Computer prediction and experimental validation of cytochrome P4502D6-dependent oxidation of GBR 12909.
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Computer Simulation↗
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Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae.
Members of the family Geobacteraceae are an important group of microorganisms from the delta subdivision of Proteobacteria that couple the oxidation of organic compounds to metal reduction. In order to uncover transcription regulatory interactions in these organisms, we used computational methods to identify conserved operons and putative cis-regulatory transcription elements. We identified 26 putative operons with gene order and function conserved among two species of Geobacteraceae, Geobacter sulfurreducens and Geobacter metallireducens. Most of these operons were also conserved in Desulfovibrio vulgaris, an additional metal reducing organism from family Desulfovibrionaceae of the delta subdivision of Proteobacteria. The predicted conserved operons were investigated for the presence of transcription factor binding sites by two different methods, (i) comparison of non-coding regions in conserved operons, and (ii) neural network promoter prediction. Predicted motifs were screened to identify most likely transcription factor binding sites and ribosome-binding sites. We provide information on motifs in Geobacteraceae similar to known transcription factor binding sites in Escherichia coli, conserved motifs in other bacterial species, putative palindromic sites, and predicted ribosome-binding sites. These predictions will aid in further elucidation of regulatory networks of gene interactions in Geobacteraceae.
Animals↗
Computational prediction of membrane-tethered transcription factors.
BACKGROUND: Sequestration of transcription factors in the membrane is emerging as an important mechanism for the regulation of gene expression. A handful of membrane-spanning transcription factors has been previously identified whose access to the nucleus is regulated by proteolytic cleavage from the membrane. To investigate the existence of other transmembrane transcription factors, we analyzed computationally all proteins in SWISS-PROT/TrEMBL for the combined presence of a DNA-binding domain and a transmembrane segment. RESULTS: Using Pfam hidden Markov models and four transmembrane-prediction programs, we identified with high confidence 76 membrane-spanning transcription factors in SWISS-PROT/TrEMBL. Analysis of the distribution of two proteins predicted by our method, MTJ1 and DMRT2, confirmed their localization to intracellular membrane compartments. Furthermore, elimination of the predicted transmembrane segment led to nuclear localization for each of these proteins. CONCLUSIONS: Our analysis uncovered a wealth of predicted membrane-spanning transcription factors that are structurally and taxonomically diverse, 56 of which lack experimental annotation. Seventy-five of the proteins are modular in structure, suggesting that a single proteolysis may be sufficient to liberate a DNA-binding domain from the membrane. This study provides grounds for investigations into the stimuli and mechanisms that release this intriguing class of transcription factors from membranes.
Active Transport, Cell Nucleus↗
Functionalized nanodiamonds part I. An experimental assessment of diamantane and computational predictions for higher diamondoids.
The structures, strain energies, and enthalpies of formation of diamantane 1, triamantane 2, isomeric tetramantanes 3-5, T(d)-pentamantane 6, and D(3d)-hexamantane 7, and the structures of their respective radicals, cations, as well as radical cations, were computed at the B3LYP/6-31G* level of theory. For the most symmetrical hydrocarbons, the relative strain (per carbon atom) decreases from the lower to the higher diamondoids. The relative stabilities of isomeric diamondoidyl radicals vary only within small limits, while the stabilities of the diamondoidyl cations increase with cage size and depend strongly on the geometric position of the charge. Positive charge located close to the geometrical center of the molecule is stabilized by 2-5 kcal mol(-1). In contrast, diamondoid radical cations preferentially form highly delocalized structures with elongated peripheral C-H bonds. The effective spin/charge delocalization lowers the ionization potentials of diamondoids significantly (down to 176.9 kcal mol(-1) for 7). The reactivity of 1 was extensively studied experimentally. Whereas reactions with carbon-centered radicals (Hal)(3)C(*) (Hal=halogen) lead to mixtures of all possible tertiary and secondary halodiamantanes, uncharged electrophiles (dimethyldioxirane, m-chloroperbenzoic acid, and CrO(2)Cl(2)) give much higher tertiary versus secondary selectivities. Medial bridgehead substitution dominates in the reactions with strong electrophiles (Br(2), 100 % HNO(3)), whereas with strong single-electron transfer (SET) acceptors (photoexcited 1,2,4,5-tetracyanobenzene) apical C(4)-H bridgehead substitution is preferred. For diamondoids that form well-defined radical cations (such as 1 and 4-7), exceptionally high selectivities are expected upon oxidation with outer-sphere SET reagents.
Journal Article↗
In vitro and in vivo transcription from a computer predicted promoter.
A fragment (172 bp) of B. subtilis phage phi29 DNA, which does not contain a functional promoter for phage transcription, has been shown to direct transcription in the promoter-probe plasmid pPV33. The promoter candidate found in this fragment by the computer method of acceptability is compared with cryptic promoters selected by this computer method. It is characterized in vitro by electron microscopic visualization of RNA polymerase binding and 'run off' transcription, and in vivo by high resolution S1 mapping.
Bacillus Phages↗
Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes.
Non-synonymous single nucleotide polymorphisms (nsSNPs) represent common genetic variation that alters encoded amino acids in proteins. All nsSNPs may potentially affect the structure or function of expressed proteins and could therefore have an impact on complex diseases. In an effort to evaluate the phenotypic effect of all known nsSNPs in human DNA repair genes, we have characterized each polymorphism in terms of different functional properties. The properties are computed based on amino acid characteristics (e.g. residue volume change); position-specific phylogenetic information from multiple sequence alignments and from prediction programs such as SIFT (Sorting Intolerant From Tolerant) and PolyPhen (Polymorphism Phenotyping). We provide a comprehensive, updated list of all validated nsSNPs from dbSNP (public database of human single nucleotide polymorphisms at National Center for Biotechnology Information, USA) located in human DNA repair genes. The list includes repair enzymes, genes associated with response to DNA damage as well as genes implicated with genetic instability or sensitivity to DNA damaging agents. Out of a total of 152 genes involved in DNA repair, 95 had validated nsSNPs in them. The fraction of nsSNPs that had high probability of being functionally significant was predicted to be 29.6% and 30.9%, by SIFT and PolyPhen respectively. The resulting list of annotated nsSNPs is available online (http://dna.uio.no/repairSNP), and is an ongoing project that will continue assessing the function of coding SNPs in human DNA repair genes.
Computational Biology↗
Computer predictions of antigenic domains in herpes simplex virus types 1 and 2 glycoprotein D as compared with experimentally proven domains.
The primary amino-acid sequence of the glycoprotein D (gD) of herpes simplex virus types 1 and 2 (HSV-1, HSV-2) was analyzed by computer programs that provided values for hydrophilicity, surface probability, flexibility, and antigenicity, as well as the secondary structure conformation. Putative antigenic domains with a high hydrophilicity, surface probability, and antigenicity index were determined and compared with the reported antigenic domains in HSV-1 and HSV-2 gD protein based on experimental data. The major experimentally proven antigenic domains were detected by the computer analyses. Additional putative antigenic domains with potential for the synthesis of antigenic viral peptides were determined.
Amino Acid Sequence↗
Computational prediction of human drug metabolism.
There is an urgent requirement within the pharmaceutical and biotechnology industries, regulatory authorities and academia to improve the success of molecules that are selected for clinical trials. Although absorption, distribution, metabolism, excretion and toxicity (ADME/Tox) properties are some of the many components that contribute to successful drug discovery and development, they represent factors for which we currently have in vitro and in vivo data that can be modelled computationally. Understanding the possible toxicity and the metabolic fate of xenobiotics in the human body is particularly important in early drug discovery. There is, therefore, a need for computational methodologies for uncovering the relationships between the structure and the biological activity of novel molecules. The convergence of numerous technologies, including high-throughput techniques, databases, ADME/Tox modelling and systems biology modelling, is leading to the foundation of systems-ADME/Tox. Results from experiments can be integrated with predictions to globally simulate and understand the likely complete effects of a molecule in humans. The development and early application of major components of MetaDrug (GeneGo, Inc.) software will be described, which includes rule-based metabolite prediction, quantitative structure-activity relationship models for major drug metabolising enzymes, and an extensive database of human protein-xenobiotic interactions. This represents a combined approach to predicting drug metabolism. MetaDrug can be readily used for visualising Phase I and II metabolic pathways, as well as interpreting high-throughput data derived from microarrays as networks of interacting objects. This will ultimately aid in hypothesis generation and the early triaging of molecules likely to have undesirable predicted properties or measured effects on key proteins and cellular functions.
Computational Biology↗
Computer prediction of neonatal conditions by sampled data analyses of the fetal heart rate and the scalp blood during labor.
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Apgar Score↗
Computer prediction of the need for dialysis and transplantation using calculated creatinine clearance.
A computerised system capable of prospective assessment of the course of chronic renal failure has been devised. Rapid analysis is possible of the progress of a large cohort of patients and therefore of the prospective load on renal unit facilities. Calculated creatinine clearance values provide a more accurate and earlier prediction of end stage failure than the reciprocals of serum creatinine values.
Adolescent↗
Computer predictions of abnormal test results. Effects on outpatient testing.
We developed statistical equations to predict abnormalities on eight commonly ordered diagnostic tests and we gave the predictions to 112 physicians practicing in an academic internal medicine practice. Half of each physician's patients were randomized to intervention status. All diagnostic tests were ordered by microcomputer, and when a physician ordered one of the eight study tests for an intervention patient, the computer displayed the probability (0% to 100%) that the test would be positive for the main abnormality being tested for. The physician could then cancel the test if desired. During a six-month controlled trial, when there were more than 15,000 scheduled patient visits, patient charges for the eight study tests were 8.8% less for the intervention patients. The largest reductions (greater than 10%) were for serum electrolyte level tests and complete blood cell counts, the two most commonly ordered tests. Physicians ordered fewer low-probability tests for intervention patients than for controls, suggesting that with timely predictive information, physicians can target tests to higher-risk patients.
Clinical Laboratory Techniques↗
Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.
Comparison of the secondary structure of the 5' non-coding region of poliovirus 3 RNA derived from the genetic algorithm with the model of Skinner et al. (J. Mol. Biol., 207, 379-392, 1989) demonstrates many of the confirmed structural elements. The genetic algorithm (Shapiro and Navetta, J. Supercomput., 8, 195-201, 1994) generates a population of all possible stems, then mixes, combines, and recombines these stems in multiple iterations on a massively parallel computer, ultimately selecting a most fit structure based on its energy. The secondary structure of the region containing the determinants of neurovirulence was better predicted using the genetic algorithm, whereas the dynamic programming algorithm (Zuker, Science, 244, 48-52, 1989) required phylogenetic comparative sequence analysis to arrive at the correct conclusion. In addition, artificial mutations were introduced throughout this region of the genome and although rearrangements in structure may occur, many structures persisted, suggesting that the given structures thus selected may have evolved to withstand isolated mutations. The genetic algorithm-derived structure for the 5' non-coding region compares favorably with the biological data and functions previously described, and contains all of the 'persistent' structures, suggesting also that the persistence factor may be an aid to validating structures.
Algorithms↗
Mapping a neutralizing epitope on the SARS coronavirus spike protein: computational prediction based on affinity-selected peptides.
Rapid elucidation of neutralizing antibody epitopes on emerging viral pathogens like severe acute respiratory syndrome (SARS) coronavirus (CoV) or highly pathogenic avian influenza H5N1 virus is of great importance for rational design of vaccines against these viruses. Here we combined screening of phage display random peptide libraries with a unique computer algorithm "Mapitope" to identify the discontinuous epitope of 80R, a potent neutralizing human anti-SARS monoclonal antibody against the spike protein. Using two different types of random peptide libraries which display cysteine-constrained loops or linear 13-15-mer peptides, independent panels containing 42 and 18 peptides were isolated, respectively. These peptides, which had no apparent homologous motif within or between the peptide pools and spike protein, were deconvoluted into amino acid pairs (AAPs) by Mapitope and the statistically significant pairs (SSPs) were defined. Mapitope analysis of the peptides was first performed on a theoretical model of the spike and later on the genuine crystal structure. Three clusters (A, B and C) were predicted on both structures with remarkable overlap. Cluster A ranked the highest in the algorithm in both models and coincided well with the sites of spike protein that are in contact with the receptor, consistent with the observation that 80R functions as a potent entry inhibitor. This study demonstrates that by using this novel strategy one can rapidly predict and identify a neutralizing antibody epitope, even in the absence of the crystal structure of its target protein.
Algorithms↗
Computational prediction of the three-dimensional structures for the Caenorhabditis elegans tubulin family.
In this article we characterize, from a structural point of view, all 16 members of the tubulin gene family of Caenorhabditis elegans (9 alpha-tubulins, 6 beta-tubulins, and 1 gamma-tubulin). We obtained their tertiary structures by computationally modifying the X-ray crystal structure of the pig brain alpha/beta-tubulin dimer published by Nogales et al. [Nature (London) 1998;391:199-203]. Our computational protocol involves changing the amino acids (with MIDAS; Jarvis et al., UCSF MIDAS. University of California, San Francisco, 1986) in the 3D structure of pig brain alpha/beta-tubulin dimer followed by geometry optimization with the AMBER force field (Perlman et al., AMBER 4. University of California, San Francisco, 1990). We subsequently analyze and compare the resulting structures in terms of the differences in their secondary and tertiary structures. In addition, we compare the pattern of hydrogen bonds and hydrophobic contacts in the guanosine triphosphate (GTP)-binding site for all members of the tubulin family. Our computational results show that, except for gamma-tubulin, all members of the C. elegans tubulin family have similar secondary and 3D structures and that the change in the pattern of hydrogen bonds in the GTP-binding site may be used to assess the relative stability of different alpha/beta-tubulin dimers formed by monomers of the tubulin family.
Animals↗
Disulfide stabilization of antibody Fv: computer predictions and experimental evaluation.
Using molecular modeling technology we have recently identified positions in conserved framework regions of Fvs which can be used to stabilize antibody Fvs by an interchain disulfide bond engineered in between the structurally conserved framework positions of the variable domains of heavy (VH) and light (VL) immunoglobulin chains (disulfide-stabilized Fv; dsFv). The computer model indicated the existence of other potential sites in the framework regions that might be suitable for disulfide bond formation between VH and VL. The possibility of obtaining dsFvs using these positions is evaluated here experimentally by constructing dsFv immunotoxins in which the Fv moiety is fused to a truncated form of Pseudomonas exotoxin. We analyzed the extent of dsFv formation and the activity of the resulting dsFv immunotoxins, and compared various dsFv molecules with the scFv immunotoxin. Our results demonstrate that position H44-L105 is the only one which gives high production yields of active dsFv. All other positions gave either low yields and activity or completely failed to produce active dsFv. With one exception, the formation and activities of the dsFvs corresponded to the C alpha-C alpha distance between the VH and VL positions, with an optimal distance of 5.7 A producing the best dsFv. Distances of 6.0-6.9 A resulted in a low yield of protein that was still capable of binding antigen, whereas distances > 7.0 A resulted in molecules in which dsFv formation was not obtained.
Amino Acid Sequence↗
Computational prediction of homodimerization of the A3 adenosine receptor.
Increasing evidence suggests that G protein-coupled receptors form functional dimers or larger oligomeric complexes through homo- or heterodimerization, and that various transmembrane (TM) domains contribute dimerization interfaces. In this study, monomeric receptor structures - either the monomeric crystallographic structure of bovine rhodopsin or an A(3) adenosine receptor (AR) homology model - were dimerized by computational methods assuming various TM contact regions, optimized, and compared. The semi-empirical oligomeric structure of mouse rhodopsin studied in a native disc membrane with atomic force microscopy was used to establish the distance between monomers in the initial dimeric models. Among eight variations of symmetrical homodimers of bovine rhodopsin, the favored dimeric assembly closely resembled the semi-empirical model, in which TM domains 4 and 5 were the contact site, thus validating this approach. We used similar methods to generate eight homodimers of the A(3)AR and found the favored dimeric interface similarly to be TM4-5. By this method, dimeric variations - TM1-2, TM2-3, TM2-4, TM3-4, TM4-5, TM5-6, TM6-7, and TM7-1 - were constructed with the SYBYL 7.0 program by using a novel "fit-centroids-normal" method. Fitting atoms considered one of eight TM-TM centroids or seven-TM centroids, two centroids of each monomer, and a normal atom passing through the plane containing all centroids. Following molecular dynamics, the most energetically favorable contact modes were identified. In addition to TM4-5, which was favored in both rhodopsin and A(3)AR dimeric models, TM1-2 dimers in which helices 8 also contacted each other were judged favorable. The largest contact surface area between the monomers among the various homodimers, determined by van der Waals calculation with the MOLCAD surface program, was for the TM4-5 dimer. This contact surface also showed a high degree of shape complementarity. In addition, the TM4-5 dimers made by this theoretical method were more stable than the semi-empirically determined dimer.
Animals↗
A topological substructural approach applied to the computational prediction of rodent carcinogenicity.
The carcinogenic activity has been investigated by using a topological substructural molecular design approach (TOPS-MODE). A discriminant model was developed to predict the carcinogenic and noncarcinogenic activity on a data set of 189 compounds. The percentage of correct classification was 76.32%. The predictive power of the model was validated by three test: an external test set (compounds not used in the develop of the model, with a 72.97% of good classification), a leave-group-out cross-validation procedure (4-fold full cross-validation, removing 20% of compounds in each cycle, with a good prediction of 76.31%) and two external prediction sets (the first and second exercises of the National Toxicology Program). This methodology evidenced that the hydrophobicity increase the carcinogenic activity and the dipole moment of the molecule decrease it; suggesting the capacity of the TOPS-MODE descriptors to estimate this property for new drug candidates. Finally, the positive and negative fragment contributions to the carcinogenic activity were identified (structural alerts) and their potentialities in the lead generation process and in the design of 'safer' chemicals were evaluated.
Animals↗
Computational prediction of the stability of lipid emulsions in total nutrient admixtures.
The relationships between the stability of lipid emulsions in a number of parenteral total nutrient admixtures (TNAs) and their electrokinetic properties were examined. Previous studies have attempted to measure or calculate zeta potentials of lipid emulsions in nutrient admixtures to rationalize their stability behavior, but there has been no demonstration that zeta potentials do actually determine emulsion stability or that such computational approaches can be successful. The present study demonstrates that emulsion stability in a range of TNAs is dependent on the emulsion zeta potential and also that van der Waals forces, influenced by the presence of glucose, are important. By accounting for these factors we show that it is possible to calculate the stability of TNAs by Deryaguin-Landau-Verwey-Overbeck-based methods and obtain reasonable agreement with experimental stability data in most systems.
Drug Stability↗