scholarly journals An Approach for a Substitution Matrix Based on Protein Blocks and Physicochemical Properties of Amino Acids through PCA

2014 ◽  
Vol 6 (4) ◽  
pp. 3.1-3.10 ◽  
Author(s):  
Youngki You ◽  
Inhwan Jang ◽  
Kyungro Lee ◽  
Heonjoo Kim ◽  
Kwanhee Lee
Keyword(s):  
Amino Acids ◽  
Physicochemical Properties ◽  
Substitution Matrix ◽  
Protein Blocks

A Study on Host Tropism Determinants of Influenza Virus Using Machine Learning

2020 ◽  
Vol 15 (2) ◽  
pp. 121-134 ◽  
Author(s):  
Eunmi Kwon ◽  
Myeongji Cho ◽  
Hayeon Kim ◽  
Hyeon S. Son
Keyword(s):  
Machine Learning ◽  
Amino Acids ◽  
Influenza Virus ◽  
Random Forest ◽  
Physicochemical Properties ◽  
Protein Sequences ◽  
Influenza Viruses ◽  
Host Tropism ◽  
Post Hoc ◽  
Ha Protein

Background: The host tropism determinants of influenza virus, which cause changes in the host range and increase the likelihood of interaction with specific hosts, are critical for understanding the infection and propagation of the virus in diverse host species. Methods: Six types of protein sequences of influenza viral strains isolated from three classes of hosts (avian, human, and swine) were obtained. Random forest, naïve Bayes classification, and knearest neighbor algorithms were used for host classification. The Java language was used for sequence analysis programming and identifying host-specific position markers. Results: A machine learning technique was explored to derive the physicochemical properties of amino acids used in host classification and prediction. HA protein was found to play the most important role in determining host tropism of the influenza virus, and the random forest method yielded the highest accuracy in host prediction. Conserved amino acids that exhibited host-specific differences were also selected and verified, and they were found to be useful position markers for host classification. Finally, ANOVA analysis and post-hoc testing revealed that the physicochemical properties of amino acids, comprising protein sequences combined with position markers, differed significantly among hosts. Conclusion: The host tropism determinants and position markers described in this study can be used in related research to classify, identify, and predict the hosts of influenza viruses that are currently susceptible or likely to be infected in the future.

scholarly journals Amino Acids as the Potential Co-Former for Co-Crystal Development: A Review

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3279
Author(s):  
Ilma Nugrahani ◽  
Maria Anabella Jessica
Keyword(s):  
Amino Acids ◽  
Physicochemical Properties ◽  
Deep Eutectic Solvent ◽  
Strong Interactions ◽  
Green Method ◽  
Pharmaceutical Ingredients ◽  
Gastrointestinal Fluid ◽  
Non Covalent Interactions ◽  
Natural Deep Eutectic Solvent ◽  
Covalent Interactions

Co-crystals are one of the most popular ways to modify the physicochemical properties of active pharmaceutical ingredients (API) without changing pharmacological activity through non-covalent interactions with one or more co-formers. A “green method” has recently prompted many researchers to develop solvent-free techniques or minimize solvents for arranging the eco-friendlier process of co-crystallization. Researchers have also been looking for less-risk co-formers that produce the desired API’s physicochemical properties. This review purposed to collect the report studies of amino acids as the safe co-former and explored their advantages. Structurally, amino acids are promising co-former candidates as they have functional groups that can form hydrogen bonds and increase stability through zwitterionic moieties, which support strong interactions. The co-crystals and deep eutectic solvent yielded from this natural compound have been proven to improve pharmaceutical performance. For example, l-glutamine could reduce the side effects of mesalamine through an acid-base stabilizing effect in the gastrointestinal fluid. In addition, some amino acids, especially l-proline, enhances API’s solubility and absorption in its natural deep eutectic solvent and co-crystals systems. Moreover, some ionic co-crystals of amino acids have also been designed to increase chiral resolution. Therefore, amino acids are safe potential co-formers, which are suitable for improving the physicochemical properties of API and prospective to be developed further in the dosage formula and solid-state syntheses.

A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction

2007 ◽  
Vol 67 (1) ◽  
pp. 142-153 ◽  
Author(s):  
Eran Eyal ◽  
Milana Frenkel-Morgenstern ◽  
Vladimir Sobolev ◽  
Shmuel Pietrokovski
Keyword(s):  
Amino Acids ◽  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Substitution Matrix

Physicochemical Properties of Adducts of Light Fullerenes and Amino Acids

2021 ◽  
Vol 95 (11) ◽  
pp. 2181-2197
Author(s):  
N. A. Charykov ◽  
V. A. Keskinov ◽  
A. V. Petrov
Keyword(s):  
Amino Acids ◽  
Physicochemical Properties

Synthesis of chelated compounds of amino acids with metals

2021 ◽  
Author(s):  
A.A. Yamskikh ◽  
L.A. Ivanova
Keyword(s):  
Amino Acids ◽  
Physicochemical Properties ◽  
Alkaline Earth ◽  
Alkaline Earth Metals ◽  
Iron Copper ◽  
Copper Zinc ◽  
Glycine Synthesis

The article describes the reactions of glycine synthesis with alkaline, alkaline-earth and divalent 3-d metals, which were carried out during the experiment. Hydroxides or sulfates of lithium, magnesium, calcium, manganese, iron, copper, zinc, cobalt and sodium were used as reagents for the synthesis. The physicochemical properties of the obtained compounds were studied. Keywords: chelates, glycinates of alkaline and alkaline earth metals, glycinates of divalent 3-d metals.

scholarly journals Karakteristik Fisiko-Kimia Konsentrat Protein Ikan Sunglir (Elagatis bipinnulatus)

Jurnal MIPA ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 164
Author(s):  
Frets Jonas Rieuwpassa ◽  
Eko Cahyono
Keyword(s):  
Amino Acids ◽  
Physicochemical Properties ◽  
Essential Amino Acids ◽  
Fat Content ◽  
Pelagic Fish ◽  
Animal Protein ◽  
Physical Analysis ◽  
Fat Absorption ◽  
Type B ◽  
High Level

Ikan merupakan sumber protein hewani yang memiliki daya cerna yang lebih baik dan jumlah kandungan asam amino essensial yang lebih banyak dibandingkan dengan sumber protein hewani lainnya. Ikan sunglir adalah jenis ikan pelagis yang banyak hidup diperairan Nusa Utara. Ekstraksi KPI umumnya dilakukan dengan menggunakan pelarut etanol. Penelitian ini bertujuan mengkarakterisasi sifat fisiko-kimia konsentrat protein ikan yang diekstrak dari ikan sunglir. Penggunaan etanol 90% dalam mengekstraksi konsentrat protein dari ikan sunglir menghasilkan rendemen berkisar 18-20%. Hasil Penelitian menunjukkan bahwa konsentrat protein ikan sunglir memiliki kandungan protein yang tinggi dan memiliki kadar lemak yang rendah. Konsentrat protein dengan kadar protein >65% dan kadar lemak <3% tergolong sebagai konsentrat protein Tipe B sesuai dengan standar Mutu FAO 1976 tentang KPI. Hasil pengujian fisik menunjukkan bahwa KPI memiliki kemampuan penyerapan air, lemak dan densitas kamba yang cukup baik untuk diaplikasikan ke dalam bahan panganFish serve as an important source of animal protein with better digestibility and higher content of essential amino acids than other sources of animal protein. Elagatis bipinnulatus or sunglir in Indonesian is a common pelagic fish caught in Sangihe Islands. FPC is commonly extracted with etanol. Therefore, this research aims to characterise the physicochemical properties of the FPC extracted from rainbow runner. The use of 90% ethanol for exraction of FPC from rainbow runner resulted in 18-20% yield. The result shows that the local rainbow runner contained FPC with high level of protein (77.34%) but low level of fat (1.22%), classified as type B on the basis of FAO’s standard on FPC Protein, which stipulated FPC with >65% protein and <3% fat content as Type B. In addition, physical analysis proved that FPC has appropriate water and fat absorption abilities as well as kamba density, suitble for food substitute or fortification

scholarly journals Isolation and Charactherization of Collagen from Swim Bladder Waste of Yellow-pike Conger (Muraenesox talabon)

2016 ◽  
Vol 19 (3) ◽  
pp. 222 ◽  
Author(s):  
I Wayan Darya Kartika ◽  
Wini Trilaksani
Keyword(s):  
Amino Acids ◽  
Body Weight ◽  
Physicochemical Properties ◽  
Functional Groups ◽  
Hydrothermal Process ◽  
Acid Extraction ◽  
Swim Bladder ◽  
Chemical Content ◽  
Wet Weight ◽  
Acid Process

<p>Indonesian capture fisheries production reached ± 6.4 million tons in 2014. This number was predicted<br />resulted a huge fishery waste, one of them was swim bladder that potentially contain collagen, so it needs to<br />be developed. This aim of this study was to determine the characteristics of the swim bladder (proportion<br />and chemical content) and collagen characteristics (yield and physicochemical properties) extracted from<br />the swim bladder cunang (Muraenesox talabon). Swim bladder waste had proportion 0.57 to 0.67% of whole<br />yellow-piked conger body weight and 24.74% protein/100 g wet weight (equivalent to 93.39% of protein/100<br />gram dry). The waste had a potency of collagen, which is characterized by the high proportion of the<br />amino acids glycine, proline, hydroxyproline and alain. Acid extraction and hydrothermal process resulted<br />collagen extracts, identified from a spectrum of amide I, amide II and amide III functional groups. Collagen<br />extracted with acid process contained a higher glycine than hydrothermal one, but instead hydrothermal<br />process produced extract with a higher proline, hydroxyproline and alanine composition.<br /><br /></p>

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