белков сои с помощью компьютерных программ (Nir 42, ISI), обеспечивающих работу ИК-сканеров типа NIR-4250 или FOSS NIRSystem 5000. Установлено, что при создании калибровочных уравнений содержание каждой аминокислоты наиболее корректно выражать в абсолютных единицах (г на 100 г белка), а не относительных (%). 17 of the 20 amino acids, included in the composition of plant proteins, are most effectively determined using liquid chromatography. The technology of high-performance liquid chromatography is to a certain extent costly in time, among other things because of sample preparation that makes it unsuitable for mass analysis, for example, when evaluating a breeding material. In this case, the technology based on scanning in the near infrared radiation band are the most acceptable. Despite the fact that IR scanners are able to determine a sufficiently large number of components on the basis of one calibration equation, a constant correction is required when determining the composition of amino acids and reducing it to a percentage ratio. The options for creating calibration equations for determining the amino acid composition of soybean proteins for computer programs (Nir 42, ISI), which provide the operation of IR scanners, such as NIR-4250 or FOSS NIRSystem 5000 are considered in the article. It was found that when creating calibration equations, it is most correct to set for each amino acid its mass content (g per 100 g of protein), and not the relative portion (in %).

scholarly journals FALCON2: a web server for high-quality prediction of protein tertiary structures

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lupeng Kong ◽  
Fusong Ju ◽  
Haicang Zhang ◽  
Shiwei Sun ◽  
Dongbo Bu
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Web Server ◽  
High Quality ◽  
Tertiary Structures ◽  
Target Proteins ◽  
High Quality Protein ◽  
Protein Functions

Abstract Background Accurate prediction of protein tertiary structures is highly desired as the knowledge of protein structures provides invaluable insights into protein functions. We have designed two approaches to protein structure prediction, including a template-based modeling approach (called ProALIGN) and an ab initio prediction approach (called ProFOLD). Briefly speaking, ProALIGN aligns a target protein with templates through exploiting the patterns of context-specific alignment motifs and then builds the final structure with reference to the homologous templates. In contrast, ProFOLD uses an end-to-end neural network to estimate inter-residue distances of target proteins and builds structures that satisfy these distance constraints. These two approaches emphasize different characteristics of target proteins: ProALIGN exploits structure information of homologous templates of target proteins while ProFOLD exploits the co-evolutionary information carried by homologous protein sequences. Recent progress has shown that the combination of template-based modeling and ab initio approaches is promising. Results In the study, we present FALCON2, a web server that integrates ProALIGN and ProFOLD to provide high-quality protein structure prediction service. For a target protein, FALCON2 executes ProALIGN and ProFOLD simultaneously to predict possible structures and selects the most likely one as the final prediction result. We evaluated FALCON2 on widely-used benchmarks, including 104 CASP13 (the 13th Critical Assessment of protein Structure Prediction) targets and 91 CASP14 targets. In-depth examination suggests that when high-quality templates are available, ProALIGN is superior to ProFOLD and in other cases, ProFOLD shows better performance. By integrating these two approaches with different emphasis, FALCON2 server outperforms the two individual approaches and also achieves state-of-the-art performance compared with existing approaches. Conclusions By integrating template-based modeling and ab initio approaches, FALCON2 provides an easy-to-use and high-quality protein structure prediction service for the community and we expect it to enable insights into a deep understanding of protein functions.

scholarly journals Determination of Amino Acid Composition in the Harpagophytum procumbens Root

2019 ◽  
Vol 18 (1) ◽  
pp. 85-91
Author(s):  
AI Kriukova ◽  
IM Vladymyrova ◽  
OL Levashova ◽  
TS Tishakova
Keyword(s):  
Amino Acids ◽  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
High Performance ◽  
Harpagophytum Procumbens

The amino acid composition of the roots of Harpagophytum procumbens was investigated by the method of high performance liquid chromatography (HPLC) with preliminary derivatization. Sixteen free and thirteen bound amino acids were quantitatively determined. The content of protein-bound amino acids was calculated. Dhaka Univ. J. Pharm. Sci. 18(1): 85-91, 2019 (June)

scholarly journals Structural and Physical Properties of a Necrosis-Inducing Toxin from Pyrenophora tritici-repentis

1997 ◽  
Vol 87 (2) ◽  
pp. 154-160 ◽  
Author(s):  
Hui-Fen Zhang ◽  
Leonard J. Francl ◽  
James G. Jordahl ◽  
Steven W. Meinhardt
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Cd Spectroscopy ◽  
Tan Spot ◽  
Pyrenophora Tritici Repentis ◽  
Membrane Adhesion ◽  
Α Helix ◽  
Β Sheet

Cultivar-specific toxic metabolites of Pyrenophora tritici-repentis are involved in the appearance of necrotic and chlorotic foliar lesions characteristic of tan spot. A P. tritici-repentis necrosis-inducing toxin, Ptr necrosis toxin, was purified from isolate 86-124, sequenced by gas-phase amino acid microsequencing, and characterized by circular dichroism (CD) spectroscopy and isoelectric focusing. The purified protein had a similar amino acid composition and molecular weight as previously reported. Analysis of the CD spectrum from 178 to 250 nm indicated a protein consisting of 13% α-helix, 36% antiparallel β-sheet, 25% turns, and 25% other structures. The Ptr necrosis toxin from isolate 86-124 has an isoelectric point near pH 10. Using overlapping proteolytic fragments obtained from the toxin, a sequence of 101 continuous amino acids was obtained, but the amino terminus was blocked and 9 to 16 amino acids could not be sequenced. Secondary structure prediction based on the amino acid sequence indicated a β-sheet protein with little α-helix, which is in agreement with the structure determined by CD spectroscopy. Sequence analysis indicated the presence of a possible membrane adhesion site and several possible phosphorylation sites that may be involved in phytotoxicity.

scholarly journals Amino Acid Compositions of 27 Food Fishes and Their Importance in Clinical Nutrition

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Bimal Mohanty ◽  
Arabinda Mahanty ◽  
Satabdi Ganguly ◽  
T. V. Sankar ◽  
Kajal Chakraborty ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Content ◽  
High Performance ◽  
Crude Protein ◽  
Cold Water ◽  
Building Blocks ◽  
Crude Protein Content ◽  
Dietary Counseling ◽  
Amino Acid Compositions

Proteins and amino acids are important biomolecules which regulate key metabolic pathways and serve as precursors for synthesis of biologically important substances; moreover, amino acids are building blocks of proteins. Fish is an important dietary source of quality animal proteins and amino acids and play important role in human nutrition. In the present investigation, crude protein content and amino acid compositions of important food fishes from different habitats have been studied. Crude protein content was determined by Kjeldahl method and amino acid composition was analyzed by high performance liquid chromatography and information on 27 food fishes was generated. The analysis showed that the cold water species are rich in lysine and aspartic acid, marine fishes in leucine, small indigenous fishes in histidine, and the carps and catfishes in glutamic acid and glycine. The enriched nutrition knowledge base would enhance the utility of fish as a source of quality animal proteins and amino acids and aid in their inclusion in dietary counseling and patient guidance for specific nutritional needs.

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