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PubMed1995

Proposed cation-pi mediated binding by factor Xa: a novel enzymatic mechanism for molecular recognition.

Factor Xa (FXa) is an important serine protease in the blood coagulation cascade. Small synthetic competitive inhibitors of FXa are under development as potential anticoagulants. To better understand FXa structural features and molecular recognition mechanisms, we have constructed three dimensional models of FXa-inhibitor complex structures via a new search approach that samples conformational space and binding space simultaneously for DABE and DX-9065a, two bis amidinoaryl derivatives that are among the most potent and selective FXa inhibitors reported to date. We find the most probable binding modes for the two inhibitors to be a folded conformation, with one distal amidino group extending into the S1 pocket, forming a salt-bridge with FXa Asp-189, and the other positively charged group fitting into the S4 subsite, and stabilized by a cation-pi interaction. We propose as a hypothesis that the cavity-like S4 subsite formed by the three pi-faces of the aromatic residues Tyr-99, Phe-174 and Trp-215 is sufficiently rich in pi electrons that it is not only a hydrophobic pocket, but also forms a cation recognition site. This proposed cation-pi binding mechanism is one of the first proposed for enzymatic molecular recognition, and for which experimental verification can be obtained without any complicating charge compensation mechanism. Our models provide plausible explanations of the structure-activity relationships observed for these inhibitors, and suggest that cation-pi interactions may provide a novel mechanism for molecular recognition.

Amino Acid Sequence↗

PubMed2003

Massive telomere loss and telomerase RNA expression in dexamethasone-induced apoptosis in mouse thymocytes.

Apoptosis is a well-recognized process of cell death occurring under several physiological and pathological conditions and represents the principal mechanism involved in cell selection in the thymus. Glucocorticoids are well known to stimulate apoptosis in rat thymocytes. However, it is unclear whether the same changes occur after in vivo glucocorticoid treatment in mice. Chromosomal stability and cell viability require a proficient telomeric end-capping function. Cells with critical telomere shortening and telomerase dysfunction undergo increased apoptosis. In turn, the change in telomere function in cells undergoing apoptosis is not fully characterized. In order to investigate this, we studied the changes in thymocytes after dexamethasone administration in BALB/c mice. The loss of normal thymocytes coincided with the appearance of small dense cells with characteristic features of apoptosis including condensed chromatin, internucleosomal DNA cleavage, and a "hypodiploid" peak on flow cytometry, which suggested that dexamethasone-induced thymocyte apoptosis in BALB/c mice could be considered a well-defined experimental model for studying apoptotic processes. Dexamethasone-treated thymocytes exhibited rapid and dynamic loss of telomeric sequences and up-regulation of telomerase RNA as an early event in the apoptotic process. Telomerase activity was unchanged in this event. Thereafter, telomere gain associated with an increase in telomerase activity occurred in the regenerative process of the thymus. These results suggest a role of telomere loss and up-regulation of telomerase RNA as key apoptosis sensors.

Animals↗

PubMed2001

Biocomplexity: adaptive behavior in complex stochastic dynamical systems.

Existing methods of complexity research are capable of describing certain specifics of bio systems over a given narrow range of parameters but often they cannot account for the initial emergence of complex biological systems, their evolution, state changes and sometimes-abrupt state transitions. Chaos tools have the potential of reaching to the essential driving mechanisms that organize matter into living substances. Our basic thesis is that while established chaos tools are useful in describing complexity in physical systems, they lack the power of grasping the essence of the complexity of life. This thesis illustrates sensory perception of vertebrates and the operation of the vertebrate brain. The study of complexity, at the level of biological systems, cannot be completed by the analytical tools, which have been developed for non-living systems. We propose a new approach to chaos research that has the potential of characterizing biological complexity. Our study is biologically motivated and solidly based in the biodynamics of higher brain function. Our biocomplexity model has the following features, (1) it is high-dimensional, but the dimensionality is not rigid, rather it changes dynamically; (2) it is not autonomous and continuously interacts and communicates with individual environments that are selected by the model from the infinitely complex world; (3) as a result, it is adaptive and modifies its internal organization in response to environmental factors by changing them to meet its own goals; (4) it is a distributed object that evolves both in space and time towards goals that is continually re-shaping in the light of cumulative experience stored in memory; (5) it is driven and stabilized by noise of internal origin through self-organizing dynamics. The resulting theory of stochastic dynamical systems is a mathematical field at the interface of dynamical system theory and stochastic differential equations. This paper outlines several possible avenues to analyze these systems. Of special interest are input-induced and noise-generated, or spontaneous state-transitions and related stability issues.

Adaptation, Physiological↗

PubMed2006

Asymmetric total synthesis of (+)- and ent-(-)-yatakemycin and duocarmycin SA: evaluation of yatakemycin key partial structures and its unnatural enantiomer.

Complementary to studies that provided the first yatakemycin total synthesis resulting in its structure revision and absolute stereochemistry assignment, a second-generation asymmetric total synthesis is disclosed herein. Since the individual yatakemycin subunits are identical to those of duocarmycin SA (alkylation subunit) or CC-1065 (central and right-hand subunits), the studies also provide an improvement in our earlier total synthesis of CC-1065 and, as detailed herein, have been extended to an asymmetric total synthesis of (+)-duocarmycin SA. Further extensions of the studies provided key yatakemycin partial structures and analogues for comparative assessments. This included the definition of the DNA selectivity (adenine central to a five-base-pair AT sequence, e.g., 5'-AAAAA), efficiency, relative rate, and reversibility of ent-(-)-yatakemycin and its comparison with the natural enantiomer (identical selectivity and efficiency), structural characterization of the adenine N3 adduct confirming the nature of the DNA reaction, and comparisons of the cytotoxic activity of the natural product (L1210, IC50 = 5 pM) with those of its unnatural enantiomer (IC50 = 5 pM) and a series of key partial structures including those that probe the role of the C-terminus thiomethyl ester. The only distinguishing features between the enantiomers is that ent-(-)-yatakemycin alkylates DNA at a slower rate (krel = 0.13) and is reversible, whereas (+)-yatakemycin is not. Nonetheless, even ent-(-)-yatakemycin alkylates DNA at a faster rate and with a greater thermodynamic stability than (+)-duocarmycin SA, illustrating the unique characteristics of such "sandwiched" agents.

Adenine↗

PubMed2005

Interplay between cubic and hexagonal phases in block copolymer solutions.

The phase behavior of a symmetric styrene-isoprene (SI) diblock copolymer in a styrene-selective solvent, diethylphthalate, was investigated by in situ small-angle X-ray scattering on isotropic and shear-oriented solutions and by rheology and birefringence. A remarkable new feature in this phase diagram is the coexistence of both body-centered cubic (bcc) and hexagonally close-packed (hcp) sphere phases, in a region between close-packed spheres (cps) and hexagonally packed cylinders (hex) over the concentration range phi approximately 0.33-0.45. By focusing on the transitions among these various ordered phases during heating and cooling cycles, we observed a strong hysteresis: supercooled cylinders persisted upon cooling. The stability of these supercooled cylinders is quite dependent on concentration, and for phi > or = 0.40, the supercooled cylinders do not revert to spheres even after quiescent annealing for 1 month. The spontaneous formation of spheres due to the dissociation of cylinders is kinetically hindered in this case, and the system is apparently not amenable to any pretransitional fluctuations of cylinders prior to the cylinder-to-sphere transition. This contrasts with the case of cylinders transforming to spheres upon heating in the melt. The application of large amplitude shear to the supercooled cylinders is effective in restoring the equilibrium sphere phases.

Journal Article↗

PubMed2004

Genetic analysis of complex demographic scenarios: spatially expanding populations of the cane toad, Bufo marinus.

Inferring the spatial expansion dynamics of invading species from molecular data is notoriously difficult due to the complexity of the processes involved. For these demographic scenarios, genetic data obtained from highly variable markers may be profitably combined with specific sampling schemes and information from other sources using a Bayesian approach. The geographic range of the introduced toad Bufo marinus is still expanding in eastern and northern Australia, in each case from isolates established around 1960. A large amount of demographic and historical information is available on both expansion areas. In each area, samples were collected along a transect representing populations of different ages and genotyped at 10 microsatellite loci. Five demographic models of expansion, differing in the dispersal pattern for migrants and founders and in the number of founders, were considered. Because the demographic history is complex, we used an approximate Bayesian method, based on a rejection-regression algorithm, to formally test the relative likelihoods of the five models of expansion and to infer demographic parameters. A stepwise migration-foundation model with founder events was statistically better supported than other four models in both expansion areas. Posterior distributions supported different dynamics of expansion in the studied areas. Populations in the eastern expansion area have a lower stable effective population size and have been founded by a smaller number of individuals than those in the northern expansion area. Once demographically stabilized, populations exchange a substantial number of effective migrants per generation in both expansion areas, and such exchanges are larger in northern than in eastern Australia. The effective number of migrants appears to be considerably lower than that of founders in both expansion areas. We found our inferences to be relatively robust to various assumptions on marker, demographic, and historical features. The method presented here is the only robust, model-based method available so far, which allows inferring complex population dynamics over a short time scale. It also provides the basis for investigating the interplay between population dynamics, drift, and selection in invasive species.

Animals↗

PubMed1997

The foldability landscape of model proteins.

Molecular evolution may be considered as a walk in a multidimensional fitness landscape, where the fitness at each point is associated with features such as the function, stability, and survivability of these molecules. We present a simple model for the evolution of protein sequences on a landscape with a precisely defined fitness function. We use simple lattice models to represent protein structures, with the ability of a protein sequence to fold into the structure with lowest energy, quantified as the foldability, representing the fitness of the sequence. The foldability of the sequence is characterized based on the spin glass model of protein folding. We consider evolution as a walk in this foldability landscape and study the nature of the landscape and the resulting dynamics. Selective pressure is explicitly included in this model in the form of a minimum foldability requirement. We find that different native structures are not evenly distributed in interaction space, with similar structures and structures with similar optimal foldabilities clustered together. Evolving proteins marginally fulfill the selective criteria of foldability. As the selective pressure is increased, evolutionary trajectories become increasingly confined to "neutral networks," where the sequence and the interactions can be significantly changed while a constant structure is maintained.

Amino Acid Sequence↗

PubMed2006

Bipolar depression: diagnostic and treatment considerations.

Bipolar affective disorder is a recurrent, disabling, and potentially lethal illness that typically begins early in life. Although the disorder is defined by the manic and hypomanic episodes, for most people the depression episodes are the more virulent aspect of the illness. Specifically, the depressive episodes are more numerous, last longer, and are more difficult to treat than the manias, and depression is the principal cause of the illness's increased mortality due to suicide. For people with early-onset depression, predictors of subsequent bipolarity include a family history, psychotic features, and reverse neurovegetative features. Initial episodes of depression are commonly misdiagnosed, which often delays initiation of appropriate therapy and increases the likelihood of treatment with antidepressants alone. Unfortunately, the correct diagnosis is often not made until there has been a treatment-emergent affective switch. There are no treatments specifically approved for bipolar disorder in youth and, among antidepressants, only fluoxetine has received approved. When bipolarity is suspected, treatment with mood stabilizers, both conventional (i.e., lithium, valproate, and carbamazapine) and more recently classified (lamotrigine) and atypical antipsychotics should be prioritized. When antidepressants are indicated in combination with mood stabilizers, first choice options include bupropion and the selective serotonin reuptake inhibitors. Studies of adults indicate that several forms of focused psychotherapy may improve longer term outcomes.

Age of Onset↗

PubMed2003

Using selected operational descriptors to examine the heterogeneity within a bulk humic substance.

The heterogeneity within a bulk humic substance (HS) was investigated for ultrafiltration (UF) fractions of purified Aldrich humic acid (PAHA) using specific ultraviolet absorbance (SUVA), weight- and number-average molecular weights (MWw and MWn), and organic carbon-normalized pyrene binding coefficients (Koc). As expected, variations in these selected operational descriptors were found for the PAHA UF fractions, but the variations were smaller than the ranges observed for a small subset of different aquatic and terrestrial HS. In general, correlations among the operational descriptors for the different HS failed to predict the correct trends for the PAHA UF fractions. More variation in Koc was observed for the different HS versus the PAHA UF fractions despite comparable molecular weight ranges, suggesting that the extent of pyrene binding is more strongly influenced by HS source and chemical structure than merely by physical structural features. Size-exclusion chromatography (SEC) confirmed the structural stability of PAHA UF fractions, as demonstrated by a near-identical mathematical reconstruction of the original bulk chromatogram from a weighted summation of the individual UF fraction chromatograms. An ideal mixture model accurately predicted some operational descriptors of PAHA properties (i.e., SUVA and MWw), but failed to predict the PAHA reactivity for pyrene binding. Our Koc results at pH 4 and 7 suggest that the relative contribution of two mechanisms, partitioning and specific interactions, may account for the interactions between HS and pyrene.

Chromatography, Gel↗

PubMed2001

Reentry in a morphologically realistic atrial model.

INTRODUCTION: Atrial fibrillation is the most common cardiac arrhythmia. In ablation procedures, identification of the reentrant pathways is vital. This has proven difficult because of the complex morphology of the atria. The purpose of this study was to ascertain the role of specific anatomic structures on reentry induction and maintenance. METHOD AND RESULTS: A computationally efficient, morphologically realistic, computer model of the atria was developed that incorporates its major structural features, including discrete electrical connections between the right and left atria, physiologic fiber orientation in three dimensions, muscle structures representing the crista terminalis (CT) and pectinate muscles, and openings for the veins and AV valves. Reentries were induced near the venous openings in the left and right atria, the mouth of the coronary sinus, and the free wall of the right atrium. The roles of certain muscular structures were ascertained by selectively removing the structures and observing how the propagation of activity was affected. CONCLUSION: (1) The muscular sheath of the coronary sinus acts as a pathway for a reentrant circuit and stabilizes any circuits that utilize the isthmus near the inferior vena cava. (2) Poor trans-CT coupling serves to stabilize flutter circuits. (3) Wall thickness is an important factor in the propagation of electrical activity, especially in the left atrium. (4) The openings of the inferior and superior venae cavae form natural anatomic anchors that make reentry easier to initiate by allowing for smaller ectopic beats to induce reentry.

Atrial Fibrillation↗

PubMed1997

The relevance of neural architecture to visual performance: phylogenetic conservation and variation in Dipteran visual systems.

In cyclorrhaphan flies, giant tangential neurons in the lobula plate are supplied by isomorphic arrays of evolutionarily conserved achromatic elementary motion detecting circuits originating in the retina. The arrangements among giant tangential neurons is characteristic of a taxon and can differ between taxa having different visual performances. Observations of 12 brachyceran and 4 nematoceran species have identified different behaviors associated with visually stabilized flight. Neuroanatomical comparisons between closely related species having different behaviors and phylogenetically distant species that have similar behaviors suggest that such differences relate to differences of giant tangential cell architecture in the lobula plate. These functionally related differences contrast to anatomical features that reflect phylogenetic affinities. For example, the lobula plates of robber flies, typified by ballistic flight behavior, all differ from other taxa in lacking cyclorrhaphan-type vertical motion-sensitive neurons; instead, they possess an extra complement of horizontal cells in their place. The results suggest that, although circuits that compute elementary motion are conserved across the Diptera, selective pressure has resulted in modifications of their target neurons, thus contributing to the wide variety of visual behaviors observed within this group of insects.

Animals↗

PubMed2001

Hypothesis: hemimelia and the maintenance of pentadactyly?

The limbs of extant terrestrial vertebrates possess five or fewer digits, yet, polydactyly is accepted as being the ancestral state. Therefore, I propose a hypothesis to account for the maintenance of digital number at five or fewer digits, based on a selective disadvantage associated with polydactylous states in terrestrial vertebrates. This disadvantage is not associated with the polydactyly per se, but rather with the hemimelia which is a common feature of polydactylies in mammals. Hemimelia causes a twisting, or luxation, of the distal segment of the limb, which is due to a malformation of the radius/tibia of the limb. This defect results in the limb being held in an abnormal gait, which causes problems in the locomotion of the animal which would compromise their ability to flourish. Therefore, the abnormal gait and torsion of the limb caused by the hemimelia is acting as a stabilizing force to maintain the dactyly of the tetrapod limb with five or fewer digits.

Animals↗

PubMed1998

Evaluation of biodegradable rifampicin-bearing microsphere formulations using a stability-indicating high-performance liquid chromatographic assay.

The validation of a rapid and selective stability-indicating high-performance liquid chromatographic procedure for the determination of rifampicin (RIF) and its decomposition products in aqueous solution is described. Direct injection and column switching HPLC procedures have been compared and, owing to the increased sensitivity and precision, the latter has been applied to the study of RIF stability in the presence of isoascorbic acid at pH 7.4. The time-dependent hydrolytic decomposition of RIF to 3-formyl rifamycin SV (RSV) was found to be biexponential. Log concentration versus time plots of RIF and RSV decomposition were found to be parallel, indicating a pseudo equilibrium decomposition process. This feature allowed corrections for the amounts lost to secondary reactions to be calculated when the assay was applied to the determination of release characteristics of RIF from biodegradable poly-d, l-lactide-co-glycolide microspheres.

Antibiotics, Antitubercular↗

PubMed2001

[A clinical investigation into the effect of comfort denture adhesive on masticatory function with complete dentures].

OBJECTIVE: The purpose of this study was to evaluate the clinical effect of the new developed form of Comfort denture adhesive (Comfort DA). METHODS: 10 edentulous patients with complete dentures were selected for this study. The maximum biting force and masticatory efficiency were recorded before and after application of the adhesive to all the new and old dentures. Subjective test was also used to evaluate this adhesive in enhancing retention and stability of complete denture using the questionnaire way. RESULTS: The data indicated that significantly greater biting forces were generated with old dentures than with the new dentures. The major findings were that the adhesive produced a statistically significant improvement in the masticatory efficiency after application. Subjective views of the patients indicated that this tested product significantly improved denture retention, stability and had other favorable features. The time of adhesion was about 6 8 hours. CONCLUSION: The generally favorable clinical performance of the developed Comfort DA formulation indicated that it might be an efficacious denture adhesive.

English Abstract↗

PubMed1996

Protein secondary structural types are differentially coded on messenger RNA.

Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. The fractional frequency values of the individual codons as they occur in mRNAs of highly expressed genes from Escherichia coli were taken as an indicative measure of the translation speed. The tricodons were classified by the sum of the frequency values of the constituent codons. Examination of the conformation of the encoded amino acid residues in the corresponding protein tertiary structures revealed a correlation between codon usage in mRNA and topological features of the encoded proteins. Alpha helices on proteins tend to be preferentially coded by translationally fast mRNA regions while the slow segments often code for beta strands and coil regions. Fast regions correspondingly avoid coding for beta strands and coil regions while the slow regions similarly move away from encoding alpha helices. Structural and mechanistic aspects of the ribosome peptide channel support the relevance of sequence fragment translation and subsequent conformation. A discussion is presented relating the observation to the reported kinetic data on the formation and stabilization of protein secondary structural types during protein folding. The observed absence of such strong positive selection for codons in non-highly expressed genes is compatible with existing theories that mutation pressure may well dominate codon selection in non-highly expressed genes.

Bacterial Proteins↗

PubMed2006

Structure based studies of the adaptive diversification process of congerins.

The isoforms of a fish galectin, congerins I and II, have several features that make them suitable for a study of accelerated process of molecular diversification based on 3D structures: They have been generated by a gene duplication, and still maintain 47% amino acid sequence identity to each other. Their genes show very high K A: /K S: ratio, and are though to be components of fish defense system. The crystal systems for a high-resolution analysis are known for both proteins. A series of works with biochemistry, molecular biology, and X-ray crystallography techniques have suggested that the two proteins might have evolved under differential selection pressures. Congerin I appeared to be a stabilized version of galectin-1. Congerin II was shown to be adapted to a new carbohydrate-ligand. The 3D structures of the wild type and mutant proteins have revealed the probable cause and consequence of the selection pressure responsible for the diversification of congerins.

Adaptation, Physiological↗

PubMed2005

Adaptive significance of avian beak morphology for ectoparasite control.

The beaks of Darwin's finches and other birds are among the best known examples of adaptive evolution. Beak morphology is usually interpreted in relation to its critical role in feeding. However, the beak also plays an important role in preening, which is the first line of defence against harmful ectoparasites such as feather lice, fleas, bugs, flies, ticks and feather mites. Here, we show a feature of the beak specifically adapted for ectoparasite control. Experimental trimming of the tiny (1-2 mm) maxillary overhang of rock pigeons (Columba livia) had no effect on feeding efficiency, yet triggered a dramatic increase in feather lice and the feather damage they cause. The overhang functions by generating a shearing force against the tip of the lower mandible, which moves forward remarkably quickly during preening, at up to 31 timesper second. This force damages parasite exoskeletons, significantly enhancing the efficiency of preening for parasite control. Overhangs longer than the natural mean of 1.6mm break significantly more often than short overhangs. Hence, stabilizing selection will favour overhangs of intermediate length. The adaptive radiation of beak morphology should be re-assessed with both feeding and preening in mind.

Adaptation, Biological↗

PubMedDate not supplied

Theoretical studies of cis-Pt(II)-diammine binding to duplex DNA.

The binding of cis-Pt(II) diammine (cis-DP) to double-stranded DNA was studied with several kinked conformations that can accommodate the formation of a square planar complex. Molecular mechanics (MM) calculations were performed to optimize the molecular fit. These results were combined with quantum mechanical (QM) calculations to ascertain the relative energetics of ligand binding through water vs direct binding of the phosphate to the ammine and platinum, and to guide the selection of DNA conformations to model complex formation. Based on QM and MM calculations, models are proposed that may be characterized by several general features. A structure involving hydrogen bonding between each ammine and distinct adjacent phosphate groups, referred to as closed conformation (CC), has already been reported. This is also found in the crystal structure of small dimers. We report alternative conformations that may be important in platination of duplex DNA. They are characterized by an intermediate conformation (IC), involving hydrogen bonding between one ammine and phosphate group, and an open conformation (OC), without ammine phosphate hydrogen bonding. The IC and OC can be stabilized by water bridges in the space between the ammine and the phosphate groups. Sugar puckers alternate from the type C(2')-endo or C(1')-exo (S), to the type C(3')-endo or C(2')-exo (N), with intermediate types near O(1')-endo (O). In general, the sugar puckers alternate from S to N to S through the platinated region (3'-TpG*pG*p-5'), with the complexed strand exhibiting, (3')-S*-N*-S-(5') alternation, while the complementary strand shows either (3')-S*-N*-S-(5') or (3')-S*-N*-O-(5') alternation. In both the OC and IC, a hydrogen bond is found between the ammine and O4(T) on thymine (T) at the (3') end, adjacent to the complex site. There is a continuous range of backbone conformations through the platinated region which relate the OC to the IC. The models presented suggest that the dynamics of the binding of the cis-Pt(II)-diammines to adjacent N7(G) in double-stranded DNA may encompass several conformational possibilities, and that water bridges may play a roll in supporting open and intermediate conformations. Proton-proton distances are reported to assist in the experimental determination of conformations.

Cisplatin↗