ChemInform Abstract: SYNTHESIS AND ATTRACTIVE PROPERTIES OF PEPTIDES CONTAINING AMINO ACID RESIDUES OF VALINE, PHENYLALANINE, PROLINE, AND GLUTAMIC ACID

1980 ◽  
Vol 11 (37) ◽  
Author(s):  
N. YA. KRASNOBRIZHII ◽  
E. M. SKRYNIK ◽  
L. G. KOVALENKO
Keyword(s):  
Amino Acid ◽  
Glutamic Acid ◽  
Amino Acid Residues

scholarly journals Analysis of proteolytic processing sites in potyvirus polyproteins revealed differential amino acid preferences of NIa-Pro protease in each of seven cleavage sites

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245853
Author(s):  
Chul Jun Goh ◽  
Yoonsoo Hahn
Keyword(s):  
Amino Acid ◽  
Glutamic Acid ◽  
Cleavage Site ◽  
Proteolytic Processing ◽  
Cleavage Sites ◽  
Amino Acid Residues ◽  
Consensus Sequences ◽  
Polyprotein Processing ◽  
Potyvirus Species ◽  
Consensus Amino Acid

Potyviruses encode a large polyprotein that undergoes proteolytic processing, producing 10 mature proteins: P1, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb-RdRp, and CP. While P1/HC-Pro and HC-Pro/P3 junctions are cleaved by P1 and HC-Pro, respectively, the remaining seven are processed by NIa-Pro. In this study, we analyzed 135 polyprotein sequences from approved potyvirus species and deduced the consensus amino acid residues at five positions (from −4 to +1, where a protease cleaves between −1 and +1) in each of nine cleavage sites. In general, the newly deduced consensus sequences were consistent with the previous ones. However, seven NIa-Pro cleavage sites showed distinct amino acid preferences despite being processed by the same protease. At position −2, histidine was the dominant amino acid residue in most cleavage sites (57.8–60.7% of analyzed sequences), except for the NIa-Pro/NIb-RdRp junction where it was absent. At position −1, glutamine was highly dominant in most sites (88.2–97.8%), except for the VPg/NIa-Pro junction where glutamic acid was found in all the analyzed proteins (100%). At position +1, serine was the most abundant residue (47.4–86.7%) in five out of seven sites, while alanine (52.6%) and glycine (82.2%) were the most abundant in the P3/6K1 and 6K2/VPg junctions, respectively. These findings suggest that each NIa-Pro cleavage site is finely tuned for differential characteristics of proteolytic reactions. The newly deduced consensus sequences may be useful resources for the development of models and methods to accurately predict potyvirus polyprotein processing sites.

scholarly journals Results supporting the concept of the oxidant-mediated protein amino acid conversion, a naturally occurring protein engineering process, in human cells

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 594
Author(s):  
Yuichiro J. Suzuki ◽  
Jian-Jiang Hao
Keyword(s):  
Amino Acid ◽  
Protein Engineering ◽  
Glutamic Acid ◽  
Human Cells ◽  
Amino Acid Residues ◽  
Engineering Process ◽  
Protein Amino Acid ◽  
Peroxiredoxin 6 ◽  
Naturally Occurring ◽  
Cultured Human Cells

Reactive oxygen species (ROS) play an important role in the development of various pathological conditions as well as aging. ROS oxidize DNA, proteins, lipids, and small molecules. Carbonylation is one mode of protein oxidation that occurs in response to the iron-catalyzed, hydrogen peroxide-dependent oxidation of amino acid side chains. Although carbonylated proteins are generally believed to be eliminated through degradation, we previously discovered the protein de-carbonylation mechanism, in which the formed carbonyl groups are chemically eliminated without proteins being degraded. Major amino acid residues that are susceptible to carbonylation include proline and arginine, both of which are oxidized to become glutamyl semialdehyde, which contains a carbonyl group. The further oxidation of glutamyl semialdehyde produces glutamic acid. Thus, we hypothesize that through the ROS-mediated formation of glutamyl semialdehyde, the proline, arginine, and glutamic acid residues within the protein structure can be converted to each other. Mass spectrometry provided results supporting that proline 45 (a well-conserved residue within the catalytic sequence) of the peroxiredoxin 6 molecule may be converted into glutamic acid in cultured human cells, opening up a revolutionizing concept that biological oxidation elicits the naturally occurring protein engineering process.

Conformation of branched polypeptides based on poly(L-lysine): The effect of terminal amino acids in the branches

1985 ◽  
Vol 50 (1) ◽  
pp. 228-244 ◽  
Author(s):  
Hana Votavová ◽  
Ferenc Hudecz ◽  
Judit Kajtár ◽  
Jaroslav Šponar ◽  
Karel Bláha ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Ionic Strength ◽  
Glutamic Acid ◽  
Amino Acid Residues ◽  
Ordered Structure ◽  
Cd Spectra ◽  
Helix Formation ◽  
Terminal Amino ◽  
Α Helix

CD Spectra of branched polypeptides based on poly(L-lysine) and containing three DL-alanine residues and one to three other L- or D-amino acid residues in the branches were measured in water, water-methanol and water-trifluoroethanol mixtures. In aqueous solutions dependence of the CD spectra on pH and ionic strength was studied. The effect of branch elongation was followed mainly with compounds containing glutamic acid. One terminal D-amino acid residue and also an extension by two L- or D-amino acid residues does not hinder the α-helix formation in the backbone but affects the conditions of its formation. In polypeptides with three L- or D-amino acids additional α-helical segments in the branches are assumed to be formed. For branches with L-amino acids the CD curves express additively the contributions of both helical components, in the case of D-amino acids the increasing population of the ordered structure in branches is manifested by compensation of dichroic contribution of the L-amino acid backbone leading even to enantiomorphous curves.

scholarly journals Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Tatyana Aleksandrovna Khrustaleva
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Glutamic Acid ◽  
Gc Content ◽  
Alpha Helix ◽  
Random Coil ◽  
Amino Acid Residues ◽  
Alpha Helices ◽  
Beta Strand ◽  
Genomic Gc Content

3D structures of proteins with coordinated Mn2+ ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used). Major Mn2+ binders are aspartic acid (6.82% of Asp residues), histidine (14.76% of His residues), and glutamic acid (3.51% of Glu residues). We found out that the motif of secondary structure “beta strand-major binder-random coil” is overrepresented around all the three major Mn2+ binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn2+ ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn2+ sites with at least one amino acid in the “beta strand-major binder-random coil” motif of secondary structure (77.88%) does not depend on genomic GC-content.

Monospecificity of the antibodies to bovine αs1-casein fragment 140–149: application to the detection of bovine milk in caprine dairy products

1995 ◽  
Vol 62 (1) ◽  
pp. 83-88 ◽  
Author(s):  
Marie-Paule Rolland ◽  
Lotfi Bitri ◽  
Pierre Besançon
Keyword(s):  
Amino Acid ◽  
Glutamic Acid ◽  
Dairy Products ◽  
Polyclonal Antibodies ◽  
Bovine Milk ◽  
Amino Acid Residues ◽  
Native Protein ◽  
Glutamic Acid Residue ◽  
Antigen Complex ◽  
Single Difference

SUMMARYComparison of the primary sequences of bovine, ovine and caprine αs1-casein shows a deletion of eight amino acid residues in the ovine casein region 141–148, which is identical in the bovine and caprine proteins except for a single difference in position 148 (Q or E). Polyclonal antibodies raised in rabbits against the bovine casein sequence 140–149 (QELAYFYPEL) appeared monospecific for bovine αsl-casein, since no antibody-antigen complex was formed with homologous ovine or caprine proteins. These antibodies remained unable to recognize the caprine sequence in the native protein even after extensive tryptic proteolysis. The lack of immunoreactivity of the antibodies against synthetic caprine αsl-casein peptide 138–149 (VNQELAYFYPQL) suggested that the glutamic acid residue in position 148 is essential for the antigenic character of the bovine peptide. From these observations, the use of these antibodies for the detection and quantitation of bovine milk present in ovine dairy products could be extended to caprine products.

α-Glutamic acid-β-naphthylamidase from Neisseria catarrhalis

1969 ◽  
Vol 15 (11) ◽  
pp. 1293-1300 ◽  
Author(s):  
Sidney T. Cox ◽  
Francis J. Behal
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Glutamic Acid ◽  
Metal Ion ◽  
Gel Filtration ◽  
Aminopeptidase Activity ◽  
Amino Acid Residues ◽  
Ph Optimum ◽  
Hydrolysis Of ◽  
Derivatives Of

A second bacterial peptidase-like enzyme, arylamidase-II, has been isolated from cell free extracts of Neisseria catarrhalis. Arylamidase-II action is limited primarily to the hydrolysis of α-glutamic acid and α-aspartic acid derivatives of β-naphthylamine and short peptides of glutamic acid. The enzyme was purified 450-fold by gel filtration, ion exchange, and calcium phosphate chromatography. Its pH optimum and molecular weight were 7.7 and 170 000, respectively. Aside from its restricted substrate specificity, arylamidase-II has been found to be closely related in its mechanism of action, molecular weight, pH optimum, and metal ion dependence to arylamidase-I, which catalyzes the hydrolysis of neutral amino acid derivatives of β-naphthylamine. Arylamidase-II exhibits aminopeptidase activity, requiring the amino acid residues in the N-terminal and penultimate position to be of the L-configuration in order for hydrolysis to occur.

scholarly journals Glutamine as a precursor to N-terminal pyrrolid-2-one-5-carboxylic acid in mouse immunoglobulin λ-type light chains. Amino acid-sequence variability at the N-terminal extra piece of λ-type light-chain precursors

1977 ◽  
Vol 165 (2) ◽  
pp. 347-354 ◽  
Author(s):  
Yigal Burstein ◽  
Israel Schechter
Keyword(s):  
Amino Acid ◽  
Carboxylic Acid ◽  
Amino Acid Sequence ◽  
Glutamic Acid ◽  
Sequence Data ◽  
Amino Acid Residues ◽  
Sequence Analyses ◽  
Methionine Residue ◽  
Mouse Immunoglobulin ◽  
V Region

The mRNA molecules coding for three mouse immunoglobulin λ-type light (L) chains (MOPC-104E λ1, RPC-20 λ1, MOPC-315 λ2) programme the cell-free synthesis of precursors larger than the mature proteins. Radioactive amino acid-sequence analyses of each of the three precursors labelled with [3H]alanine, [3H]serine, [3H]glutamine, [3H]glutamic acid and [3H]threonine showed that an extra piece, at least 18 residues long, is linked to the N-terminus of the mature L-chains. The N-terminal extra-peptide segment may be 19 residues long, since analyses of precursors labelled with [35S]methionine indicated an additional N-terminal methionine residue which was recovered in low yields. Presumably this is the initiator methionine, which is known to be short lived in eukaryotes. The mature forms of MOPC-104E, RPC-20 and MOPC-315 λ L-chains are blocked at the N-termini by pyrrolid-2-one-5-carboxylic acid (pyroglutamic acid). Sequence analyses of precursors labelled with [3H]glutamine and [3H]glutamic acid showed incorporation only of glutamine in a position that matches with the position of pyrrolid-2-one-5-carboxylic acid in the mature forms of all three precursors, and incorporation of glutamic acid in other positions. The data showed the absence of glutamine–glutamic acid interconversion, since the radioactive peaks obtained from either3H-labelled amino acid were discrete, and free from cross-contamination. These results prove that glutamine is the precursor amino acid of pyrrolid-2-one-5-carboxylic acid at the N-termini of the mature MOPC-104E λ1, RPC-20 λ1 and MOPC-315 λ2 L-chains. Thus the formation of pyrrolid-2-one-5-carboxylic acid by cyclization of glutamine is a post-translational event which occurs after, or concomitant with, cleavage of the extra piece from the precursor to yield the mature L-chain. The variable (V) regions (110 amino acid residues) of mouse λ L-chains are quite similar: when compared with that of MOPC-104E λ1 chain, the V-region of RPC-20 λ1 chain differs in one residue, and the V-region of MOPC-315 λ2 chain differs in 11 residues. The partial sequence data show that the N-terminal extra pieces of the two λ1 L-chain precursors have, so far, identical partial sequences; the extra piece of the λ2 L-chain precursor differs from these in at least three out of 19 positions.

Effect of Glycylglycine on Absorption from Human Jejunum of an Amino Acid Mixture Simulating Casein and a Partial Enzymic Hydrolysate of Casein Containing Small Peptides

1977 ◽  
Vol 53 (1) ◽  
pp. 27-33
Author(s):  
P. D. Fairclough ◽  
D. B. A. Silk ◽  
M. L. Clark ◽  
D. M. Matthews ◽  
T. C. Marrs ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Glutamic Acid ◽  
Free Amino Acids ◽  
Free Amino ◽  
Amino Acid Mixture ◽  
Acid Mixture ◽  
Acid Uptake ◽  
Amino Acid Residues ◽  
Small Peptides

1. A jejunal perfusion technique has been used in normal volunteer subjects to study jejunal absorption of amino acid residues from a partial enzymic hydrolysate of casein in which about 50% of the amino acids existed as small peptides, and also from an equivalent mixture of free amino acids. 2. The effect of a high concentration of the dipeptide glycylglycine on the absorption of amino acid residues from these preparations was studied to quantify the importance of mucosal uptake of intact peptides during absorption of the partial hydrolysate of casein. 3. The results were unexpected. Glycylglycine significantly inhibited absorption of several amino acid residues (aspartic acid + asparagine, serine, glutamic acid + glutamine, proline, alanine, phenylalanine, threonine and isoleucine) from the free amino acid mixture, whereas it significantly inhibited the absorption of only two (serine, glutamic acid + glutamine) from the peptide-containing partial casein hydrolysate. 4. The effect of glycylglycine on absorption of amino acids from the mixture of free amino acids was apparently due to inhibition of amino acid uptake by free glycine liberated from the dipeptide during perfusion. The reason for the failure of glycylglycine to cause extensive inhibition of absorption from the partial hydrolysate is not clear. It may be due to glycylglycine being only a weak inhibitor of peptide uptake, but the possibility that some peptides are taken up by a system unavailable to glycylglycine has to be considered.

scholarly journals Evidence for the oxidant-mediated amino acid conversion, a naturally occurring protein engineering process, in human cells

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 594 ◽  
Author(s):  
Yuichiro J. Suzuki ◽  
Jian-Jiang Hao
Keyword(s):  
Amino Acid ◽  
Protein Engineering ◽  
Glutamic Acid ◽  
Human Cells ◽  
Amino Acid Residues ◽  
Engineering Process ◽  
Peroxiredoxin 6 ◽  
Naturally Occurring ◽  
Cultured Human Cells ◽  
Major Amino Acid

Reactive oxygen species (ROS) play an important role in the development of various pathological conditions as well as aging. ROS oxidize DNA, proteins, lipids, and small molecules. Carbonylation is one mode of protein oxidation that occurs in response to the iron-catalyzed, hydrogen peroxide-dependent oxidation of amino acid side chains. Although carbonylated proteins are generally believed to be eliminated through proteasome-dependent degradation, we previously discovered the protein de-carbonylation mechanism, in which the formed carbonyl groups are chemically eliminated without proteins being degraded. Major amino acid residues that are susceptible to carbonylation include proline and arginine, both of which are oxidized to become glutamyl semialdehyde, which contains a carbonyl group. The further oxidation of glutamyl semialdehyde produces glutamic acid. Thus, we hypothesize that through the ROS-mediated formation of glutamyl semialdehyde, the proline, arginine, and glutamic acid residues within the protein structure are interchangeable. In support of this hypothesis, mass spectrometry demonstrated that proline 45 (a well-conserved residue within the catalytic sequence) of the peroxiredoxin 6 molecule can be converted into glutamic acid in cultured human cells, establishing a revolutionizing concept that biological oxidation elicits the naturally occurring protein engineering process.

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