scholarly journals Virtual 2-D map of the fungal proteome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Awdhesh Kumar Mishra ◽  
Adil Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd-Allah ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Isoelectric Point ◽  
Synonymous Codon ◽  
Average Molecular Weight ◽  
Protein Sequences ◽  
Bimodal Distribution ◽  
Fungal Proteome ◽  
Fungal Kingdom ◽  
Abundant Amino Acid

AbstractThe molecular weight and isoelectric point (pI) of the proteins plays important role in the cell. Depending upon the shape, size, and charge, protein provides its functional role in different parts of the cell. Therefore, understanding to the knowledge of their molecular weight and charges is (pI) is very important. Therefore, we conducted a proteome-wide analysis of protein sequences of 689 fungal species (7.15 million protein sequences) and construct a virtual 2-D map of the fungal proteome. The analysis of the constructed map revealed the presence of a bimodal distribution of fungal proteomes. The molecular mass of individual fungal proteins ranged from 0.202 to 2546.166 kDa and the predicted isoelectric point (pI) ranged from 1.85 to 13.759 while average molecular weight of fungal proteome was 50.98 kDa. A non-ribosomal peptide synthase (RFU80400.1) found in Trichoderma arundinaceum was identified as the largest protein in the fungal kingdom. The collective fungal proteome is dominated by the presence of acidic rather than basic pI proteins and Leu is the most abundant amino acid while Cys is the least abundant amino acid. Aspergillus ustus encodes the highest percentage (76.62%) of acidic pI proteins while Nosema ceranae was found to encode the highest percentage (66.15%) of basic pI proteins. Selenocysteine and pyrrolysine amino acids were not found in any of the analysed fungal proteomes. Although the molecular weight and pI of the protein are of enormous important to understand their functional roles, the amino acid compositions of the fungal protein will enable us to understand the synonymous codon usage in the fungal kingdom. The small peptides identified during the study can provide additional biotechnological implication.

scholarly journals Virtual 2D mapping of the viral proteome reveals host-specific modality distribution of molecular weight and isoelectric point

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Awdhesh Kumar Mishra ◽  
Yugal Kishore Mohanta ◽  
Ahmed Al-Harrasi
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Isoelectric Point ◽  
Viral Proteins ◽  
Bimodal Distribution ◽  
Bacterial Host ◽  
Protein Coding ◽  
Specific Amino Acid ◽  
Vertebrate Hosts

AbstractA proteome-wide study of the virus kingdom based on 1.713 million protein sequences from 19,128 virus proteomes was conducted to construct an overall proteome map of the virus kingdom. Viral proteomes encode an average of 386.214 amino acids per protein with the variation in the number of protein-coding sequences being host-specific. The proteomes of viruses of fungi hosts (882.464) encoded the greatest number of amino acids, while the viral proteome of bacterial host (210.912) encoded the smallest number of amino acids. Viral proteomes were found to have a host-specific amino acid composition. Leu (8.556%) was the most abundant and Trp (1.274%) the least abundant amino acid in the collective proteome of viruses. Viruses were found to exhibit a host-dependent molecular weight and isoelectric point of encoded proteins. The isoelectric point (pI) of viral proteins was found in the acidic range, having an average pI of 6.89. However, the pI of viral proteins of algal (pI 7.08) and vertebrate (pI 7.09) hosts was in the basic range. The virtual 2D map of the viral proteome from different hosts exhibited host-dependent modalities. The virus proteome from algal hosts and archaea exhibited a bimodal distribution of molecular weight and pI, while the virus proteome of bacterial host exhibited a trimodal distribution, and the virus proteome of fungal, human, land plants, invertebrate, protozoa, and vertebrate hosts exhibited a unimodal distribution.

Series of sequential polypeptides containing lysine or arginine: Preparation and characterization

1988 ◽  
Vol 53 (1) ◽  
pp. 145-156 ◽  
Author(s):  
Jana Pírková ◽  
Svetlana Churkina ◽  
Vladimír Gut ◽  
Ivo Frič ◽  
Karel Bláha
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Peptide Synthesis ◽  
Average Molecular Weight ◽  
Basic Amino Acid ◽  
Cd Spectra ◽  
Active Esters ◽  
Marked Tendency

The sequential polypeptides (Lys-Ala)n, (Lys-Ala-Ala)n, (Lys-Ala-Ala-Ala)n, (Lys-Leu-Ala)n, (Lys-Leu-Ala-Ala)n, (Lys-Leu-Ala-Ala-Ala)n, (Lys-Ala-Leu)n, (Lys-Ala-Leu-Ala)n, (Orn-Leu-Ala)n,(Arg-Ala-Ala)n, (Arg-Leu-Ala)n, (Arg-Leu-Ala-Ala)n, (Arg-Ala-Leu)n, and (Arg-Ala-Leu-Ala)n were synthesized by polymerization of active esters (1-succinimidyl or pentafluorophenyl) of the corresponding Nα-deblocked monomers. The monomers were prepared using the usual methods of peptide synthesis in solution. Upon dialysis, the average molecular weight of the polymer was 6 000-9 000 as determined by sedimentation in ultracentrifuge. Polypeptides, containing leucine in addition to the basic amino acid, showed a marked tendency to aggregation. CD spectra of the products were measured for characterization.

scholarly journals Purification and Properties of Staphylocoagulase

1975 ◽  
Author(s):  
A.D. Muller ◽  
B. M. Bas ◽  
H. C. Hemker
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Aspartic Acid ◽  
Acid Composition ◽  
Isoelectric Point ◽  
Terminal Amino Acid ◽  
Purification And Properties ◽  
Terminal Amino

Staphylocoagulase, an exoprotein of coagulase positive staphylocoagulase, has been purified to a state in which only trace amounts of contaminating proteins are detectable.Purification was more than 35,000 fold, which is 7 times more than the highest value reported in the literature. The yield was about 15%.Aspartic acid was found as a single N-terminal amino acid in this preparation. The molecular weight is 61,000 and the isoelectric point lies at pH 4.53.The amino acid composition was determined.

scholarly journals The Molecular Mass and Isoelectric Point of Plant Proteomes

2019 ◽  
Author(s):  
Tapan Kumar Kumar Mohanta ◽  
Abdulatif Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
Ahmed Al-Harrasi
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Molecular Mass ◽  
Plant Species ◽  
Isoelectric Point ◽  
Polyketide Synthase ◽  
Type I ◽  
Plant Proteins ◽  
Higher Plant

Abstract Background Cell contain diverse array of proteins with different molecular weight and isoelectric point (pI). The molecular weight and pI of protein play important role in determining the molecular biochemical function. Therefore, it was important to understand the detail regarding the molecular weight and pI of the plant proteins. Results A proteome-wide analysis of plant proteomes from 145 species revealed a pI range of 1.99 (epsin) to 13.96 (hypothetical protein). The spectrum of molecular mass of the plant proteins varied from 0.54 to 2236.8 kDa. A putative Type-I polyketide synthase (22244 amino acids) in Volvox carteri was found to be the largest protein in the plant kingdom. However, Type-I polyketide synthase was not found in higher plant species. Titin (806.46 kDa) and misin/midasin (730.02 kDa) were the largest proteins identified in higher plant species. The pI and molecular weight of the plant proteins showed a trimodal distribution. An acidic pI (56.44% of proteins) was found to be predominant over a basic pI (43.34% of proteins) and the abundance of acidic pI proteins was higher in unicellular algae species relative to multicellular higher plants. In contrast, the seaweed, Porphyra umbilicalis, possesses a higher proportion of basic pI proteins (70.09%). Plant proteomes were also found to contain selenocysteine (Sec), amino acid that was found only in lower eukaryotic aquatic plant lineage. Amino acid composition analysis showed Leu was high and Trp was low abundant amino acids in the plant proteome. Additionally, the plant proteomes also possess ambiguous amino acids Xaa (unknown), Asx (asparagine or aspartic acid), Glx (glutamine or glutamic acid), and Xle (leucine or isoleucine) as well. Conclusion The diverse molecular weight and isoelectric point range of plant proteome will be helpful to understand their biochemical and functional aspects. The presence of selenocysteine proteins in lower eukaryotic organism is of interest and their expression in higher plant system can help us to understand their functional role.

Protein

1995 ◽  
Author(s):  
Roland Lüthy ◽  
David Eisenberg
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Isoelectric Point ◽  
Extinction Coefficient ◽  
Titration Curve ◽  
Side Chains ◽  
Pka Values ◽  
Extinction Coefficients ◽  
Molecular Weights

Given a protein sequence, the amino acid composition can be determined by counting the number of residues of each type. Then a molecular weight can be calculated by summing the molecular weights of the individual amino acid residues, taking into account the loss of one H2O molecule per peptide bond. Table 1 lists the molecular weights of the twenty amino acids and water. This approach assumes that the protein has not been covalently modified. Because of extensive glycosylation of some proteins, this approach can significantly underestimate the actual molecular weight. With the pKa values of Table 1, it is possible to calculate the theoretical charge of a protein at a given pH by summing the charges of the amino acid side chains and of the amino terminus and carboxyl terminus. By performing this calculation over a pH range, one obtains a theoretical titration curve and an isoelectric point (the pH at which the protein hasanetchargeof zero). This method assumes that all normally titratable groups are accessible to water, and that all side chains have the intrinsic pKa values listed in Table 1. This assumption is not completely correct, and consequently, the theoretical isoelectric point may differ from the experimentally determined value. Figure 1 shows the calculated titration curve for pancreatic ribonuclease: the calculated isoelectric point is 8.2, whereas the measured value is 9.6 (Lehninger, 1977). The calculation of extinction coefficients (Gill and von Hippel, 1989) is performed in much the same way as that of the isoelectric point Individual residues are treated as if they are free amino acids, and the overall extinction coefficient is calculated as the sum of the extinction coefficients of the residues. The same basic assumption is made: Residues are assumed to be in typical environments and not to show unusual absorption due to their local environments. In the case of the extinction coefficient, however, this assumption seems to be generally acceptable; calculated extinction coefficients are typically within a few percent of the experimentally determined value, and errors of more than 15% are rare (Gill and von Hippel, 1989).

scholarly journals The sialic acid content and isoelectric point of human kininogen

1975 ◽  
Vol 145 (2) ◽  
pp. 401-403 ◽  
Author(s):  
J C Londesborough ◽  
U Hamberg
Keyword(s):  
Molecular Weight ◽  
Sialic Acid ◽  
Amino Acid ◽  
Isoelectric Point ◽  
Acid Content ◽  
Low Molecular Weight ◽  
Sialic Acid Content

The sialic acid content of highly purified human kininogen was found to be about 8.6 mol/mol(mol.wt. 50,000). The isoelectric point (pH 4.9 +/- 0.2) is much higher than that of bovine low-molecular-weight kininogen, but is close to that expected from the amino acid and sialic acid analyses.

Amino Acid Sequence of the Small Subunit of Ribulose-1,5-Bisphosphate Carboxylase from Spinach

1979 ◽  
Vol 6 (3) ◽  
pp. 401
Author(s):  
P.G Martin
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Data ◽  
Average Molecular Weight ◽  
Small Subunit ◽  
Bisphosphate Carboxylase ◽  
N Terminus ◽  
Proline Substitution ◽  
Ribulosebisphosphate Carboxylase

The complete amino acid sequence of the small subunit of ribulosebisphosphate carboxylase from spinach has been determined. There are 120 amino acids. The N-terminus of the protein is frequently blocked. There is a tyrosine-proline substitution at position 91 and the average molecular weight of the two forms is 13 897. The interest of the sequence data for students of physiology and evolution is discussed.

Structural study on liver gelactin

1984 ◽  
Vol 62 (11) ◽  
pp. 1072-1075 ◽  
Author(s):  
Julian Gruda ◽  
Hélène-Marie Thérien
Keyword(s):  
Electron Microscopy ◽  
Molecular Weight ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Structural Study ◽  
Isoelectric Focusing ◽  
Isoelectric Point ◽  
Gel Filtration ◽  
Rabbit Liver

Electron microscopy, ultracentrifugation, gel filtration, and isoelectric focusing were carried out with gelactin, an actin-gelling protein from rabbit liver. Gelactin is a dimeric acidic protein (isoelectric point (pI) = 5.45), with a molecular weight of 190 000, a Svedberg constant of 6.25, and a Stoke's radius and length of 7.0 and 28 nm, respectively. While different from α-actinin by pI and amino acid composition, gelactin belongs by its dimensions to the class of α-actinins.

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