iSP-RAAC: Identify Secretory Proteins of Malaria Parasite Using Reduced Amino Acid Composition

2020 ◽  
Vol 23 (6) ◽  
pp. 536-545
Author(s):  
Haoyue Zhang ◽  
Qilemuge Xi ◽  
Shenghui Huang ◽  
Lei Zheng ◽  
Wuritu Yang ◽  
...  

Background: As the pathogen of malaria, malaria parasite secretes a variety of proteins for its growth and reproduction. Objective: The identification of the secretory proteins of malaria parasite has crucial reference significance for the development of anti-malaria vaccines as well as medicine. Methods: In this study, a computational classification method was developed to identify the secreted proteins of Plasmodium. Amino acid composition, dipeptide composition, and tripeptide composition as well as reduced amino acids alphabets were proposed to illuminate protein sequences. We further used SVM to train and predict respectively and optimized the features. Results: 74 types of reduced amino acids alphabets were employed to predict secretory proteins. The results showed that the accuracy improved to 91.67% with 0.84 Mathew’s correlation coefficient (MCC) by dipeptide composition, and the highest prediction accuracy reached 92.26% after feature selection, which demonstrated that our method is prominent and reliable in the field of malaria parasite secreted proteins prediction. Conclusion: A intuitive web server iSP-RAAC (http://bioinfor.imu.edu.cn/isppseraac) was established for the convenience of most experimental scientists.

2018 ◽  
Vol 1 (4) ◽  
pp. e201800017 ◽  
Author(s):  
Luz P Blanco ◽  
Bryan L Payne ◽  
Felix Feyertag ◽  
David Alvarez-Ponce

Pathogens differ in their host specificities, with species infecting a unique host (specialist pathogens) and others having a wide host range (generalists). Molecular determinants of pathogen’s host range remain poorly understood. Secreted proteins of generalist pathogens are expected to have a broader range of intermolecular interactions (i.e., higher promiscuity) compared with their specialist counterparts. We hypothesize that this increased promiscuity of generalist secretomes may be based on an elevated content of primitive amino acids and intrinsically disordered regions, as these features are known to increase protein flexibility and interactivity. Here, we measure the proportion of primitive amino acids and percentage of intrinsically disordered residues in secreted, membrane, and cytoplasmic proteins from pathogens with different host specificity. Supporting our prediction, there is a significant general enrichment for primitive amino acids and intrinsically disordered regions in proteins from generalists compared to specialists, particularly among secreted proteins in prokaryotes. Our findings support our hypothesis that secreted proteins' amino acid composition and disordered content influence the pathogens' host range.


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.


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