Characterization of the Hydrophobic Properties of Amino Acids. II. How Hydrophobic, Hydrophilic and Lipophilic Is Tryptophan?

1993 ◽  
Vol 58 (5) ◽  
pp. 996-1000 ◽  
Author(s):  
Josef Chmelík
Keyword(s):  
Amino Acids ◽  
Partition Coefficient ◽  
Hydrophobic Properties

The model for the characterization of hydrophobicity, hydrophilicity and lipophilicity of compounds is presented. It is based on the vapour-to-solvent coefficients for hydrophilicity and lipophilicity and the partition coefficient for hydrophobicity. It is shown that some apparently contradictory facts can be understood on the basis of this model.

Characterization of the hydrophobic properties of amino acids on the basis of their partition and distribution coefficients in the 1-octanol-water system

1991 ◽  
Vol 56 (10) ◽  
pp. 2030-2041 ◽  
Author(s):  
Josef Chmelík ◽  
Jiří Hudeček ◽  
Karol Putyera ◽  
Jiří Makovička ◽  
Vítěz Kalous ◽  
...  
Keyword(s):  
Amino Acids ◽  
Water System ◽  
Distribution Coefficients ◽  
Published Data ◽  
Hydrophobic Properties ◽  
Charged Amino Acids ◽  
Hydrophobic Amino Acids ◽  
Partition Process

The hydrophobic properties of amino acid side chains were characterized on the basis of the partition process in the 1-octanol-water system. The partition coefficients were calculated from the published data and the distribution coefficients were determined experimentally on the basis of a double partition process utilizing the fact that the amino acids pass almost completely into the aqueous phase in the partition process. When the volumes of water and 1-octanol are suitably selected, this fact permits avoidance of the difficulties associated with the determination of amino acids in 1-octanol, where their solubilities are very low. Our scale is the only complete experimental scale based on the partition process of amino acids in the 1-octanol-water system. It follows from comparison of the calculated and the experimental data with the values published for the distribution coefficients of N-acetyl amides of amino acids that the best agreement was achieved for hydrophobic amino acids, while greater differences were observed for hydrophilic amino acids. These differences, expressed as the logarithm of the distribution coefficients, correspond to an average of 0.08 for nonpolar amino acids and 0.30 for acidic and basic amino acids: expressed as relative deviations, these values correspond to 2-10% for nonpolar amino acids, and 5-30% for charged amino acids.

Post-proline endopeptidase, further characterization of the enzyme from pig kidneys

1984 ◽  
Vol 49 (8) ◽  
pp. 1846-1853 ◽  
Author(s):  
Karel Hauzer ◽  
Tomislav Barth ◽  
Linda Servítová ◽  
Karel Jošt
Keyword(s):  
Amino Acids ◽  
Aspartic Acid ◽  
Ion Exchange Chromatography ◽  
Exchange Chromatography ◽  
Relative Molecular Mass ◽  
Enzyme Molecule ◽  
Thiol Compounds ◽  
Modified Method ◽  
N Terminus

A post-proline endopeptidase (EC 3.4.21.26) was isolated from pig kidneys using a modified method described earlier. The enzyme was further purified by ion exchange chromatography on DEAE-Sephacel. The final product contained about 95% of post-proline endopeptidase. The enzyme molecule consisted of one peptide chain with a relative molecular mass of 65 600 to 70 000, containing a large proportion of acidic and alifatic amino acids (glutamic acid, aspartic acid and leucine) and the N-terminus was formed by aspartic acid or asparagine. In order to prevent losses of enzyme activity, thiol compounds has to be added.

scholarly journals Avoided motifs: short amino acid strings missing from protein datasets

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Function ◽  
Large Protein ◽  
New Approach ◽  
Cellular Context ◽  
Human Proteins ◽  
Context Specific ◽  
Protein Datasets

Abstract According to the amino acid composition of natural proteins, it could be expected that all possible sequences of three or four amino acids will occur at least once in large protein datasets purely by chance. However, in some species or cellular context, specific short amino acid motifs are missing due to unknown reasons. We describe these as Avoided Motifs, short amino acid combinations missing from biological sequences. Here we identify 209 human and 154 bacterial Avoided Motifs of length four amino acids, and discuss their possible functionality according to their presence in other species. Furthermore, we determine two Avoided Motifs of length three amino acids in human proteins specifically located in the cytoplasm, and two more in secreted proteins. Our results support the hypothesis that the characterization of Avoided Motifs in particular contexts can provide us with information about functional motifs, pointing to a new approach in the use of molecular sequences for the discovery of protein function.

scholarly journals Genetic and Molecular Characterization of sting, a Gene Involved in Crystal Formation and Meiotic Drive in the Male Germ Line of Drosophila melanogaster

Genetics ◽  
1999 ◽  
Vol 151 (2) ◽  
pp. 749-760 ◽  
Author(s):  
Armin Schmidt ◽  
Gioacchino Palumbo ◽  
Maria P Bozzetti ◽  
Patrizia Tritto ◽  
Sergio Pimpinelli ◽  
...  
Keyword(s):  
Amino Acids ◽  
Drosophila Melanogaster ◽  
Null Allele ◽  
Germ Line ◽  
Meiotic Drive ◽  
P Element ◽  
Crystal Formation ◽  
Male Sterile ◽  
Male Sterile Mutation

Abstract The sting mutation, caused by a P element inserted into polytene region 32D, was isolated by a screen for male sterile insertions in Drosophila melanogaster. This sterility is correlated with the presence of crystals in spermatocytes and spermatids that are structurally indistinguishable from those produced in males carrying a deficiency of the Y-linked crystal (cry) locus. In addition, their morphology is needle-like in Ste+ flies and star-shaped in Ste flies, once again as observed in cry– males. The sti mutation leads to meiotic drive of the sex chromosomes, and the strength of the phenomenon is correlated with the copy number of the repetitive Ste locus. The same correlation is also true for the penetrance of the male sterile mutation. A presumptive sti null allele results in male sterility and lethal maternal effect. The gene was cloned and shown to code for a putative protein that is 866 amino acids long. A C-terminal domain of 82 amino acids is identified that is well conserved in proteins from different organisms. The gene is expressed only in the germline of both sexes. The interaction of sting with the Ste locus can also be demonstrated at the molecular level. While an unprocessed 8-kb Ste primary transcript is expressed in wild-type males, in X/Y homozygous sti males, as in X/Y cry– males, a 0.7-kb mRNA is produced.

Cloning and characterization of a human brain Na + -independent transporter for small neutral amino acids that transports d -serine with high affinity

2000 ◽  
Vol 287 (3) ◽  
pp. 231-235 ◽  
Author(s):  
Jun Nakauchi ◽  
Hirotaka Matsuo ◽  
Do Kyung Kim ◽  
Akiteru Goto ◽  
Arthit Chairoungdua ◽  
...  
Keyword(s):  
Amino Acids ◽  
Human Brain ◽  
Neutral Amino Acids ◽  
High Affinity

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.

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