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PubMed2000

PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins.

A novel tool for computer-aided design of single-site mutations in proteins and peptides is presented. It proceeds by performing in silico all possible point mutations in a given protein or protein region and estimating the stability changes with linear combinations of database-derived potentials, whose coefficients depend on the solvent accessibility of the mutated residues. Upon completion, it yields a list of the most stabilizing, destabilizing or neutral mutations. This tool is applied to mouse, hamster and human prion proteins to identify the point mutations that are the most likely to stabilize their cellular form. The selected mutations are essentially located in the second helix, which presents an intrinsic preference to form beta-structures, with the best mutations being T183-->F, T192-->A and Q186-->A. The T183 mutation is predicted to be by far the most stabilizing one, but should be considered with care as it blocks the glycosylation of N181 and this blockade is known to favor the cellular to scrapie conversion. Furthermore, following the hypothesis that the first helix might induce the formation of hydrophilic beta-aggregates, several mutations that are neutral with respect to the structure's stability but improve the helix hydrophobicity are selected, among which is E146-->L. These mutations are intended as good candidates to undergo experimental tests.

Algorithms↗
PubMed1992

Development of a real-time algorithm for predicting sufentanil plasma levels during cardiopulmonary-bypass surgery using a systems approach.

During cardiopulmonary-bypass (CB) procedures, anesthesiologists have traditionally based the administration of narcotics on general dosage recommendations and past experience. Initial doses are usually based on body weight and supplemental amounts are given in anticipation of, or in response to, the effects of surgical stimuli. There has been considerable recent interest in using the population pharmacokinetics of narcotics to optimize the attainment and maintenance of drug plasma concentrations at analgesic target levels which will blunt the hemodynamic responses to noxious stimuli. Moreover, the undershooting or overshooting of the target can be reduced by application of these principles making drug administration more effective and safer. The present study concerns the development of a model for the computer-guided administration of sufentanil throughout surgical procedures involving CB; there is a paucity of studies which have attempted to model the pharmacokinetics of drugs during CB because of the lack of information on the effects of bypass conditions on the pharmacokinetic parameters. We have attempted to approach the effects of hypothermia on sufentanil clearance by applying a continuous temperature correction to the ultimate elimination rate constant (the terminal eigenvalue). This correction is based primarily on the anticipated effects of temperature on the enzyme-catalyzed reactions which are essential for the elimination of drug from the body. An algorithm for the application of the model is also presented.

Algorithms↗
PubMed2005

An experiment-based algorithm for predicting the partitioning of unfolded peptides into phosphatidylcholine bilayer interfaces.

Knowing the partitioning free energy of unfolded polypeptides into membrane interfaces is necessary for understanding membrane protein stability and for designing antimicrobial and other peptides. Experiment-based whole-residue free-energy (hydropathy) scales for amino acids in unfolded peptides, derived from the partitioning of host-guest pentapeptides (Ac-WLXLL) into the interfaces of phosphatidylcholine bilayers and into n-octanol, have been determined by W. C. Wimley, S. H. White, and colleagues [(1996) Nat. Struc. Biol. 3, 842; Wimley, W. C. et al. (1996) Biochemistry 35, 5109]. These scales offer the possibility of computing absolute partitioning free energies of unfolded peptides given only their amino acid sequences. However, the scales are incomplete, because partitioning free energies of N- and C-terminal groups are missing. To complete the scales, we have measured the pH-dependent partitioning of the host-guest pentapeptide variants AcWL-X-LL-NH(2) and WL-X-LL-NH(2) (X = G or W) into palmitoyloleoylphosphatidylcholine (POPC) bilayer interfaces and n-octanol. These measurements, in combination with the earlier ones, lead to hydrophobicity scale values for protonation, deprotonation, or acetylation of the N terminus and protonation, deprotonation, or amidation of the C terminus. A surprising finding is that a charged N terminus has a much smaller effect on bilayer partitioning than a charged C terminus. We present a simple algorithm for computing the absolute partitioning free energies of unfolded peptides into the phosphatidylcholine bilayer interface.

Algorithms↗
PubMed1997

Localization of antigenic sites on Der p 2 using oligonucleotide-directed mutagenesis targeted to predicted surface residues.

BACKGROUND: Understanding the molecular nature of allergen-antibody interactions is important to understanding the mechanism of conventional immunotherapy as well as to designing alternative immunotherapeutic strategies. Many important allergens have been cloned and expressed, making it possible to apply recombinant DNA techniques to dissect antigenic determinants. OBJECTIVE: The aim of this study was to use predictive algorithms and site-directed mutagenesis to investigate monoclonal antibody and IgE antibody epitopes of the major house dust mite allergen Der p 2. METHODS: Computer algorithms were used to assess the primary amino acid sequence of Der p 2 and to identify regions of hydrophilic and flexible sequence. Subsequently, site-directed mutagenesis was used to generate amino acid substitutions at hydrophilic residues at positions 44-46 and at position 100. The variants were tested in a competitive inhibition ELISA with four group 2-specific murine monoclonal antibodies and with human IgE antibody from mite allergic patients. RESULTS: Conservative amino acid substitutions at position 44-46 did not distinguish IgE antibody epitopes, but did suggest that these residues are involved in the epitope defined by one monoclonal antibody, 15E11. Non-conservative substitution of proline at this position reduced binding to all four monoclonal antibodies, as well as IgE antibody, by 50-80%. Point mutants at position 100 mapped the epitopes of two monoclonal antibodies, 7A1 and 13A4, previously shown to bind the same region of Der p 2. In addition, the two variants tested at this position showed distinct inhibition curves with these two monoclonal antibodies indicating differences in fine specificity. CONCLUSIONS: Using predictive algorithms, in the absence of tertiary structural information, we have been able to localize important B cell determinants on Der p 2. The results suggest that it is possible to modulate antibody recognition of allergens using site-directed mutagenesis and that this approach may provide a new strategy for allergen specific immunotherapy.

Antibodies, Monoclonal↗
PubMed2001

Assessing spectral algorithms to predict atherosclerotic plaque composition with normalized and raw intravascular ultrasound data.

Spectral analysis of backscattered intravascular ultrasound (IVUS) data has demonstrated the ability to characterize plaque. We compared the ability of spectral parameters (e.g., slope, midband fit and y-intercept), computed via classic Fourier transform (CPSD), Welch power spectrum (WPSD) and autoregressive (MPSD) models, to classify plaque composition. Data were collected ex vivo from 32 human left anterior descending coronary arteries. Regions-of-interest (ROIs), selected from histology, comprised 64 collagen-rich, 24 fibrolipidic, 23 calcified and 37 calcified-necrotic regions. A novel quantitative method was used to correlate IVUS data with corresponding histologic sections. Periodograms of IVUS samples, identified for each ROI, were used to calculate spectral parameters. Statistical classification trees (CT) were computed with 75% of the data for plaque characterization. The remaining data were used to assess the accuracy of the CTs. The overall accuracies for normalized spectra with CPSD, WPSD and MPSD were, respectively, 84.7%, 85.6% and 81.1% (training data) and 54.1%, 64.9% and 37.8% (test data). These numbers were improved to 89.2%, 91.9% and 89.2% (training) and 62.2%, 73% and 59.5% (test) when the calcified and calcified-necrotic regions were combined for analysis. Most CTs misclassified a few fibrolipidic regions as collagen, which is histologically acceptable, and the unnormalized and normalized spectra results were similar.

Adult↗
PubMed2005

Evaluation of Helicobacter hepaticus bacterial shedding in fostered and sex-segregated C57BL/6 mice.

Neonatal fostering has been evaluated as a means of eliminating Helicobacter hepaticus infection in laboratory mouse colonies. The purpose of the present study was to evaluate cross-fostering of neonatal C57BL/6 pups from experimentally infected dams after male-absent parturition and to determine the effects of sex and housing strategy on H. hepaticus populations. Approximately 20 C57BL/6 mice (age, 1 to 4 days) were fostered daily. In all fostered mice, fecal samples collected at 21 and 42 days of age and cecal samples collected at 42 days of age tested negative for H. hepaticus by polymerase chain reaction analysis. Our results demonstrate that removal of the male prior to parturition extends the fostering period to yield Helicobacter-free mice. In a second experiment, the effects of time of infection, housing strategy, and sex on fecal H. hepaticus shedding and cecal colonization were evaluated. Neither time nor housing strategy affected bacterial shedding. In contrast, fecal and cecal bacterial loads were higher in male mice versus female mice. A novel predictive algorithm was developed to predict cecal bacterial colonization levels in light of fecal bacterial loads. Our findings likely will prove useful in Helicobacter eradication efforts and in studies designed to further elucidate the role of H. hepaticus in disease.

Algorithms↗
PubMed2001

Protein-protein interaction map inference using interacting domain profile pairs.

UNLABELLED: A number of predictive methods have been designed to predict protein interaction from sequence or expression data. On the experimental front, however, high-throughput proteomics technologies are starting to yield large volumes of protein-protein interaction data. High-quality experimental protein interaction maps constitute the natural dataset upon which to build interaction predictions. Thus the motivation to develop the first interaction-based protein interaction map prediction algorithm. A technique to predict protein-protein interaction maps across organisms is introduced, the 'interaction-domain pair profile' method. The method uses a high-quality protein interaction map with interaction domain information as input to predict an interaction map in another organism. It combines sequence similarity searches with clustering based on interaction patterns and interaction domain information. We apply this approach to the prediction of an interaction map of Escherichia coli from the recently published interaction map of the human gastric pathogen Helicobacter pylori. Results are compared with predictions of a second inference method based only on full-length protein sequence similarity - the "naive" method. The domain-based method is shown to i) eliminate a significant amount of false-positives of the naive method that are the consequences of multi-domain proteins; ii) increase the sensitivity compared to the naive method by identifying new potential interactions. AVAILABILITY: Contact the authors.

Algorithms↗
PubMed2004

Identification and characterization of a T-helper peptide from carcinoembryonic antigen.

PURPOSE: The purpose of this research was to identify promiscuous T-helper cell determinants (THd) from carcinoembryonic antigen (CEA) to be used to prime T-cell help for cancer therapy. CEA was selected because this antigen is expressed in an important variety of carcinomas. EXPERIMENTAL DESIGN: Potential promiscuous THd from CEA were predicted using available computer algorithms. Predicted peptides were synthesized and tested in binding experiments to different HLA-DR molecules. Binder peptides were then used to prime T-cell responses both in vitro and in vivo. RESULTS: Twenty 15-mer peptides from CEA were predicted to bind to different HLA-DR molecules. The promiscuous character of these peptides was demonstrated in binding experiments. Fifteen of 20 peptides tested were able to bind to HLA-DR4, but only CEA (625-639) was shown to be presented after processing of recombinant CEA. CEA (625-639) was also found to be presented by HLA-DR53. Moreover, immunization of HLA-DR4 transgenic mice with CEA (625-639) in conjunction with class I epitope OVA (257-264), induced a CTL response specific of OVA (257-264). CONCLUSIONS: CEA (625-639) might be a relevant promiscuous THd peptide for cancer therapy.

Algorithms↗
PubMed2006

Determining OMP topology by computation, surface plasmon resonance and cysteine labelling: the test case of OMPG.

Bacterial outer-membrane proteins (OMP) are important in pathogenicity and the recently solved structure of OmpG provides an excellent test case for topological predictions since it is monomeric. Here we compare the results of applying several computerised structure prediction algorithms to the sequence of OmpG. Furthermore, we probe the OmpG topology by both an established chemical labelling approach and a new method which combines epitope insertion and surface plasmon resonance. The computational approaches are broadly accurate but the exact choice of the number of beta strands remains difficult. The algorithms also tend to predict the entire beta strand rather than just the transmembrane region. Epitope insertion clearly pinpoints exposed loops but its utility in defining buried or periplasmic sites is less clear cut. Cysteine-mutant labelling is largely confined to exposed residues but one periplasmic cysteine may be labelled by reagents entering via the OmpG pore.

Bacterial Outer Membrane Proteins↗
PubMed2005

A dipstick protein and specific gravity algorithm accurately predicts pathological proteinuria.

BACKGROUND: The proper strategy to screen for early chronic kidney disease is debatable, but protein-creatinine ratio from a random urine sample (UPC) commonly is used. The purpose is to determine whether dipstick data effectively identify patients with increased UPC ratios. Because urine concentration affects proteinuria interpretation, we hypothesized that dipstick protein (DSP) and specific gravity (SG) are sufficient for screening. METHODS: A hospital laboratory database was searched for urine samples simultaneously assayed for UPC ratio, DSP, and SG (n = 2,098). A random 70% of the cohort was used to generate a development model, which was validated in the remaining 30%. Samples were stratified according to DSP and SG values. A DSP versus SG matrix was created, and each sample was allocated to a discrete DSP-SG category. Proportions of samples with overt (UPC ratio > or = 500 mg/g) and nephrotic-range proteinuria (UPC ratio > or = 3,000 mg/g) were calculated for all 40 cells. RESULTS: Optimum correlations between DSP-SG cells and UPC ratios were determined for the development model, yielding 97.0% negative predictive value (NPV) for a UPC ratio of 500 mg/g or less and 97.5% positive predictive value (PPV) for a UPC ratio of 500 mg/g or greater. NPV for a UPC ratio of 3,000 mg/g or less was 99.7%. Application of the model to the validation sample showed a 96.5% NPV for a UPC ratio of 500 mg/g or less, 99.4% PPV for a UPC ratio of 500 mg/g or greater, and 99.0% NPV for a UPC ratio of 3,000 mg/g or less. CONCLUSION: DSP and SG values effectively identify patients requiring proteinuria quantification by means of UPC ratio. A Web-based tool was developed that allows DSP and SG value entry and provides a recommendation regarding the need for proteinuria quantification.

Biomarkers↗
PubMed1996

Membrane topology of the human Na+/glucose cotransporter SGLT1.

The membrane topology of the human Na+/glucose cotransporter SGLT1 has been probed using N-glycosylation scanning mutants and nested truncations. Functional analysis proved essential for establishment of signal-anchor topology. The resultant model diverges significantly from previously held suppositions of structure based primarily on hydropathy analysis. SGLT1 incorporates 14 membrane spans. The N terminus resides extracellularly, and two hydrophobic regions form newly recognized membrane spans 4 and 12; the large charged domain near the C terminus is cytoplasmic. This model was evaluated further using two advanced empirically-based algorithms predictive of transmembrane helices. Helix ends were predicted using thermo-dynamically-based algorithms known to predict x-ray crystallographically determined transmembrane helix ends. Several considerations suggest the hydrophobic C terminus forms a 14th transmembrane helix, differentiating the eukaryotic members of the SGLT1 family from bacterial homologues. Our data inferentially indicate that these bacterial homologues incorporate 13 spans, with an extracellular N terminus. The model of SGLT1 secondary structure and the predicted helix ends signify information prerequisite for the rational design of further experiments on structure/function relationships.

Amino Acid Sequence↗
PubMed2004

Predictive scheduling algorithms for real-time feature extraction and spatial referencing: application to retinal image sequences.

Real-time spatial referencing is an important alternative to tracking for designing spatially aware ophthalmic instrumentation for procedures such as laser photocoagulation and perimetry. It requires independent, fast registration of each image frame from a digital video stream (1024 x 1024 pixels) to a spatial map of the retina. Recently, we have introduced a spatial referencing algorithm that works in three primary steps: 1) tracing the retinal vasculature to extract image feature (landmarks); 2) invariant indexing to generate hypothesized landmark correspondences and initial transformations; and 3) alignment and verification steps to robustly estimate a 12-parameter quadratic spatial transformation between the image frame and the map. The goal of this paper is to introduce techniques to minimize the amount of computation for successful spatial referencing. The fundamental driving idea is to make feature extraction subservient to registration and, therefore, only produce the information needed for verified, accurate transformations. To this end, the image is analyzed along one-dimensional, vertical and horizontal grid lines to produce a regular sampling of the vasculature, needed for step 3) and to initiate step 1). Tracing of the vascular is then prioritized hierarchically to quickly extract landmarks and groups (constellations) of landmarks for indexing. Finally, the tracing and spatial referencing computations are integrated so that landmark constellations found by tracing are tested immediately. The resulting implementation is an order-of-magnitude faster with the same success rate. The average total computation time is 31.2 ms per image on a 2.2-GHz Pentium Xeon processor.

Algorithms↗
PubMed1998

Selective versus non-selective antiarrhythmic approach for prevention of atrial fibrillation after coronary surgery: is there a need for pre-operative risk stratification? A prospective placebo-controlled study using low-dose sotalol.

AIM: This study evaluated the advantages of 'selective' over 'non-selective' antiarrhythmic prevention of atrial fibrillation after coronary surgery based on a new risk prediction algorithm. METHODS AND RESULTS: In a retrospective analysis of a prospective randomized trial, a model for risk prediction was determined based on clinical data of the control group (A; n = 107) and tested in a test group (B; n = 107, treated with low dose sotalol). Using this algorithm, the effect of a 'selective' antiarrhythmic approach in high-risk patients was compared to a 'non-selective' approach, where all patients were treated. In total, 75 (35%) patients developed atrial fibrillation and 14 (7%) side-effects led to discontinuation of study medication. Based on the risk prediction algorithm, 36% of group A patients were classified as high-risk patients with an incidence of atrial fibrillation of 76% compared to 26% in low-risk patients (P < 0.0001). The selective approach, i.e. treatment of high-risk patients only reduced the incidence of atrial fibrillation from 76% to 50% (P = 0.0295) compared to a reduction from 44% to 26% (P = 0.0065) when all patients were treated. More importantly, with the non-selective approach 100% of patients were exposed to the possible side-effects of sotalol and costs compared to 24% only with the selective approach (P < 0.0001). CONCLUSIONS: Thus, a selective approach based on a clinical risk prediction algorithm should improve the cost-effectiveness and safety of low-dose sotalol in the prevention of atrial fibrillation after coronary bypass surgery.

Adult↗
PubMed1998

Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments.

The feasibility of predicting the global fold of small proteins by incorporating predicted secondary and tertiary restraints into ab initio folding simulations has been demonstrated on a test set comprised of 20 non-homologous proteins, of which one was a blind prediction of target 42 in the recent CASP2 contest. These proteins contain from 37 to 100 residues and represent all secondary structural classes and a representative variety of global topologies. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that incorporates multiple sequence information. Predicted tertiary restraints are derived from multiple sequence alignments via a two-step process. First, seed side-chain contacts are identified from correlated mutation analysis, and then a threading-based algorithm is used to expand the number of these seed contacts. A lattice-based reduced protein model and a folding algorithm designed to incorporate these predicted restraints is described. Depending upon fold complexity, it is possible to assemble native-like topologies whose coordinate root-mean-square deviation from native is between 3.0 A and 6.5 A. The requisite level of accuracy in side-chain contact map prediction can be roughly 25% on average, provided that about 60% of the contact predictions are correct within +/-1 residue and 95% of the predictions are correct within +/-4 residues. Precision in tertiary contact prediction is more critical than absolute accuracy. Furthermore, only a subset of the tertiary contacts, on the order of 25% of the total, is sufficient for successful topology assembly. Overall, this study suggests that the use of restraints derived from multiple sequence alignments combined with a fold assembly algorithm holds considerable promise for the prediction of the global topology of small proteins.

Amino Acid Sequence↗
PubMed2005

Toward robotized beating heart TECABG: assessment of the heart dynamics using high-speed vision.

Active robotic filtering is a promising solution for beating heart Totally Endoscopic Coronary Artery Bypass Grafting (TECABG). n this work, we assess the heart motion dynamics using simultaneously igh speed imaging of optical markers attached to the heart, ECG signals and ventilator airflow acquisitions. Our goal is to make an assessment of the heart motion (shape, velocity, acceleration) in order to be able to make more accurate specifications for a dedicated robot that could follow this motion in real-time. Furthermore, using the 2 additional inputs (ECG, airflow), we propose a prediction algorithm of the motion that could be used with a predictive control algorithm to improve the tracking accuracy.

Algorithms↗