Computer simulation of the conformational properties of retro-inverso peptides. II. Ab initio study, spatial electron distribution, and population analysis of N-formylglycine methylamide, N-formyl N'-acetyldiaminomethane, and N-methylmalonamide

Ab initio minimal and split-valence basis set calculations have been performed on compounds that are involved in retro–inverso modifications, i.e., gem-diaminoalkyl and malonyl structures. These calculations are compared with empirical force field calculations and the minor differences discussed. All calculations agree that the preferred helical conformation of the isolated gem-diaminoalkyl and malonyl derivatives of residues found in the retro-inverso modified peptides is 5–8 kcal/mol lower than the C conformation preferred by the isolated peptide residues. Population analysis and contour plots of the charge distribution are used to help explain the differences between the model compounds.     

Conformational transitions and geometry differences between low-energy conformers of N-acetyl-N′-methyl alanineamide: An ab initio study at the 4-21G level with gradient relaxed geometries

Energy pathways between the α_R, β′, C, and β-regions of the conformational energy surface of N-acetyl-N′-methylalanyl amide were obtained by SCF ab initio calculations on the 4-21G level, with gradient geometry optimization at each point. The calculations indicate that no barrier exists at this computational level between α_R and β′. The variation of geometry (bond distances and bond angles) with conformation is analyzed in detail, and the most important geometrical parameters that should be treated as variables in both empirical energy calculations and in the fitting of polypeptide chains in proteins by x-ray methods are identified. In addition to the ?,ψ correlation discussed previously for the helical state, a correlation of these dihedral angles in the β-region is described.     

Etude experimentale de L′auto-association des molécules modèles dipeptidiques. III. Influence de la dimerisation stéréosélective sur les spectres de résonance magnétique protonique

Proton magnetic resonance spectra of model dipeptide molecules R₁–C′₁O₁–N₂H₂–CHR₂–C′₂O₂–N₃H₃–R₃ in CCl₄ solutions exhibit splited signals when investigating on mixtures of L and D enantiomers differing from the racemic composition. The major effect is observed on amide proton signals which are the ones most sensitive to the ratio of aggregation. The stereoselective dimerization of enantiomeric molecules in the so-called C₅ conformational state is shown to be responsible for such a phenomenon, the intensity of which depends on the bulkiness of the side chain R₂. A theoretical approach is proposed which gives predictions in close agreement with our own experimental findings.     

Apparent molar volumes of some amino acids and peptides in aqueous urea solutions

Densities of solutions of several α-amino acids and peptides in 3 and 6m aqueous urea solvents have been determined at 298.15 K. These data have been used to evaluate the infinite-dilution apparent molar volumes of the solutes and the volume changes due to transfer (V ) of the α-amino acids and peptides at infinite dilution from water to aqueous urea solutions. The sign and magnitude of the V values have been rationalized in the framework of Friedman's cosphere-overlap model. The V values for the glycyl group (? CH₂CONH? ) and alkyl side chains have been estimated.     

Equi-replicated balanced block designs generated by a balanced matrix

In this paper it is shown that if N= \documentclass{article}\pagestyle{empty}\begin{document}$ \mathop \sum \limits_{i = 1}^{S_h} $\end{document} c_ihN_ih, where c_ih are some non-negative integer numbers and N_ih are such incidence matrices that A_h = \documentclass{article}\pagestyle{empty}\begin{document}$ \mathop \sum \limits_{i = 1}^{S_h} $\end{document} i N_ih is a balanced matrix defined by SHAH (1959), for h = 1, 2,…, p, then a block design with an incidence matrix Ñ = [N, N,…,N] is an equi-replicated balanced block design. Here the balance of a block design is defined in terms of the matrix M₀ introduced by CALI?SKI (1971).     

On the blue color of triiodide ions in starch and starch fractions. I. Characterization and assignment of absorption and circular dichroism spectra of triiodide ions in amylose

Four fundamental Raman lines were observed at 159, 111, 55 and 27 cm^-1 corresponding to the I bound (I) in amyloses with DP from 20 to 100, regardless of the degree of polymerization of I and the excitation wavelength. The spectral resolution was based on the molar extinction coefficient and molar ellipticity spectra of I. Eight bands, named, S₁, S₂, ?, S₈ from long to short wavelength, were isolated. These were found regardless of the DP. By a resonance excitation Raman study, the characteristics of S₃ and S₄, comprising the shoulder around 480 nm, were found to be different from those of S₁ and S₂, comprising the blue band. The assignment of the spectra was based on the electronic states of the monomeric I in the exciton-coupled dimeric unit. It was concluded that the blue band (S₁,S₂) belonged to the long-axis transitions and the shoulder band (S₃,S₄) to the short-axis ones on the monmeric coordinate system.     

On the “filterable aggregates and other particles” interpretation of the extraordinary regime of polyelectrolytes

Quasi-elastic light scattering studies on some polyelectrolyte systems exhibit a somewhat “bizarre” behavior in the profile of the apparent diffusion coefficient D_app as a function of the salt concentration C_s. As C_s is decreased, D_app first increases in accordance with polyelectrolyte theories, and then undergoes a precipitous drop in value by over an order of magnitude at a well-defined critical value C_s = C. This “transition” from C_s > C (ordinary) to C_s < C (extraordinary) is referred to as the “ordinary-extraordinary” (o-e) transition. Ghosh, Peitzsch, and Reed [(1992) Biopolymers, Vol. 32, pp. 1105–1122] proposed a “filterable aggregate” (FA) and “other particle” interpretation for the o-e transition and its reversibility in regard to ionic strength changes. The present communication examines in detail the FA model as applied to the o-e transition. It is shown that the FA model fails to account of the established characteristics of the o-e transition. © 1993 John Wiley & Sons, Inc.     

Characterization of the transition state of Lysozyme unfolding. I. Effect of protein-solvent interactions on the transition state

The influence of proline cis-trans isomerization on the kinetics of lysozyme unfolding was examined carefully according to the theory of Hagerman and Baldwin [(1976) Biochemistry 15, 1462–1473]. As a result, the kinetics of lysozyme unfolding was found to follow the two-state transition model well. The temperature dependencies of k_uf and k_f over a wide temperature range showed that ΔC = 0 and ΔC = ?6.7 kJ K^?1 mol^?1 in solutions of different concentrations of GuHCl. The data observed in solutions containing other denaturants also supported the conclusion that ΔC is nearly equal to zero. The activation enthalpies of unfolding (ΔH) were observed at various concentrations of several kinds of denaturants. They were independent of species and concentrations of denaturants ΔH = 200 kJ mol^?1). These facts indicate that the aspect of interaction between protein and different kinds of solvent molecules varies only slightly during the unfolding to the transition state, that is, the transition state is at compact as the native one. Therefore, it is also suggested that ΔH of 200 kJ mol^?1 is primarily required for the disruption of long-range interactions among different structural domains through a subtle conformational change. We compared the effects of several kinds of denaturants on the unfolding rate. The addition of PrOH more remarkably increases the unfolding rate than do other hydrophilic denaturants. This is probably because PrOH molecules can penetrate into the hydrophobic core of lysozyme, but hydrophilic reagents cannot because of the compactness of the transition state.     

Hetero-α-helical,two-chain coiled-coils. Clam–worm hybrid paramyosins

The specificity of the interaction between the α-helices in two-chain coiled-coils is investigated by studying the formation of hybrid molecules in which one α-helix is a clam paramyosin chain and the other a worm paramyosin chain. Hybrids are formed by mixing, denaturation, and subsequent renaturation. Comparison is made with a blank solution in which renaturation precedes mixing, thus precluding hybridization. Hybrids are detected by a ruse based on the presence of free sulfhydryl functions on calm chains. This allows molecules comprising two clam chains to be covalently crosslinked by oxidation with 5,5′-dithiobis(2-nitrobenzoate). Worm paramyosin chains have no sulfhydryl, so molecules comprising two worm chains or hybrid molecules comprising one chain of each type cannot crosslink. When run on sodium dodecyl sulfate polyacrylamide gel electrophoresis, therefore, the protein separates into two well-resolved regions, one containing one-chain species and the other two-chain species. When the gels are scanned and quantitated, the hybrids show up as an increase in the fraction of material in the one-chain band compared with the fraction in the blank solution. When renaturation is direct, we find that the fraction of renaturated molecules that are hybrids varies from ～10% at 5°C to ～5% at 25°C. These are judged to be nonequilibrium (quenched) values. When renaturation is by slow annealing, the equilibrium fraction hybrids are ～4% and show a modest, but measurable, increase with increasing temperature. These data allow calculation of the equilibrium constant K_h and standard free energy for the hybridization reaction: (1/2)CC + (½)WW = CW, in which C(W) stands for an α-helical clam (worm) polypeptide chain. The temperature dependence gives the standard enthalpy and entropy of the reaction. We find ΔH ? 1800 cal mol^?1 and ΔH ? 1.4 cal mol^?1 K^?1, using molarity concentration units and the infinitely dilute solution in NaCl/phosphate buffer as reference state. The possible molecular significance of these values is discussed, and it is concluded that the observed standard entropy arises essentially entirely from the rotational dissymmetry of the hybrids.     

Effects of temperature on microbial ethanol production. II. A thermodynamic interpretation of the temperature profile curve of ethanol production

An attempt is made to give a thermodynamic interpretation of the complete temperature profile curve of ethanol formation. Taking into consideration an enhancing competition between thermal activation and thermal deactivation of ethanol formation at increasing temperatures and supposing that the ethanol production is affected by a reversible and an irreversible term of thermal deactivation of a modified ARRHENIUS equation being current for the total biokinetic sphere may be derived: . The quantities ΔH and ΔH^D_2T are identical with the temperature functions of the change of entropy caused by reversible and irreversible deactivation of ethanol formation, respectively. Accordingly for the yeast strain Saccharomyces cerevisiae Sc 5 the calculated entropy coefficients of reversible and irreversible thermal deactivation of ethanol formation amount to C = (0.245± 0.013) kJ/mol · deg.² and C = (1.657 ± 0.046) kJ/mol · deg.².     

Construction of Equi-replicated Balanced Block Designs with Block Sizes Exceeding the Number of Treatments

In this note it is shown that the block design with incidence matrix Ñ = [NN… N], where N = c_1hN_h + c_oh (11′–N_h). c_oh and c_1h are any non-negative integers and N_h,h = 1, 2,…,p, are incidence matrices of balanced incomplete block designs with the same number of treatments t, is a balanced block design with the block sizes exceeding the number of treatments. In derivation the matrix M₀, introduced by CALIński (1971) is utilized.     

Conformational flexibility of peptides containing α,β-unsaturated amino acid residues. I. Conformational analysis of N-acetyl-N′-methylamides of dehydroalanine and N-methyldehydroalanine

Conformational energy calculations on the N-acetyl-N′-methylamides of dehydroalanine and N-methyldehydroalanine indicate that their conformational behavior is very different from that of the corresponding saturated compounds. The conformational data in the literature from x-ray and nmr investigations on peptides containing α,β-unsaturated residues are discussed on the basis of these theoretical results.     

Ground‐ and excited‐state proton transfer and antioxidant activity of 3‐hydroxyflavone in egg yolk phosphatidylcholine liposomes: absorption and fluorescence spectroscopic studies

Excited‐state intramolecular proton transfer (ESIPT) and dual luminescence behaviour of 3‐hydroxyflavone (3‐HF) have been utilized to monitor its binding to liposomal membranes prepared from egg yolk phosphatydilcholine (EYPC). Additionally, absorption spectrophotometric assay has been performed to evaluate the antioxidant activity of 3‐HF against lipid peroxidation in this membrane system. When 3‐HF molecules are partitioned into EYPC liposomes, a weak long‐wavelength absorption band with λ ～410 nm appears in addition to the principal absorption at ～λ = 345 nm. Selective excitation of the 410 nm band produces the characteristic emission (λ～460 nm) of the ground‐state anionic species, whereas excitation at the higher energy absorption band leads to dual emission with predominatly ESIPT tautomer fluorescence (λ = 528 nm). Both ESIPT tautomer and the anionic species exhibit fairly high fluorescence anisotropy (r) values (r = 0.122 and 0.180, respectively). Biexponential fluorescence decay kinetics are observed for the ESIPT tautomer as well as the ground‐state anionic forms, indicating heterogeneity in the microenvironments of the corresponding emitting species. Furthermore, we demonstrate that lipid peroxidation of EYPC liposomes is significantly inhibited upon 3‐HF binding, suggesting that 3‐HF can be potentially useful as an inhibitor of peroxidative damage of cell membranes. Copyright © 2008 John Wiley & Sons, Ltd.     

Molecular conformation of polysaccharides in solution. Changes in the optical rotation and in the elution pattern of gel filtration

Molecular conformation of some polysaccharides in aqueous solution in evidenced by changes in the optical rotation and in the elution pattern of gel filtration. The changes in the specific rotation against that in water are expressed as a molar conformational value [K]: ?495° for colominic acid in 1.0 N NaOH solution, and ?180° for hyaluronate (HA), +85° for corneal keratin sulfate, and +234° for amylose in 8 M urea solution. The gel filtration of amylose and HA dissolved in 8 M urea solution shows elution patterns distinctly different from those dissolved in water. The phenomena are attributable to a molecular conformational transition of polysaccharide molecules in aqueous solution.     

Effects of cavity-creating mutations on conformational stability and structure of the dimeric 4-α-helical protein ROP: Thermal unfolding studies

The structural and energetic perturbations caused by cavity-creating mutations (Leu-41 → Val and Leu-41 → Ala) in the dimeric 4-α-helical-bundle protein ROP have been characterized by CD spectroscopy and differential scanning calorimetry (DSC). Deconvolution of the CD spectra showed a decrease in α -helicity as a result of the amino acid exchanges that follows qualitatively the overall decrease in conformational stability. Transition enthalpies are sensitive probes of the energetic change associated with point mutations. ΔH⁰ values at the respective transition temperatures, T_1/2 (71.0, 65.3, and 52.9°C at 0.5 mg/ml) decrease from 580 ± 20 to 461 ± 20 kJ/(mol of dimmer) and 335 ± 20 kJ/(mol of dimmer) for wildtype ROP (Steif, C., Weber, P., Hinz, H.-J., Flossdorf, J., Cesareni, G., Kokkinidis, M. Biochemistry 32:3867-3876, 1993), L⁴¹V, and L⁴¹A, respectively. The conformational stabilities at 25°C expressed by the standard Gibbs energies of denaturation, ΔG, are 71.7, 61.1, and 46.1 kJ/(mol of dimmer). The corresponding transition enthalpies have been obtained from extrapolation using the c(T)and c(T) functions. Their values at 25°C are 176.3, 101.9, and 141.7 kJ/(mol of dimmer) for wild-type ROP, L⁴¹V, and L⁴¹A, respectively. When the stability perturbation resulting from the cavity creating mutations is referred to the exchange of 1 mol of CH₂ group, the average ΔΔG value is ?5.0 ± 1 kJ/(mol of CH₂ group). This decrease in conformation stability suggests that dimeric ROP exhibits the same susceptibility to Leu → Yal and Leu → Ala exchanges as small monomeric proteins. Careful determinations of the partial specific heat capacities of wild-type and mutated protein solutions suggest that the mutational effects are predominantly manifested in the native rather than the unfolded state. © 1995 Wiley-Liss, Inc.     

Heat capacity changes and partial molal heat capacities of some di- and tripeptides in water

Integral enthalpies of solution of several dipeptides and tripeptides in water at low concentrations have been determined at 25 and 35°C. These data have been used to derive the changes in heat capacity on dissolution at infinite dilution ΔC at 30°C. Limiting partial molal heat capacities ΔC have been determined by combining ΔC with C_p2 (heat capacity of pure solid peptides). Using the data on ω-amino acids and these peptides, the partial molal heat capacity of a peptide group ? CONH? was semiquantitatively estimated.     

Kinetics of ethidium's intercalation in packaged bacteriophage T7 DNA: effects of DNA packing density

The kinetics of ethidium's intercalative binding to DNA packaged in bacteriophage T7 and two T7 deletion mutants have been determined, using enhancement of fluorescence to quantitate binding. At a constant ethidium concentration, the results can be described as first-order binding with two different rate constants, k (= k₁ + k_?1) and k (= k₂ + k_?2). The larger rate constant (k) was at least four orders of magnitude smaller than the comparable first-order forward rate constant for binding to DNA released from its capsid. At 25°C values of k decreased as the amount of DNA packaged per internal volume increased. This latter observation indicates that the rate of ethidium's binding to packaged T7 DNA is limited by an event that occurs inside of the DNA-containing region of T7, not by the crossing of T7 capsid's outer shell. Arrhenius plots of kM are biphasic, indicating a transition for packaged DNA at a temperature of 20°C. The data indicate that k s are limited by either sieving of ethidium during its passage through the packaged DNA or subsequent hindered intercalation.     

A population genetic study of the Banks and Torres Islands (Vanuatu) and of the Santa Cruz Islands and polynesian outliers (Solomon Islands)

As part of a multidisciplinary survey of populations in the Banks and Torres Islands of Vanuatu and the Southern and Central Districts of the Solomon Islands, nearly 2,400 persons have been tested for ABO blood groups and a number of serum protein and red cell enzyme genetic marker systems. For the ABO system, the populations are characterized in general by high gene O and low gene B frequencies except in two of the Polynesian Outlier Islands, Rennell and Bellona, which have high frequencies of B. Among the serum proteins, several alleles have distributions indicating significant movement of people between islands. These include Albumin ^{New Guinea} and the transferrin alleles Tf, and Tf, and Tf. Similar specific alleles for red cell enzymes also show distributions reflecting interisland population movement as well as contact with persons from outside the southern Pacific region. Examples are ACP in the acid phosphatase system, PGM and PGM, PGM and PGM, PGK⁴ and also HbJ^Tongariki. The data available for 11 polymorphic systems were used to generate genetic distances. Of the four Polynesian Outlier Islands, Anuta is most remote genetically, with Rennell and Bellona also relatively isolated. The fourth Polynesian Outlier, Tikopia, occupies a position genetically close to the Melanesian populations of the Banks and Torres Islands and the southern Solomons. The history of early European contact and voyaging in the Pacific, as well as archaeological and linguistic evidence and local legends, indicate that significant movements of people occurred between islands and provided opportunities for genes to be introduced from Europeans, Africans, and Asians. The genetic marker studies give evidence for genes from all these sources, though at a low level. Despite this admixture, the Polynesian Outlier and Melanesian populations have preserved their own distinctive genetic patterns.     

Application of the nearest-neighbor Ising model to the helix-coil transition of polypeptides in mixed organic solvents.

Using the formalism of nearest-neighbor Ising model and assuming that the allowed states for a monomeric unity of a polypeptide chain in solutions containing strong acids are E (helix), C (coil), and CS (solvent-bonded coil), the partition function of the system was deduced analytically. Equations were obtained which permitted the prediction of the characteristic thermodynamic behavior of the helix–coil transition under these conditions. These equations were used to examine critically the possible correlations between experimental data obtained using different techniques. Particular attention was devoted to quantities called “transition enthalpies,” obtained from the slope of the transition curves at the point where the helix fraction is one-half (ΔH), or for measurements of the heat of solution of the polymer over the total range of solvent composition (ΔH), or from heat capacity measurements taken at various temperatures (ΔH). Literature data of ΔH(j = opt, sol, cal) for the system poly-γ-benzyl-L -glutamate in mixtures of dichloroacetic acid and 1,2-dichloroethane were carefully analyzed.     

Physical association of two simple alkylators to some DNA sequences

Molecular mechanics calculations have been used to determine the preferred physical association sites of the known alkylating agent dimethyl aziridinium ion (Az⁺) and a CH prototype test probe with B-form, tetrameric DNA sequences. Electrostatic interactions are most important in determining these preferential physical association sites. In turn, the intermolecular energy minima depend on the charge distribution assigned to the DNA sequence. However, for three reported DNA charge distributions, only two distinct sets of energy minima were obtained for the CH-like ion interacting with (G-C)₄, (A-T)₄, and [(G-C)·(A-T)]₂ deoxyribonucleic acids. These minima correspond to physical association geometries in which the CH-like ion is near known alkylation sites. The results of the Az⁺ … [(G-C)·(A-T)]₂ interaction are virtually identical to those found for the CH-like ion. Aqueous solvation energetics have little effect on the physical association of Az⁺ with [(G-C)·(A-T)]₂.