Constructing a Syntheses Table of the Standard Amino Acid Based on the PAM250 Matrix

2011 ◽  
Vol 335-336 ◽  
pp. 1279-1284
Author(s):  
Xiao Hong Shi ◽  
Xiang Hong Wang
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Physicochemical Properties ◽  
Side Chain ◽  
Side Chains ◽  
Chemical Structures ◽  
Naturally Occurring ◽  
Standard Amino Acid ◽  
Similar Amino Acid

It is well known that there are some similarities among various naturally occurring amino acids. The standard amino acids have been grouped by their general properties and the chemical structures of their side chains. In this paper we divided the molecular weight of amino acid into two parts: backbone molecular weight Mband side chain molecular weight Ms. We naturally grouped the amino acids into two sets according to the rate of Ms/ Mb. We developed a method to construct a syntheses table to reflect the relevant physicochemical properties based on the PAM250 matrix and successfully established an elegant table of the twenty amino acids. Our work proved that PAM250 matrix could be used not only in finding reasonable alignments but also in grouping similar amino acid.

Synthesis and evaluation of chiral β-amino acid-based low-molecular-weight organogelators possessing a methyl/trifluoromethyl side chain

2019 ◽  
Vol 43 (7) ◽  
pp. 2882-2887 ◽  
Author(s):  
Koichi Kodama ◽  
Ryuta Kawamata ◽  
Takuji Hirose
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Supramolecular Structures ◽  
Side Chain ◽  
Low Molecular Weight ◽  
Side Chains ◽  
Low Molecular Weight Organogelators

Impacts of side-chains and chirality of organogelators derived from β-amino acids are described with their supramolecular structures.

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).

Molecular aggregation in crystalline 1:1 complexes of hydrophobic D- and L-amino acids. I. The L-isoleucine series

1999 ◽  
Vol 55 (3) ◽  
pp. 424-431 ◽  
Author(s):  
Bjørn Dalhus ◽  
Carl Henrik Görbitz
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aminobutyric Acid ◽  
Side Chain ◽  
Side Chains ◽  
Amino Acid Side Chain ◽  
Molecular Aggregation ◽  
Plane Symmetry ◽  
Hydrogen Bond Pattern ◽  
Polar Parts

The amino acid L-isoleucine has been cocrystallized with seven selected D-amino acids including D-methionine [L-isoleucine–D-methionine (1/1), C6H13NO2.C5H11NO2S, amino-acid side chain R = —CH2—CH2—S—CH3] and a homologous series from D-alanine [L-isoleucine–D-alanine (1/1), C6H13NO2.C3H7NO2, R = —CH3] through D-α-aminobutyric acid [L-isoleucine–D-α-aminobutyric acid (1/1), C6H13NO2.C4H9NO2, R = —CH2—CH3] and D-norvaline [L-isoleucine–D-norvaline (1/1), C6H13NO2.C5H11NO2, R = —CH2—CH2—CH3] to D-norleucine [L-isoleucine–D-norleucine (1/1), C6H13NO2.C6H13NO2, R = —CH2—CH2—CH2—CH3] with linear side chains, and D-valine [L-isoleucine–D-valine (1/1), C6H13NO2.C5H11NO2, R = —CH—(CH3)2] and D-leucine [L-isoleucine–D-leucine (1/1), C6H13NO2.C6H13NO2, R = —CH2—CH—(CH3)2] with branched side chains. All the crystal structures are divided into distinct hydrophilic and hydrophobic layers. In the five complexes with amino acids with linear side chains the polar parts of the D- and L-amino acids are related by pseudo-glide-plane symmetry, and four of them have remarkably similar molecular arrangements. The D-valine and D-leucine complexes, on the other hand, are structurally quite different with the polar parts of the D- and L-amino acids related by pseudo-inversion. Differences in the hydrogen-bond pattern in the two molecular arrangements are discussed.

Discussing the Syntheses Table of the Standard Amino Acid Based on the Graph Theory

2011 ◽  
Vol 105-107 ◽  
pp. 1784-1787
Author(s):  
Xiao Hong Shi ◽  
Xiang Hong Wang
Keyword(s):  
Amino Acids ◽  
Graph Theory ◽  
Amino Acid ◽  
Connected Graph ◽  
Network Graph ◽  
Standard Amino Acid ◽  
Similar Amino Acid

We discussed the syntheses table of the standard amino acid based on the graph theory that transformed the syntheses table into a network graph and using the connected-graph concept to discuss the performance of the table based on the various classification results. Finally, we selected a set with 29 specific representative classifications of twenty amino acids to calculate each connected-rate and on average connected-rate of 29 specific reached to 0.944. It means the similar amino acid have been arranged together and get a suitable position in the table, meanwhile the performance of this table reached our required

Complete Covalent Structure of Human Platelet Factor 4

1979 ◽  
Vol 42 (05) ◽  
pp. 1652-1660 ◽  
Author(s):  
Francis J Morgan ◽  
Geoffrey S Begg ◽  
Colin N Chesterman
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Human Platelet ◽  
Platelet Factor 4 ◽  
Platelet Factor ◽  
Disulphide Bonds ◽  
Covalent Structure

SummaryThe amino acid sequence of the subunit of human platelet factor 4 has been determined. Human platelet factor 4 consists of identical subunits containing 70 amino acids, each with a molecular weight of 7,756. The molecule contains no methionine, phenylalanine or tryptophan. The proposed amino acid sequence of PF4 is: Glu-Ala-Glu-Glu-Asp-Gly-Asp-Leu-Gln-Cys-Leu-Cys-Val-Lys-Thr-Thr-Ser- Gln-Val-Arg-Pro-Arg-His-Ile-Thr-Ser-Leu-Glu-Val-Ile-Lys-Ala-Gly-Pro-His-Cys-Pro-Thr-Ala-Gin- Leu-Ile-Ala-Thr-Leu-Lys-Asn-Gly-Arg-Lys-Ile-Cys-Leu-Asp-Leu-Gln-Ala-Pro-Leu-Tyr-Lys-Lys- Ile-Ile-Lys-Lys-Leu-Leu-Glu-Ser. From consideration of the homology with p-thromboglobulin, disulphide bonds between residues 10 and 36 and between residues 12 and 52 can be inferred.

Characterization of an isozyme of S-adenosylmethionine synthetase from rat liver

1984 ◽  
Vol 62 (5) ◽  
pp. 276-279 ◽  
Author(s):  
C. H. Lin ◽  
W. Chung ◽  
K. P. Strickland ◽  
A. J. Hudson
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Enzymatic Synthesis ◽  
Gel Filtration ◽  
Deae Cellulose ◽  
Aromatic Amino Acids ◽  
Adenosylmethionine Synthetase ◽  
Cellulose Column

An isozyme of S-adenosylmethionine synthetase has been purified to homogeneity by ammonium sulfate fractionation, DEAE-cellulose column chromatography, and gel filtration on a Sephadex G-200 column. The purified enzyme is very unstable and has a molecular weight of 120 000 consisting of two identical subunits. Amino acid analysis on the purified enzyme showed glycine, glutamate, and aspartate to be the most abundant and the aromatic amino acids to be the least abundant. It possesses tripolyphosphatase activity which can be stimulated five to six times by S-adenosylmethionine (20–40 μM). The findings support the conclusion that an enzyme-bound tripolyphosphate is an obligatory intermediate in the enzymatic synthesis of S-adenosylmethionine from ATP and methionine.

scholarly journals Regulation of rat magnocellular neurosecretory system by D-aspartate: evidence for biological role(s) of a naturally occurring free D-amino acid in mammals

2000 ◽  
Vol 167 (2) ◽  
pp. 247-252 ◽  
Author(s):  
H Wang ◽  
H Wolosker ◽  
J Pevsner ◽  
SH Snyder ◽  
DJ Selkoe
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Amino Acid ◽  
Physiological Function ◽  
Neurosecretory System ◽  
Milk Ejection ◽  
Magnocellular Neurons ◽  
Rat Hypothalamus ◽  
Naturally Occurring

Little evidence is available for the physiological function of D-amino acids in species other than bacteria. Here we demonstrate that naturally occurring freed -aspartate (D-Asp) is present in all magnocellular neurons of rat hypothalamus. The levels of this naturally occurring D-amino acid were elevated during lactation and returned to normal thereafter in the magnocellular neurosecretory system, which produces oxytocin, a hormone responsible for milk ejection during lactation. Intraperitoneal injections of D-Asp reproducibly increased oxytocin gene expression and decreased the concentration of circulating oxytocin in vivo. Similar changes were observed in the vasopressin system. These results provide evidence for the role(s) of naturally occurring free D-Asp in mammalian physiology. The findings argue against the conventional concept that only L-stereoisomers of amino acids are functional in higher species.

The C-terminal sequence of amino acid residues of κ-casein isolated from buffalo's milk

1967 ◽  
Vol 34 (1) ◽  
pp. 85-88 ◽  
Author(s):  
M. H. Abd El-Salam ◽  
W. Manson
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Peptide Chain ◽  
Amino Acid Residues ◽  
Terminal Sequence ◽  
Carboxypeptidase A ◽  
Phosphorous Content ◽  
Single Peptide

SummaryWhen κ-casein from buffalo's milk was treated with carboxypeptidase A (EC 3. 4. 2. 1),4 amino acids, valine, threonine, serine and alanine were released from the protein in a manner consistent with the view that they originate in the C-terminal sequence of a single peptide chain. The amounts produced suggest a minimum molecular weight for buffalo κ-casein of approximately 17000, in agreement with the value calculated from the phosphorous content on the basis of the presence of 2 phosphorus atoms/molecule. A comparison is made with the C-terminal sequence reported for bovine κ-casein.

Isolation and characterization of some novel genes of the apolipoprotein A-I family in Japanese eel, Anguilla japonica

2011 ◽  
Vol 6 (4) ◽  
pp. 545-557 ◽  
Author(s):  
Malay Choudhury ◽  
Takahiro Oku ◽  
Shoji Yamada ◽  
Masaharu Komatsu ◽  
Keita Kudoh ◽  
...  
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Consensus Sequence ◽  
Structural Features ◽  
Lipid Binding ◽  
Japanese Eel ◽  
Amino Acid Sequences ◽  
Novel Genes ◽  
Isolation And Characterization

AbstractApolipoproteins such as apolipoprotein (apo) A-I, apoA-IV, and apoE are lipid binding proteins synthesized mainly in the liver and the intestine and play an important role in the transfer of exogenous or endogenous lipids through the circulatory system. To investigate the mechanism of lipid transport in fish, we have isolated some novel genes of the apoA-I family, apoIA-I (apoA-I isoform) 1–11, from Japanese eel by PCR amplification. Some of the isolated genes of apoIA-I corresponded to 28kDa-1 cDNAs which had already been deposited into the database and encoded an apolipoprotein with molecular weight of 28 kDa in the LDL, whereas others seemed to be novel genes. The structural organization of all apoIA-Is consisted of four exons separated by three introns. ApoIA-I10 had a total length of 3232 bp, whereas other genes except for apoIA-I9 ranged from 1280 to 1441 bp. The sequences of apoIA-Is at the exon-intron junctions were mostly consistent with the consensus sequence (GT/AG) at exon-intron boundaries, whereas the sequences of 3′ splice acceptor in intron 1 of apoIA-I1-7 were (AC) but not (AG). The deduced amino acid sequences of all apoIA-Is contained a putative signal peptide and a propeptide of 17 and 5 amino acid residues, respectively. The mature proteins of apoIA-I1-3, 7, and 8 consisted of 237 amino acids, whereas those of apoIA-I4-6 consisted of 239 amino acids. The mature apoIA-I10 sequence showed 65% identity to amino acid sequence of apoIA-I11 which was associated with an apolipoprotein with molecular weight of 23 kDa in the VLDL. All these mature apoIA-I sequences satisfied the common structural features depicted for the exchangeable apolipoproteins such as apoA-I, apoA-IV, and apoE but apoIA-I11 lacked internal repeats 7, 8, and 9 when compared with other members of apoA-I family. Phylogenetic analysis showed that these novel apoIA-Is isolated from Japanese eel were much closer to apoA-I than apoA-IV and apoE, suggesting new members of the apoA-I family.

Amino acid uptake systems in Bacteroides ruminicola

1979 ◽  
Vol 25 (10) ◽  
pp. 1161-1168 ◽  
Author(s):  
Roselynn M. W. Stevenson
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Nitrogen Sources ◽  
Amino Acid Uptake ◽  
Defined Medium ◽  
High Rate ◽  
Transport Systems ◽  
Acid Uptake ◽  
Chemical Structures ◽  
Kinetic Inhibition

Uptake of amino acids by Bacteroides ruminicola was observed in cells grown in a complete defined medium, containing ammonia as the nitrogen source. A high rate of uptake occurred only in fresh medium, as an inhibitory substance, possibly acetate, apparently accumulated during growth. All amino acids except proline were taken up and incorporated into cold trichloroacetic acid precipitable material. Different patterns of incorporation and different responses to 2,4-dinitrophenol and potassium ferricyanide indicated multiple uptake systems were involved. Kinetic inhibition patterns suggested six distinct systems were present for amino acid uptake, with specificities related to the chemical structures of the amino acids. Thus, the failure of free amino acids to act as sole nitrogen sources for growth of B. ruminicola is not due to the absence of transport systems for these compounds.

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