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PubMed2004

Protein structure prediction and analysis using the Robetta server.

The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis. For structure prediction, sequences submitted to the server are parsed into putative domains and structural models are generated using either comparative modeling or de novo structure prediction methods. If a confident match to a protein of known structure is found using BLAST, PSI-BLAST, FFAS03 or 3D-Jury, it is used as a template for comparative modeling. If no match is found, structure predictions are made using the de novo Rosetta fragment insertion method. Experimental nuclear magnetic resonance (NMR) constraints data can also be submitted with a query sequence for RosettaNMR de novo structure determination. Other current capabilities include the prediction of the effects of mutations on protein-protein interactions using computational interface alanine scanning. The Rosetta protein design and protein-protein docking methodologies will soon be available through the server as well.

Alanine↗

PubMedDate not supplied

Development of patient-specific three-dimensional pediatric cardiac models.

The availability of algorithms to create three-dimensional (3D) models from medical images has made it possible to render and build patient-specific reconstructions of individual body parts. In the present study, this technology was used to create 3D models of pediatric hearts for use in medical device development. Digital models were created using CT datasets of pediatric hearts and commercially available 3D image processing software. Using this software, stacked CT data were viewed, and pixels representing the heart and rib cage were selected and rendered as 3D models. Stereolithography and 3D printing technology were used to create rigid and flexible physical heart models (biomodels) from the digital models. Twelve on-screen models of the thorax and cardiac structures were created from cardiac CT scans obtained from 11 patients with and without congenital heart disease (median age, 3 years; range, 2 days to 13 years). Rigid and flexible physical heart models were generated from the digital models to provide tactile and visual information. 3D models of pediatric cardiac and chest anatomy provide enhanced understanding and tactile representation of complex anatomy. Precise representation of the spatial relationships between anatomic structures is particularly useful during the development and placement of medical devices.

Algorithms↗

PubMed2002

Up and down cascades: three-dimensional magnetic field model.

In our previous works we already have proposed a two-dimensional model of geodynamo. Now we use the same approach to build a three-dimensional self-excited geodynamo model that generates a large scale magnetic field from whatever small initial field, using the up and down cascade effects of a multiscale turbulent system of cyclones. The multiscale system of turbulent cyclones evolves in six domains of an equatorial cylindrical layer of the core. The appearance of new cyclones is realized by two cascades: a turbulent direct cascade and an inverse cascade of coupling of similar cyclones. The interaction between the different domains is effected through a direct cascade parameter which is essential for the statistics of the long-life symmetry breaking. Generation of the secondary magnetic field results from the interaction of the components of the primary magnetic field with the turbulent cyclones. The amplification of the magnetic field is due to the transfer of energy from the turbulent helical motion to the generated magnetic field. The model demonstrates a phase transition through the parameter characterizing this energy transfer. In the supercritical domain we obtain long-term intervals of constant polarity (chrons) and quick reversals; relevant time constants agree with paleomagnetic observations. Possible application of the model to the study of the geometrical structure of the geomagnetic field (and briefly other planetary fields) is discussed.

Journal Article↗

PubMed2004

Tissue transglutaminase acylation: Proposed role of conserved active site Tyr and Trp residues revealed by molecular modeling of peptide substrate binding.

Transglutaminases (TGases) catalyze the cross-linking of peptides and proteins by the formation of gamma-glutamyl-epsilon-lysyl bonds. Given the implication of tissue TGase in various physiological disorders, development of specific tissue TGase inhibitors is of current interest. To aid in the design of peptide-based inhibitors, a better understanding of the mode of binding of model peptide substrates to the enzyme is required. Using a combined kinetic/molecular modeling approach, we have generated a model for the binding of small acyl-donor peptide substrates to tissue TGase from red sea bream. Kinetic analysis of various N-terminally derivatized Gln-Xaa peptides has demonstrated that many CBz-Gln-Xaa peptides are typical in vitro substrates with K(M) values between 1.9 mM and 9.4 mM, whereas Boc-Gln-Gly is not a substrate, demonstrating the importance of the CBz group for recognition. Our binding model of CBz-Gln-Gly on tissue TGase has allowed us to propose the following steps in the acylation of tissue TGase. First, the active site is opened by displacement of conserved W329. Second, the substrate Gln side chain enters the active site and is stabilized by hydrophobic interaction with conserved residue W236. Third, a hydrogen bond network is formed between the substrate Gln side chain and conserved residues Y515 and the acid-base catalyst H332 that helps to orient and activate the gamma-carboxamide group for nucleophilic attack by the catalytic sulphur atom. Finally, an H-bond with Y515 stabilizes the oxyanion formed during the reaction.

Acylation↗

PubMed2007

The utility of magnetic resonance imaging and spectroscopy for predicting insignificant prostate cancer: an initial analysis.

OBJECTIVE: To design new models that combine clinical variables and biopsy data with magnetic resonance imaging (MRI) and MR spectroscopic imaging (MRSI) data, and assess their value in predicting the probability of insignificant prostate cancer. PATIENTS AND METHODS: In all, 220 patients (cT stage T1c or T2a, prostate-specific antigen level <20 ng/mL, biopsy Gleason score 6) had MRI/MRSI before surgery and met the inclusion criteria for the study. The probability of insignificant cancer was recorded retrospectively and separately for MRI and combined MRI/MRSI on a 0-3 scale (0, definitely insignificant; - 3, definitely significant). Insignificant cancer was defined from surgical pathology as organ-confined cancer of </= 0.5 cm(3) with no poorly differentiated elements. The accuracy of predicting insignificant prostate cancer was assessed using areas under receiver operating characteristic curves (AUCs), for previously reported clinical models and for newly generated MR models combining clinical variables, and biopsy data with MRI data (MRI model) and MRI/MRSI data (MRI/MRSI model). RESULTS: At pathology, 41% of patients had insignificant cancer; both MRI (AUC 0.803) and MRI/MRSI (AUC 0.854) models incorporating clinical, biopsy and MR data performed significantly better than the basic (AUC 0.574) and more comprehensive medium (AUC 0.726) clinical models. The P values for the differences between the models were: base vs medium model, <0.001; base vs MRI model, <0.001; base vs MRI/MRSI model, <0.001; medium vs MRI model, <0.018; medium vs MRI/MRSI model, <0.001. CONCLUSIONS: The new MRI and MRI/MRSI models performed better than the clinical models for predicting the probability of insignificant prostate cancer. After appropriate validation, the new MRI and MRI/MRSI models might help in counselling patients who are considering choosing deferred therapy.

Aged↗

PubMed2003

Structural basis of regulation and substrate specificity of protein kinase CK2 deduced from the modeling of protein-protein interactions.

BACKGROUND: Protein Kinase Casein Kinase 2 (PKCK2) is an ubiquitous Ser/Thr kinase expressed in all eukaryotes. It phosphorylates a number of proteins involved in various cellular processes. PKCK2 holoenzyme is catalytically active tetramer, composed of two homologous or identical and constitutively active catalytic (alpha) and two identical regulatory (beta) subunits. The tetramer cannot phosphorylate some substrates that can be phosphorylated by PKCK2alpha in isolation. The present work explores the structural basis of this feature using computational analysis and modeling. RESULTS: We have initially built a model of PKCK2alpha bound to a substrate peptide with a conformation identical to that of the substrates in the available crystal structures of other kinases complexed with the substrates/ pseudosubstrates. In this model however, the fourth acidic residue in the consensus pattern of the substrate, S/T-X-X-D/E where S/T is the phosphorylation site, did not result in interaction with the active form of PKCK2alpha and is highly solvent exposed. Interaction of the acidic residue is observed if the substrate peptide adopts conformations as seen in beta turn, alpha helix, or 3(10) helices. This type of conformation is observed and accommodated well by PKCK2alpha in calmodulin where the phosphorylation site is at the central helix. PP2A carries sequence patterns for PKCK2alpha phosphorylation. While the possibility of PP2A being phosphorylated by PKCK2 has been raised in the literature we use the model of PP2A to generate a model of PP2A-PKCK2alpha complex. PKCK2beta undergoes phosphorylation by holoenzyme at the N-terminal region, and is accommodated very well in the limited space available at the substrate-binding site of the holoenzyme while the space is insufficient to accommodate the binding of PP2A or calmodulin in the holoenzyme. CONCLUSION: Charge and shape complimentarity seems to play a role in substrate recognition and binding to PKCK2alpha, along with the consensus pattern. The detailed conformation of the substrate peptide binding to PKCK2 differs from the conformation of the substrate/pseudo substrate peptide that is bound to other kinases in the crystal structures reported. The ability of holoenzyme to phosphorylate substrate proteins seems to depend on the accessibility of the P-site in limited space available in holoenzyme.

Amino Acid Sequence↗

PubMed2006

Fibrous dysplasia as a stem cell disease.

At a time when significant attention is devoted worldwide to stem cells as a potential tool for curing incurable diseases, fibrous dysplasia of bone (FD) provides a paradigm for stem cell diseases. Consideration of the time and mechanism of the causative mutations and of nature of the pluripotent cells that mutate in early embryonic development indicates that, as a disease of the entire organism, FD can be seen as a disease of pluripotent embryonic cells. As a disease of bone as an organ, in turn, FD can be seen as a disease of postnatal skeletal stem cells, which give rise to dysfunctional osteoblasts. Recognizing FD as a stem cell disease provides a novel conceptual angle and a way to generate appropriate models of the disease, which will continue to provide further insight into its natural history and pathogenesis. In addition, skeletal stem cells may represent a tool for innovative treatments. These can be conceived as directed to alter the in vivo behavior of mutated stem cells, to replace mutated cells through local transplantation, or to correct the genetic defect in the stem cells themselves. In vitro and in vivo models are currently being generated that will permit exploration of these avenues in depth.

Bone and Bones↗

PubMed2000

Transgenic mouse models to study the role of the macrophage scavenger receptor class A in atherosclerosis.

Several in vivo studies have been performed on the role of the macrophage scavenger receptor class A (SR-A) in atherosclerosis using SR-A knockout mice. The results indicate both an antiatherogenic and a proatherogenic role of SR-A, depending on the nature of the animal model serving as the athero-susceptible background. To study the role of SR-A in a different model, we generated a transgenic mouse model with high level expression of the human SR-A gene using a 180 Kb yeast artificial chromosome (MSR1 transgenic mice). These mice show increased expression of SR-A according to the natural expression pattern. The MSR1 transgenic mice were crossed onto a low-density lipoprotein receptor deficient background and were fed a high fat diet for 10 weeks. After this period, the size of the atherosclerotic lesions in the proximal aorta was measured. Surprisingly, atherosclerosis was significantly reduced in the MSR1 transgenic mice. In a second study, the effect of SR-A was examined in APOE-3 Leiden mice providing a different athero-susceptible background. To exclude nonmacrophage effects, bone marrow was transplanted from MSR1 mice and wild-type littermates to APOE-3 Leiden transgenic mice. After 8 weeks on a high fat diet, atherosclerosis in the mice that had received MSR1 bone marrow was reduced compared with mice that had received wild-type bone marrow. This difference reached statistical significance when individual cholesterol exposure of the mice was taken into account. Both experiments indicated an antiatherogenic role of the SR-A. This observation cannot be explained easily by SR-A function in foam cell formation because in MSR1 macrophages in vitro foam cell formation is increased. Alternatively, however, SR-A may affect the activation of macrophages. Hence the response to lipopolysaccharide was measured in MSR1-transgenic macrophages. These macrophages showed a reduction in their activation in response to lipopolysaccharide, as measured by nitric oxide production. These data show that an elevated level of SR-A expression reduces atherosclerosis, potentially by modifying the response of macrophages to activation signals in the plaque.

Animals↗

PubMedDate not supplied

Finding meaning: antecedents of uncertainty in illness.

In this study a portion of the uncertainty in illness model was tested. Antecedents to uncertainty tested were the stimuli frame variables of symptom pattern and event familiarity and the structure provider variables of education, social support, and credible authority. Data were collected on a convenience sample of 61 women with gynecological cancer at the time of major treatment effect. Findings supported the proposed model with an empirically generated revised model presenting the influence of antecedents on specific areas of uncertainty. Divergent paths for reducing uncertainty were found. Social support, credible authority, and event familiarity had the greatest influence on lowering the level of uncertainty. Event familiarity and credible authority were primarily effective in reducing the complexity surrounding treatment and the system of care. Social support functioned to decrease the level of ambiguity concerning the state of the illness. Findings generally support the proposed explantation for uncertainty arousal and have substantive significance in identifying the sources of stimuli leading to uncertainty arousal and modification.

Adult↗

PubMed2003

Construction of varicella-zoster virus recombinants from parent Oka cosmids and demonstration that ORF65 protein is dispensable for infection of human skin and T cells in the SCID-hu mouse model.

We generated an ORF65 deletion mutant by using a cosmid system constructed from the genome of a low-passage clinical isolate (P-Oka). Using the SCID-hu mouse model, we demonstrated that the ORF65 protein is dispensable for viral replication in skin and T cells, which are critical host cell targets during primary varicella-zoster virus infection.

Animals↗

PubMed2000

Renal antioxidant enzymes and fibrosis-related markers in the rat adriamycin model.

Excessive generation of reactive oxygen intermediates can induce changes in the cellular antioxidant defence system. In this study we examine the antioxidant enzyme status and the expression of fibrosis-related marker proteins in the Adriamycin model of chronic renal failure in the rat. Twenty weeks after Adriamycin treatment, rats have overt nephrotic syndrome and renal failure with development of tubulo-interstitial fibrosis and glomerulosclerosis. Lipids accumulate in blood and in both glomeruli and tubulo-interstitial tissue. Desmin and alpha-smooth muscle actin expression increases in glomeruli and in the tubulo-interstitial area. Renal cortex antioxidant enzyme activities are decreased 20 weeks after Adriamycin injection (to 41% for catalase, to 56% for total superoxide dismutase and to 69% for glutathione peroxidase). The mRNA levels of catalase, Cu/Zn-superoxide dismutase and glutathione peroxidase-1 evaluated by Northern blot are decreased by more than 50% for catalase, Cu/Zn-superoxide dismutase and glutathione peroxidase-1. We conclude that in the rat Adriamycin-induced model of chronic renal failure with fibrosis, the combination of decreased antioxidant enzyme status in renal cortex with high concentrations of lipids in blood and renal tissue facilitates oxidative damage. Development of fibrosis is paralleled by increased expression of desmin and alpha-smooth muscle actin.

Animals↗

PubMed2003

Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials.

A new approach, MOBILE, is presented that models protein binding-sites including bound ligand molecules as restraints. Initially generated, homology models of the target protein are refined iteratively by including information about bioactive ligands as spatial restraints and optimising the mutual interactions between the ligands and the binding-sites. Thus optimised models can be used for structure-based drug design and virtual screening. In a first step, ligands are docked into an averaged ensemble of crude homology models of the target protein. In the next step, improved homology models are generated, considering explicitly the previously placed ligands by defining restraints between protein and ligand atoms. These restraints are expressed in terms of knowledge-based distance-dependent pair potentials, which were compiled from crystallographically determined protein-ligand complexes. Subsequently, the most favourable models are selected by ranking the interactions between the ligands and the generated pockets using these potentials. Final models are obtained by selecting the best-ranked side-chain conformers from various models, followed by an energy optimisation of the entire complex using a common force-field. Application of the knowledge-based pair potentials proved efficient to restrain the homology modelling process and to score and optimise the modelled protein-ligand complexes. For a test set of 46 protein-ligand complexes, taken from the Protein Data Bank (PDB), the success rate of producing near-native binding-site geometries (rmsd<2.0A) with MODELLER is 70% when the ligand restrains the homology modelling process in its native orientation. Scoring these complexes with the knowledge-based potentials, in 66% of the cases a pose with rmsd <2.0A is found on rank 1. Finally, MOBILE has been applied to two case studies modelling factor Xa based on trypsin and aldose reductase based on aldehyde reductase.

Binding Sites↗

PubMed2001

Diagnostics and a qualitative model.

First generation expert systems were using shallow knowledge based on heuristic information to solve a diagnostic problem. This approach has many disadvantages, which can be avoided by using deep knowledge. Diagnostic reasoning based on deep knowledge is called model-based diagnostics. Recently, the use of qualitative modeling in relation to deep knowledge in expert systems has become increasingly important. The main purpose of our contribution is to present the model-based diagnostic approach at a formal level. The originality of the presented formalization is the concept of the diagnostic space, the characterization of the minimal diagnoses, and the measurement. The formalization serves as the theoretical background to prove our view to the design of qualitative system models and to establish the diagnostic architecture called DISY. The qualitative system model in our diagnostic approach needs not to be specially adopted for use in the diagnostic domain. The only requirement is that it must simulate the system behavior expressed by normal or abnormal functioning of its components. Proposed DISY architecture is not complex and simply takes into an account the previous diagnostic result to obtain a new one from the additional observation-measurement (medical tests or examinations) of the system.

Decision Support Techniques↗

PubMed2005

Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling.

The utility of previously generated microarray data is severely limited owing to small study size, leading to under-powered analysis, and failure of replication. Multiplicity of platforms and various sources of systematic noise limit the ability to compile existing data from similar studies. We present a model for transformation of data across different generations of Affymetrix arrays, developed using previously published datasets describing technical replicates performed with two generations of arrays. The transformation is based upon a probe set-specific regression model, generated from replicate measurements across platforms, performed using correlation coefficients. The model, when applied to the expression intensities of 5069 shared, sequence-matched probe sets in three different generations of Affymetrix Human oligonucleotide arrays, showed significant improvement in inter generation correlations between sample-wide means and individual probe set pairs. The approach was further validated by an observed reduction in Euclidean distance between signal intensities across generations for the predicted values. Finally, application of the model to independent, but related datasets resulted in improved clustering of samples based upon their biological, as opposed to technical, attributes. Our results suggest that this transformation method is a valuable tool for integrating microarray datasets from different generations of arrays.

Algorithms↗

PubMed1997

Large scale protein modelling and model repository.

Knowledge-based molecular modelling of proteins has proven useful in many instances including the rational design of mutagenesis experiments, but it has been generally limited by the availability of expensive computer hardware and software. To overcome these limitations, we have developed the SWISS-MODEL server for automated knowledge-based protein modelling. The SWISS-MODEL server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates protein models for sequences which share significant similarities with at least one protein of known 3D-structure. We now use the software framework of the server to generate large collections of protein models. To store these models, we have established the SWISS-MODEL Repository, a new database for protein models generated by theoretical approaches. This repository is directly integrated with SWISS-PROT and other databases through the ExPASy World-Wide Web server (URL is http:(/)/www.expasy.ch).

Amino Acid Sequence↗

PubMed2002

Specificity determinants in MAPK signaling to transcription factors.

One critical component in determining the specificity, fidelity, and efficiency of MAPK substrate phosphorylation is the presence of distinct docking domains in the substrate proteins. These docking domains are found in a range of substrates, including the transcription factors myocyte enhancer factor-2A and SAP-1. However, the sequences of these motifs differ, as does their targeting preferences by MAPKs, with SAP-1 being targeted by both the ERK and p38 isoforms, whereas myocyte enhancer factor-2A is targeted only by certain members of the p38 subfamily. Here, we have investigated the specificity determinants within these motifs and generated a model for how specificity is generated. We demonstrate that residues throughout the docking domains play important roles in the recognition process. However, residues located at different positions are important for discriminating between ERK and p38 MAPKs. Furthermore, the docking domains can be further subdivided into submotifs, which are differentially required for phosphorylation by ERK or p38 MAPKs. We have used loss- and gain-of-function mutagenesis to identify residues that discriminate between ERK and p38 MAPKs, residues that act to promote suboptimal interactions, and regions that are differentially required depending on the kinase involved. A model is proposed to explain how specificity is generated within these short docking domains.

Alanine↗

PubMed2002

Reaching to grasp with a multi-jointed arm. I. Computational model.

The generation of goal-directed movements requires the solution of many difficult computational problems. Among these are transformations from extrinsic to intrinsic reference frames, specifying solution paths, removing under-specification due to excess degrees of freedom and path multiplicity, constraint satisfaction, and error correction. There are no current motor-control computational models that address these issues in the context of realistic arm movement with redundant degrees of freedom. In this paper, we conjecture there is a geometric stage between sensory input and physical execution. The geometric stage determines movement trajectories independently of forces. It uses a gradient technique that relies on the metric of the space of postures to resolve endpoint path selection, posture-change specification, error correction, and multiple constraint satisfaction on-line without preplanning. The model is instantiated in an arm with seven degrees of freedom that moves in three-dimensional space. Simulated orientation-matching movements are compared with actual human movement data to assess the validity of several of the model's behavioral predictions.

Algorithms↗

PubMed1998

31P-magnetic resonance spectroscopy and 2H-magnetic resonance imaging studies of a panel of early-generation transplanted murine tumour models.

The objective of this study was first to determine whether three slowly growing early-generation murine transplantable tumours, the T40 fibrosarcoma, T115 mammary carcinoma and T237 lung carcinoma, exhibit patterns of energetics and blood flow during growth that are different from those of the faster growing RIF-1 fibrosarcoma. Serial measurements were made with 31P-magnetic resonance spectroscopy (MRS), relating to nutritive blood flow and 2H-magnetic resonance imaging (MRI), which is sensitive to both nutritive and large-vessel (non-nutritive) flow. All four tumour lines showed a decrease in betaNTP/Pi and pH with growth; however, each line showed a different pattern of blood flow that did not correlate with the decrease in energetics. Qualitative histological analysis strongly correlated with the 2H-MRI. Second, their response to 5 mg kg(-1) hydralazine i.v. was monitored by 31P-MRS. A marked decrease in betaNTP/Pi and pH was observed in both the RIF-1 fibrosarcoma and the third-generation T115 mammary carcinoma after hydralazine challenge. In contrast, the fourth generation T40 fibrosarcoma and T237 lung carcinoma showed no change in 31P-MRS parameters. However, a fifth-generation T237 cohort, which grew approximately three times faster than fourth-generation T237 cohorts, exhibited a significant deterioration in betaNTP/Pi and pH in response to hydralazine. These data are consistent with a decoupling between large-vessel and nutritive blood flow and indicate that early-generation transplants that have a slow growth rate and vascular tone are more appropriate models of human tumour vasculature than more rapidly growing, repeatedly transplanted tumours.

Animals↗