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Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase.

Combined QM/MM molecular dynamics simulations have been carried out for the dehalogenation reaction of the nucleophilic displacement of dichloroethane catalyzed by haloalkane dehalogenase. The computed chlorine kinetic isotope effects and free energies of activation in the wild-type and the Phe172Trp mutant enzyme are found to be consistent with experiment. In comparison with the uncatalyzed model reaction in water, the enzyme lowers the activation barrier by about 16 kcal/mol. The enormous enzymatic action was attributed to a combination of contributions from a change in the solvation effect and transition state stabilization. The unique features of tryptophan's ability to interact favorably with hydrophobic substrates and to form hydrogen bonds to the leaving group chloride ion at the transition state enable both factors to make significant contributions to the barrier lowering mechanism in the enzyme. This is in contrast to the reference reaction in water, in which hydrogen bonding interactions are weakened at the transition state because of dispersed charge distribution at the transition state relative to that in the reactant and product states.

Amino Acid Substitution↗

Theoretical study on tertiary structural elements of beta-peptides: nanotubes formed from parallel-sheet-derived assemblies of beta-peptides.

Parallel or polar strands of beta-peptides spontaneously form nanotubes of different sizes in a vacuum as determined by ab initio calculations. Stability and conformational features of [CH3CO-(beta-Ala)k-NHCH3]l (1 < or = k < or = 4, 2 < or = l < or = 4) models were computed at different levels of theory (e.g., B3LYP/6-311++G(d,p)// B3LYP/6-31G(d), with consideration of BSSE). For the first time, calculations demonstrate that sheets of beta-peptides display nanotubular characteristics rather than two-dimensional extended beta-layers, as is the case of alpha-peptides. Of the configurations studied, k = l = 4 gave the most stable nanotubular structure, but larger assemblies are expected to produce even more stable nanotubes. As with other nanosystems such as cyclodextrane, these nanotubes can also incorporate small molecules, creating a diverse range of applications for these flexible, biocompatible, and highly stable molecules. The various side chains of beta-peptides can make these nanosystems rather versatile. Energetic and structural features of these tubular model systems are detailed in this paper. It is hoped that the results presented in this paper will stimulate experimental research in the field of nanostructure technology involving beta-peptides.

Hydrogen Bonding↗

Design of potent dicyclic (4-10/5-8) gonadotropin releasing hormone (GnRH) antagonists.

With the ultimate goal of identifying a consensus bioactive conformation of GnRH antagonists, the compatibility of a number of side chain to side chain bridges in bioactive analogues was systematically explored. In an earlier publication, cyclo[Asp(4)-Dpr(10)]GnRH antagonists with high potencies in vitro and in vivo had been identified.(1) Independently from Dutta et al. (2) and based on structural considerations, the cyclic [Glu(5)-Lys(8)] constraint was also found to be tolerated in GnRH antagonists. We describe here a large number of cyclic (4-10) and (5-8) and dicyclic (4-10/5-8) GnRH antagonists optimized for affinity to the rat GnRH receptor and in vivo antiovulatory potency. The most potent monocyclic analogues were cyclo(4-10)[Ac-DNal(1), DFpa(2),DTrp(3),Asp(4),DArg(6),Xaa(10)]GnRH with Xaa = D/LAgl (1, K(i) = 1.3 nM) or Dpr (2, K(i) = 0.36 nM), which completely blocked ovulation in cycling rats after sc administration of 2.5 microgram at noon of proestrus. Much less potent were the closely related analogues with Xaa = Dbu (3, K(i) = 10 nM) or cyclo(4-10)[Ac-DNal(1), DFpa(2),DTrp(3),Glu(4),DArg(6),D/LAgl(10)]GnRH (4, K(i) = 1.3 nM). Cyclo(5-8)[Ac-DNal(1),DCpa(2),DTrp(3),Glu(5),DArg++ +(6),Lys(8), DAla(10)]GnRH (13), although at least 20 times less potent in the AOA than 1 or 2 with similar GnRHR affinity (K(i) = 0.84 nM), was found to be one of the most potent in a series of closely related cyclo(5-8) analogues with different bridge lengths and bridgehead chirality. The very high affinity of cyclo(5,5'-8)[Ac-DNal(1), DCpa(2),DPal(3),Glu(5)(betaAla),DArg(6),(D or L)Agl,(8)DAla(10)]GnRH 14 (K(i) = 0.15 nM) correlates well with its high potency in vivo (full inhibition of ovulation at 25 microgram/rat). Dicyclo(4-10/5-8)[Ac-DNal(1),DCpa(2),DTrp(3),Asp (4),Glu(5),DArg(6), Lys(8),Dpr(10)]GnRH (24, K(i) = 0.32 nM) is one-fourth as potent as 1 or 2, in the AOA; this suggests that the introduction of the (4-10) bridge in 13, while having little effect on affinity, restores functional/conformational features favorable for stability and distribution. To further increase potency of dicyclic antagonists, the size and composition of the (5-8) bridge was varied. For example, the substitution of Xbb(5') by Gly (30, K(i) = 0.16 nM), Sar (31, K(i) = 0.20 nM), Phe (32, K(i) = 0.23 nM), DPhe (33, K(i) = 120 nM), Arg (36, K(i) = 0.20 nM), Nal (37, K(i) = 4.2 nM), His (38, K(i) = 0.10 nM), and Cpa (39, K(i) = 0.23 nM) in cyclo(4-10/5,5'-8)[Ac-DNal(1),DCpa(2),DPal(3),Asp(4),G lu(5)(Xbb(5')), DArg(6),Dbu,(8)Dpr(10)]GnRH yielded several very high affinity analogues that were 10, ca. 10, 4, >200, 1, ca. 4, >2, and 2 times less potent than 1 or 2, respectively. Other scaffolds constrained by disulfide (7, K(i) = 2.4 nM; and 8, K(i) = 450 nM), cyclo[Glu(5)-Aph(8)] (16, K(i) = 20 nM; and 17, K(i) = 0.28 nM), or cyclo[Asp(5)-/Glu(5)-/Asp(5)(Gly(5'))-Amp(8)] (19, K(i) = 1.3 nM; 22, K(i) = 3.3 nM; and 23, K(i) = 3.6 nM) bridges yielded analogues that were less potent in vivo and had a wide range of affinities. The effects on biological activity of substituting DCpa or DFpa at position 2, DPal or DTrp at position 3, and DArg, DNal, or DCit at position 6 are also discussed. Interestingly, monocyclo(5-8)[Glu(5), DNal(6),Lys(8)]GnRH (18, K(i) = 1. (ABSTRACT TRUNCATED)

Animals↗

Synthesis of new macrocyclic chiral manganese(III) Schiff bases as catalysts for asymmetric epoxidation.

We describe a general synthetic strategy for the preparation of a series of macrocyclic chiral manganese(III) salen complexes. The developed reaction pathway allows the modulation of the different key groups, namely, the chiral diimine, the bulky substituents in positions 3 and 3', and the linker used in the macrocyclization of the Schiff base. The different complexes presented here illustrate these readily available structural variations. The catalytic properties of the catalysts (5 mol %) were improved for the asymmetric epoxidation of 2,2'-dimethylchromene with NaOCl or H2O2 as oxygen atom donor. A large range of enantiomeric excesses was obtained (ee values from 30% to 96%), depending on the features and the stability of the complexes. The most efficient catalyst, in terms of stereoinduction (ee value = 96%), contains a diiminocyclohexyl moiety, ethyl groups in positions 3 and 3', and a short polyether junction arm.

Catalysis↗

Theoretical study on structures and stability of Si2CP isomers.

The structures, energetics, spectroscopies, and isomerization of various doublet Si2CP species are explored theoretically. In contrast to the previously studied SiC2N and SiC2P radicals that have linear SiCCN and SiCCP ground states, the title Si2CP radical has a four-membered-ring form cSiSiPC 1 (0.0 kcal/mol) with Si-C cross-bonding as the ground-state isomer at the CCSD(T)/6-311G(2df)//B3LYP/6-311G(d)+ZPVE level, similar to the Si2CN radical. The second low-lying isomer 2 at 11.6 kcal/mol has a SiCSiP four-membered ring with C-P cross-bonding, yet it is kinetically quite unstable toward conversion to 1 with a barrier of 3.5 kcal/mol. In addition, three cyclic species with divalent carbene character, i.e., cSiSiCP 7, 7' with C-P cross-bonding and cSiCSiP 8 with Si-Si cross-bonding, are found to possess considerable kinetic stability, although they are energetically high lying at 44.4, 46.5, and 41.4 kcal/mol, respectively. Moreover, a linear isomer SiCSiP 5 at 44.3 kcal/mol also has considerable kinetic stability and predominantly features the interesting cumulenic /Si=C=Si=P/* form with a slight contribution from the silicon-phosphorus triply bonded form /Si=C*-Si[triple bond]P/. The silicon-carbon triply bonded form *Si[triple bond]C-Si[triple bond]P/ has negligible contribution. All five isomers are expected to be observable in low-temperature environments. Their bonding nature and possible formation strategies are discussed. For relevant species, the QCISD/6-311G(d) and CCSD(T)/6-311+G(2df) (single-point) calculations are performed to provide more reliable results. The calculated results are compared to those of the analogous C3N, C3P, SiC2N, and Si2CN radicals with 17 valence electrons. Implications in interstellar space and P-doped SiC vaporization processes are also discussed.

Journal Article↗

Separating the contributions to 15N transverse relaxation in a fibronectin type III domain.

In proteins, dynamic mobility is an important feature of structure, stability, and biomolecular recognition. Uniquely sensitive to motion throughout the milli- to picosecond range, rates of transverse relaxation, R2, are commonly obtained for the characterization of chemical exchange, and the construction of motional models that attempt to separate overall and internal mobility. We have performed an in-depth study of transverse relaxation rates of backbone 15N nuclei in TNfn3(1-90), the third fibronectin type III domain from human tenascin. By combining the results of spin-echo (CPMG) and off-resonance T1 rho experiments, we present R2 rates at effective field strengths of 2 to 40 krad/s, obtaining a full spectrum of 16 independent R2 data points for most residues. Collecting such a large number of replicate measurements provides insight into intrinsic uncertainties. The median standard deviation in R2 for non-exchanging residues is 0.31, indicating that isolated measurements may not be sufficiently accurate for a precise interpretation of motional models. Chemical exchange events on a timescale of 570 microseconds were observed in a cluster of residues at the C terminus. Rates of exchange for five other residues were faster than the sampled range of frequencies and could not be determined. Averaged 'exchange free' transverse relaxation rates, R2(0), were used to calculate the diffusion tensor for rotational motion. Despite a highly asymmetric moment of inertia, the narrow angular dispersion of N-H vectors within the beta sandwich proves insufficient to define deviations from isotropic rotation. Loop residues provide exclusive evidence for axially symmetric diffusion (Dpar/Dper = 1.55).

Diffusion↗

Acoustic dimensions of hearing-impaired speakers' intelligibility.

Regression and principal components analyses were employed to study the relationship between three measures of speech intelligibility and 12 segmental, prosodic, and hearing ability parameters in 20 severely to profoundly hearing-impaired speakers. Regression analyses on the original 12 parameters revealed that cognate pair voice onset time differences and mean sentence duration strongly predicted speech intelligibility based on readings of isolated word and contextual speech material. A principal components analysis derived four factors that accounted for the majority of the variance in the original 12 parameters. Subsequent regression analyses using the four factors as predictor variables revealed two factors with strong relationships to the speech intelligibility measures. One factor primarily reflected segmental production processes related to the temporal and spatial differentiation of phonemes, whereas the other factor reflected prosodic features and production stability. These results are consistent with prior research that suggests independent primary and secondary roles for segmental and prosodic speech characteristics, respectively, in determining intelligibility in severely to profoundly hearing-impaired speakers.

Adult↗

The prosequence of human lactase-phlorizin hydrolase modulates the folding of the mature enzyme.

The efficient transport of proteins along the secretory pathway requires that the polypeptide adopts a stably folded conformation to egress the endoplasmic reticulum (ER). The transport-competent precursor of the brush border enzyme LPH, pro-LPH, undergoes an intracellular cleavage process in the trans-Golgi network between Arg(734) and Leu(735) to yield LPH beta(initial). The role of the prodomain comprising the N-terminally located 734 amino acids of pro-LPH, LPH alpha, in the folding events of LPH beta(initial) has been analyzed by the individual expression of both forms in COS-1 cells. Following synthesis at 37 degrees C LPH beta(initial) acquires a misfolded and enzymatically inactive conformation that is degraded by trypsin. A temperature shift to 20 degrees C generates a stable, trypsin-resistant, and enzymatically active LPH beta(initial) indicating that the individual expression of LPH beta(initial) results in a temperature-sensitive conformation. This form interacts at non-permissive temperatures sequentially with the ER chaperones immunoglobulin-binding protein and calnexin resulting in an ER retention. The LPH alpha prodomain resides in the ER when individually expressed. It reveals compact structural features that are stabilized by disulfide bridges. LPH alpha and LPH beta(initial) readily interact with each other upon coexpression, and this interaction appears to trigger the formation of a trypsin-resistant, correctly folded, enzymatically active, and transport-competent LPH beta(initial) polypeptide. These data clearly demonstrate that the proregion of pro-LPH is an intramolecular chaperone that is critically essential in facilitating the folding of the intermediate form LPH beta(initial) in the context of the pro-LPH polypeptide.

Animals↗

Proton gradients during salt adaptation of Synechococcus.

The ability of cells to energize their membranes during salt-adaptation as measured by delta pH was studied using the electron spin resonance (ESR) spin probe technique. Salt-adaptated cells have the following features: an increased stability of delta pH across the cytoplasmic membrane and a significantly lower rate of delta pH formation across the thylakoid membrane. Therefore, during salt-adaptation, the cytoplasmic membrane takes over the role of primary energizing membrane from the thylakoid membrane. In contrast to non-adapted cells, delta pH across the thylakoid membrane of salt-grown cells is higher under respiratory than under photosynthetic conditions.

Adaptation, Physiological↗

Incidence of arrhythmias in dental anaesthesia: a cross-over comparison of halothane and isoflurane.

Fifty patients received halothane anaesthesia during the surgical removal of 3rd molars from one side of the mouth and isoflurane during extractions on the other. Degree of surgical difficulty was matched, and end-tidal PCO2 did not differ significantly between sides. A significantly higher incidence of arrhythmias occurred during halothane, compared with isoflurane, anaesthesia. This difference occurred primarily when halothane was given for the first operated side. A clinically important feature of the stability of cardiac rhythm during isoflurane anaesthesia was demonstrated--when frequent ectopic beats occur during halothane anaesthesia, a significant decrease in the rate of premature contractions occurs within 3 min of discontinuing halothane and introducing isoflurane.

Adult↗

Hyperthermostable mutants of Bacillus licheniformis alpha-amylase: thermodynamic studies and structural interpretation.

This paper provides further understanding of the thermodynamic and structural features determining the stability of Bacillus licheniformis alpha-amylase (BLA) at two crucial positions, His133 and Ala209. Results of protein modelling and saturated site-directed mutagenesis at position 133 and 209 have been reported in a previous paper (Declerck et al., 1995, Prot. Engng, 8, 1029-1037). In the first part of the present work, evidence is presented supporting the hypothesis that the stabilizing mutations reduce the rate of initial unfolding of the enzyme during the reversible step of the inactivation reaction and do not modify the irreversible processes undergone subsequently by the unfolded molecules. In the second part, we have examined the three-dimensional structure of BLA which has been determined recently by X-ray analysis (Machius et al., 1995, J. Mol. Biol., 246, 545-559). This analysis showed that our previous predictions made from molecular modelling were partly correct. At position 209, the effect of the stabilizing substitutions can be explained by a groove-filling effect reinforcing the hydrophobic packing between two helices of the central domain, while preserving a well-ordered water structure at the surface. At position 133, the stabilizing substitutions must compensate the loss of the hydrogen bond network in which the original histidine side-chain is involved; this compensation could be achieved through enhanced hydrophobic side-chain interactions within the beta-sheet where residue 133 is located, which correlates with the propensity of the residue to form and maintain a beta-strand conformation of the main chain at this position.

Alanine↗

The surgical treatment of nerve root compression caused by scoliosis of the lumbar spine.

Twenty patients with radicular compression caused by scoliosis of the lumbar spine with attendant spondyloarthrosis have been relieved of pain with restoration of function following surgical decompression. The stenosis caused by arthropathy is alleviated by foraminotomy and facetectomy after laminectomy over multiple levels along the concavity of the scoliotic curve. The spinous processes and attached ligaments are reconstructed to maintain the normal intermuscular septum contributing to stability. The clinical features are described with documentation by means of radiographic studies, myelography, and CAT scanning in all patients. In addition, the histopathologic findings of the facets removed at the time of surgery are described and the relationship of these findings to the symptomatology is indicated. The long-term results have been gratifying, supporting the efficacy of this means of therapy.

Adult↗

Smooth muscle cell phenotypes in atherosclerotic lesions.

Recently, there has been a dramatic change in the way we think about the role of vascular smooth muscle cells in atherosclerosis, and it is now generally accepted that a dearth of vascular smooth muscle cells in an atherosclerotic plaque is a detrimental feature of the disease. Indeed, it is now recognized that the phenotypes of vascular smooth muscle cells within a plaque dictate its features, progression and stability. Therefore an understanding of the processes that generate and regulate vascular smooth muscle cell heterogeneity are of critical importance for future therapeutic advancement in the treatment of atherosclerosis.

Apoptosis↗

Two-dimensional solitons in saturable media with a quasi-one-dimensional lattice potential.

We study families of solitons in a two-dimensional model of the light transmission through a photorefractive medium equipped with a (quasi-)one-dimensional photonic lattice. The soliton families are bounded from below by finite minimum values of the peak and total power. Narrow solitons have a single maximum, while broader ones feature side lobes. Stability of the solitons is checked by direct simulations. The solitons can be set in motion across the lattice (actually, made tilted in the spatial domain), provided that the respective boost parameter does not exceed a critical value. Collisions between moving solitons are studied too. Collisions destroy the solitons, unless their velocities are sufficiently small. In the latter case, the colliding solitons merge into a single stable pulse.

Journal Article↗

Onset of dendritic flux avalanches in superconducting films.

We report a detailed comparison of experimental data and theoretical predictions for the dendritic flux instability, believed to be a generic behavior of type-II superconducting films. It is shown that a thermomagnetic model published very recently [Phys. Rev. B 73, 014512 (2006)10.1103/PhysRevB.73.014512] gives an excellent quantitative description of key features like the stability onset (first dendrite appearance) magnetic field, and how the onset field depends on both temperature and sample size. The measurements were made using magneto-optical imaging on a series of different strip-shaped samples of MgB2. Excellent agreement is also obtained by reanalyzing data previously published for Nb.

Journal Article↗

Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure.

Until recently, it has only been possible to grow crystals of peanut lectin when complexed with sugar ligands. It is now shown that it is possible to grow peanut lectin crystals at acidic pH in the presence of oligopeptides corresponding to a loop in the lectin molecule. Crystals have also been prepared in the presence of these peptides as well as lactose. Low-pH crystal forms of the lectin-lactose complex similar to those obtained at neutral pH have also been grown. Thus, crystals of peanut lectin grown under different environmental conditions, at two pH values with and without sugar bound to the lectin, are now available. They have been used to explore the plasticity and hydration of the molecule. A detailed comparison between different structures shows that the lectin molecule is sturdy and that the effect of changes in pH, ligand binding and environment on it is small. The region involving the curved front beta-sheet and the loops around the second hydrophobic core is comparatively rigid. The back beta-sheet involved in quaternary association, which exhibits considerable variability, is substantially flexible, as is the sugar-binding region. The numbers of invariant water molecules in the hydration shell are small and they are mainly involved in metal coordination or in stabilizing unusual structural features. Small consistent movements occur in the combining site upon sugar binding, although the site is essentially preformed.

Binding Sites↗

Etomidate in a new solvent. A clinical evaluation.

The introduction of polyethylene glycol as a solvent for etomidate appears to markedly reduce the incidence of pain on injection while maintaining the previously demonstrated advantageous features of cardiovascular stability and rapid recovery.

Anesthesia, Intravenous↗

Parents teaching their young mentally handicapped children.

This paper reports a fine-grained analysis of interaction between 21 mothers and fathers and their young mentally handicapped children. Parent-child dyads were videotaped at home on two occasions with a 'roundabout' toy. The sessions were analysed by means of a detailed coding system which reflected the reciprocal nature of interaction and which attended to sequences of behaviour. Results are reported on short-term stability of various features of communication and comparisons of dyads involving mothers and fathers. Implications of the results are outlined for interventions designed to help parents to teach their young mentally handicapped children.

Adult↗