Dendrimers: properties and applications.

Dendrimers are a new class of polymeric materials. They are highly branched, monodisperse macromolecules. The structure of these materials has a great impact on their physical and chemical properties. As a result of their unique behaviour dendrimers are suitable for a wide range of biomedical and industrial applications. The paper gives a concise review of dendrimers' physico-chemical properties and their possible use in various areas of research, technology and treatment.     

Sodium cholate sorption on cationic dextran hydrogel microspheres. 1. Influence of the chemical structure of functional groups

New hydrogel microspheres based on crosslinked dextran, containing pendant quaternary ammonium groups with different chemical structures have been synthesized and tested as possible bile acid sorbents The in vitro sodium cholate sorption by these hydrogels has been followed in the absence or in the presence of competing anions The sorption results have indicated a strong influence of the chemical structure of functional groups on both the affinity and selectivity towards cholate ions. The best sorption performances were obtained with hydrogels having in the structure of functional groups an alkyl substituent with the length higher than C(8).     

Histone-histone interactions. II. Structural stability of the histone H3-H4 complex.

The stability of the histone H3-H4 complex toward urea, changes in pH and ionic strength, and certain chemical modifications have been examined by gel electrophoresis anc circular dichronism. When uncomplexed, the two cysteine residues of histone H3 become rapidly oxidized, forming an intramolecular disulfide bridge which apparently blocks complex formation on return to complexing conditions. The complex was found to be unstable toward low values of pH and ionic strength, concentrations of urea exceeding 1 M, modifications of the cysteine residues, and fragmention in which the C terminal portions of either H3 or H4 are removed. A possible structure for this complex is proposed.     

The interaction of N alpha-alkylenkephalins with opiate receptors. Tissue-dependent shifts in the opiate activity of methionine-enkephalin following N alpha-alkylation

Experimental conditions for the small scale alkylation of the alpha-amino group of the opioid peptide methionine-enkephalin using the method of reductive alkylation are described. The generality of the method is established by describing in detail the synthesis, purification, and structure elucidation of the N alpha-ethyl, isopropyl, phenethyl, and cyclopropylmethyl derivatives of methionine-enkephalin. By a combination of amino acid and mass spectral analysis it is possible to carry out the structure analysis of nanomole quantities of these modified peptides, making direct chemical modification and structure elucidation of carrier-free tritiated and radioiodinated enkephalins feasible. Using these chemical procedures, a homologous series of N alpha-n-alkyl derivatives of methionine-enkephalin has has been synthesized. It is shown that the relative binding and opiate activity of these N alpha-alkyl derivatives, using several standard in vitro assay systems, depends on the tissue source used. The results of this study are analyzed by considering recent reports indicating the existence of multiple opiate receptors.     

Distance constraints on macromolecular conformation.

Many physico-chemical studies are made on proteins to determine something of their solution conformation. For example the coat protein of Tobacco Mosaic Virus has been subjected to more non-crystallographic experimental studies to determine its native conformation than perhaps any other protein. Yet the sum of the experimentally determined constraints on its tertiary structure are surprisingly inadequate to fix its conformation. We are able to detect and remove minor inconsistencies in the data and then calculate a sampling of conformations consistent with all the data, which differ among themselves by r.m.s. deviations of the respective interresidue distances ranging from 5.7 angstrom to 15.8 angstrom. Some individual interresidue distances differ by as much as 50 angstrom from structure to structure. In order to restrict the range of possible conformations to something corresponding to the errors in a 10 angstrom resolution X-ray crystal structure, chemical and spectroscopic studies will have to be much more detailed than anything done to date. Our calculations appear to be useful in deciding which further experiments would be most productive.     

A computer-assisted structural analysis of regular polysaccharides on the basis of 13C-n.m.r. data

A computerised approach to the structural analysis of unbranched regular polysaccharides is described, which is based on an evaluation of the 13C-n.m.r. spectra for all possible primary structures within the additive scheme starting from the chemical shifts of the 13C resonances of the constituent monosaccharides and the average values of the glycosylation effects. The analysis reveals a structure (or structures), the evaluated spectrum of which resembles most closely that observed. The approach has been verified by using a series of bacterial polysaccharides of known structure and, in combination with methylation analysis data, for the determination of the presently unknown structures of the O-specific polysaccharides from Salmonella arizonae O59 and O63, and Proteus hauseri O19.     

Expressed protein ligation. Method and applications.

The introduction of noncanonical amino acids and biophysical probes into peptides and proteins, and total or segmental isotopic labelling has the potential to greatly aid the determination of protein structure, function and protein-protein interactions. To obtain a peptide as large as possible by solid-phase peptide synthesis, native chemical ligation was introduced to enable synthesis of proteins of up to 120 amino acids in length. After the discovery of inteins, with their self-splicing properties and their application in protein synthesis, the semisynthetic methodology, expressed protein ligation, was developed to circumvent size limitation problems. Today, diverse expression vectors are available that allow the production of N- and C-terminal fragments that are needed for ligation to produce large amounts and high purity protein(s) (protein alpha-thioesters and peptides or proteins with N-terminal Cys). Unfortunately, expressed protein ligation is still limited mainly by the requirement of a Cys residue. Of course, additional Cys residues can be introduced into the sequence by site directed mutagenesis or synthesis, however, those mutations may disturb protein structure and function. Recently, alternative ligation approaches have been developed that do not require Cys residues. Accordingly, it is theoretically possible to obtain each modified protein using ligation strategies.     

Molecular effects of nitrosamine toxicity.

Nitrosamines are toxic chemical compounds found low in quantity, but widespread in the environment. This work investigated the kinetics of chemical reaction of activated nitrosamines with various organic substrates. The mechanism by which nitrosamines react demonstrates possible pathways in which the toxicity is expressed. Once activated nitrosamines are very reactive. Chemical compounds which can act as nucleophilic substrates may be alkylated by the activated nitrosamines. A broad category of chemical compounds are shown to be suitable substrates for nitrosamine induced alkylation. This large category of substrates suggests a substantial potential for toxic activity in vivo. By investigating the reaction kinetics of activated nitrosamines a greater understanding of their toxic effects may be possible.     

The sequence of 28S ribosomal RNA varies within and between human cell lines.

The primary structure of 28S ribosomal RNA constitutes a conserved core which is similar among most 23S-like rRNAs and expansion segments which occur at specific positions in the sequence. The expansion segments account for most of the size difference between prokaryotic (archaeal and eubacterial) and eukaryotic rRNAs and they exhibit a sequence variation which is unique among rRNAs. We have investigated the sequence variation of one of the expansion segments, V8, by sequencing a total of 111 V8 segments from 9 different human cell lines and tissues and have found 35 different variants. The variation occur mainly at two 'hot spots' which are separated by 170 nucleotides in the primary sequence but are neighbours in the secondary structure. The sequence of V8 segments varies both within and between human cell lines and tissues. The implications for the evolution of the eukaryotic 28S rRNA are discussed together with possible functions of the expansion segments. We also present a secondary structure model for the V8 segment based on comparative sequence analysis and chemical and enzymatic foot printing.     

Secondary structure model for 23S ribosomal RNA.

A secondary structure model for 23S ribosomal RNA has been constructed on the basis of comparative sequence data, including the complete sequences from E. coli. Bacillus stearothermophilis, human and mouse mitochondria and several partial sequences. The model has been tested extensively with single strand-specific chemical and enzymatic probes. Long range base-paired interactions organize the molecule into six major structural domains containing over 100 individual helices in all. Regions containing the sites of interaction with several ribosomal proteins and 5S RNA have been located. Segments of the 23S RNA structure corresponding to eucaryotic 5.8S and 25 RNA have been identified, and base paired interactions in the model suggest how they are attached to 28S RNA. Functionally important regions, including possible sites of contact with 30S ribosomal subunits, the peptidyl transferase center and locations of intervening sequences in various organisms are discussed. Models for molecular 'switching' of RNA molecules based on coaxial stacking of helices are presented, including a scheme for tRNA-23S RNA interaction.     

Glucosamine oligomers: 2. N.m.r. studies on a DP3.

This paper concerns the characterization of the chemical structure of a DP3 glucosamine oligomer. The assignments of nearly all protons are reported. Variations of 1H chemical shifts with pD and temperature are correlated to the pKa of amino groups, and not with substantial conformational changes.     

13C-N.M.R. spectra of methyl 3,4-dideoxy-DL-glyc-3-enopyranosides

¹³C-N.m.r., proton-decoupled spectra of 22 isomeric methyl 3,4-dideoxy-DL- glyc-3-enopyranosides are presented. Comparison of the data for compounds having HO-2 unsubstituted and acetylated enabled assignment of all of the resonances. Specific up- and down-field shifts made possible an unequivocal assignment of structure to 3,4-unsaturated methyl glycenopyranosides. On the basis of the chemical shifts of the signal for C-1, the position of the conformational equilibrium of methyl 3,4-dideoxy-DL-pent-3-enopyranosides could be estimated.     

Effects of chemical modification on enzymatic activities and stabilities

The influence of chemical modification on the initial specific activity, residual activity, and deactivation kinetics of various enzymes is analyzed using a series mechanism. This straightforward multistate sequential model presented is consistent with the enzyme deactivation data obtained from different fields. The enzymes are placed in five different categories depending on the effect of chemical modification on initial specific activity and residual activity or stability. Wherever possible, structure-function relationships are described for the enzymes in the different categories. The categorization provides one avenue that leads to further physical insights into enzyme deactivation processes and into the enzyme structure itself.     

The application of 1H NMR chemical shift calculations to diastereotopic groups in proteins.

We have calculated chemical shifts for a range of diastereotopic protons in proteins (i.e. methylene protons, and the methyl groups of valine and leucine residues), using a recently optimised method for chemical shift calculation. The calculations are based on crystal structure coordinates, and have been compared with experimental stereospecific assignments. The results indicate that chemical shifts can be used to suggest stereospecific assignments with about 80% probability of being correct, in cases where both the experimental and the calculated chemical shift differences between a pair of diastereotopic protons are greater than 0.3 ppm. Inaccurate calculations are shown to be caused in most cases by differences between crystal and solution structures. Furthermore, chemical shift calculations based on NMR structures are shown to be capable of acting as a further constraint on structure, by limiting the range of side-chain conformations adopted in structures calculated from NMR data.     

Molecular preservation.

The differing patterns of molecular abundances in organisms are fundamental to the understanding of the biomolecular palaeontological record. All organisms contain DNA, RNA, protein, polysaccharides and lipid components, together with glycolipids, lipopolysaccharides and other complex molecules. Certain biopolymers, however, are restricted in their distributions; for example, lignin, cutin and sporopollenin are found only in terrestrial plants. The detailed chemical structures, namely the bond types present and their precise intramolecular environments, determine resistance to degradation. Observations of biomolecular preservation are compared with predictions based on chemical structure and on conditions encountered during decay.     

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study.

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG3) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.     

Genetic control of a structural polymer of the Neurospora crassa cell wall.

The heteropolysaccharide present in fraction 1 of the Neurospora crassa cell wall has been characterized in wild-type and morphological mutant strains of this fungus. Single and double mutations have been studied to determine possible genetic interactions controlling the chemical composition of such heteropolysaccharides . Single mutations studied were peak-2, scumbo ( FGSC 49), ragged ( FGSC 296), and crisp -1 ( FGSC 488). Double mutations studied were peak-2, scumbo ( FGSC 419), and ragged crisp -1. In all these strains, the main constituents of the heteropolysaccharide were glucose, mannose and galactose. Glycosidic linkages binding these neutral sugars have been identified by gas-liquid chromatography. A chemical structure of fraction I heteropolysaccharide is proposed. The results obtained with double mutants suggest the existence of genetic interactions, such as complementation or additive effects of lesions of different genes, to control the chemical composition and structure of the cell wall and the morphology of N. crassa mycelium.     

Navigating molecular space for reaction mechanisms: an efficient,automated procedure

Mechanism is a core chemical concept that has vital implications for reaction rate, efficiency and selectivity. The discovery of mechanism is not easy due to the great diversity of possible chemical rearrangements in even relatively simple systems. For this reason, mechanisms involving bond breaking and forming are usually proposed via chemical intuition – which limits the scope of considered possibilities – and these hypotheses are then tested using simulation or experiment. This article discusses an automated simulation strategy for investigating multiple elementary step reaction mechanisms in chemical systems. The method starts from a single input structure and seeks out nearby intermediates, optimises the proposed structures and then determines the kinetic viability of each elementary step. The kinetically accessible intermediates are catalogued and new searches are performed on each unique structure. This process is repeated for an arbitrary number of steps without human intervention, and massively parallel computation enables fast searches in chemical space. Importantly, this strategy can be empirically shown to lead to a finite number of accessible structures, not a combinatorial explosion of intermediates. Therefore, the method should be able to predict multi-step reaction pathways in many interesting chemical systems. Demonstrations on organic reactions and a hydrogen storage material, ammonia borane, show that the herein proposed strategy can uncover complex reactivity without relying on existing chemical intuition.     

Structure of oxidatively damaged nucleic acid adducts. 3. Tautomerism, ionization and protonation of 8-hydroxyadenosine studied by 15N NMR spectroscopy.

Natural abundance 15N NMR spectroscopy and ancillary spectroscopic techniques have been employed to study the solution structure of 8-hydroxyadenosine. 8-Hydroxyadenosine is a naturally occurring oxidized nucleic acid adduct that is generally implied to have an 8-hydroxy tautomeric structure. 15N NMR chemical shifts and coupling constants, however, indicate that the modified base exists as an 8-keto tautomer. The pH dependence of 15N NMR and UV spectra showed the presence of two pKa's, at 2.9 and 8.7, corresponding to protonation at N1 and ionization at N7, respectively. The latter results in the formation of an 8-enolate structure. Unusual upfield shifts of the 1H and 15N resonances of the NH2 group, and a reduction in the one-bond coupling constant 1JN6-H6, is indicative of an unfavorable steric or electronic interaction between the NH2 group and the adjacent N7-H proton. This interaction results in a subtle change in the structure of the NH2 group. In addition to being a possible mechanism for alteration of hydrogen bonding in oxidized DNA, this type of interaction gives a better understanding into N7-N9 tautomerism of adenine. Furthermore, the structure of 8-hydroxyadenosine has been related to possible mechanisms for mutations.     

Alpha-, beta-, and gamma-tubulins: sequence comparisons and structural constraints.

Comparison of congruent to 160 alpha-, beta-, and gamma-tubulins, and excluding the highly divergent C-terminal peptide, indicates that the three subclasses have similar tertiary structures. Conserved sequences within or between the subclasses have been identified, together with the locations of known epitopes, chemical modifications, and mutations. Evidence is also reviewed concerning the identity of the GTP-binding sites, about which residues are exposed in the assembled microtubule and at subunit:subunit interfaces. These characteristics constrain the possible tertiary structure of the tubulin subunit.