Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

Mutations of PCDH15, encoding protocadherin 15, can cause either combined hearing and vision impairment (type 1 Usher syndrome; USH1F) or nonsyndromic deafness (DFNB23). Human PCDH15 is reported to be composed of 35 exons and encodes a variety of isoforms with 3-11 ectodomains (ECs), a transmembrane domain and a carboxy-terminal cytoplasmic domain (CD). Building on these observations, we describe an updated gene structure that has four additional exons of PCDH15 and isoforms that can be subdivided into four classes.

Ab initio molecular dynamics study on the initial chemical events in nitramines: thermal decomposition of CL-20.

CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitramine explosive. To improve atomistic understanding of the thermal decomposition of CL-20 gas and solid phases, we performed a series of ab initio molecular dynamics simulations. We found that during unimolecular decomposition, unlike other nitramines (e.

The effect of nitroaromatics' composition on their toxicity in vivo: novel, efficient non-additive 1D QSAR analysis.

Novel 1D QSAR approach that allows analysis of non-additive effects of molecular fragments on toxicity has been proposed. Twenty-eight nitroaromatic compounds including some well-known explosives have been chosen for this study. The 50% lethal dose concentration for rats (LD50) was used as the estimation of toxicity in vivo to develop 1D QSAR models on the framework of Simplex representation of molecular structure.

The effects of characteristics of substituents on toxicity of the nitroaromatics: HiT QSAR study.

The present study applies the Hierarchical Technology for Quantitative Structure-Activity Relationships (HiT QSAR) for (i) evaluation of the influence of the characteristics of 28 nitroaromatic compounds (some of which belong to a widely known class of explosives) as to their toxicity; (ii) prediction of toxicity for new nitroaromatic derivatives; (iii) analysis of the effects of substituents in nitroaromatic compounds on their toxicity in vivo. The 50% lethal dose concentration for rats (LD50) was used to develop the QSAR models based on simplex representation of molecular structure. The preliminary 1D QSAR results show that even the information on the composition of molecules reveals the main tendencies of changes in toxicity.

CL-20 photodecomposition: ab initio foundations for identification of products.

1,5-Dihydrodiimidazo[4,5-b:4'5'e]pyrazine, 1H-imidazo[4,5-b]pyrazine, and 1H-imidazole were considered as possible products of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) photodecomposition. Since we took as a reference the product obtained after CL-20 irradiation in methanol solution, the nature of intermolecular bonds between heterocycles under study and methanol molecules was analyzed in detail. Existing hydrogen bonds were found to be quite strong, so dependence of calculations results on an influence of solvent was taken into account using both the polarizable continuum model (PCM) and the supermolecular approach.

Application of quantum-chemical approximations to environmental problems: Prediction of physical and chemical properties of TNT and related species.

This paper presents accurate predictions of ecologically important properties of nitroaromatic compounds and their derivatives, including vapor pressure, Henry's law constants, water solubility, octanol/water partition coefficients, heats of formation and ionization potentials. The proposed technique of calculations was based on quantum-chemical methods. The relationship between the chemical structure and mentioned physico-chemical parameters of such widespread military produced contaminants as trinitrotoluene and its derivatives was considered.

Structural insights into the non-additivity effects in the sequence-to-reactivity algorithm for serine peptidases and their inhibitors.

Sequence-to-reactivity algorithms (SRAs) for proteins have the potential of being broadly applied in molecular design. Recently, Laskowski et al. have reported an additivity-based SRA that accurately predicts most of the standard free energy changes of association for variants of turkey ovomucoid third domain (OMTKY3) with six serine peptidases, one of which is streptogrisin B (commonly known as Streptomyces griseus peptidase B, SGPB).

Despite having a common P1 Leu, eglin C inhibits alpha-lytic proteinase a million-fold more strongly than does turkey ovomucoid third domain.

Results of the inhibition of alpha-lytic proteinase by two standard mechanism serine proteinase inhibitors, turkey ovomucoid third domain (OMTKY3) and eglin C, and many of their variants are presented. Despite similarities, including an identical P1 residue (Leu) in their primary contact regions, OMTKY3 and eglin C have vastly different association equilibrium constants toward alpha-lytic proteinase, with Ka values of 1.8 x 10(3) and 1.

The mechanism of unimolecular decomposition of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane. A computational DFT study.

By using the B3LYP level of density functional theory, possible decomposition reaction pathways of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) in the gas phase have been investigated. We have found several types of reactions for this process: homolytic cleavage of an N-N bond to form the NO2* group; HONO elimination; C-C and C-N bonds breaking leading to ring opening; and H-migration. On the basis of the results of computation scanning of the potential energy surface, the most favorite pathway of CL-20 unimolecular decomposition that results in the formation of the stable aromatic compound 1,5-dihydrodiimidazo[4,5-b:4',5'-e]pyrazine has been proposed.

Functional evolution within a protein superfamily.

The ability to predict and characterize distributions of reactivities over families and even superfamilies of proteins opens the door to an array of analyses regarding functional evolution. In this article, insights into functional evolution in the Kazal inhibitor superfamily are gained by analyzing and comparing predicted association free energy distributions against six serine proteinases, over a number of groups of inhibitors: all possible Kazal inhibitors, natural avian ovomucoid first and third domains, and sets of Kazal inhibitors with statistically weighted combinations of residues. The results indicate that, despite the great hypervariability of residues in the 10 proteinase-binding positions, avian ovomucoid third domains evolved to inhibit enzymes similar to the six enzymes selected, whereas the orthologous first domains are not inhibitors of these enzymes on purpose.

Ring-Toss: Capping highly exposed tyrosyl or tryptophyl residues in proteins with beta-cyclodextrin.

We have used UV difference spectroscopy and fluorescence spectroscopy to study the perturbation by beta-cyclodextrin of tyrosyl or tryptophyl residues located at each of the 10 variable consensus contact positions in the third domain of turkey ovomucoid. The goal was to monitor the accessibility of the side chain rings of these residues when located at these positions. The results indicated that the tyrosyl or tryptophyl rings are most highly exposed when located in the P1 position followed by the P4 position.

Prediction of CL-20 chemical degradation pathways, theoretical and experimental evidence for dependence on competing modes of reaction.

Highest occupied and lowest unoccupied molecular orbital energies, formation energies, bond lengths and FTIR spectra all suggest competing CL-20 degradation mechanisms. This second of two studies investigates recalcitrant, toxic, aromatic CL-20 intermediates that absorb from 370 to 430 nm. Our earlier study (Struct.

The role of scaffolding in standard mechanism serine proteinase inhibitors.

In single domain, "standard mechanism" protein inhibitors of serine proteinases, about a dozen residues make contact with the cognate enzyme. The remainder of the molecule, the scaffolding, holds the reactive site region of the inhibitor in a canonical conformation, improves the binding by about six orders of magnitude and protects it from proteolysis. However, the stability and global structure of the scaffolding is irrelevant to inhibition, provided that inhibition is measured much below the melting temperature, Tm.

From the discovery of the reactive site of inhibitors to their sequence to reactivity algorithm.

Michael Laskowski Jr. (1930-2004) was a pioneer in the field of Standard mechanism serine proteinase inhibitors. He made numerous important contributions in the field.

Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations.

One of the most studied protein proteinase inhibitors is the turkey ovomucoid third domain, OMTKY3. This inhibitor contains a reactive-site loop (Lys13I-Arg21I) that binds in a nearly identical manner to all studied serine proteinases, regardless of their clan or specificity. The crystal structure of OMTKY3 bound to subtilisin Carlsberg (CARL) has been determined.

Theoretical predictions of chemical degradation reaction mechanisms of RDX and other cyclic nitramines derived from their molecular structures.

Analysis of environmental degradation pathways of contaminants is aided by predictions of likely reaction mechanisms and intermediate products derived from computational models of molecular structure. Quantum mechanical methods and force-field molecular mechanics were used to characterize cyclic nitramines. Likely degradation mechanisms for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) include hydroxylation utilizing addition of hydroxide ions to initiate proton abstraction via 2nd order rate elimination (E2) or via nucleophilic substitution of nitro groups, reductive chemical and biochemical degradation, and free radical oxidation.

A kinetic model of aqueous-phase alkali hydrolysis of 2,4,6-trinitrotoluene.

Alkali hydrolysis of 2,4,6-trinitrotoluene (TNT) was studied using batch experiments with starting pH values 11 and 12 in glass conical flasks covered with aluminum foil. Isothermal (25 and 40 degrees C) as well as non-isothermal experiments were conducted. Experiments starting at pH 12 resulted in >95% reduction in the concentration of TNT; those starting at pH 11 had a maximum reduction of 20-25% in TNT concentration.

Testing of the additivity-based protein sequence to reactivity algorithm.

The standard free energies of association (or equilibrium constants) are predicted for 11 multiple variants of the turkey ovomucoid third domain, a member of the Kazal family of protein inhibitors, each interacting with six selected enzymes. The equilibrium constants for 38 of 66 possible interactions are strong enough to measure, and for these, the predicted and measured free energies are compared, thus providing an additional test of the additivity-based sequence to reactivity algorithm. The test appears to be unbiased as the 11 variants were designed a decade ago to study furin inhibition and the specificity of furin differs greatly from the specificities of our six target enzymes.

Two conformational states of Turkey ovomucoid third domain at low pH: three-dimensional structures, internal dynamics, and interconversion kinetics and thermodynamics.

Turkey ovomucoid third domain (OMTKY3) is shown to exist at low pH as two distinctly folded, interconverting conformations. Activation parameters were determined for the transition, and these were of the type reported previously for cis/trans isomerizations of prolyl peptide bonds. Multidimensional, multinuclear NMR spectroscopy was used to determine the three-dimensional structure of each of the two states of P(5)-Pro(14)Asp OMTKY3 at pH 2.

NMR determination of pKa values for Asp, Glu, His, and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain.

From the larger set of 191 variants at all the variable contact positions in the turkey ovomucoid third domain, we selected a subset that consists of Asp, Glu, His, and Lys residues at eight of the nine contiguous P6-P3' positions (residues 13-21), the exception being P3-Cys16 which is involved in a conserved disulfide bridge. Two-dimensional [1H,1H]-TOCSY data were collected for each variant as a function of sample pH. This allowed for the evaluation of 31 of the 32 pK(a) values for these residues, the exception being that of P5-Lys14, whose signals at high pH could not be resolved from those of other Lys residues in the molecule.

Additivity-based prediction of equilibrium constants for some protein-protein associations.

For many protein families, such as serine proteinases or serine proteinase inhibitors, the family assignment predicts reactivity only in general terms. Both detailed specificity and quantitative reactivity are lacking. We believe that, for many such protein families, algorithms can be devised by defining the subset of n functionally important sequence positions, making the 19n possible single mutants and measuring their reactivity.

Alkali hydrolysis of trinitrotoluene.

Data for alkali hydrolysis of 2,4,6-trinitrotoluene (TNT) in aqueous solution at pH 12.0 under static (pH-controlled) as well as dynamic (pH-uncontrolled) conditions are reported. The experiments were conducted at two different molar ratios of TNT to hydroxyl ions at room temperature.

Appropriateness of nitrate use in a general medicine population.

Background: Nitrates are one of the most commonly prescribed drug groups for cardiac disease, especially for angina pectoris and congestive heart failure. The chronic efficacy of nitrates is limited by the development of tolerance, which can be attenuated by use of sustained-release preparations or administration of regular-release preparations asymmetrically.

Objective: To determine whether patients receiving isosorbide 5-mononitrate (ISMN) use the drug in a pharmacologically appropriate manner and whether they had been instructed in the prophylactic use of sublingual nitrates prior to effort.

The fate of hydrogen peroxide as an oxygen source for bioremediation activities within saturated aquifer systems.

In situ bioremediation is an innovative technique for the remediation of contaminated aquifers that involves the use of microorganisms to remediate soils and groundwaters polluted by hazardous substances. During its application, this process may require the addition of nutrients and/or electron acceptors to stimulate appropriate biological activity. Hydrogen peroxide has been commonly used as an oxygen source because of the limited concentrations of oxygen that can be transferred into the groundwater using above-ground aeration followed by reinjection of the oxygenated groundwater into the aquifer or subsurface air sparging of the aquifer.