Conformational analysis of cyclic dipeptides: I. , , , and

Conformational analysis of two pairs of synthetic cyclodipeptides formed by interaction of both side chain functional groups ( , and ) and of the main and side chains ( , and ) was achieved by the method of molecular mechanics. The energetically optimal conformational states of the molecules under study were determined. It was shown that the conformational motility of cyclic system of the compounds under study depends on the relative arrangement of the amide groups and the number of atoms in the cycle.     

Ethane and n-pentane in exhaled breath are biomarkers of exposure not effect

The relationship of exhaled ethane and n-pentane to exhaled NO, carbonylated proteins, and indoor/outdoor atmospheric pollutants were examined in order to evaluate ethane and n-pentane as potential markers of airway inflammation and/or oxidative stress. Exhaled NO and carbonylated proteins were found to have no significant associations with either ethane (p = 0.96 and p = 0.81, respectively) or n-pentane (p = 0.44 and 0.28, respectively) when outliers were included. In the case where outliers were removed n-pentane was found to be inversely associated with carbonylated proteins. Exhaled hydrocarbons adjusted for indoor hydrocarbon concentrations were instead found to be positively associated with air pollutants (NO, NO₂ and CO), suggesting pollutant exposure is driving exhaled hydrocarbon concentrations. Given these findings, ethane and n-pentane do not appear to be markers of airway inflammation or oxidative stress.     

Conformational analysis of glycosaminoglycans. I. Charge distributions, torsional potentials, and steric maps

An initial study of the charge distributions and torsional potentials for (1→4)-linked disaccharides, and a steric energy-map for (1→4)-linked disaccharides is reported for six acidic glycosaminoglycans. The charge distributions have been computed by the CNDO quantum-mechanical procedure, together with a molecular-decomposition technique. The intrinsic torsional potential has been computed by using CNDO energies and empirical potential-energies. The intrinsic torsional potential is two-dimensional. The general steric-map for a (1→4)-linked disaccharide will be useful for simplifying future conformational analyses of glycosaminoglycans. Wherever possible, comparisons between theory and experiment are presented or cited.     

Conformational analysis of Amphotericin B I. Isolated molecule

Theoretical conformational analysis have been performed on an isolated Amphotericin B molecule as a first step toward theoretical investigations of molecular association. Analysis of the conformational space of this cyclic molecule have been performed using a constrained energy minimization procedure in order to keep the molecule closed in the right way. Results show that Amphotericin B can be seen as a rigid molecule and that a unique energetically stable conformer can be found for this molecule under different physico-chemical conditions.     

Synthesis and secretion of hydroxyproline containing macromolecules in carrots. I. Kinetic analysis

When disks of carrot (Daucus carota) phloem parenchyma are incubated for 6 days there is a 10-fold increase in cell wall hydroxyproline due to the synthesis and secretion of hydroxyproline-containing macromolecules. The synthesis of these molecules and their secretion are demonstrated by measuring the kinetics of incorporation and of chase of ¹⁴C-proline and hydroxyproline in different fractions of the cytoplasm and the cell wall. The hydroxyproline-containing molecules which are secreted are associated with the membranous organelles of the cytoplasm. They can be fractionated into trichloroacetic acid-soluble and trichloroacetic acid-precipitated fractions. The properties of the trichloroacetic acid-soluble fraction associated with the membranous organelles are consistent with its role as a cell wall precursor.     

Conformational analysis of tachykinins. I. N-terminal fragments of substance P, physalemin, hylambatin, and uperolein]

Theoretical conformational analysis of N-terminal fragments of the title peptides has been carried out using the potential energy calculations. The number of conformational states for each fragment is very limited, and they are easily interconverted. Since these fragments cannot form alpha-helises, it is unlikely that upon binding of tachikinins to their receptors, their N-terminal fragments could overcome the hydrophobic barrier of the cell membrane's lipid belayer.     

Spatial structure of myelopeptides: I. Conformational analysis of MP-1, MP-2, and MP-3

Theoretical conformational analysis was used to study the spatial structure and conformational properties of myelopeptides, bone-marrow peptide mediators. The low-energy conformations of three hexapeptides MP-1 (Phe-Leu-Gly-Phe-Pro-Thr), MP-2 (Leu-Val-Val-Tyr-Pro-Trp), and MP-3 (Leu-Val-Cys-Tyr-Pro-Gln) were found, the values of dihedral angles of the backbone and side chains of the amino acid residues constituting these peptides were determined, and the energies of intra- and interresidual interactions were estimated.     

Conformational analysis of amino acids and peptides using specific isotope substitution. I. Conformation of L-phenylalanylglycine.

L-Phenylalanyl-(R)-[²H]glycine, L-valyl-(R)-[²H]glycine, and L-phenylalanyl [¹⁵N]glycine were prepared. Assignments for pro-R and pro-S proton NMR signals of the glycine residue were done and coupling constants between proton and ¹⁵N were obtained. Based on the data an attempt to explain the origin of the nonequivalence of the glycine methylene protons was made, and a conformational model for L-phenylalanylglycine is proposed.     

Evolution of macromolecules: I. Dual coding systems

The evolution of proteins determined by two independently mutable coding mechanisms (e.g., one in which nucleic acids operate with unit coding ratio) has been analyzed kinetically in two ways. The first presumes a system of mutating and reproducing proteins; the dependent variables are the numbers of the various kinds of proteins—wild types, and mutants obtained by mutations in one or another of the two coding mechanisms. The second approach deals with kinds rather than numbers of proteins; the reproductive element in the evolving system is dealt with by assuming a specific rate of extinction for members of each protein class, due to the occurrence of lethal mutations in the proteins themselves or in other proteins in the organisms that carry them. If the two kinds of mutants occur at different rates, it is shown in both treatments that time will not necessarily extinguish the initial advantage of one of them—that is, the notion that the slower class will eventually occur often enough to produce a random distribution of the two classes after long periods of evolution is not in general true. The effects of mutation rate, reproduction rate, and extinction rate on the distribution of the various protein classes are analyzed. Contribution No. 666 from the Division of Basic Health Sciences.     

Tertiary structure of myelopeptides. II. Conformational analysis of Phe-Arg-Pro-Arg-Ile-Met-Thr-Pro, Val-Val-Tyr-Pro-Asp, and Val-Asp-Pro-Pro

Theoretical conformational analysis was used to study the spatial structure and conformational properties of myelopeptides, bone marrow peptide mediators. The low-energy conformations of myelopeptides MP-4 (Phe-Arg-Pro-Arg-Ile-Met-Thr-Pro), MP-5 (Val-Val-Tyr-Pro-Asp), and MP-6 (Val-Asp-Pro-Pro) were found; the values of dihedral angles of backbone and side chains of the amino acid residues were determined; and the energies of intra- and interresidual interactions were estimated.     

Vibrational analysis of peptides,polypeptides, and proteins. I. Polyglycine I

A force field has been refined for the antiparallel chain-rippled sheet structure of polyglycine I. Transition dipole coupling and hydrogen bonding are explicitly taken into account. Amide I and amide II mode splittings are well accounted for, the latter also providing a quantitative explanation of the amide A and amide B mode frequencies and intensities. In addition to predicting other features of the vibrational spectrum of polyglycine I, this force field is completely transferable to other β polypeptides, even though these have the antiparallel chainpleated sheet structure.     

Conformational changes in transfer RNA. I. Equilibrium theory

We report the results of semi-empirical calculations describing thermodynamic properties of transfer RNA conformations. The most important new features of the procedure are: (1) the use of parameters obtained from model oligoribonucleotides to evaluate the free energy of helical regions and small hairpin loops, and (2) the use of a model which is somewhat more realistic than the freely jointed chain for evaluating internal loops and intermediate size hairpin loops. The new parameters lead to important quantitative and qualitative differences from predictions which would have been made in the past and lead to a priori predictions of tRNA melting temperatures which are within about 6°C of the experimental values. The results suggest the following conclusions: (1) The early melting transition observed in several tRNA's is partly the result of tertiary unfolding, and partly the result of the loss of some secondary structure. (2) The part of the secondary structure which melts during the early transition is different for different tRNA's. For fMet and Tyr from E. coli, the calculations predict that the dihydrouradiene arm melts out early. For yeast Phe the acceptor stem and anticodon helix melt first. (3) The results also suggest the possibility that tertiary unfolding and early secondary structural melting do not occur independently but are coupled, so that the two types of structure are probably mutually stabilizing.     

Conformational changes in E. coli DNA topoisomerase I.

DNA topoisomerases are the enzymes responsible for maintaining the topological states of DNA. In order to change the topology of DNA, topoisomerases pass one or two DNA strands through transient single or double strand breaks in the DNA phosphodiester backbone. It has been proposed that both type IA and type II enzymes change conformation dramatically during the reaction cycle in order to accomplish these transformations. In the case of Escherichia coli DNA topoisomerase I, it has been suggested that a 30 kDa fragment moves away from the rest of the protein to create an entrance into the central hole in the protein. Structures of the 30 kDa fragment reveal that indeed this fragment can change conformation significantly. The fragment is composed of two domains, and while the domains themselves remain largely unchanged, their relative arrangement can change dramatically.