Barrier to rotation and conformation of the NB2 group in cytosine and its derivatives. Part I. Theoretical study of cytosine.

A theoretical investigation of the conformation of the amino group in cytosine has been performed by the CNDO/2 and INDO methods. The results suggest that from the energetical point of view the conformation of the amino group is not stable in the course of rotation. It changes its hybridization from sp2-like in the planar case to sp3-like in the transition state. The physical basis of the barrier to rotation of this group around the C4-N7 bond are discussed. Some comments on the solvent dependence of the electronic absorption spectra of cytosine are presented.     

Theoretical study of the electronic structure and conformation of polysilole and its derivatives

The electronic structures and conformations in the optimized geometries of polysilole and its derivatives are studied theoretically, using the one-dimensional tight-binding self-consistent field crystal orbital (SCF-CO) method. It has been found that the copolymer formed by alternating aromatic silole and quinoid thiophene has a relatively small bandgap value. We observe that polysilole may show an interesting thermochromic behavior, because the conformation of polysilole is considerably easier to change at lower temperature than that of polythiophene.     

Interaction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system. 1. Biochemical studies.

Lipoamide dehydrogenase or dihydrolipoamide dehydrogenase (EC 1.8.1. 4) is the E3-protein component of the mitochondrial 2-oxoacid dehydrogenase multienzyme complexes. It is also the L-protein component of the glycine decarboxylase system. Although the enzymology of this enzyme has been studied exhaustively using free lipoamide as substrate, no data are available concerning the kinetic parameters of this enzyme with its physiological substrates, the dihydrolipoyl domain of the E2 component (dihydrolipoyl acyltransferase) of the 2-oxoacid dehydrogenase multienzyme complexes or the dihydrolipoyl H-protein of the mitochondrial glycine decarboxylase. In this paper, we demonstrate that Tris(2-carboxyethyl)phosphine, a specific disulfide reducing agent, allows a continuous reduction of the lipoyl group associated with the H-protein during the course of the reaction catalysed by the L-protein. This provided a valuable new tool with which to study the catalytic properties of the lipoamide dehydrogenase. The L-protein displayed a much higher affinity for the dihydrolipoyl H-protein than for free dihydrolipoamide. The oxidation of the dihydrolipoyl H-protein was not affected by the presence of structurally related analogues (apoH-protein or octanoylated H-protein). In marked contrast, these analogues strongly and competitively inhibited the decarboxylation of the glycine molecule catalysed by the P-protein component of the glycine decarboxylase system. Small unfolded proteolytic fragments of the H-protein, containing the lipoamide moiety, displayed Km values for the L-protein close to that found for the H-protein. On the other hand, these fragments were not able to promote the decarboxylation of the glycine in the presence of the P-protein. New highly hydrophilic lipoate analogues were synthesized. All of them showed Km and kcat/Km values very close to that found for the H-protein. From our results we concluded that no structural interaction is required for the L-protein to catalyse the oxidation of the dihydrolipoyl H-protein. We discuss the possibility that one function of the H-protein is to maintain a high concentration of the hydrophobic lipoate molecules in a nonmicellar state which would be accessible to the catalytic site of the lipoamide dehydrogenase.     

Theoretical study of prostaglandin E2 conformation

The theoretical conformational analysis of PGE2 has been performed using semiempirical approach and fixed values of the bond length and valence angles. A set of low-energy conformations was obtained for the alpha-chain and the whole PGE2 molecule. Unlike the PGE1 molecule, PGE2 alpha-chain prefers semifolded conformations. The hairpin structures with the parallel orientation of alpha- and omega-chains are the lowest-energy conformations of PGE2 conformations of PGE1 and PGE2. Sterically similar explain the similar biological activity of the two molecules.     

On the conformation of the disulphide group in L-cystine and its derivatives.

The terminal groups in cystine are asymmetric and hence the dissulphide group with right and left chirality may not have equal energy. An attempt is made to resolve this problem through energy calculation using semi-empirical methods involving non-bonded and electrostatic interactions and simple Pauling type torsional potential for the disulphide group. The results are discussed in the light of experimental data.     

DNA flexibility as a function of allomorphic conformation and of base sequence.

Systematic theoretical modeling of symmetric DNA oligomers, carried out earlier for the B conformation, is now extended to A-DNA. In contrast to the previous results, it is found that A-DNA shows no multiplicity of low-energy substate conformations. The possibilities of the Jumna algorithm are subsequently applied to studying deformations of the oligomers. Controlled winding and stretching deformations are used to study how the two allomorphs and different base sequences absorb such external stress. The results help explain the internal mechanics of the DNA double helix and the extent to which fine structure influences this behavior. The results point to some differences between the A and B double helices, but also to many similarities. Sequence effects on flexibility are relatively limited compared to their impact on optimal energy conformations. It is also shown that the conformational substates detected for B-DNA oligomers are preserved under deformation, but have little influence on its energetics.     

Effect of the terminal amino group of a linker arm and its length at the C5 position of a pyrimidine nucleoside on the thermal stability of DNA duplexes

2'-Deoxyuridine derivatives bearing a substituent at the C5-position, which has a different chain length and a different functional group (methyl or amino), were synthesized and incorporated into oligodeoxyribonucleotides. The effect of the substituent groups in the major groove on the stability of the duplexes was investigated by UV melting experiments. It was found that the stabilization of these duplexes by a terminal amino group depended on the length of a linker arm.     

Interaction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system 2. Crystal structures of H- and L-proteins.

The glycine decarboxylase complex consists of four different component enzymes (P-, H-, T- and L-proteins). The 14-kDa lipoamide-containing H-protein plays a pivotal role in the complete sequence of reactions as its prosthetic group (lipoic acid) interacts successively with the three other components of the complex and undergoes a cycle of reductive methylamination, methylamine transfer and electron transfer. With the aim to understand the interaction between the H-protein and its different partners, we have previously determined the crystal structure of the oxidized and methylaminated forms of the H-protein. In the present study, we have crystallized the H-protein in its reduced state and the L-protein (lipoamide dehydrogenase or dihydrolipoamide dehydrogenase). The L-protein has been overexpressed in Escherichia coli and refolded from inclusion bodies in an active form. Crystals were obtained from the refolded L-protein and the structure has been determined by X-ray crystallography. This first crystal structure of a plant dihydrolipoamide dehydrogenase is similar to other known dihydrolipoamide dehydrogenase structures. The crystal structure of the H-protein in its reduced form has been determined and compared to the structure of the other forms of the protein. It is isomorphous to the structure of the oxidized form. In contrast with methylaminated H-protein where the loaded lipoamide arm was locked into a cavity of the protein, the reduced lipoamide arm appeared freely exposed to the solvent. Such a freedom is required to allow its targeting inside the hollow active site of L-protein. Our results strongly suggest that a direct interaction between the H- and L-proteins is not necessary for the reoxidation of the reduced lipoamide arm bound to the H-protein. This hypothesis is supported by biochemical data [Neuburger, M., Polidori, A.M., Piètre, E., Faure, M., Jourdain, A., Bourguignon, J., Pucci, B. & Douce, R. (2000) Eur. J. Biochem. 267, 2882-2889] and by small angle X-ray scattering experiments reported herein.     

Circular dichroism of polynucleotides: dimers as a function of conformation

Working within the restrictions of a model, we have calculated the circular dichroism of the dinucleoside phosphates ApA, CpC, and CpA for various conformations. Comparing the calculated curves with those measured in aqueous solution we find agreement for (1) ApA as a right-handed helix with both bases either as in B-form DNA, or else rotated 180° around the glycosidic bond, (2) CpC as the right-handed conformation with both bases as in DNA, (3) ApC as either the right-handed conformation with both bases as in DNA, or else as a left-handed helix with both bases rotated 180°, and (4) CpA as either a left-handed helix with both bases in a left-handed DNA, or else in the right-handed conformation with both bases rotated 180°. In addition, we have investigated circular dichroism as a measure of unstacking. We find that opening the bases to a 90° total angle (base planes perpendicular) reduces the intensity of the calculated bands to 20% of their original value. Further, we find that allowing the sliding of one base past the other does not lead to a temperature dependence consistent with experiment.     

A parametric model of muscle moment arm as a function of joint angle: Application to the dorsiflexor muscle group in mice

A parametric model was developed to describe the relationship between muscle moment arm and joint angle. The model was applied to the dorsiflexor muscle group in mice, for which the moment arm was determined as a function of ankle angle. The moment arm was calculated from the torque measured about the ankle upon application of a known force along the line of action of the dorsiflexor muscle group. The dependence of the dorsiflexor moment arm on ankle angle was modeled as r=R sin(a+Δ), where r is the moment arm calculated from the measured torque and a is the joint angle. A least-squares curve fit yielded values for R, the maximum moment arm, and Δ, the angle at which the maximum moment arm occurs as offset from 90°. Parametric models were developed for two strains of mice, and no differences were found between the moment arms determined for each strain. Values for the maximum moment arm, R, for the two different strains were 0.99 and 1.14 mm, in agreement with the limited data available from the literature. While in some cases moment arm data may be better fitted by a polynomial, use of the parametric model provides a moment arm relationship with meaningful anatomical constants, allowing for the direct comparison of moment arm characteristics between different strains and species.     

The terminal web. A reevaluation of its structure and function

The apical cytoplasm of epithelial cells of the small and large intestines has been examined by freeze-etch techniques as well as conventional and high voltage electron microscopy of sectioned material to gain a better understanding of the fine structural organization of the terminal web region. In the small intestine the terminal web exhibits a distinct stratification caused by the association of different sets of filaments with the three members of the junctional complex. Individual filaments of this network are closely associated with the sealing elements of the tight junctions, the surface of the core microfilament bundles, and the intermicrovillar plasma membrane. This region of the terminal web is the apical zone. The adherens zone appears as a band of interwoven filaments of two different diameters extending across the cytoplasm at the level of the intermediate junction. Within this region of the terminal web, individual 60-70 A actin-like filaments separate from the bundles of core microfilaments to interact with one another and with filaments of similar diameter from the zonula adherens. 100 A tonofilaments also contribute to the adherens zone, presumably stabilizing the orientation of the actin-like filaments. The basal zone which underlies the adherens zone consists of closely interwoven bundles of tonofilaments that are anchored to and interconnect the spot desmosomes. Within the large intestine the cytoplasmic microfilaments form a looser and less clearly stratified network which nevertheless retains the same basic organization found in the small intestine. Transmembrane linkers appear to originate within the cytoplasmic plaques of the spot desmosomes, pass through the plasma membranes, and meet in a staggered configuration in the intercellular space; these linkers may thus mediate the actual mechanical coupling between the cytoskeletal networks of tonofilament bundles of adjacent cells. This integrated system of cytoplasmic filaments and intercellular junctions endows the apical cytoplasm with both the flexibility and the stability necessary for the normal functioning of the epithelium.     

Theoretical studies on the electrical activity of pancreatic beta-cells as a function of glucose.

The electrical activity of pancreatic beta-cells, which has been closely correlated both with intracellular Ca2+ concentration and insulin release, is characterized by a biphasic response to glucose and bursts of spiking action potentials. Recent voltage clamp and single channel patch clamp experiments have identified several transmembrane ionic channels that may play key roles in the electrophysiological behavior of beta-cells. There is a hypothesis that Ca2+-activated K+ channels are responsible for both the resting potential during low glucose concentration and the silent phase during bursting. The discovery of the ATP-inactivated K+ channel raises the possibility that the current for this latter K+ channel may dominate the resting potential, while the Ca2+-activated K+ current dominates the silent phase potential between bursts. The recent discovery that Ca2+-activated K+ channels are pH sensitive raises an interesting possibility for the biphasic electrical response. In this paper, numerical methods are presented for evaluating these hypotheses against experimental evidence.     

Structure and function of the myoglobin containing octaethylhemin as a prosthetic group

Spectrophotometric titration of ferric octaethylporphyrin (OEP) with apomyoglobin revealed their 1:1 complex formation. Proton NMR spectrum of the OEP-reconstituted deoxymyoglobin exhibits an exchangeable peak from the proximal F8 histidine at 78.5 ppm, indicating the incorporation of iron OEP into the heme cavity to form the Fe-N(His-F8) bond. OEP metmyoglobin without external ligand has an iron-bound water that deprotonates above pH 7.8. Affinities of the aquometmyoglobin for several ionic ligands were comparable with those of native metmyoglobin. Deoxy OEP myoglobin at 25 degrees C reversibly binds oxygen with an affinity of P50 = 0.8 mm Hg, which is similar to that of native protein. These results indicate that iron OEP serves as a prosthetic group for myoglobin with normal function, despite the significant structural and electronic difference between OEP and protoporphyrin. The unexpected functional similarity between native and OEP myoglobins was interpreted in terms of a structural perturbation at the heme distal site caused by introduction of bulky OEP into the heme pocket.     

Vibrational CD studies of the solution conformation of simple alanyl peptides as a function of pH

The CH-stretching vibrational CD (VCD) spectra of glycyl-L-alanine, L-alanylglycine, and L-alanyl-L-alanine have been studied at neutral, high, and low pH in D2O solution. The intense positive VCD band attributed to the C alpha H stretch of the alanyl residue in glycyl-L-alanine at neutral pH is absent in L-alanylglycine. In contrast to the VCD spectra of L-alanine, the positive methine-stretching VCD band in glycyl-L-alanine and L-alanyl-L-alanine is still present at pH 2. Based on the ring current mechanism, the VCD spectra are consistent with the presence of a five-membered CO...HN intramolecular hydrogen-bonded ring between the C-terminal carboxylate and peptide NH groups at neutral and high pH; and a seven-membered COH...O = C hydrogen-bonded ring between the C-terminal carboxyl OH and peptide C = O groups at low pH. In the N-terminal alanyl residue, the peptide C = O group is hydrogen bonded to the NH trans to the methine bond. The CH-stretching VCD spectra of L-alanyl-L-alanyl-L-alanine at neutral pH are consistent with two intramolecularly hydrogen-bonded conformations for the central alanyl residue.     

Reconstruction of shoulder function using a reflected long head biceps: a moment arm study

A tendon transfer technique is proposed for the reconstruction of the paralyzed shoulders secondary to brachial plexus injury. This innovative technique does not require bone-to-bone or tendon to-bone fixation, and attempts to overcome other clinical limitations such as those due to insufficient length of donor muscle. The approach is referred to as the reflected long head biceps (RLHB) technique. The long head of biceps tendons is utilized as a bridging tendon graft. Two surgical alternatives, namely the through-deltoid (TD) pathway and the sub-deltoid (SD) pathway, were studied. The moment arms of the transferred tendons were assessed and reported. The TD technique yielded a larger moment than the SD technique. In the plane 30 degrees anterior to the scapular plane, the average moment arms were 3.8cm TD and 3.0cm SD at zero elevation. Such differences tended to further widen with increasing elevation. At 80 degrees elevation, the moment arms became 3.2cm TD and 1.2cm SD. The results supported the clinical feasibility of this RLHB tendon transfer approach.     

Preferred conformation of the benzyloxycarbonyl-amino group in peptides

Structural parameters, derived from X-ray crystallographic data, have been compiled for 35 derivatives of amino acids, peptides, and related compounds, which contain the N-terminal benzyloxycarbonyl (Z) group. The geometry of the urethane moiety of this end group is closely similar to that of the tert-butoxycarbonyl (Boc) group, except for a relaxation of some bond angles because the Z group is sterically less crowded than the Boc group. For the same reason, the Z group has greater conformational flexibility. As a result, packing forces in the crystal may cause greater deformations of bond angles, resulting in larger variations of observed bond lengths and bond angles than in Boc-peptide crystals. The aromatic rings of the Z end groups tend to stack in crystals. Conformational energy calculations indicate that most conformations of Z-amino acid-N'-methylamides and of corresponding Boc derivatives have similar dihedral angles and relative energies, i.e. the nature of the N-terminal end group has little effect on the conformational preferences of the residue next to it. In particular, the computed fraction of molecules with a cis urethane (C-N) bond is similar for the two derivatives: 0.51 and 0.42 in Boc-Pro-NHCH3 and Z-Pro-NHCH3, respectively, and 0.02 in the two Ala derivatives. There exist several computed conformations of Z-Ala-NHCH3 and Z-Pro-NHCH3 in which the phenyl ring and the C-terminal methylamide group are close to each other. Because of favorable nonbonded interactions, such conformations are of low energy.