scholarly journals Characterization and Prediction of Dengue Virus Targeting Peptides Based on Combined Amino Acid Composition Descriptors Using Random Forest Algorithm.

Author(s):  
Elakkiya Elumalai ◽  
Suresh Kumar Muthuvel

Abstract Dengue virus peptides are emerging as potential therapeutics for dengue infection. Due to the important role of dengue peptides in curbing dengue infection, their identification has proven crucial in terms of infection biology. To calculate differences between amino acids and physiochemical attributes, statistical tests and F-scores were used in this work. The random forest algorithm was used to predict dengue peptides using grouped amino acid composition, transition and distribution. Here, we have used three descriptors; Amino acid content, Grouped Amino acid composition and Composition, transition and distribution features (CTDC). We have created models and compared with combined model. Using the grouped amino acid composition as input parameters for the random forest algorithm, Our classifier's overall accuracy increased to 88.80%, which was the greatest overall accuracy found in this investigation. Our classifier produced superior predicting outcomes when compared to previously developed algorithms. In conclusion, we looked at the differences in amino acids and physiochemical properties between dengue viral peptides, using the grouped amino acid composition to build a classifier that predicts these dengue virus inhibitory peptides.

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhixia Teng ◽  
Zitong Zhang ◽  
Zhen Tian ◽  
Yanjuan Li ◽  
Guohua Wang

Abstract Background Amyloids are insoluble fibrillar aggregates that are highly associated with complex human diseases, such as Alzheimer’s disease, Parkinson’s disease, and type II diabetes. Recently, many studies reported that some specific regions of amino acid sequences may be responsible for the amyloidosis of proteins. It has become very important for elucidating the mechanism of amyloids that identifying the amyloidogenic regions. Accordingly, several computational methods have been put forward to discover amyloidogenic regions. The majority of these methods predicted amyloidogenic regions based on the physicochemical properties of amino acids. In fact, position, order, and correlation of amino acids may also influence the amyloidosis of proteins, which should be also considered in detecting amyloidogenic regions. Results To address this problem, we proposed a novel machine-learning approach for predicting amyloidogenic regions, called ReRF-Pred. Firstly, the pseudo amino acid composition (PseAAC) was exploited to characterize physicochemical properties and correlation of amino acids. Secondly, tripeptides composition (TPC) was employed to represent the order and position of amino acids. To improve the distinguishability of TPC, all possible tripeptides were analyzed by the binomial distribution method, and only those which have significantly different distribution between positive and negative samples remained. Finally, all samples were characterized by PseAAC and TPC of their amino acid sequence, and a random forest-based amyloidogenic regions predictor was trained on these samples. It was proved by validation experiments that the feature set consisted of PseAAC and TPC is the most distinguishable one for detecting amyloidosis. Meanwhile, random forest is superior to other concerned classifiers on almost all metrics. To validate the effectiveness of our model, ReRF-Pred is compared with a series of gold-standard methods on two datasets: Pep-251 and Reg33. The results suggested our method has the best overall performance and makes significant improvements in discovering amyloidogenic regions. Conclusions The advantages of our method are mainly attributed to that PseAAC and TPC can describe the differences between amyloids and other proteins successfully. The ReRF-Pred server can be accessed at http://106.12.83.135:8080/ReRF-Pred/.


1955 ◽  
Vol 8 (4) ◽  
pp. 537 ◽  
Author(s):  
DH Simmonds

The amino acid composition of 16-hr 6N HCI hydrolysates of three qualities of commercially classified wools has now been determined using the technique of Moore and Stein (1951). In this paper the results obtained on samples of Merino 70's and Corriedale 56's wool are compared with those previously reported for Merino wool of 64's quality. The overall pattern of the amino acid composition of the three wools is similar although small variations between the wools are observed with some of the amino acids.


1973 ◽  
Vol 134 (2) ◽  
pp. 431-436 ◽  
Author(s):  
W. Ferdinand ◽  
W. Bartley ◽  
V. Broomhead

Amino acid analyses of mitochondrial membranes are compared with the amino acid composition of whole mitochondria (Alberti, 1964) and found to be very similar except in the cystine content. The composition of the endogenous amino acids found in freshly prepared mitochondria has been established and shown to differ considerably from the amino acid composition of membranes or whole mitochondria. The amino acids produced during anaerobic incubation of mitochondria at pH7.4, on the other hand, resemble the membrane in composition, supporting the view that neutral proteinase activity is responsible for their appearance. Aerobic incubation produces a similar pattern of amino acids except that amino acids such as proline, serine, asparagine, glutamic acid and glutamine, which can be metabolically utilized under aerobic conditions, are present to a smaller extent. The presence of large relative concentrations of endogenous taurine, cysteic acid and oxidized glutathione and the accumulation of taurine during incubation is found. The selective retention of taurine and cysteic acid within the mitochondria is established. It is proposed that the first step in the degeneration of isolated mitochondria results from lipid hydroperoxide accumulation caused by the lack of glutathione reductase in isolated mitochondria.


1955 ◽  
Vol 102 (4) ◽  
pp. 435-440 ◽  
Author(s):  
Leonard T. Skeggs ◽  
Walton H. Marsh ◽  
Joseph R. Kahn ◽  
Norman P. Shumway

A preparation of hypertensin I was purified by countercurrent distribution and was shown to migrate as a single component in starch blocks at pH 9.3 and 4.2. It had an isoelectric point of 7.7. Quantitative analysis by ion exchange column chromatography showed eight amino acids in approximately unimolar proportion: aspartic, proline, valine, isoleucine, leucine, tyrosine, phenylalanine, and arginine. There were in addition two moles of histidine.


2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Karidia Konate ◽  
Emilie Josse ◽  
Milana Tasic ◽  
Karima Redjatti ◽  
Gudrun Aldrian ◽  
...  

AbstractRecently, we designed novel amphipathic cell-penetrating peptides, called WRAP, able to transfer efficiently siRNA molecules into cells. In order to gain more information about the relationship between amino acid composition, nanoparticle formation and cellular internalization of these peptides composed of only three amino acids (leucine, arginine and tryptophan), we performed a structure–activity relationship (SAR) study. First, we compared our WRAP1 and WRAP5 peptides with the C6M1 peptide also composed of the same three amino acids and showing similar behaviors in siRNA transfection. Afterwards, to further define the main determinants in the WRAP activity, we synthesized 13 new WRAP analogues harboring different modifications like the number and location of leucine and arginine residues, the relative location of tryptophan residues, as well as the role of the α-helix formation upon proline insertions within the native WRAP sequence. After having compared the ability of these peptides to form peptide-based nanoparticles (PBNs) using different biophysical methods and to induce a targeted gene silencing in cells, we established the main sequential requirements of the amino acid composition of the WRAP peptide. In addition, upon measuring the WRAP-based siRNA transfection ability into cells compared to several non-peptide transfection agents available on the markets, we confirmed that WRAP peptides induced an equivalent level of targeted gene silencing but in most of the cases with lower cell toxicity as clearly shown in clonogenic assays.


Author(s):  
С.Е. НИЗКИЙ ◽  
Г.А. КОДИРОВА ◽  
Г.В. КУБАНКОВА

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 %).


Author(s):  
F.I. Vasilevich ◽  
V.M. Bachinskaya ◽  
Yu.V. Petrova

Экспериментальные исследования кормовых добавок Абиотоник и Чиктоник проводили на базе вивария кафедры эпизоотологии и организации ветеринарного дела, а ветеринарносанитарную экспертизу продуктов убоя цыплятбройлеров проводили на кафедре паразитологии и ветеринарносанитарной экспертизы ФГБОУ ВО МГАВМиБ МВА имени К.И. Скрябина и ФГБНУ ФНЦ ВИЭВ РАН, аминокислотный состав мяса перепелов в Государственном бюджетном учреждении Краснодарского края Кропоткинская краевая ветеринарная лаборатория . Из цыплят в суточном возрасте кросса Кобб500 было сформировано три группы по 10 голов в каждой две опытные и контрольная опытным группам выпаивали кормовые добавки из расчета 1 мл/кг живой массы птицы до 50 суток выращивания, убой птицы проводили на 56 сутки. Тушки птицы после 24х часов созревания в холодильной камере при температуре 4 С подвергали исследованиям по общепринятым методикам: ГОСТ Р 519442002. Мясо птицы. Методы органолептических показателей, температуры и массы ГОСТ 314702012. Мясо птицы, субпродукты и полуфабрикаты из мяса птицы. Методы органолептических и физикохимических исследований аминокислотный состав мяса исследовали согласно М 0438 2009. Корма, комбикорма и сырье для их производства. Методика измерений массовой доли аминокислот методом капиллярного электрофореза с использованием системы капиллярного электрофореза Капель. Применение кормовых добавок в дозе 1 мл/кг живой массы способствовало увеличению живой массы птицы при применении Абиотоника на 54,23, а при применении Чиктоника на 37,70 по отношению к контролю. Во всех исследуемых пробах количество ЛЖК находится в пределах нормы и составило: в 1й опытной 1,390,03 мг КОН, во 2й опытной 1,420,04 мг КОН и в контрольной группе 1,810,06 мг КОН, что говорит о свежести и доброкачественности мяса. Значение рН мяса цыплятбройлеров находилось в трех группах в пределах нормы и не превышало 6,0. По результатам проведенных исследований аминокислотного состава красной и белой мышечной ткани цыплятбройлеров было установлено, что применение кормовой добавки Абиотоник способствовало увеличению незаменимых аминокислот на 12,14 и на 22,84 соответственно, а заменимых на 8,11 и на 22,51 по отношению к контрольной группеExperimental studies of feed additives Abiotonik and Chiktonik were conducted on the basis of the vivarium of the Department of Epizootology and Organization of Veterinary, and the veterinarysanitary examination of the products of slaughter broiler chickens was carried out at the Department of Parasitology and VeterinarySanitary Expertise of FSBEI HE MGAVMiB MBA named after KI Scriabin and the FSBI of the Federal Research Center of the VIEW RAS, the amino acid composition of quail meat in the State budget institution of the Krasnodar Territory Kropotkinskaya regional veterinary laboratory. Three groups of 10 animals each were formed from chickens at the daily age of the Cobb500 crosscountry, the experimental groups were fed feed additives at the rate of 1 ml / kg of live weight of poultry for up to 50 days of cultivation, and poultry were slaughtered for 56 days. Poultry carcasses after 24 hours of maturation in a refrigerating chamber at a temperature of 4 C were subjected to research according to generally accepted methods: GOST R 519442002. Poultry meat Methods of organoleptic characteristics, temperature and mass GOST 314702012 Poultry meat, offal and semifinished products from poultry meat. Methods of organoleptic and physicochemical studies) Amino acid composition of meat was carried out according to M 04382009. Feed, feed and raw materials for their production. Methods of measuring the mass fraction of amino acids by capillary electrophoresis using the Cappel capillary electrophoresis system. The use of feed additives in a dose of 1 ml / kg of live weight contributed to an increase in live weight of the bird when using Abiotonics by 54.23, and when using Chictonics by 37.70 relative to the control. In all studied samples, the number of VFAs is within the normal range and amounted to 1.39 0.03 mg KOH in 1 experimental group, 1.42 0.04 mg KOH in 2 experimental groups and 1.81 0.06 in the control group. mg KOH, which speaks of the freshness and goodness of meat. The pH of broiler chicken meat was in three groups within the normal range and did not exceed 6.0. According to the results of studies of the amino acid composition of red and white muscle tissue of broiler chickens, it was found that the use of the feed additive Abiotonik contributed to an increase in essential amino acids by 12.14 and by 22.84, and by replaceable ones by 8.11 and by 22.51 relative to the control group.Экспериментальные исследования кормовых добавок Абиотоник и Чиктоник проводили на базе вивария кафедры эпизоотологии и организации ветеринарного дела, а ветеринарносанитарную экспертизу продуктов убоя цыплятбройлеров проводили на кафедре паразитологии и ветеринарносанитарной экспертизы ФГБОУ ВО МГАВМиБ МВА имени К.И. Скрябина и ФГБНУ ФНЦ ВИЭВ РАН, аминокислотный состав мяса перепелов в Государственном бюджетном учреждении Краснодарского края Кропоткинская краевая ветеринарная лаборатория . Из цыплят в суточном возрасте кросса Кобб500 было сформировано три группы по 10 голов в каждой две опытные и контрольная опытным группам выпаивали кормовые добавки из расчета 1 мл/кг живой массы птицы до 50 суток выращивания, убой птицы проводили на 56 сутки. Тушки птицы после 24х часов созревания в холодильной камере при температуре 4 С подвергали исследованиям по общепринятым методикам: ГОСТ Р 519442002. Мясо птицы. Методы органолептических показателей, температуры и массы ГОСТ 314702012. Мясо птицы, субпродукты и полуфабрикаты из мяса птицы. Методы органолептических и физикохимических исследований аминокислотный состав мяса исследовали согласно М 0438 2009. Корма, комбикорма и сырье для их производства. Методика измерений массовой доли аминокислот методом капиллярного электрофореза с использованием системы капиллярного электрофореза Капель. Применение кормовых добавок в дозе 1 мл/кг живой массы способствовало увеличению живой массы птицы при применении Абиотоника на 54,23, а при применении Чиктоника на 37,70 по отношению к контролю. Во всех исследуемых пробах количество ЛЖК находится в пределах нормы и составило: в 1й опытной 1,390,03 мг КОН, во 2й опытной 1,420,04 мг КОН и в контрольной группе 1,810,06 мг КОН, что говорит о свежести и доброкачественности мяса. Значение рН мяса цыплятбройлеров находилось в трех группах в пределах нормы и не превышало 6,0. По результатам проведенных исследований аминокислотного состава красной и белой мышечной ткани цыплятбройлеров было установлено, что применение кормовой добавки Абиотоник способствовало увеличению незаменимых


InterConf ◽  
2021 ◽  
pp. 363-369
Author(s):  
Nadira Turganbaeva ◽  
Dinara Isakova

The objective of this paper was to study the amino acid composition of donkey milk inhabiting the Kegety gorge of the Chui region. As well as human milk, donkey and mare’s milk is albumin; the amount of casein is 35-45%, while cow’s milk is casein milk with casein content over 75%. The peculiarity of albumin milk is a higher biological and nutritional value, due to better amino acid balance, high sugar content and the ability to form small, delicate flakes when souring. In terms of its properties, albumin milk is closest to human milk and is the best substitute for it. The obtained results showed that the quantitative content of 7 essential amino acids out of 8, such as lysine, phenylalanine, leucine, isoleucine, methionine, valine, threonine is relatively high compared to other amino acids. Despite the absence of tryptophan in donkey milk, the percentage of 8 essential amino acids in donkey milk protein exceeds that in mare and cow’s milk.


Vestnik MGTU ◽  
2020 ◽  
Vol 23 (3) ◽  
pp. 205-213
Author(s):  
N. V. Linovskaya ◽  
E. V. Mazukabzova ◽  
O. S. Rudenko ◽  
T. V. Savenkova

Milk chocolate is particularly popular with different age groups. It is characterized by low protein content with a large amount of fats and carbohydrates determining the food imbalance of the product. In conditions of high-grade animal proteins deficiency the selection of high-quality protein-containing ingredients for food production is very relevant. The aim of this work is to study the protein adequacy of various components of milk chocolate to enhance its biological value. The amino acid scale method has been used to assess the biological value of proteins; it is based on the determination of amino acid (chemical) score. It has been found that the limiting biological value amino acid for classical white raw ingredients of milk chocolate (cocoa products and milk powder) is methionine + cysteine. For constructing chocolate formulas with increased biological value it is advisable to use protein-containing raw materials (whey protein concentrate, oat flour, etc.) to compensate for the limiting amino acids. The indicator of amino acids utilitarianity of proteins of raw milk chocolate components has been calculated. On the basis of the utilitarian index we have established the coefficient of utilitarian of the amino acid composition of the raw materials characterizing essential amino acids' balance. We have determined the biological value of protein and the amino acid composition imbalance coefficient. It has been found that the amino acid composition of milk and whey protein concentrates is most balanced compared to the amino acid composition of traditional protein-containing raw components of milk chocolate. The limiting acid of whey protein concentrate is valine, which makes its use in the manufacture of chocolate products more attractive compared to milk protein concentrate (the limiting amino acid is methionine + cysteine). In the group of vegetable non-conventional raw materials oat and buckwheat flour are characterized by the best indicators of biological value. The amino acid adequacy of oat flour is comparable to the qualitative protein indicators of cocoa products, the limiting amino acid is lysine. Buckwheat flour is characterized by the smallest imbalance in amino acid composition, which distinguishes the proteins of this raw material with the highest degree of digestibility compared with the proteins of all the studied protein-containing components of milk chocolate.


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