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PubMed2006

Synthesis, crystal structure and DNA binding studies of a binuclear copper(II) complex with phenanthroline.

A new binuclear copper(II) complex, [Cu2Phen2Cl4] (Phen=1,10-phenanthroline), has been synthesized and characterized. Single crystal X-ray diffraction results suggest that this complex structure belongs to monoclinic crystal system, Cc (no. 9) with the cell dimensions: a=9.849(2)A, b=17.833(4)A, c=13.374(3)A, beta=106.61(3) degrees , V=2251.0(8)A(3), Dc=1.8569 Mgm(-3), F(000)=1256.0, Z=4. One Cu(II) central atom situated in a distorted square planar geometry is four-coordinated. The other situated in a distorted square pyramidal geometry is five-coordinated. Only one bridging Cl atom exists in the complex. Spectroscopic studies, including electronic absorption and fluorescence spectra, conductivity measurements and parallel factor analysis (PARAFAC) of fluorescence excitation-emission three-way data array, were carried out on the DNA binding behavior of the complex. All the results suggested that the breakage of DNA secondary structure took place at low molar ratio of complex to DNA (0.3 at most) and intercalation into the base pair of DNA took place at high molar ratio. Additionally, the equilibrium concentration of EB-DNA and EB (EB: ethidium bromide) could be directly obtained by PARAFAC algorithm, proved to be a convincing method for studying the interaction of complexes with DNA.

Copper↗
PubMed1991

[Study of the pyruvate dehydrogenase complex by circular dichroism].

A comparative study of the pyruvate dehydrogenase complex and its pyruvate dehydrogenase component was carried out by using the circular dichroism method. It was found that the spectral properties of the pyruvate dehydrogenase complex are determined by those of its first component: i) the spectrum of the thiamine pyrophosphate-free pyruvate dehydrogenase complex displayed the main characteristics of the pyruvate dehydrogenase component; ii) the appearance of the charge transfer complex band during thiamine pyrophosphate saturation was revealed for the both proteins; iii) in both cases the charge transfer complex band disappeared after the interaction of the holoform with pyruvate and reappeared after the addition of dithiothreitol used as a deacetylating reagent. Coenzyme A in the same reaction selectively deacetylated the pyruvate dehydrogenase complex (but not its pyruvate dehydrogenase component). The spectral dynamics of pyruvate dehydrogenase reflects the functional changes in the enzyme active centers during the catalytic act. The similarity of the spectral behaviour of pyruvate dehydrogenase within the complex structure and in the isolated state provides support for the earlier proposed mechanism of the pyruvate dehydrogenase action and ensures a methodological basis for its direct investigation within the complex structure.

Acetylation↗
PubMedDate not supplied

Catfishes as a case study for discussions on general evolution: the importance of functional uncouplings in morphological macroevolution.

Many evolutionary biologists have stressed that functional uncouplings play an important role in morphological macroevolution, as they facilitate diversification and speciation by increasing the number of degrees of freedom and allowing more mechanical solutions for functional problems. In the present paper, the importance of functional uncouplings in the evolution of six major catfish structural complexes is briefly discussed, namely those constituted by the mandibular barbels and associated structures, the pectoral girdle complex, the elastic spring apparatus, the suspensorium, the palatine-maxillary system, and the adductor mandibulae complex. The overview of these major structural complexes indicates that functional uncouplings did effectively play an essential role on catfish evolutionary history. The study of this cosmopolitan and particularly diverse group representing about one-third of all freshwater fishes thus supports the importance of functional uncouplings in morphological macroevolution.

Animals↗
PubMed2004

Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes.

Amino acid sequence alignments of orthologous ribosomal proteins found in Bacteria, Archaea, and Eukaryota display, relative to one another, an unusual segment or block structure, with major evolutionary implications. Within each of the prokaryotic phylodomains the sequences exhibit substantial similarity, but cross-domain alignments break up into (a) universal blocks (conserved in both phylodomains), (b) bacterial blocks (unalignable with any archaeal counterparts), and (c) archaeal blocks (unalignable with any bacterial counterparts). Sequences of those eukaryotic cytoplasmic riboproteins that have orthologs in both Bacteria and Archaea, exclusively match the archaeal block structure. The distinct blocks do not correlate consistently with any identifiable functional or structural feature including RNA and protein contacts. This phylodomain-specific block pattern also exists in a number of other proteins associated with protein synthesis, but not among enzymes of intermediary metabolism. While the universal blocks imply that modern Bacteria and Archaea (as defined by their translational machinery) clearly have had a common ancestor, the phylodomain-specific blocks imply that these two groups derive from single, phylodomain-specific types that came into existence at some point long after that common ancestor. The simplest explanation for this pattern would be a major evolutionary bottleneck, or other scenario that drastically limited the progenitors of modern prokaryotic diversity at a time considerably after the evolution of a fully functional translation apparatus. The vast range of habitats and metabolisms that prokaryotes occupy today would thus reflect divergent evolution after such a restricting event. Interestingly, phylogenetic analysis places the origin of eukaryotes at about the same time and shows a closer relationship of the eukaryotic ribosome-associated proteins to crenarchaeal rather than euryarchaeal counterparts.

Amino Acid Sequence↗
PubMed2000

Sensory organ generation in the chicken inner ear: contributions of bone morphogenetic protein 4, serrate1, and lunatic fringe.

The chicken inner ear is a remarkably complex structure consisting of eight morphologically distinct sensory organs. Unraveling how these sensory organs are specified during development is key to understanding how such a complex structure is generated. Previously, we have shown that each sensory organ in the chicken inner ear arises independently in the rudimentary otocyst based on Bone morphogenetic protein 4 (Bmp4) expression. Here, we compare the expression of Bmp4 with two other putative sensory organ markers, Lunatic Fringe (L-fng) and chicken Serrate1 (Ser1), both of which are components of the Notch signaling pathway. L-fng and Ser1 expression domains were asymmetrically distributed in the otic cup. At this early stage, expression of L-fng is similar to Delta1 (Dl1), in an anteroventral domain apparently corresponding to the neurogenic region, while Ser1 is expressed at both the anterior and posterior poles. By the otocyst stage, the expression of both L-fng and Ser1 largely coincided in the medial region. All presumptive sensory organs, as identified by Bmp4 expression, arose within the broad L-fng- and Ser1-positive domain, indicating the existence of a sensory-competent region in the rudimentary otocyst. In addition, there is a qualitative difference in the levels of expression between L-fng and Ser1 such that L-fng expression was stronger in the ventral anterior, whereas Ser1 was stronger in the dorsal posterior region of this broad domain. This early difference in expression may presage the differences among sensory organs as they arise from this sensory competent zone.

Age Factors↗
PubMed1991

Self-assembly in supramolecular systems.

The complex structural and functional properties of many natural molecules have spawned innumerable attempts to understand and mimic biological activity. This has often involved preparing extremely complex structures of carefully designed geometries. In natural systems the primary structure of a protein (the amino acid sequence) establishes all of the structural relationships within the molecule, although many of these are not apparent until the molecule folds, coils, or otherwise adopts the appropriate conformation. Nature has selected suitable amino acid sequences for various applications during eons of evolution. In this paper, we report our efforts to achieve similar results by providing all of the required structural elements on a flexible framework. This concept is illustrated in three ways: the design and preparation of a redox-switched vesicle and a small-molecule molecular receptor (both based on the ferrocene system) and of a functional cation channel.

Amino Acid Sequence↗
PubMed2001

Thermodynamics of Ras/effector and Cdc42/effector interactions probed by isothermal titration calorimetry.

Proliferation, differentiation, and morphology of eucaryotic cells is regulated by a large network of signaling molecules. Among the major players are members of the Ras and Rho/Rac subfamilies of small GTPases that bind to different sets of effector proteins. Recognition of multiple effectors is important for communicating signals into different pathways, leading to the question of how an individual GTPase achieves tight binding to diverse targets. To understand the observed specificity, detailed information about binding energetics is expected to complement the information gained from the three-dimensional structures of GTPase/effector protein complexes. Here, the thermodynamics of the interaction of four closely related members of the Ras subfamily with four different effectors and, additionally, the more distantly related Cdc42/WASP couple were quantified by means of isothermal titration calorimetry. The heat capacity changes upon complex formation were rationalized in light of the GTPase/effector complex structures. Changes in enthalpy, entropy, and heat capacity of association with various Ras proteins are similar for the same effector. In contrast, although the structures of the Ras-binding domains are similar, the thermodynamics of the Ras/Raf and Ras/Ral guanine nucleotide dissociation stimulator interactions are quite different. The energy profile of the Cdc42/WASP interaction is similar to Ras/Ral guanine nucleotide dissociation stimulator, despite largely different structures and interface areas of the complexes. Water molecules in the interface cannot fully account for the observed discrepancy but may explain the large range of Ras/effector binding specificity. The differences in the thermodynamic parameters, particularly the entropy changes, could help in the design of effector-specific inhibitors that selectively block a single pathway.

Animals↗
PubMed2003

Spatial analysis of archaeal community structure in grassland soil.

The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.

Crenarchaeota↗
PubMed2006

Structure-based discovery and optimization of potential cancer therapeutics targeting the cell cycle.

Progress has been made recently in the structure-based optimization of novel cell cycle antitumor therapeutics based on cyclin-dependent kinase (CDK) inhibition. A novel inhibitor series based on the 2-amino-4-heteroaryl-pyrimidine scaffold was discovered using the LIDAEUS high-throughput docking methodology, and was subsequently optimized for CDK2 potency through information provided by crystallographic complex structures. A computational study of CDK4 inhibitors led to the incorporation of selectivity determinants into a pyrimidine pharmacophore to generate isoform-specific inhibitors. In addition, molecules from the inhibitor series have been crystallized in complex structures with both monomeric inactive CDK2 and an active complex of CDK2 bound to cyclin A or E. This crystallization revealed that significant differences exist in the affinity of the inhibitors for active and inactive states of CDK2. Information on differences in affinity facilitates the prediction of experimental binding of inhibitors and allows for the further development of structure-guided design.

Antineoplastic Agents↗
PubMed1990

Stimulus complexity and autistic children's responsivity: assessing and training a pivotal behavior.

Interdisciplinary research suggests that autistic children's limitations in responding to environmental stimuli may be directly related to the number of components contained in the stimuli; as the number of components increases, such children hypothetically would exhibit greater difficulties in responding. The central purpose of this experiment was to assess whether such children indeed exhibit greater difficulties in responding as the number of components contained in an environmental stimulus was increased from one to four. If the children's responsivity was a function of stimulus complexity, a second focus of this experiment was to assess the feasibility of teaching them to respond to a complex environmental stimulus containing up to four components and to determine whether the effects of the intervention would generalize to other situations involving complex structured and social stimuli. Data gathered using a multiple baseline design across behaviors and children indicate that all of the children exhibited fewer correct responses to a stimulus as the number of stimulus components was increased from one to four. The results further showed that the training program used in this investigation was effective in producing some generalized increases in the children's responses to complex structured and social stimuli. Conceptualizing autistic children's responses to complex multicomponent stimuli as a pivotal target behavior that can be operationally defined may have important implications for understanding and altering the children's responsivity and development.

Adolescent↗
PubMed2003

Stereospecific interactions of proline residues in protein structures and complexes.

The constrained backbone torsion angle of a proline (Pro) residue has usually been invoked to explain its three-dimensional context in proteins. Here we show that specific interactions involving the pyrrolidine ring atoms also contribute to its location in a given secondary structure and its binding to another molecule. It is adept at participating in two rather non-conventional interactions, C-H...pi and C-H...O. The geometry of interaction between the pyrrolidine and aromatic rings, vis-à-vis the occurrence of the C-H...pi interactions has been elucidated. Some of the secondary structural elements stabilized by Pro-aromatic interactions are beta-turns, where a Pro can interact with an adjacent aromatic residue, and in antiparallel beta-sheet, where a Pro in an edge strand can interact with an aromatic residue in the adjacent strand at a non-hydrogen-bonded site. The C-H groups at the Calpha and Cdelta positions can form strong C-H...O interactions (as seen from the clustering of points) and such interactions involving a Pro residue at C' position relative to an alpha-helix can cap the hydrogen bond forming potentials of the free carbonyl groups at the helix C terminus. Functionally important Pro residues occurring at the binding site of a protein almost invariably engage aromatic residues (with one of them being held by C-H...pi interaction) from the partner molecule in the complex, and such aromatic residues are highly conserved during evolution.

Binding Sites↗
PubMed2003

Software systems as complex networks: structure, function, and evolvability of software collaboration graphs.

Software systems emerge from mere keystrokes to form intricate functional networks connecting many collaborating modules, objects, classes, methods, and subroutines. Building on recent advances in the study of complex networks, I have examined software collaboration graphs contained within several open-source software systems, and have found them to reveal scale-free, small-world networks similar to those identified in other technological, sociological, and biological systems. I present several measures of these network topologies, and discuss their relationship to software engineering practices. I also present a simple model of software system evolution based on refactoring processes which captures some of the salient features of the observed systems. Some implications of object-oriented design for questions about network robustness, evolvability, degeneracy, and organization are discussed in the wake of these findings.

Journal Article↗
PubMed2003

Seasonal shift from bottom-up to top-down impact in phytophagous insect populations.

Although many studies now examine how multiple factors influence the dynamics of herbivore populations, few studies explicitly attempt to document where and when each is important and how they vary and interact. In fact, how temporal variation in top-down (natural enemies) and bottom-up (host plant resources) factors affect herbivore dynamics has been suggested as a particularly important yet poorly understood feature of terrestrial food webs. In this study we examined how temporal changes in predator density (wolf spiders, sheet-web builders, and mirid egg predators) and host-plant resources (plant quality and structural complexity) influence the population dynamics of the dominant phytophagous insects on Atlantic-coast salt marshes, namely Prokelisia planthoppers (Homoptera: Delphacidae). We designed a factorial experiment in meadows of Spartina alterniflora to mimic natural variation in vegetation quality and structure by establishing two levels of plant nutrition (leaf nitrogen content) by fertilization, and two levels of habitat complexity by adding leaf litter (thatch). We then assessed seasonal changes in the strength of bottom-up (plant quality) and top-down (predator) impacts on planthopper populations. Planthopper populations responded positively to increased plant quality treatments in late summer. Despite the greater number of planthopper adults colonizing fertilized Spartina plots compared to unfertilized controls, the offspring of these colonists were much less abundant at the end of the season in fertilized plots, particularly those with thatch. The initial colonization effect was later erased because arthropod predators selectively accumulated in fertilized plots where they inflicted significant mortality on all stages of planthoppers. Predators rapidly colonized fertilized plots and reached high densities well in advance of planthopper colonization, a response we attribute to their rapid aggregation in complex-structured habitats with readily available alternative prey. Our results suggest that plant resources not only mediate the strength of predator impacts on herbivore populations, but they also promote the coupling of predator and prey populations and thus influence when enemy impacts are realized.

Animals↗
PubMed2005

Imidazolin-2-iminato titanium complexes: synthesis, structure and use in ethylene polymerization catalysis.

The Staudinger reaction of the imidazolin-2-ylidenes, 1,3-di-tert-butylimidazolin-2-ylidene (1a), 1,3-diisopropylimidazolin-2-ylidene (1b), 1,3-diisopropyl-4,5-dimethylimidazolin-2-ylidene (1c), 1,3-bis(2,4,6-trimethylphenyl)imidazolin-2-ylidene (1d) and 1,3-bis(2,6-diisopropylphenylimidazolin-2-ylidene (1e), with trimethylsilyl azide furnishes the corresponding N-silylated 2-iminoimidazolines 2a-e, which react with [(eta-C5H5)TiCl3] to afford half-sandwich cyclopentadienyl titanium complexes of the type [CpTi(L)Cl2] (3) (L = imidazolin-2-iminato ligand). Similarly, the reactions of 1,3-di-tert-butyl-2-(trimethylsilylimino)imidazoline (2a) with [(eta-tBuC5H4)TiCl3] results in the formation of [(eta-tBuC5H4)Ti(L)Cl2] (4) (L = 1,3-di-tert-butylimidazolin-2-imide). Bis(1,3-di-tert-butylimidazolin-2-iminato)titanium dichloride (5) is obtained from the reaction of two eq. of 2a with TiCl4. Treatment of 5 with methyllithium results in the formation of the corresponding dimethyl complex [L2Ti(CH3)2] (6), whereas [CpTi(L)(CH3)2] (7) is similarly obtained from 3a. The molecular structures of 3a, 3b, 3c, 3e x C7H8, 4 and 7 are reported revealing linearly coordinated imidazolin-2-iminato ligands together with very short Ti-N bond distances. All dichloro complexes (3a-e, 4 and 5) can be activated with methylaluminoxane (MAO) to give active catalysts for ethylene homopolymerization. In most cases, moderate to high activities are observed together with the formation of high (HMWPE) or even ultra high molecular weight polyethylene (UHMWPE).

Catalysis↗
PubMed2006

Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex.

For structural studies of proteins and their complexes, chemical cross-linking combined with mass spectrometry presents a promising strategy to obtain structural data of protein interfaces from low quantities of proteins within a short time. We explore the use of isotope-labeled cross-linkers in combination with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry for a more efficient identification of cross-linker containing species. For our studies, we chose the calcium-independent complex between calmodulin and a 25-amino acid peptide from the C-terminal region of adenylyl cyclase 8 containing an "IQ-like motif." Cross-linking reactions between calmodulin and the peptide were performed in the absence of calcium using the amine-reactive, isotope-labeled (d0 and d4) cross-linkers BS3 (bis[sulfosuccinimidyl]suberate) and BS2G (bis[sulfosuccinimidyl]glutarate). Tryptic in-gel digestion of excised gel bands from covalently cross-linked complexes resulted in complicated peptide mixtures, which were analyzed by nano-HPLC/nano-ESI-FTICR mass spectrometry. In cases where more than one reactive functional group, e.g., amine groups of lysine residues, is present in a sequence stretch, MS/MS analysis is a prerequisite for unambiguously identifying the modified residues. MS/MS experiments revealed two lysine residues in the central alpha-helix of calmodulin as well as three lysine residues both in the C-terminal and N-terminal lobes of calmodulin to be cross-linked with one single lysine residue of the adenylyl cyclase 8 peptide. Further cross-linking studies will have to be conducted to propose a structural model for the calmodulin/peptide complex, which is formed in the absence of calcium. The combination of using isotope-labeled cross-linkers, determining the accurate mass of intact cross-linked products, and verifying the amino acid sequences of cross-linked species by MS/MS presents a convenient approach that offers the perspective to obtain structural data of protein assemblies within a few days.

Adenylyl Cyclases↗
PubMed1993

The interosseous membrane of the forearm: structure and its role in Galeazzi fractures.

A cadaveric study was performed to anatomically describe and mechanically document the interosseous membrane of the forearm using gross, histologic, scanning electron microscopic, and mechanical testing. The membrane was found to be a complex structure composed of nerves and vessels but mainly of collagen fibers that thicken to form bands coursing from radius to ulna. Strain-gauge studies demonstrated that the load transfer occurs from the radius to the ulna via the membrane and changes with supination or pronation. With specimens under a specific test load, sectioning of the membrane allowed the fractured radius to shorten by 6.25 mm and sectioning of the triangular fibrocartilage complex resulted in shortening of 7.7 mm. Total shortening after osteotomy and sectioning of the complex structure and membrane ranged from 15 to 40 mm. In Galeazzi fractures, the interosseous membrane acts as a constraint to radial shortening. Anatomic reduction with internal fixation is indicated for this fracture-dislocation.

Aged↗
PubMed2006

Mitochondrial complex I: structure, function and pathology.

Oxidative phosphorylation (OXPHOS) has a prominent role in energy metabolism of the cell. Being under bigenomic control, correct biogenesis and functioning of the OXPHOS system is dependent on the finely tuned interaction between the nuclear and the mitochondrial genome. This suggests that disturbances of the system can be caused by numerous genetic defects and can result in a variety of metabolic and biochemical alterations. Consequently, OXPHOS deficiencies manifest as a broad clinical spectrum. Complex I, the biggest and most complicated enzyme complex of the OXPHOS system, has been subjected to thorough investigation in recent years. Significant progress has been made in the field of structure, composition, assembly, and pathology. Important gains in the understanding of the Goliath of the OXPHOS system are: exposing the electron transfer mechanism and solving the crystal structure of the peripheral arm, characterization of almost all subunits and some of their functions, and creating models to elucidate the assembly process with concomitant identification of assembly chaperones. Unravelling the intricate mechanisms underlying the functioning of this membrane-bound enzyme complex in health and disease will pave the way for developing adequate diagnostic procedures and advanced therapeutic treatment strategies.

Animals↗
PubMed2000

Resonant response of complex shell structures

Resonances of shell structures play a prominent role in determining their acoustic characteristics. Among the most important of such characteristics are radiated noise, scattering, and self-noise levels. The nature of the structural resonances, for example the number of modes within a particular frequency band or the overall spatial dependence of the response, determines the importance of these phenomena in various contexts and what steps may be taken to modify their acoustic impact. In the past, knowledge of the resonant response of highly idealized systems has been used to guide the development of quiet platforms. The results of a scale model investigation of the effects of increased complexity on the nature of the resonances of submerged shell structures are reported. Effects presented here are flexural Bloch mode resonances, localized resonances resulting from structural irregularity, and the effects of non-axisymmetry on these phenomena. The implications of these results on acoustic design and the development of systems is discussed.

Journal Article↗