Contribution of side-chain chromophores to the optical activity of proteins: Model compound studies. IV. The indole chromophore of yohimbinic acid.

The optical properties of the indole chromophore of the indole alkaloid yohimbinic acid have been investigated as a function of molecular conformation. Theoretical rotatory strengths have been calculated and compared with experimental circular dichroism spectra. Optical data that may be suitable for calculating the chiroptical properties of the near ultraviolet electronic transitions of the indole chromophores, which occur in tryptophan residues of proteins, have been developed. The far ultraviolet transitions of yohimbinic acid have also been investigated.     

Study by circular dichroism and optical rotatory dispersion of polypeptides with aromatic side-chain chromophores

Poly(ortho-, meta-, and para-γ-nitrobenzyl-L -glutamates) were studied by circular dichroism (CD) and optical rotatory dispersion (ORD) in two helicogenic solvents, hexafluoroisopropanol (HFIP) and dichloroethane (EDC), and two non-helicogenic solvents, dichloracetic acid (DCA) and trifluoroacetic acid (TFA). The corresponding glutamates were also studied in DCA and TFA. The symmetric nitrobenzylic chromophore is optically active when the polymers are in solution in DCA and TFA. The corresponding glutamates are also optically active under the same conditions. Thus, it was not possible to explain the origin of the optical activity of the side-chain chromophore when the polymer is in solution in a helicogenic solvent. Nevertheless, from a side-chain dichroic band, a helix–coil transition curve was determined and the stability of each poly(γ-nitrobenzyl-L -glutamate) given; this stability depends on the position of the nitro substituent on the aromatic ring.     

Aromatic side-chain interactions in proteins. I. Main structural features

In a data set of 593 nonhomologous proteins from the PDB, we have analyzed the pairing of phenylalanine, tyrosine, tryptophan, and histidine residues with their closest aromatic partner. The frequency distribution of the shortest interatomic distance of partners is bimodal with a sharp peak at approximately 3.8 A and a wider one at a longer distance. Only the 3.8 A peak corresponds to direct ring-ring interactions thus aromatic pairs. The aromatic pairs were separated into two classes, near-sequence pairs and far-sequence pairs. Near sequence pairs stabilize local structure, and far-sequence pairs stabilize tertiary structure. Far-sequence pairs (74% of all pairs) mainly bridge two beta-strands, followed by pairs that bridge a beta-strand and a helix, and pairs that bridge a beta-strand and a random coil structure. Pairs that bridge helices are rare. The secondary structure of the near-sequence pairs depends on the partner distance in the sequence. When the partners are 1, 3, or 4 residues apart in the sequence, pairs are mostly found in helical structures. When the partners are two apart, pairs are mostly found in the same beta-strand. Analysis of the frequency of near sequence pairs supports the hypothesis that aromatic pairing occurs after, rather than before, the formation of secondary structures.     

Conformational studies of proteins with aromatic side-chain effects

We present here a brief analysis of ultraviolet isotropic absorption and related circular dichroism of the n–π* and π–π* transitions for the peptide (amide) chromophore in the 185–240 mμ region. Investigations by ultraviolet absorption and circular dichroism techniques on natural amino acids with aromatic chromophores in their side chains are also reported. By taking into account both the peptide and aromatic transitions we discuss the conformational studies of proteins with aromatic side-chain effects. Our attention is largely focused on the optical rotatory dispersion and circular dichroism spectra of these proteins in the near ultraviolet region, where characteristic aromatic side-chain bands occur. The 185–240 mμ region is also discussed when evidence exists of overlapping Cotton effects of aromatic and peptide groups.     

Optical activity of aromatic chromophores. I. O, m, and p-tyrosine

The optical activity and the conformational energy of the amino acids tyrosine, o-tyrosine, and m-tyrosine have been calculated as a function of molecular conformation. A new graphic technique, rotatory strength–conformational energy maps, was developed for the presentation of these calculations. Experimental circular dichroism spectra were determined by utilization of a new experimental technique that involves complete computer control of a Cary spectropolarimeter. This permitted repetitive scanning with signal averaging over extended time periods and resulted in a greatly enhanced signal to noise ratio. On the basis of these calculations, it, was concluded that the Kirkwood “coupled oscillator” mechanism is capable of explaining the observed optical activity of the aromatic chromophores of the molecules that were investigated.     

EPR studies on compound I of horseradish peroxidase.

Compound I of horseradish peroxidase (donor: hydrogen-peroxide oxidoreductase EC 1.11.1.7) was studied by EPR at low temperatures. An asymmetric signal was found, about 15 Gauss wide and with a g-value of 1.995, which could be detected only at temperatures below 20 K and which had an intensity corresponding to about 1% of the heme content. In a titration with H2O2, the signal intensity was proportional to the concentration of Compound I, reaching a maximum when equivalent amounts of H2O2 were added. This indicates that the signal is not due to an impurity, and it is suggested that a free radical is formed, relaxed by a near-by fast-relaxing iron.     

Energetics of hydrogen bonding in proteins: a model compound study.

Differences in the energetics of amide-amide and amide-hydroxyl hydrogen bonds in proteins have been explored from the effect of hydroxyl groups on the structure and dissolution energetics of a series of crystalline cyclic dipeptides. The calorimetrically determined energetics are interpreted in light of the crystal structures of the studied compounds. Our results indicate that the amide-amide and amide-hydroxyl hydrogen bonds both provide considerable enthalpic stability, but that the amide-amide hydrogen bond is about twice that of the amide-hydroxyl. Additionally, the interaction of the hydroxyl group with water is seen most readily in its contributions to entropy and heat capacity changes. Surprisingly, the hydroxyl group shows weakly hydrophobic behavior in terms of these contributions. These results can be used to understand the effects of mutations on the stability of globular proteins.     

An analysis of side-chain conformation in proteins.

The crystal structures of a number of globular proteins are currently available. An analysis of the distribution of side-chains among different allowed conformations in these proteins has been carried out. The observed conformations of individual residues are discussed on the basis of well-known stereochemical criteria. The population distribution of side-chains in different allowed regions in conformational space can be explained largely on the basis of simple steric considerations. In addition to examining the conformational behaviour of individual residues, some population distributions of conformational angles of general interest involving groups of residues have also been analyzed.     

Population genetic studies in the Balkans. I. Serum proteins

Within a study of the genetics of Southeastern European populations seven serum protein polymorphisms (AMY2, BF, C3, CP, GC, HPA, TF) were examined in three samples of Aromuns (Albania: the village of Andon Poci, province Gjirocaster, Republic of Macedonia: Stip region, Romania: the village Kogalniceanu, province Dobruja) and four reference samples (Albanians: Tirana, Romanians: Constanta and Ploiesti as well as Greeks (Northeastern Greece)). The Aromun samples from Albania and Romania form one separate cluster and the reference samples together with the Aromuns from Macedonia (Stip region) form a second one.     

Diamide model for the optical activity of collagen and polyproline I and II

A diamide, N-acetyl-L -proline-N,N-dimethylamide (AcProDMA), in water solution has optical rotatory dispersion (ORD) and circular dichroism (CD) spectra very similar to those of poly-L -proline II and the fibrous protein collagen. In contrast, AcProDMA in cyclohexane solution has optical activity resembling that of poly-L -proline I. Conformational analysis shows that AcProDMA is confined by steric constraints to either of two narrow regions of conformational space. The trans isomer of AcProDMA assumes conformations near those of polyproline II and collagen nearest neighbors, while cis-AcProDMA assumes conformations near that of polyproline I nearest neighbors. Nuclear magnetic resonance (NMR) experiments show that an equilibrium mixture of the cis and trans isomers of AcProDMA is present in solution. The trans isomer predominates in aqueous solution, but the equilibrium shifts to favor the cis isomer in nonpolar organic solvents such as cyclohexane. Analysis of the ORD spectra in terms of two basic spectra reveals a solvent dependent isomerization which parallels that observed by NMR. The optical activity of the pure isomers of AcProDMA can be derived from the ORD, CD and NMR data. A comparison of component cotton effects confirms the similarity in optical activity of trans-AcProDMA, polyproline II, and collagen on the one hand, and of cis-AcProDMA and Polyproline I on the other.     

Oxidation of horseradish peroxidase compound II to compound I.

In the reaction between equimolar amounts of horseradish peroxidase and chlorite, the native enzyme is oxidized directly to Compound II (Hewson, W.D., and Hager, L.P. (1979) J. Biol. Chem. 254, 3175-3181). At acidic pH but not at alkaline values, this initial reaction is followed by oxidation of Compound II to Compound I. The highly pH-dependent chemistry of Compound II can be readily demonstrated by the reduction of Compound I, with ferrocyanide at acidic, neutral, and alkaline pH values. Titration at low pH yields very little Compound II, whereas at high pH, the yield is quantitative. Similarly, the reaction of horseradish peroxidase and chlorite at low pH yields Compound I while only Compound II is formed at high pH. At intermediate pH values both the ferrocyanide reduction and the chlorite reaction produce intermediate yields of Compound II. This behavior is explained in terms of acidic and basic forms of Compound II. The acidic form is reactive and unstable relative to the basic form. Compound II can be readily oxidized to Compound I by either chloride or chlorine dioxide in acidic solution. The oxidation does not occur in alkaline solution, nor will hydrogen peroxide cause the oxidation of Compound II, even at low pH.     

Contribution to the Embryology of Indian Euphorbiaceae: I. Euphorbia rothiana Spreng.

The paper presents an account of the embryology of Euphorbiarothiana Spreng.     

Interaction of halides with the cyanide complex of myeloperoxidase: a model for substrate binding to compound I.

EPR spectra of the low-spin cyanide complex of myeloperoxidase have been measured in the absence and presence of halide substrates; chloride, bromide and iodide. Halide-dependent spectral changes are found at acidic pH. The electronic structure of the low-spin ferric iron in cyanide complex appears to be modulated by halide binding to a protonated amino acid in the distal heme cavity. These findings suggest halide substrates can interact with ferryl oxygen in compound I during enzyme catalysis to form hypohalous acid.     

Contribution to the linkage theory of autopolyploids: I

A theory of linkage of autopolyploids is developed under consideration ofm loci andr alleles. The simplifying assumption of chromosome segregation, which may be considered as an approximation to the more adequate theory of chromatid segregation, is made throughout. Random mating and distinct, non-overlapping generations are assumed. Under these assumptions the problem is determined by three basic probability distributions—the distributions of genotypes and of gametes, and the segregation distribution. The segregation distribution is assumed to be the same for males and for females. The aim of the paper is to establish recurrence formulas (which allow to find the distributions of gametes and of genotypes from generation to generation, if the distribution of genotypes for an initial generation is known) and to investigate the limit behavior of these distributions as the number of generations increases indefinitely. In the present paper (hereafter referred to as I) the problem is explained, and the three characteristic distributions are introduced for the general case of a 2s-ploid,m loci, andr alleles. Recurrence relations are established for tetraploids,s=2 andm=2 loci, while the recurrence relations for the general case as well as the limit theorems will be given in the second part of this paper (hereafter referred to as II).     

Heterosis in the codominance model: electrophoretic studies of proteins in the chicken-quail hybrid.

1. Electrophoretical comparisons was carried out on qualitative and quantitative differences of three proteins in the cock-quail hybrid: albumin, immunoglobulin and hemoglobin. All three components correspond to situations of codominance. 2. Heterosis was demonstrated twice: the immunological potentialities of the hybrid are increased by its possession of two types of Ig G; the affinity of hemoglobin for oxygen can be better regulated in the hybrid than in both parental species. 3. Proportions of the codominant parental components in the hybrid are different in the case of the three investigated proteins; this fact probably reflects the relative importance of the quantitative regulation of gene products in the hybrid.     

An evaluation of the charge-transfer model for the chromophores of the retinal-containing proteins,rhodopsin and bacteriorhodopsin

The chromophores of rhodopsin and bacteriorhodopsin are believed to result from an electrostatic interaction between the protonated Schiff base of retinal and amino acid side chains. It has been proposed from ESR measurements on rhodopsin (Shirane, K. (1975) Nature, 254, 722–723) and model studies using retinal and tryptophan (Ishigami, M., Maeda, Y. and Mishima, K. (1966) Biochim. Biophys. Acta 112, 372–375) that the interaction is one of charge transfer and that the amino acid involved is tryptophan. Our re-examination of this work does not support the existence of a charge-transfer complex. However, additional similarities between the model system and bateriorhodopsin were observed. It is concluded that further studies in this area may yield information about the nature of the protein chromophores.