scholarly journals ANALYSIS AND PREDICTION OF MAJOR BLOOD PROTEINS BASED ON THEIR AMINO ACID AND DIPEPTIDE COMPOSITION

2013 ◽  
Vol 5 (1) ◽  
pp. 285-288 ◽  
Author(s):  
MUTHUKRISHNAN S ◽  
◽  
PURI M ◽  
LEFEVRE C
Keyword(s):  
Amino Acid ◽  
Blood Proteins ◽  
Dipeptide Composition

Consistency and Change

2019 ◽  
Author(s):  
Alan Kelly
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Living Organism ◽  
Peptide Bond ◽  
The Body ◽  
Blood Proteins ◽  
Genes Encoding ◽  
Fundamental Phenomenon ◽  
P Proteins

Proteins are, in my view, the most impressive molecules in food. They influence the texture, crunch, chew, flow, color, flavor, and nutritional quality of food. Not only that, but they can radically change their properties and how they behave depending on the environment and, critically for food, in response to processes like heating. Even when broken down into smaller components they are important, for example giving cheese many of its critical flavor notes. Indeed, I would argue that perhaps the most fundamental phenomenon we encounter in cooking or processing food is the denaturation of proteins, as will be explained shortly. Beyond food, the value of proteins and their properties is widespread across biology. Many of the most significant molecules in our body and that of any living organism (including plants and animals) are proteins. These include those that make hair and skin what they are, as well as the hemoglobin that transports oxygen around the body in our blood. Proteins are built from amino acids, a family of 20 closely related small molecules, which all have in chemical terms the same two ends (chemically speaking, an amino end and an acidic end, hence the name) but differ in the middle. This bit in the middle varies from amino acid to amino acid, from simple (a hydrogen atom in the case of glycine, the simplest amino acid) to much more complex structures. Amino acids can link up very neatly, as the amino end of one can form a bond (called a peptide bond) with the acid end of another, and so forth, so that chains of amino acids are formed that, when big enough (more than a few dozen amino acids), we call proteins. Our bodies produce thousands of proteins for different functions, and the instructions for which amino acids combine to make which proteins are essentially what the genetic code encrypted in our DNA specifies. We hear a lot about our genes encoding the secrets of life, but what that code spells is basically P-R-O-T-E-I-N. Yes, these are very important molecules!

The Influence of Dipeptide Composition on Protein Folding Rates

2011 ◽  
Vol 378-379 ◽  
pp. 157-160
Author(s):  
Jian Xiu Guo ◽  
Ni Ni Rao
Keyword(s):  
Protein Folding ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Dipeptide Composition ◽  
Coupling Effects ◽  
Jackknife Test ◽  
Folding Rates ◽  
Important Challenge ◽  
The Relationship

Understanding the relationship between amino acid sequences and folding rates of proteins is an important challenge in computational and molecular biology. All existing algorithms for predicting protein folding rates have never taken into account the sequence coupling effects. In this work, a novel algorithm was developed for predicting the protein folding rates from amino acid sequences. The prediction was achieved on the basis of dipeptide composition, in which the sequence coupling effects are explicitly included through a series of conditional probability elements. Based on a non-redundant dataset of 99 proteins, the proposed method was found to provide an excellent agreement between the predicted and experimental folding rates of proteins when evaluated with the jackknife test. The correlation coefficient was 87.7% and the standard error was 2.04, which indicated the important contribution from sequence coupling effects to the determination of protein folding rates.

Protein Synthesis and Uptake by Isolated Cecropia Oocytes

1971 ◽  
Vol 8 (3) ◽  
pp. 735-750
Author(s):  
LUCY M. ANDERSON
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Perchloric Acid ◽  
Selection Process ◽  
Ovarian Follicle ◽  
Follicle Cell ◽  
Follicle Cells ◽  
Follicular Epithelium ◽  
Blood Proteins ◽  
Cell Product

A procedure has been developed for separating the oocytes and follicular epithelium-nurse cell complexes making up the vitellogenic ovarian follicle of the Cecropia moth. Both components remained viable during short-term in vitro incubation in female blood. Isolated epithelial cells were found by autoradiography to incorporate tritiated amino acids and to secrete a fixable, non-dialysable labelled material. Isolated oocytes incubated in a blood medium containing this tritiated, dialysed follicle cell product incorporated it in small cortical yolk bodies, presumably by pinocytosis. Quantitative perchloric acid-precipitation and scintillation counting indicated that the amount of labelled material incorporated by the oocytes increased with time. These results provide direct confirmation of a follicle contribution to the yolk. Isolated oocytes were also tested for their ability to incorporate labelled amino acids. Fixable label was observed autoradiographically throughout the oocyte cytoplasm, with the greatest concentration in the cortex, but little appeared in the yolk spheres. The amount of perchloric acid-precipitable amino acid in oocytes incubated in female blood increased with time for up to 2 h and then remained constant or decreased slightly. In medium that had been previously conditioned by follicle cells and dialysed, however, incorporation of labelled amino acid continued for at least 4 h. A possible interpretation of this result is that stimulation of pinocytosis by the epithelial cell products causes increased turnover of cell membrane and demands continued synthesis of new proteins. Labelled female blood proteins were not incorporated into yolk to an appreciable extent by isolated oocytes, even in the presence of follicle cell product. Perhaps extracellular preconcentration, as occurs in the intact follicle, is necessary for effective accrual of blood proteins. The female blood proteins did become associated with the oocyte cortex, however, and exhibited a higher affinity for the oocyte than male blood proteins. Thus preferential adsorption to the oocyte surface may be a component of the selection process in vitellogenesis.

Detecting thermophilic proteins through selecting amino acid and dipeptide composition features

Amino Acids ◽  
2011 ◽  
Vol 42 (5) ◽  
pp. 1947-1953 ◽  
Author(s):  
Songyot Nakariyakul ◽  
Zhi-Ping Liu ◽  
Luonan Chen
Keyword(s):  
Amino Acid ◽  
Dipeptide Composition

scholarly journals HEMOGLOBIN AND PLASMA PROTEIN

1943 ◽  
Vol 77 (4) ◽  
pp. 375-396 ◽  
Author(s):  
F. S. Robscheit-Robbins ◽  
L. L. Miller ◽  
G. H. Whipple
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Plasma Protein ◽  
The Body ◽  
Acid Mixture ◽  
Blood Proteins ◽  
Body Protein ◽  
Growth Mixture ◽  
Amino Acid Mixtures ◽  
Hemoglobin Production

Given healthy dogs, fed abundant iron and protein-free or low protein diets, with sustained anemia due to bleeding, we can study the capacity of these animals to produce simultaneously new hemoglobin and plasma protein. The reserve stores of blood protein producing materials in this way are very largely depleted, and levels of 6 to 8 gm. per cent for hemoglobin and 4 to 5 gm. per cent for plasma protein can be maintained for considerable periods of time. These dogs are very susceptible to infection and to injury by many poisons. Under such conditions, these anemic and hypoproteinemic dogs will use very efficiently a variety of digests (serum, hemoglobin, and casein) and the growth mixture (Rose) of pure amino acids. Nitrogen balance is maintained and considerable new blood proteins are produced. Dog plasma by vein is used freely in these doubly depleted dogs to make new hemoglobin in abundance (Table 1). Serum digests by vein are well utilized to make new hemoglobin and plasma protein in the same dogs (Table 1). Serum digests by mouth are effectively used to make new blood proteins (Table 5). Dog or sheep hemoglobin given in large amounts intraperitoneally are remarkably well utilized to form hemoglobin and plasma protein (Table 6). It must be obvious that the globin of the hemoglobin is saved in these protein-depleted dogs and used to make large amounts of hemoglobin and plasma protein. Hemoglobin digests are also well utilized whether given by mouth (Table 7) or by vein (Table 8) and liberal amounts of plasma protein are manufactured from digests presumably ideally suited for hemoglobin production. Casein digests are well used (Table 8) and form as much new plasma protein as any material tested—even serum digests. Amino acid mixtures are of especial interest. The growth mixture of 10 amino acids (Rose) is well utilized by mouth or by vein and favors new hemoglobin production more than any material tested (Table 2). Cystine replacing methionine in the amino acid mixture increases the plasma protein—hemoglobin output ratio, that is it favors plasma protein production. Digests of various sorts and amino acid mixtures or combinations of digests and amino acid mixtures can be used rapidly and effectively to build new hemoglobin or plasma protein, to maintain nitrogen equilibrium, and to replete reserve protein stores. These experiments point to clinical problems. The unexplained preference given to hemoglobin production in these hypoproteinemic dogs is observed under all conditions, even when whole plasma or serum digests are given by vein. In general, 2 to 4 gm. of hemoglobin are formed for every gram of plasma protein. This all adds up to a remarkable fluidity in the use of plasma protein or hemoglobin which can contribute directly to the body protein pool from which are evolved, without waste of nitrogen, the needed proteins, whether hemoglobin, plasma protein, or tissue proteins.

scholarly journals Control of blood proteins by functional disulfide bonds

Blood ◽  
2014 ◽  
Vol 123 (13) ◽  
pp. 2000-2007 ◽  
Author(s):  
Diego Butera ◽  
Kristina M. Cook ◽  
Joyce Chiu ◽  
Jason W. H. Wong ◽  
Philip J. Hogg
Keyword(s):  
Amino Acid ◽  
Blood Cell ◽  
Blood Coagulation ◽  
Disulfide Bonds ◽  
Blood Proteins ◽  
Peptide Bonds ◽  
Major Mechanism ◽  
Chemically Modified ◽  
Amino Acid Side Chains ◽  
Core Features

Abstract Most proteins in nature are chemically modified after they are made to control how, when, and where they function. The 3 core features of proteins are posttranslationally modified: amino acid side chains can be modified, peptide bonds can be cleaved or isomerized, and disulfide bonds can be cleaved. Cleavage of peptide bonds is a major mechanism of protein control in the circulation, as exemplified by activation of the blood coagulation and complement zymogens. Cleavage of disulfide bonds is emerging as another important mechanism of protein control in the circulation. Recent advances in our understanding of control of soluble blood proteins and blood cell receptors by functional disulfide bonds is discussed as is how these bonds are being identified and studied.

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 ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Malaria Parasite ◽  
Secreted Proteins ◽  
Secretory Proteins ◽  
Dipeptide Composition ◽  
Malaria Vaccines ◽  
Growth And Reproduction

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.

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