TREND OF AMINO ACID COMPOSITION OF PROTEINS OF DIFFERENT TAXA

2006 ◽  
Vol 04 (02) ◽  
pp. 597-608 ◽  
Author(s):  
NATALYA S. BOGATYREVA ◽  
ALEXEI V. FINKELSTEIN ◽  
OXANA V. GALZITSKAYA
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Correlation Coefficient ◽  
Acid Composition ◽  
Amino Acid Compositions ◽  
Universal Genetic Code ◽  
Eukaryotic Proteins ◽  
Eukaryotic Proteomes ◽  
Random Frequency ◽  
Unstructured Proteins

Archaea, bacteria and eukaryotes represent the main kingdoms of life. Is there any trend for amino acid compositions of proteins found in full genomes of species of different kingdoms? What is the percentage of totally unstructured proteins in various proteomes? We obtained amino acid frequencies for different taxa using 195 known proteomes and all annotated sequences from the Swiss–Prot data base. Investigation of the two data bases (proteomes and Swiss–Prot) shows that the amino acid compositions of proteins differ substantially for different kingdoms of life, and this difference is larger between different proteomes than between different kingdoms of life. Our data demonstrate that there is a surprisingly small selection for the amino acid composition of proteins for higher organisms (eukaryotes) and their viruses in comparison with the "random" frequency following from a uniform usage of codons of the universal genetic code. On the contrary, lower organisms (bacteria and especially archaea) demonstrate an enhanced selection of amino acids. Moreover, according to our estimates, 12%, 3% and 2% of the proteins in eukaryotic, bacterial and archaean proteomes are totally disordered, and long (> 41 residues) disordered segments are found to occur in 16% of arhaean, 20% of eubacterial and 43% of eukaryotic proteins for 19 archaean, 159 bacterial and 17 eukaryotic proteomes, respectively. A correlation between amino acid compositions of proteins of various taxa, show that the highest correlation is observed between eukaryotes and their viruses (the correlation coefficient is 0.98), and bacteria and their viruses (the correlation coefficient is 0.96), while correlation between eukaryotes and archaea is 0.85 only.

scholarly journals Homologies in amino acid composition and structure of histone F2al isolated from human leukaemic cells

1970 ◽  
Vol 119 (2) ◽  
pp. 165-170 ◽  
Author(s):  
Laxman S. Desai ◽  
George E. Foley
Keyword(s):  
Gene Regulation ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Neoplastic Cells ◽  
Amino Acid Compositions ◽  
Composition And Structure ◽  
Leukaemic Cells ◽  
Rf Values ◽  
Similar Amino Acid

Histones F2al extracted from normal and neoplastic cells possess similar amino acid compositions. Tryptic and chymotryptic peptides of the F2al histones have identical chromato-electrophoretic RF values. It is concluded that histones F2al from various sources have similar overall structures. The observed differences in the ratios of ∈-N-monomethyl- and di-∈-N-methyl-lysine in the histones from normal and neoplastic cells may be of significance with respect to gene regulation.

scholarly journals Analysis of Heterodimeric “Mutual Synergistic Folding”-Complexes

2019 ◽  
Vol 20 (20) ◽  
pp. 5136 ◽  
Author(s):  
Mentes ◽  
Magyar ◽  
Fichó ◽  
Simon
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Intrinsically Disordered Proteins ◽  
Driving Forces ◽  
Disordered Proteins ◽  
Subunit Interactions ◽  
Amino Acid Compositions ◽  
Intrinsically Disordered ◽  
Β Sheet

Several intrinsically disordered proteins (IDPs) are capable to adopt stable structures without interacting with a folded partner. When the folding of all interacting partners happens at the same time, coupled with the interaction in a synergistic manner, the process is called Mutual Synergistic Folding (MSF). These complexes represent a discrete subset of IDPs. Recently, we collected information on their complexes and created the MFIB (Mutual Folding Induced by Binding) database. In a previous study, we compared homodimeric MSF complexes with homodimeric and monomeric globular proteins with similar amino acid sequence lengths. We concluded that MSF homodimers, compared to globular homodimeric proteins, have a greater solvent accessible main-chain surface area on the contact surface of the subunits, which becomes buried during dimerization. The main driving force of the folding is the mutual shielding of the water-accessible backbones, but the formation of further intermolecular interactions can also be relevant. In this paper, we will report analyses of heterodimeric MSF complexes. Our results indicate that the amino acid composition of the heterodimeric MSF monomer subunits slightly diverges from globular monomer proteins, while after dimerization, the amino acid composition of the overall MSF complexes becomes more similar to overall amino acid compositions of globular complexes. We found that inter-subunit interactions are strengthened, and additionally to the shielding of the solvent accessible backbone, other factors might play an important role in the stabilization of the heterodimeric structures, likewise energy gain resulting from the interaction of the two subunits with different amino acid compositions. We suggest that the shielding of the β-sheet backbones and the formation of a buried structural core along with the general strengthening of inter-subunit interactions together could be the driving forces of MSF protein structural ordering upon dimerization.

scholarly journals Studies of haemoglobin types in barbary sheep (Ammotragus lervia)

1968 ◽  
Vol 107 (6) ◽  
pp. 745-751 ◽  
Author(s):  
G. van Vliet ◽  
T. H. J. Huisman ◽  
G. A. Dasher ◽  
W. H. Moretz ◽  
A. M. Dozy ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Domestic Sheep ◽  
Amino Acid Residues ◽  
Amino Acid Compositions ◽  
Ammotragus Lervia ◽  
Peptide T ◽  
Barbary Sheep ◽  
Β Chain

1. Two haemoglobin types, haemoglobins Amm-C and Amm-B, were observed in five Barbary sheep (Ammotragus lervia). One animal was homozygous for haemoglobin Amm-C, a second was homozygous for haemoglobin Amm-B, and three were heterozygous for both. 2. Amino acid analyses of the globin from haemoglobin Amm-B showed that this type was related to, but not identical with, haemoglobin B of the domestic sheep. 3. The β-chain of haemoglobin Amm-C was found to be composed of 141 amino acid residues. Its amino acid composition differed from that of the βC-chain of the anaemic domestic sheep in at least 14 residues. The Amm-βC-chain contained one isoleucyl residue. 4. The amino acid compositions of tryptic peptides T-1, T-2, T-13 and T-14 of the Amm-βC-chain were similar to those of the sheep βC-chain. Peptides T-3, T-4, T-6, T-7, T-8, T-11 and T-15 were the same as the corresponding peptides of the sheep βA- and βC-chains. Peptide T-5 and to a smaller extent peptide T-9 resembled the corresponding peptides of the sheep βA-chain, and peptide T-10 was identical with peptide γT-10 of sheep haemoglobin F. Peptide T-12 was not recovered. 5. The results of these investigations were interpreted as being indicative that the structural Amm-βC-gene is closely related to the βC-gene of sheep, from which through domestication the present domestic sheep originated.

scholarly journals Pathway-Specific Protein Domains (PSPD) Discrimination by Using a Hybrid Feature Space Based on Deep Neural Network(DNN)

2020 ◽  
Author(s):  
Ali Ghulam ◽  
XiuJuan Lei ◽  
Yuchen Zhang ◽  
Zhenqiang Wu
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Correlation Coefficient ◽  
Acid Composition ◽  
Deep Neural Network ◽  
Protein Domains ◽  
Specific Protein ◽  
Matthew’S Correlation Coefficient

Abstract The Pathway-specific protein domains (PSPDs) are important tools in examining drug growth as they provide a fast, reliable, and inexpensive way of estimating complex new molecular targets in specific diseases. The protein architecture prevents the formation of a direct correlation between signal transduction behavior and cellular structure. Accordingly, protein–tissue factor pathway inhibitor 2 isotypes 1 precursors have been used to encode peptide sequence information into specific feature structures. The measurable structure-activity classification model obtained by machine learning technology can predict pathway-specific protein interactions and new signaling peptides. We introduce deep neural network (DNN)-based PSPDs, abbreviated as DNNPSPDs, as the first pathway-specific protein domain that is built based on five extant models, namely, the AAindex, pseudo-amino acid composition, amino acid composition, composition mood of pseudoamino acids, and dipeptide composition. A total of 900 proteins with undetermined roles collected from the PDB data base are tested to evaluate the predictive power of this model. Various combinations of the available feature selection technologies are also combined to process a hybrid function space. DNNPSPDs predicts PSPDs by using features that are automatically learned from primary protein sequences. The sequences of pathway-associated proteins are sequentially fed into and decoded in neural network layers. Several classifications are also employed. DNNPSPDs achieves a prediction accuracy of 0.957 at a Matthew’s correlation coefficient (MCC) of 91.86%, with DPC, and 2nd achieve high prediction score 0.936 at Matthew’s correlation coefficient (MCC) of 88.02%, accuracy which is probably better. In terms of ROC–AUC, DNNPSPDs achieves a ROC–AUC curve of 0.982, which is larger than that of the other machine learning classifiers. A study using an alternative dataset reveals that our primary pathways, as pathway-specific protein domains, have accurate and reliable associations, thereby proving the viability of the proposed DNNPSPDs.

Carboxylesterases (EC 3.1.1). Amino Acid Composition of Liver Carboxylesterases

1975 ◽  
Vol 53 (5) ◽  
pp. 561-564 ◽  
Author(s):  
Keith Scott ◽  
Burt Zerner
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Homologous Series ◽  
Evolutionary History ◽  
Amino Acid Compositions ◽  
General Similarity ◽  
History Of

The amino acid compositions of the carboxylesterases from chicken, horse, ox, sheep, and pig livers are reported and compared. As would be expected for this homologous series, the compositions show a general similarity. However, there are some significant differences, but the degree to which particular pairs of enzymes differ is consistent with the evolutionary history of the species from which they were isolated.

The isolation and properties of 1·6 S γ -histone from calf thymocytes

1958 ◽  
Vol 149 (934) ◽  
pp. 36-41 ◽  
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Physicochemical Properties ◽  
Amino Acid Composition ◽  
High Molecular Weight ◽  
Acid Composition ◽  
The Other ◽  
Amino Acid Compositions

The isolation of 1·6 S γ -histone is described, its amino-acid composition recorded and an account given of some of its physicochemical properties. Its molecular weight has been calculated from sedimentation velocities to be 74000 in its unaggregated condition. It thus represents a second histone of high molecular weight present in the nuclei of calf thymocytes. Both β and 1·6 S γ -histone are distinguished from the other four components in their ability to undergo aggregation. The γ -histone, however, does not aggregate so readily or so extensively as does β -histone. These two histones are also clearly distinguished by their amino-acid compositions.

Amino acid composition of sperm histones in the house cricket Acheta domesticus

1976 ◽  
Vol 54 (1) ◽  
pp. 56-61 ◽  
Author(s):  
Dominick Pallotta ◽  
Anne Tessier
Keyword(s):  
Amino Acid ◽  
Glutamic Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Acheta Domesticus ◽  
House Cricket ◽  
Amino Acid Compositions ◽  
Calf Thymus ◽  
The Individual

Histones were isolated from late spermatids and spermatozoa of the house cricket Acheta domesticus, and the individual histone fractions were separated by electrophoresis on polyacrylamide–urea gels. The stained gels were cut so as to isolate the different histone fractions, and the amino acid compositions were determined using the technique of Houston (Houston, L. L.: Anal. Biochem. 44, 81–88 (1971)). Five of the histones had amino acid compositions resembling those for the histones of calf thymus and were thus identified as fractions F1, F3, F2a2, F2b, and F2a1. Another protein (SH) located exclusively in the late spermatids and spermatozoa was found to be basic and histone-like. It is a protein containing relatively high amounts of arginine (12.6%) and low amounts of lysine (7.6%), and, as a result, it has a low ratio of lysine–arginine (0.6). Other noteworthy features are its high contents of serine, glutamic acid, and glycine. It is an arginine rich histone and in this regard resembles other such proteins, but it does contain unique features which distinguish it from all previously described histones.

scholarly journals THE AMINO ACID COMPOSITION AND SOME PROPERTIES OF HISTONES

1951 ◽  
Vol 34 (4) ◽  
pp. 439-450 ◽  
Author(s):  
Marie M. Daly ◽  
A. E. Mirsky ◽  
Hans Ris
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Amino Acid Compositions ◽  
Calf Thymus ◽  
Sperm Chromosomes

Some of the properties and the amino acid compositions of the histones of calf thymus, calf liver, fowl erythrocytes, and of a protamine-like material isolated from rooster sperm were described. The amino acid compositions of the histones were rather similar except that no methionine was found in the fowl erythrocyte histone. In the fowl, histones are found in the somatic chromosomes and protamines are found in the sperm chromosomes. This shows that great variations in chromosome composition can exist in an organism. Histone is digested by pepsin both when isolated and when in the chromosome.

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