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PubMed2006

Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes.

ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin remodeling activities in eukaryotes from yeast to man. Many of these complexes have been found to reposition nucleosomes but with different directionalities. We find that the yeast Isw1a, Isw2, and Chd1 enzymes preferentially move nucleosomes toward more central locations on short DNA fragments whereas Isw1b does not. Importantly, the inherent positioning properties of the DNA play an important role in determining where nucleosomes are relocated to by all of these enzymes. However, a key difference is that the Isw1a, Isw2, and Chd1 enzymes are unable to move nucleosomes to positions closer than 15 bp from a DNA end, whereas Isw1b can. We also find that there is a correlation between the inability of enzymes to move nucleosomes close to DNA ends and the preferential binding to nucleosomes bearing linker DNA. These observations suggest that the accessibility of linker DNA together with the positioning properties of the underlying DNA play important roles in determining the outcome of remodeling by these enzymes.

Adenosine Triphosphatases↗
PubMed2002

A density functional study of S(N)2 substitution at square-planar platinum(II) complexes.

The energetics and reaction path in a series of S(N)2 substitution reactions at square-planar Pt(II) complexes have been studied by the application of density functional theory (DFT). Calculated free energies show excellent correlation with their experimental counterparts, while the enthalpic and entropic contributions individually indicate the presence of weak intermolecular interactions not accounted for in the present model. The nature of the leaving ligand has been shown to be much more significant in determining the activation barrier than that of the entering ligand; it is inferred (and confirmed by analysis of individual bond energies) that the reaction is driven by the dissociation of the leaving ligand, with the entering ligand playing a more passive role. Analysis of the intrinsic reaction coordinate indicates, further, that the trans ligand plays an unexpectedly dynamic role in stabilizing the transition state due to competition between stabilization and the steric effects of the entering and leaving ligands. The cis ligands, by contrast, are shown to move only slightly through the course of the reaction.

Journal Article↗
PubMed2003

A systematic approach to modeling, capturing, and disseminating proteomics experimental data.

Both the generation and the analysis of proteome data are becoming increasingly widespread, and the field of proteomics is moving incrementally toward high-throughput approaches. Techniques are also increasing in complexity as the relevant technologies evolve. A standard representation of both the methods used and the data generated in proteomics experiments, analogous to that of the MIAME (minimum information about a microarray experiment) guidelines for transcriptomics, and the associated MAGE (microarray gene expression) object model and XML (extensible markup language) implementation, has yet to emerge. This hinders the handling, exchange, and dissemination of proteomics data. Here, we present a UML (unified modeling language) approach to proteomics experimental data, describe XML and SQL (structured query language) implementations of that model, and discuss capture, storage, and dissemination strategies. These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository.

Database Management Systems↗
PubMed2004

Analysis of the thyrotropin receptor-thyrotropin interaction by comparative modeling.

We have used the most advanced programs currently available to construct the first three-domain structure of the human thyrotropin receptor (TSHR) using comparative modeling. The model consists of a leucine-rich domain (LRD; amino acids 36-281; porcine ribonuclease inhibitor used as a template for modeling), a cleavage domain (CD; amino acids 282-409; tissue inhibitor of matrix metalloproteinases 2 as template) and transmembrane domain (TMD amino acids 410-699; bovine rhodopsin as template). Models of human, porcine, and bovine TSH were also constructed (human chorionic gonadotropin [hCG] and human follicle stimulating hormone [hFSH] as templates). The LRD has a characteristic horseshoe shape with 10 tandem homologous repeats. The CD consists of beta-barrel and alpha helix structures (OB-like fold) with two disulfide bridges and the structure around these disulfide bridges remains stable after cleavage. The TMD presents the typical seven membrane-spanning helices. The TSH, LRD, CD, and TMD models were brought together in an extensive series of docking experiments. Known features of the TSH-TSHR interaction were used for selection of appropriate complexes that were then validated using a different set of experimental data. A similar approach was used to build a model of a complex between the TSHR and a monoclonal TSHR antibody with weak thyroid stimulating activity. Human thyrotropin (hTSH) alpha chains were found to make contact with many amino acids on the LRD surface and CD surface whereas no interaction between the beta chains and the CD were found. The higher affinity of bovine thyrotropin (bTSH) and porcine thyrotropin (pTSH) (relative to hTSH) for the TSHR is explained well by the models in terms of charge-charge interactions between their alpha chains and the receptor. Experimental observations showing increased sensitivity of the TSHR to hCG after mutation of TSHR Lys209 to Glu are explained well by our model. Furthermore, several mutations in the TMD that are associated with increased TSHR basal activity are predicted from our model to be caused by the formation of new interactions that stabilize the activated form of the TMD.

Animals↗
PubMed2005

Molecular genetics of T cell development.

T cell development is guided by a complex set of transcription factors that act recursively, in different combinations, at each of the developmental choice points from T-lineage specification to peripheral T cell specialization. This review describes the modes of action of the major T-lineage-defining transcription factors and the signal pathways that activate them during intrathymic differentiation from pluripotent precursors. Roles of Notch and its effector RBPSuh (CSL), GATA-3, E2A/HEB and Id proteins, c-Myb, TCF-1, and members of the Runx, Ets, and Ikaros families are critical. Less known transcription factors that are newly recognized as being required for T cell development at particular checkpoints are also described. The transcriptional regulation of T cell development is contrasted with that of B cell development, in terms of their different degrees of overlap with the stem-cell program and the different roles of key transcription factors in gene regulatory networks leading to lineage commitment.

Animals↗
PubMed2004

Crystal complex structures reveal how substrate is bound in the -4 to the +2 binding sites of Humicola grisea Cel12A.

As part of an ongoing enzyme discovery program to investigate the properties and catalytic mechanism of glycoside hydrolase family 12 (GH 12) endoglucanases, a GH family that contains several cellulases that are of interest in industrial applications, we have solved four new crystal structures of wild-type Humicola grisea Cel12A in complexes formed by soaking with cellobiose, cellotetraose, cellopentaose, and a thio-linked cellotetraose derivative (G2SG2). These complex structures allow mapping of the non-covalent interactions between the enzyme and the glucosyl chain bound in subsites -4 to +2 of the enzyme, and shed light on the mechanism and function of GH 12 cellulases. The unhydrolysed cellopentaose and the G2SG2 cello-oligomers span the active site of the catalytically active H.grisea Cel12A enzyme, with the pyranoside bound in subsite -1 displaying a S31 skew boat conformation. After soaking in cellotetraose, the cello-oligomer that is found bound in site -4 to -1 contains a beta-1,3-linkage between the two cellobiose units in the oligomer, which is believed to have been formed by a transglycosylation reaction that has occurred during the ligand soak of the protein crystals. The close fit of this ligand and the binding sites occupied suggest a novel mixed beta-glucanase activity for this enzyme.

Ascomycota↗
PubMed2002

[Ni(0)L]-catalyzed cyclodimerization of 1,3-butadiene: a density functional investigation of the influence of electronic and steric factors on the regulation of the selectivity.

We present a comprehensive theoretical investigation of the influence of the ligand L on the regulation of the product selectivity for the [Ni(0)L]-catalyzed cyclodimerization of 1,3-butadiene. The investigation was based on density functional theory (DFT) and a combined DFT and molecular mechanics (QM/MM) approach for the real [bis(butadiene)Ni(0)L] catalysts with L = PMe(3), I; PPh(3), II; P((i)Pr)(3), III; and P(OPh)(3), IV. The role of electronic and steric effects has been elucidated for all crucial elementary steps of the entire catalytic cycle. Allylic isomerization, allylic enantioface conversion, as well as oxidative coupling are shown to be influenced to a minor extent by electronic and steric effects. In contrast, the ligand's properties have a distinct influence on the preestablished equilibrium between the eta(3),eta(1)(C(1)) and bis-eta(3) forms 2 and 4, respectively, of the [(octadienediyl)Ni(II)L] complex and on the rate-determining reductive elimination following competing routes for generation of either VCH, cis-1,2-DVCB, or cis,cis-COD. Electronic factors are shown to predominantly determine the position of the kinetically mobile 2 right harpoon over left harpoon 4 equilibrium. 4 is the prevailing species for ligands L that are pi-acceptors (L = P(OPh)(3)) or weak sigma-donors (L = PPh(3)), while stronger sigma-donors (L = PMe(3), P((i)Pr)(3)) displace the equilibrium to the left. Steric bulk on the ligand as well as its pi-acceptor ability act to facilitate the reductive elimination, while sigma-donor abilities serve to retard this process. Electronic and steric factors are found to not influence uniformly the reductive elimination routes with either 2 or 4 involved. The regulation of the product selectivity is elucidated on the basis of both thermodynamic and kinetic considerations.

Journal Article↗
PubMed2006

Stress and strain analysis of the hip joint using FEM.

Many disorders of the hip can be treated with a suitable osteotomy based on the improvement of mechanical conditions in the hip joint. These operations, such as osteotomies are very complex. The surface replacement has also been developed as an alternative to a total hip replacement for young and more active people. It is up-to-date to concern with biomechanics of pathological hips and it is necessary to supplement the existing clinical findings with the results of mechanical analyses. Several finite element (FE) models are presented in this paper. The first one offers solutions to the strain-stress analysis of the physiological hip. The second one represents dysplastic hip joint. Another two computational models of both hips of a young patient were created (FE model of physiological hip and pathological hip affected by Perthes disease with a deformed shape of the femoral head). Also a computational model is presented, which enables us to investigate strain and stress parameters in the hip joint with applied surface replacement. The strain and stress analysis was performed by means of finite element method (FEM) in ANSYS system.

Arthroplasty, Replacement, Hip↗
PubMed2005

On the origin of optical activity in tris-diamine complexes of Co(III) and Rh(III): a simple model based on time-dependent density function theory.

Time-dependent density functional theory (TD-DFT) is applied to the CD spectra of Lambda(deltadeltadelta)-(+)-[Co(S-pn)n(en)(3-n)]3+ (n = 1, 2, 3) and Lambda(deltadeltadelta)-(+)-[Co(en)3]3+ as well as the stereoisomers Delta-((delta)n(lambda)(3-n))-(-)-[Co(S-pn)n(en)(3-n)]3+ (n = 1, 2, 3) and Delta(deltadeltadelta)-(-)-[Co(en)3]3+. Theory is able to reproduce the major differences in the CD spectra of the species with a Lambda-configuration and their isomers with a Delta-configuration in both the d-d and ligand-to-metal CT region. It is further possible to rationalize the trend in terms of a larger azimuthal distortion away from the octahedral geometry in the Lambda-conformation compared to the Delta-configuration. Considerations were also given to the CD spectra of the lel3-isomer, Delta(lambdalambdalambda)-(-)-[Rh(R-pn)3]3+ and the ob-isomer, Lambda(lambdalambdalambda)-(+)-[Rh(S-pn)3]3+.

Journal Article↗
PubMed2006

TOM22, a core component of the mitochondria outer membrane protein translocation pore, is a mitochondrial receptor for the proapoptotic protein Bax.

The association of Bax with mitochondria is an essential step in the implementation of apoptosis. By using a bacterial two-hybrid assay and crosslinking strategies, we have identified TOM22, a component of the translocase of the outer mitochondrial membrane (TOM), as a mitochondrial receptor of Bax. Peptide mapping showed that the interaction of Bax with TOM22 involved the first alpha helix of Bax and possibly two central alpha helices, which are homologous to the pore forming domains of some toxins. Antibodies directed against TOM22 or an antisense knockdown of the expression of TOM22 specifically inhibited the association of Bax with mitochondria and prevented Bax-dependent apoptosis. In yeast, a haploid strain for TOM22 exhibited a decreased expression of TOM22 and mitochondrial association of ectopically expressed human Bax. Our data provide a new perspective on the mechanism of association of Bax with mitochondria as it involves a classical import pathway.

Animals↗
PubMed2003

DNannotator: Annotation software tool kit for regional genomic sequences.

Sequence annotation is essential for genomics-based research. Investigators of a specific genomic region who have developed abundant local discoveries such as genes and genetic markers, or have collected annotations from multiple resources, can be overwhelmed by the difficulty in creating local annotation and the complexity of integrating all the annotations. Presenting such integrated data in a form suitable for data mining and high-throughput experimental design is even more daunting. DNannotator, a web application, was designed to perform batch annotation on a sizeable genomic region. It takes annotation source data, such as SNPs, genes, primers, and so on, prepared by the end-user and/or a specified target of genomic DNA, and performs de novo annotation. DNannotator can also robustly migrate existing annotations in GenBank format from one sequence to another. Annotation results are provided in GenBank format and in tab-delimited text, which can be imported and managed in a database or spreadsheet and combined with existing annotation as desired. Graphic viewers, such as Genome Browser or Artemis, can display the annotation results. Reference data (reports on the process) facilitating the user's evaluation of annotation quality are optionally provided. DNannotator can be accessed at http://sky.bsd.uchicago.edu/DNannotator.htm.

Chromosomes, Human, Pair 13↗
PubMed2007

Application of raman spectroscopy and sequential injection analysis for pH measurements with water dispersion of polyaniline nanoparticles.

A novel method for pH measurements between pH 7.5 and 10.4 is reported in this paper. The method combines Raman spectroscopy and the automated sequential injection analysis system (SIA) and makes use of the acid-base properties of a commercially available water dispersion of polyaniline (PANI) nanoparticles with a mean particle size of 46 nm. The useful pH range of the PANI nanoparticles is broader than for conventional acid-base indicators, due to the 1:2 reaction stoichiometry of the proton-ligand complex of the nanoparticles. The pH measurements were conducted with the 633-nm laser excitation wavelength by calculating the difference between the Raman intensities of the primary and reference wavenumbers. In this study, the pH-sensitive CH=CH stretching band at 1422 cm-1 and C-H in-plane bending band of the quinoid form at 1163 cm-1 were chosen as the primary wavenumbers. The presented method is fast and allows pH to be measured with a precision of 0.2 pH unit. The advantage of the proposed method is that the hysteresis effect, which is usually observed for PANI films, can be overcome with the PANI nanoparticles, because a fresh nanoparticle solution is used in each measurement. It should be pointed out, that this work is a fundamental study showing the applicability of Raman spectroscopy in combination with the SIA technique for pH measurements in specific applications, where the conventional glass pH electrode cannot be used.

Journal Article↗
PubMed2002

Optimisation of the monitoring strategy of macroinvertebrate communities in the river Dender, in relation to the EU Water Framework Directive.

The Dender basin in Flanders (Belgium) was used as a case study to implement the European Union (EU) Water Framework Directive. During the last 5 years, ample research on pollution loads and ecological water quality has been done on the Dender River. In addition to biological sampling of macroinvertebrates and fish, automated measurement stations were also used to investigate the spatial-temporal variability of the physical-chemical water quality. This research revealed that the pollution of the Dender River is highly variable. The high nutrient loads result in severe algae blooms during summer, leading to very complex diurnal processes. In this paper, the monitoring strategy for the assessment of the biological water quality in the Dender basin has been reviewed in relation to the EU Water Framework Directive. For this, seasonal macroinvertebrate data were collected and assessed. General trends and hidden structures in these data were analysed by means of classification trees, using different inputs (seasons, river types, and subbasins). Validation of the results was obtained by applying statistical methods. Analysis about the presence and abundance of the macroinvertebrates revealed that there is a distinct difference between the biological water quality in the Dender stem river and its tributaries. There are also seasonal differences between the macroinvertebrate communities when the Dender and its tributaries are examined separately. An optimised monitoring strategy is proposed based on these results and the EU Water Framework Directive. This includes two monitoring campaigns in summer and winter every 3 years. Furthermore, a cyclic monitoring scheme was developed to minimise sampling efforts.

Animals↗
PubMedDate not supplied

Characterization of a human import component of the mitochondrial outer membrane, TOMM70A.

Functional mitochondria require up to 1000 proteins to function properly, with 99% synthesized as precursors in the cytoplasm and transported into the mitochondria with the aid of cytosolic chaperones and mitochondrial translocators (import components). Proteins to be imported are chaperoned to the mitochondria by the cytosolic heat shock protein (cHSP70) and are immediately pursued by Translocators of the Outer Membrane (TOMs), followed by transient interactions of the unfolded proteins with Translocators of the Inner Membrane (TIMs). In the present study, we describe a human gene, TOMM70A, orthologous to the yeast Tom70 import component. TOMM70A is ubiquitously expressed in human tissues, maps on chromosome 3q13.1-q13.2 and consists of 12 coding exons spanning over 37 kb. TOMM70A localizes in the mitochondria of COS-7 cells, and in organello import assays confirmed its presence in the Outer Mitochondrial membrane (OM) of rat liver mitochondria. TOMM70A could play a significant role in the import of nuclear-encoded mitochondrial proteins with internal targeting sites such as ADP/ATP carriers and the uncoupling proteins.

Amino Acid Sequence↗
PubMed2003

Stochastic model for heart-rate fluctuations.

A normal human heart rate shows complex fluctuations in time, which is natural, because the heart rate is controlled by a large number of different feedback control loops. These unpredictable fluctuations have been shown to display fractal dynamics, long-term correlations, and 1/f noise. These characterizations are statistical and they have been widely studied and used, but much less is known about the detailed time evolution (dynamics) of the heart-rate control mechanism. Here we show that a simple one-dimensional Langevin-type stochastic difference equation can accurately model the heart-rate fluctuations in a time scale from minutes to hours. The model consists of a deterministic nonlinear part and a stochastic part typical to Gaussian noise, and both parts can be directly determined from the measured heart-rate data. Studies of 27 healthy subjects reveal that in most cases, the deterministic part has a form typically seen in bistable systems: there are two stable fixed points and one unstable one.

Cardiovascular System↗
PubMed2003

Theoretical investigation of the apparently irregular behavior of pt-pt nuclear spin-spin coupling constants.

One-bond Pt-Pt nuclear spin-spin coupling constants J(Pt-Pt) for closely related dinuclear Pt complexes can differ by an order of magnitude without any obvious correlation with Pt-Pt distances. As representative examples, the spin-spin couplings of the dinuclear Pt(I) complexes [Pt(2)(CO)(6)](2+) (1) and [Pt(2)(CO)(2)Cl(4)](2-) (2) have been computationally studied with a recently developed relativistic density functional method. The experimental values are (1)J((195)Pt-(195)Pt) = 5250 Hz for 2 but 551 Hz for 1. Many other examples are known in the literature. The experimental trends are well reproduced by the computations and can be explained based on the nature of the ligands that are coordinated to the Pt-Pt fragment. The difference for J(Pt-Pt) of an order of magnitude is caused by a sensitive interplay between the influence of different ligands on the Pt-Pt bond, and relativistic effects on metal-metal and metal-ligand bonds as well as on "atomic orbital contributions" to the nuclear spin-spin coupling constants. The results can be intuitively rationalized with the help of a simple qualitative molecular orbital diagram.

Journal Article↗
PubMed1996

Non-Template-Centered, Closed Tetravanadium Phosphate and Phosphonate Clusters.

Tetranuclear V(III) complexes, [HB(pz)(3)](4)V(4)(&mgr;-C(6)H(5)OPO(3))(4) (I), its acetonitrile solvate (I.4CH(3)CN), and [HB(pz)(3)](4)V(4)(&mgr;-O(2)NC(6)H(4)OPO(3))(4).4C(7)H(8).H(2)O (II), and tetranuclear vanadyl complexes, (t-Bupz)(4)V(4)O(4)(&mgr;-C(6)H(5)PO(3))(4).2H(2)O (III) and (t-Bupz)(5)V(4)O(4)(&mgr;-C(6)H(5)PO(3))(4).4CH(3)CN.0.6 H(2)O (IV), have been prepared and characterized by spectroscopic, magnetic, and electrochemical methods (pz = pyrazole, t-Bupz = tert-butylpyrazole). The use of organic solvents and bulky organic groups as ancillary ligands leads to formation of neutral species instead of the anionic clusters commonly found in the hydrothermal synthesis of vanadium organophosphate/phosphonate systems. Complexes I.4CH(3)CN and IV have also been characterized by single-crystal X-ray diffraction. Crystal data: I.4CH(3)CN, triclinic, P&onemacr;, a = 15.495(3) Å, b = 17.000(3) Å, c = 17.949(4) Å, alpha = 89.17(3) degrees, beta = 86.00(3) degrees, gamma = 78.60(3) degrees, Z = 2; IV, triclinic, P&onemacr;, a = 15.541(3) Å, b = 16.340(2) Å, c = 19.069(5) Å, alpha = 83.58(2) degrees, beta = 79.67(2) degrees, gamma = 63.68(1) degrees, Z = 2. Both are closed clusters, the core structure of the first consisting of a cubane-like arrangement of metal octahedra and phosphate tetrahedra and the core structure of the second consisting of a distorted, collapsed variant of the first. Unlike other vanadium phosphate clusters, these compounds form in the absence of a central, templating agent. As such they represent the simplest form of a closed cluster in which steric forces and cluster connectivity requirements play the primary role in organizing the cluster framework.

Journal Article↗
PubMed2003

Fission yeast Rad26 responds to DNA damage independently of Rad3.

BACKGROUND: The Rad26/Rad3 complex in fission yeast detects genotoxic insults and initiates the cell cycle arrest and recovery activities of the DNA damage checkpoint. To investigate how the Rad26/Rad3 complex performs these functions, we constructed and characterized Rad26-GFP. RESULTS: Rad26-GFP localized to approximately six nuclear dots in cycling cells. Following treatment with a DNA damaging agent, Rad26-GFP localization changed. Damaged cells contained one or two bright Rad26-GFP spots, in addition to smaller, more numerous Rad26-GFP speckles. Genetic analyses demonstrated that these Rad26-GFP patterns (dots, spots and speckles) were unaffected by null mutations in other DNA damage checkpoint genes, including rad3+. Data obtained with our Rad26.T12-GFP fusion protein correlate spots with cell cycle arrest activities and speckles with DNA repair activities. In addition, physiological experiments demonstrated that rad26Delta and rad3Delta alleles confer sensitivity to a microtubule-depolymerizing drug. CONCLUSION: We have discovered three distinct Rad26-GFP cellular structures. Formation of these structures did not require other checkpoint proteins. These data demonstrate that Rad26 can respond to genotoxic insult in the absence of Rad3 and the other checkpoint Rad proteins.

Cell Cycle↗