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PubMed2005

Structural classification of thioredoxin-like fold proteins.

Protein structure classification is necessary to comprehend the rapidly growing structural data for better understanding of protein evolution and sequence-structure-function relationships. Thioredoxins are important proteins that ubiquitously regulate cellular redox status and various other crucial functions. We define the thioredoxin-like fold using the structure consensus of thioredoxin homologs and consider all circular permutations of the fold. The search for thioredoxin-like fold proteins in the PDB database identified 723 protein domains. These domains are grouped into eleven evolutionary families based on combined sequence, structural, and functional evidence. Analysis of the protein-ligand structure complexes reveals two major active site locations for the thioredoxin-like proteins. Comparison to existing structure classifications reveals that our thioredoxin-like fold group is broader and more inclusive, unifying proteins from five SCOP folds, five CATH topologies and seven DALI domain dictionary globular folding topologies. Considering these structurally similar domains together sheds new light on the relationships between sequence, structure, function and evolution of thioredoxins.

Amino Acid Motifs↗
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↗
PubMed2004

The handedness of Leonardo da Vinci: a tale of the complexities of lateralisation.

The handedness of Leonardo da Vinci is controversial. Although there is little doubt that many of his well-attributed drawings were drawn with the left hand, the hatch marks of the shading going downwards from left to right, it is not clear that he was a natural left-hander, there being some suggestion that he may have become left-handed as the result of an injury to his right hand in early adulthood. Leonardo's lateralisation may be illuminated by an obscure passage in his notebooks in which he describes crouching down to look into a dark cave, putting his left hand on his knee, and shading his eyes with his right hand. We carried out a questionnaire survey, using 33 written and photographic items, to find whether this behaviour was typical of right handers or left handers. In fact the 'Leonardo task' showed almost no direct association with handedness, meaning that it contributes little to the immediate problem of elucidating Leonardo's handedness. However, the lateralisation of the task did relate to other aspects of behavioural laterality in surprisingly complex ways. This suggests that individual differences in handedness, and behavioural laterality in general, have a structural complexity which is not fully encompassed by simple measures of direction or degree of handedness.

Adult↗
PubMed2005

A two-state homology model of the hERG K+ channel: application to ligand binding.

Homology models based on available K+ channel structures have been used to construct a multiple state representation of the hERG cardiac K+ channel. These states are used to capture the flexibility of the channel. We show that this flexibility is essential in order to correctly model the binding affinity of a set of diverse ligands. Using this multiple state approach, a binding affinity model was constructed for set of known hERG channel binders. The predicted pIC50s are in good agreement with experiment (RMSD: 0.56 kcal/mol). In addition, these calculations provide structures for the bound ligands that are consistent with published mutation studies. These computed ligand bound complex structures can be used to guide synthesis of analogs with reduced hERG liability.

ERG1 Potassium Channel↗
PubMed2000

Single-molecule X-ray diffraction.

Free-electron lasers could provide femtosecond X-ray flashes with a peak brilliance 10-11 orders of magnitude higher than that which is currently available from synchrotrons. Such pulses may allow structural studies of single biomolecules before radiation damage destroys them and may permit the imaging of complex structures without the need to amplify scattered radiation through Bragg reflections.

Lasers↗
PubMed2003

A symbolic methodology to improve disassembly process design.

Millions of end-of-life electronic components are retired annually due to the proliferation of new models and their rapid obsolescence. The recovery of resources such as plastics from these goods requires their disassembly. The time required for each disassembly and its associated cost is defined by the operator's familiarity with the product design and its complexity. Since model proliferation serves to complicate an operator's learning curve, it is worthwhile to investigate the benefits to be gained in a disassembly operator's preplanning process. Effective disassembly process design demands the application of green engineering principles, such as those developed by Anastas and Zimmerman (Environ. Sci. Technol. 2003, 37, 94A-101A), which include regard for product complexity, structural commonality, separation energy, material value, and waste prevention. This paper introduces the concept of design symbolsto help the operator more efficiently survey product complexity with respect to location and number of fasteners to remove a structure that is common to all electronics: the housing. With a sample of 71 different computers, printers, and monitors, we demonstrate that appropriate symbols reduce the total disassembly planning time by 13.2 min. Such an improvement could well make efficient the separation of plastic that would otherwise be destined for waste-to-energy or landfill. The symbolic methodology presented may also improve Design for Recycling and Design for Maintenance and Support.

Computers↗
PubMed2004

Total synthesis of brevetoxin-B.

Brevetoxin-B (BTX-B), produced by the red tide organism, Gymnodium breve Davis, is the first member of marine polycyclic ethers to be structurally elucidated and one of the most potent neurotoxins. The structural feature is a trans-fused polycyclic ether ring system with 23 stereocenters. Its unique, complex structure and potent biological activity have attracted the attention of synthetic organic chemists. Total synthesis of BTX-B has been accomplished via the coupling of the ABCDEFG and IJK-ring segments, each ether ring of which was stereoselectively and efficiently constructed on the basis of SmI2-induced intramolecular cyclization, 6-endo-cyclization of hydroxy epoxide, ring-closing olefin metathesis, and SmI2-induced intramolecular Reformatsky-type reaction. Several kinds of double reactions at the left and right sides were efficiently used through the synthesis.

Animals↗
PubMed2003

From the Cover: Segmented spiral waves in a reaction-diffusion system.

Pattern formation in reaction-diffusion systems is often invoked as a mechanism for biological morphogenesis. Patterns in chemical systems typically occur either as propagating waves or as stationary, spatially periodic, Turing structures. The spiral and concentric (target) waves found to date in spatially extended chemical or physical systems are smooth and continuous; only living systems, such as seashells, lichens, pine cones, or flowers, have been shown to demonstrate segmentation of these patterns. Here, we report observations of segmented spiral and target waves in the Belousov-Zhabotinsky reaction dispersed in water nanodroplets of a water-in-oil microemulsion. These highly ordered chemical patterns, consisting of short wave segments regularly separated by gaps, form a link between Turing and trigger wave patterns and narrow the disparity between chemistry and biology. They exhibit aspects of such fundamental biological behavior as self-replication of structural elements and preservation of morphology during evolutionary development from a simpler precursor to a more complex structure.

Biophysical Phenomena↗
PubMed1996

Targeting nucleic acid secondary structures by antisense oligonucleotides designed through in vitro selection.

Using an in vitro selection approach, we have isolated oligonucleotides that can bind to a DNA hairpin structure. Complex formation of these oligonucleotides with the target hairpin involves some type of triple-stranded structure with noncanonical interaction, as indicated by bandshift assays and footprinting studies. The selected oligomers can block restriction endonuclease cleavage of the target hairpin in a sequence-specific manner. We demonstrate that in vitro selection can extend the antisense approach to functional targeting of secondary structure motifs. This could provide a basis for interfering with regulatory processes mediated by a variety of nucleic acid structures.

Binding Sites↗
PubMed1990

The thermodynamics of bipolarity: a bifurcation model of bipolar illness and bipolar character and its psychotherapeutic applications.

Two models dominate current formulations of bipolar illness: the homeostatic model implicit in Freud's psychodynamics and most neuroamine deficit/excess theories; and the oscillatory model of exaggerated biological rhythms. The homeostatic model is based on the closed systems approach of classic thermodynamics, while the oscillatory model requires the open systems approach of modern thermodynamics. Here we present a thermodynamic model of bipolarity that includes both homeostatic and oscillatory features and adds the most important feature of open systems thermodynamics: the creation of novel structures in bifurcation processes. According to the proposed model, bipolarity is the result of exaggerated biological energy that augments homeostatic, oscillatory and creative psychological processes. Only low-energy closed systems tend to rest ("point attractor") and entropic disorder. Open processes containing and exchanging energy fluctuate between opposite states ("periodic attractors"); they are characteristic of most physiological rhythms and are exaggerated in bipolar subjects. At higher energies, their strong fluctuations destroy pre-existing patterns and structures, produce turbulence ("chaotic attractors"), which sudden switches between opposite states, and create new and more complex structures. Likewise, high-energy bipolars develop high spontaneity, great fluctuations between opposite moods, internal and interpersonal chaos, and enhanced creativity (personal, artistic, professional) as well as psychopathology (personality deviations, psychotic delusions). Offered here is a theoretical explanation of the dual--creative and destructive--nature of bipolarity in terms of the new enantiodromic concept of entropy generalized by process theory. Clinically, this article offers an integrative model of bipolarity that accounts for many clinical features and contributes to a definition of the bipolar personality.

Adult↗
PubMed2005

The phaseolin vacuolar sorting signal promotes transient, strong membrane association and aggregation of the bean storage protein in transgenic tobacco.

Vacuolar storage proteins of the 7S class are co-translationally introduced into the endoplasmic reticulum and reach storage vacuoles via the Golgi complex and dense vesicles. The signal for vacuolar sorting of one of these proteins, phaseolin of Phaseolus vulgaris, consists of a four-amino acid hydrophobic propeptide at the C-terminus. When this sequence is deleted, phaseolin is secreted instead of being sorted to vacuoles. It is shown here that in transgenic tobacco plants newly-synthesized phaseolin has unusual affinity to membranes and forms SDS-resistant aggregates, but mutated phaseolin polypeptides that are either secreted or defective in assembly do not have these characteristics. Association to membranes and aggregation are transient events: phaseolin accumulated in vacuoles is soluble in the absence of detergents and is not aggregated. Association to membranes starts before the phaseolin glycan acquires a complex structure and therefore before the protein reaches the medial or trans-cisternae of the Golgi complex. These results support the hypothesis of a relationship between aggregation and vacuolar sorting of phaseolin and indicate that sorting may start in early compartments of the secretory pathway.

Cell Membrane↗
PubMed2005

Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup.

The large number of currently available group I intron sequences in the public databases provides opportunity for studying this large family of structurally complex catalytic RNA by large-scale comparative sequence analysis. In this study, the detailed secondary structures of 211 group I introns in the IE subgroup were manually predicted. The secondary structure-favored alignments showed that IE introns contain 14 conserved stems. The P13 stem formed by long-range base-pairing between P2.1 and P9.1 is conserved among IE introns. Sequence variations in the conserved core divide IE introns into three distinct minor subgroups, namely IE1, IE2 and IE3. Co-variation of the peripheral structural motifs with core sequences supports that the peripheral elements function in assisting the core structure folding. Interestingly, host-specific structural motifs were found in IE2 introns inserted at S516 position. Competitive base-pairing is found to be conserved at the junctions of all long-range paired regions, suggesting a possible mechanism of establishing long-range base-pairing during large RNA folding. These findings extend our knowledge of IE introns, indicating that comparative analysis can be a very good complement for deepening our understanding of RNA structure and function in the genomic era.

Base Pairing↗
PubMed2005

Layered poly[mu2-aqua-mu3-dimethylformamide-di-mu3-phenylphosphonato-dipotassium].

The first structurally characterized alkali metal phosphonate, the title compound, [K2(C6H6O3P)2(C3H7NO)(H2O)]n, has a complex structure, with layers parallel to the crystallographic bc plane consisting of two crystallographically independent K atoms sandwiched between the three types of ligands present in the structure, viz. water molecules, dimethylformamide molecules and two crystallographically independent phenylphosphonate ligands. Six O atoms coordinate to one K atom and seven to the other. The interlayer distance is 15.327 (4) A. The K-O distances are in the range 2.739 (2)-2.932 (2) A for the seven-coordinate K atom and 2.650 (2)-2.821 (2) A for the six-coordinate K atom.

Journal Article↗
PubMed1996

Current status in extracorporeal immunomodulation: immune disorders.

Today, clinicians can choose from a variety of extracorporeal immunomodulatory procedures such as plasma exchange, double filtration, immunoadsorption, chemoadsorption, photopheresis, and cytoapheresis. The mechanisms underlying extracorporeal immunomodulation (ECIM) comprise removal of pathogenic antibodies and circulating immune complexes as well as reticuloendothelial system deblockage; modification of immune complex structure and processing can be induced by changing the antigen/antibody ratio and by modulation of immune complex solubility via complement activation. Finally, cellular components like lymphocyte subsets, can be modified. Clinical examples of ECIM include lupus erythematosus, Goodpasture's syndrome, anti-neutrophil cytoplasmatic antibodies-mediated systemic vasculitis, myasthenia gravis, and, hypothetically, sepsis.

Adjuvants, Immunologic↗
PubMed2006

Specific and randomly derived immunoactive peptide mimotopes of mycobacterial antigens.

The mycobacterial cell surface contains complex nonprotein antigens that are highly immunoactive in nature. However, these antigens are chemically heterogeneous and structurally complex, thereby limiting their applications. To identify their peptide mimotopes, phage-displayed peptide libraries Ph.D.-7 and Ph.D.-12 were panned on either defined template, monoclonal antibody (MAb) CS-35 against lipoarabinomannan (LAM), or a polyclonal rabbit immune serum reactive against whole cells of Mycobacterium bovis BCG. Panning on anti-LAM MAb CS-35 yielded two confirmed mimotopes of LAM, a 7-mer and a 12-mer, whereas panning on polyclonal serum yielded a large repertoire of mimotopes reactive against sera from BCG-immunized rabbits, one of which turned out to have the same sequence as the 7-mer LAM mimotope. The dissociation constant of the interaction between MAb CS-35 and a synthetic peptide corresponding to the 7-mer LAM mimotope was determined to be 7.55 microM. Dot blot assays were performed with peptides corresponding to the two LAM mimotopes to evaluate their diagnostic potential. Both peptides gave discernibly higher signals with a panel of tuberculosis (TB) patient sera than with sera from healthy controls. The peptides were also found to stimulate the release of tumor necrosis factor alpha and interleukin-12 cytokines in the J774A.1 cell line and primary bone marrow-derived macrophages, indicating that they may have immunomodulatory potential. The present study demonstrates that peptide mimotopes of known and unknown mycobacterial antigens could be isolated by using subtractive phage display techniques and that these peptides could have potential applications in areas such as TB diagnostics and immunotherapy.

Animals↗
PubMed1988

Differentiation of rat small intestinal epithelial cells by extracellular matrix.

The role of extracellular matrix as a determinant of intestinal cell maturation was explored by growing a normal, but immature, rat small intestinal cell line (IEC-6) on basement membrane extract from Engelbreth-Holm-Swarm (EHS) sarcoma cells (ECM). Grown on plastic or glass, these cells are relatively immature and proliferate rapidly. In contrast, cells on ECM attached more rapidly, stopped proliferating, and rapidly organized into multicellular complex structures. Ultrastructurally, cells grown on ECM displayed significantly more mitochondria, rough endoplasmic reticulum, apical microvilli, and complex golgi apparatus, consistent with greater maturity and synthetic activity. By indirect immunofluorescence, sucrase, alkaline phosphatase, and cellular apolipoprotein B were present in cells grown on ECM only. In contrast to cells grown on glass, these cells also demonstrated Na-dependent glucose absorption, a function unique to mature villus cells (7). We conclude that the basement membrane may be a key determinant of intestinal epithelial cell maturation. The development of a mature villuslike intestinal cell in vitro may have wide application for future studies of induction and regulation of intestinal maturation and function.

Animals↗
PubMed2002

Genetically engineered gold-binding polypeptides: structure prediction and molecular dynamics.

The biological control of inorganic crystal formation, morphology, and assembly is of interest to biologists and biotechnologists studying hard tissue growth and regeneration, as well as to materials scientists using biomimetic approaches for the control of inorganic material fabrication and assembly. Biomimetics requires an accurate understanding of natural mechanisms at the molecular level. Such understanding can be derived from the use of metal surfaces to study surface recognition by proteins together with combinatorial genetics techniques for the selection of suitable peptides. Polymerization of these peptides produces engineered polypeptides large enough to encode their own folding information with low structural complexity, while enhancing binding affinity to surfaces. The low complexity of such polypeptides can aid in analyses, leading to modeling and eventual manipulation of the structure of the folded polypeptide. This paper presents structure predictions for gold-binding protein sequences, originally selected by combinatorial techniques. Molecular dynamics simulations lasting 5 ns were carried out using solvated polypeptides at the gold surface to assess the dynamics of the binding process and the effects of surface topography on the specificity of protein binding.

Amino Acid Sequence↗
PubMed2004

FR182876, a new microtubule modulator with high water-solubility, from a Streptomyces.

In the course of seeking new anti-tumor drugs, a new microtubule modulator with high water-solubility, FR182876, was isolated from a Streptomyces which also produces FR182877. Even modern spectroscopic methods could not solve the structure of FR182876 due to its structural complexity and chemical instability. Thus, we have combined chemical correlations with spectroscopic methods and determined its structure, which features a highly fused ring system and 3-methylhistidine. The latter is believed to contribute to both solubility in water and activity in promoting tubulin polymerization. FR182876 showed potent cytotoxicity against a panel of cancer cells at concentrations of 28-75 ng/ml.

Antibiotics, Antineoplastic↗