Distribution Of Amino Acid Residues Research Articles

The spatial distribution of physical, chemical, energetic and conformational properties of amino acid residues in globular proteins

An attempt is made to obtain information as to the spatial distribution of amino acid residues in globular proteins in terms of their chemical, physical, energetic and conformational properties. The crystallographic data on twenty-one protein molecules form the basis for the study. The properties of the residues, namely, hydrophobicity, polarity, acidity, molecular weight, bulkness, chromatographic index, refractivity, short/medium/long-range energetics, and powers to adopt a-helical, extended and bend structures are analysed by dividing the protein globule into six concentric shells containing equal numbers of residues. The results show that the decisive factor in determining the spatial position of a residue in a protein molecule is of composite nature involving a compromise between the various properties of the residue. The observed deviations from the general hydrophobic interior and hydrophilic exterior in globular proteins are nicely brought out. A valuable clue is obtained as to the directional properties of α-helical and extended structure segments in proteins. The relative buried, exposed and intermediate characters of the residues in protein globules are obtained in a very realistic approach.

Propriétés Physico-Chimiques et Composition en Acides Aminés des Fractions de Protéines de Soya, de Féverole, de Colza et de Feuilles de Luzeme

Fractions were prepared and purified from proteins of four different vegetable sources by a method based on differences of solubility in ammonium sulfate solutions. Sedimentation coefficient SW25, distribution of amino-acid residues, absorption coefficient at 280 and 260 nm and solubility in ammonium sulfate solutions of various concentrations have been determined with the isolated fractions. Results indicated that solubility decreased logarithmically with increases in concentration of ammonium sulfate. It is shown for the five fractions studied that solubility is related to the ratio of the number of polar/neutral residues.

Structure of the α-keratin microfibril

The fine detail in the X-ray diffraction pattern of α-keratin has been explored out to spacings of 4 Å by a direct mapping of the cylindrically averagedintensity transform. The meridional maxima lie on a set of layer lines corresponding to an axially projected repeat of structure of 470 Å, and the distribution of nonmeridional maxima is consistent with a helical symmetry in which the basic helix has a pitch† of ±3447 Å, and a line group which does not involve a rotation axis parallel to the screw axis. In addition, there is evidence for a pseudo repeat with a unit height of 67·1 Å and a unit twist of ±109·9° associated with the coiled-coil rope segments that are believed to constitute the framework of the microfibril. Possible packing arrangements of the coiled-coil rope segments within the pseudo repeat have been analyzed and two models derived; the first is based on 2-strand rope segments in which the major helix of the coiled-coil has a pitch of −151 Å and the second is based on 3-strand rope segments in which the major helix of the coiled-coil has a pitch of −220 Å. Inter-rope contacts in the two models have been analyzed, and these can be correlated with the distribution of amino acid residues in the sequences of helical segments isolated from the low-sulphur wool proteins.

The structural code for proteins: Zonal distribution of amino acid residues and stabilization of helices by hydrophobic triplets

Abstract The general distribution of 2259 amino acid residues in α-helical and in non-helical regions has been calculated using data from 12 proteins. The irregular distribution of hydrophobic residues in the helical parts of the sample permits classification of the helical regions in hydrophobic-clustered and hydrophobic-depleted zones. In comparison with the composition of α-helices, Ala, Leu, Val, Ile and Tyr predominate in hydrophobic-clustered zones, whereas Cys and Gln tend to accumulate in hydrophobic-depleted zones. The N-terminal part of the helices is rich in Asp and Pro and poor in Leu and His, whereas the C-terminal is rich in Lys and Gin and does not contain Pro. For helical regions, hydrophobic residues, located along the sequence with a relation of 1-2-5 or 1-4-5, are more frequent than those with a relation of 1-2-3, 1-2-4, 1-3-4 or 1-3-5. The opposite is found for non-helical regions. All these deviations are statistically significant. It is concluded that hydrophobic triplets 1-2-5 and 1-4-5 are required for stabilizing the helices. The relevance of our results, and others reported in the bibliography, towards a better understanding of the structural code for proteins is discussed.

Statistical analysis of the distribution of amino acid residues among helical and non-helical regions in globular proteins

A statistical analysis of the distribution of different amino acid residues among helical and non-helical regions of seven globular proteins: myoglobin, α-and β-haemoglobin, lysozyme, ribonuclease, α-chymotrypsin and papain, has been made. It was found that the distribution of a number of amino acid residues differs essentially from the distribution averaged over all amino acids. Hydrophobic amino acids—alanine and leucine—show a tendency to occupy internal turns of helical regions. Negatively and positively charged amino acids have a tendency to concentrate, correspondingly, at the amino- and carbonyl-ends of helical regions. Amino acids with hetero-atoms (O or S atoms) near the main chain (serine, threonine, cystine, asparagine) have a tendency to concentrate in non-helical regions (including the regions with β-structure). Proline can be located either on the amino-ends of helical regions or in non-helical regions. The regularities found correlate with properties of the corresponding synthetic polypeptides and can be explained on the basis of the influence of hydrophobic, electrostatic and sterical interactions on the secondary structure of polypeptide chains. A check was made of Guzzo's and Prothero's empirical rules concerning the relationship between the amino acid composition of the given region of the polypeptide chain and its secondary structure, and it was shown that Guzzo's rule is in disagreement with the results of statistical analysis, whereas Prothero's rule agrees with them.

Fractionation of plant material. IV.—Distribution of amino acid residues in fractions obtained from leaves of broad bean (Vicia faba L.)

AbstractThe quantitative distribution of amino‐acid residues amongst some fractions derived from broad‐bean leaves was determined. Among the free amino acids, asparagine predominated and 3,4‐dihydroxyphenylalanine (DOPA) was abundant. DOPA was absent from the protein fractions. Aggregated N recovery and amino acid composition resembled those found for leafy materials by previous workers. Material extracted by ethanol from the TCA‐precipitated fraction resembled the bulk protein in molecular size and amino acid composition. A fraction not migrating during electrophoresis in phenol‐acetic acid‐water gave, on hydrolysis, amino acids presumed to be bound in neutral or weakly acid compounds, mostly of low molecular weight.

The Structure of Collagen Fibrils

Publisher Summary This chapter discusses the available information, concerning collagen and featuring in particular X-ray diffraction, electron optics and certain phases of chemical evidence developed, covering the characterization of various members of the collagen class of fibrous protein and a derivation of the principal structural features of the unitary element of connective tissues, the collagen fibril. Typical mesenchymal or mesogleal collagens are found in many animal phyla and other members are derived from secretions of epithelial tissues. The differences between collagens resemble those of isomorphous simpler substances in various collagens and there are differences in the content and distribution of amino-acid residues within similar sized frameworks. More chemical evidence regarding the collagens of lower vertebrate and invertebrate animals is needed to make the meaning of these differences clearer. Judging from the evidence drawn largely from the vertebrate animal sources, collagen fibrils are composed of thinner fundamental units, protofibrils. Collagen molecules are isolated when certain weak links occurring periodically along protofibrils are broken. The collagen molecule, like the protofibril, can become extended or randomly contracted. Interbands contain the average sized, hydroxyl-containing side-chains, as hydroxyproline and serine.

Points from Foregoing Letters

Dr. W. T. Astbury summarizes accumulating X-ray evidence for the belief that ultimately there will be found no real distinction between 'fibrous' and 'globular' proteins, and points out that the stoichio-metrical data of Bergmann and Niemann indicate the same thing. He shows how X-ray measurements can be used to supplement the Bergmann argument, and calculates a stoichiometrical distribution of amino acid residues and provisional molecular weight for keratin, which also appears to fit into the new scheme.