Gene Section PTPN14 (protein tyrosine phosphatase, non receptor type 14) -
... Localisation to the golgi apparatus in epithelial cell types (Wyatt and Khew-Goodall, 2008) and mitochondria in human sperm has also been reported (Chao et al., 2011). ...
... Localisation to the golgi apparatus in epithelial cell types (Wyatt and Khew-Goodall, 2008) and mitochondria in human sperm has also been reported (Chao et al., 2011). ...
Lecture 3
... CS (envelope) conformation of Cg-endo L-proline peptide group at the trans position with respect to Ca-H (Y=120o), as in collagene ...
... CS (envelope) conformation of Cg-endo L-proline peptide group at the trans position with respect to Ca-H (Y=120o), as in collagene ...
Proteins * Structure and Function
... The R group represents a side chain from the central ‘alpha’ carbon atom, and can be anything from a simple hydrogen atom to a more complex ring structure. 3 of 29 ...
... The R group represents a side chain from the central ‘alpha’ carbon atom, and can be anything from a simple hydrogen atom to a more complex ring structure. 3 of 29 ...
The influence of membrane lipid structure on plasma
... gene products, and its network link means simple physical binding rather than in-depth knowledge of biological process. In this paper, we suggest a protein functional flow model which is a directed network based on a protein functions’ relation of signaling transduction pathway. The vertex of the su ...
... gene products, and its network link means simple physical binding rather than in-depth knowledge of biological process. In this paper, we suggest a protein functional flow model which is a directed network based on a protein functions’ relation of signaling transduction pathway. The vertex of the su ...
Science Take-Out: From DNA to Protein Structure and Function
... DNA is sometimes referred to as the blueprint of life. It holds the letters that code for almost all life on earth. Because DNA is so important, it has several proofreading and editing mechanisms in place to avoid errors as it replicates itself millions of times. However, occasionally there are mist ...
... DNA is sometimes referred to as the blueprint of life. It holds the letters that code for almost all life on earth. Because DNA is so important, it has several proofreading and editing mechanisms in place to avoid errors as it replicates itself millions of times. However, occasionally there are mist ...
Computational design of entry inhibitor scaffolds targeting the third
... tropism [1]. Specific binding to the V3 loop was accomplished primarily by nonconventional XH···π interactions between CH/OH sugar groups of the glycolipids and the conserved V3 residues with π-conjugated side chains. Along with XH···π interactions, πstacking and the standard H-bonds involving the f ...
... tropism [1]. Specific binding to the V3 loop was accomplished primarily by nonconventional XH···π interactions between CH/OH sugar groups of the glycolipids and the conserved V3 residues with π-conjugated side chains. Along with XH···π interactions, πstacking and the standard H-bonds involving the f ...
Biology 162: Computational Genetics
... • Related to phylogenetic methods we will see later – Calculate probability of each residue having been the common ancestor of the residues in a column – Calculate probability of each residue as a descendent – Use these probabilities as priors with appropriate weighting ...
... • Related to phylogenetic methods we will see later – Calculate probability of each residue having been the common ancestor of the residues in a column – Calculate probability of each residue as a descendent – Use these probabilities as priors with appropriate weighting ...
Databases
... NCBI - RefSeq • The RefSeq database is a curated collection of DNA, RNA, and protein sequences built by NCBI. • RefSeq provides only one example of each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes. • For each model organism, RefSeq aims to provide ...
... NCBI - RefSeq • The RefSeq database is a curated collection of DNA, RNA, and protein sequences built by NCBI. • RefSeq provides only one example of each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes. • For each model organism, RefSeq aims to provide ...
Click for format template in MS Word file
... known history will help to elucidate conserved sites, and characterize their correspondence to other pathogens and their relevance to the immune system. We describe a large-scale analysis of the entire WNV proteome, aimed at identifying and characterizing evolutionarily conserved amino acid sequence ...
... known history will help to elucidate conserved sites, and characterize their correspondence to other pathogens and their relevance to the immune system. We describe a large-scale analysis of the entire WNV proteome, aimed at identifying and characterizing evolutionarily conserved amino acid sequence ...
Helicobacter-Mammalian Host jump is mediated by targeted gene
... IP31758 genome Designation (Figure 1a) ...
... IP31758 genome Designation (Figure 1a) ...
Heme Redox State Triggers Conformational Changes in the Ec DOS
... oxidized and reduced states enable us to reveal the UVRR spectra of the Trp53 and W110 residues, separately. The difference spectra between the reduced and oxidized forms reflect the environmental changes of Trp residues. The W18, W17, W16, W7, and W3 bands of Trp53 near the heme vinyl side chain at ...
... oxidized and reduced states enable us to reveal the UVRR spectra of the Trp53 and W110 residues, separately. The difference spectra between the reduced and oxidized forms reflect the environmental changes of Trp residues. The W18, W17, W16, W7, and W3 bands of Trp53 near the heme vinyl side chain at ...
Macromolecular Interactions
... Protein-protein interfaces tend to be large (600 – 1300 Å2), involve 10 – 40 residues from each protein that interdigitate into multiple residues from the other protein, and are rich in aromatic residues (His, Phe, Tyr, Trp) and Arg Protein interactions are determined by hydrophobic effects and shap ...
... Protein-protein interfaces tend to be large (600 – 1300 Å2), involve 10 – 40 residues from each protein that interdigitate into multiple residues from the other protein, and are rich in aromatic residues (His, Phe, Tyr, Trp) and Arg Protein interactions are determined by hydrophobic effects and shap ...
Chap. 4. "Proteins: Three-Dimensional Structure and Function
... restricted when there is a bulky R-group such as in tyrosine, or the R-group has a branch at the ßcarbon position as in isoleucine. By using models and analyzing the possibility of steric clash between R-groups, Ramachandran developed a plot showing the permissible values for phi and psi angles (Fi ...
... restricted when there is a bulky R-group such as in tyrosine, or the R-group has a branch at the ßcarbon position as in isoleucine. By using models and analyzing the possibility of steric clash between R-groups, Ramachandran developed a plot showing the permissible values for phi and psi angles (Fi ...
homeostasis in cortical neurons nicotinamide adenine dinucleotide
... transcription protein elicits mitochondrial hyperpolarization and respiratory deficit, with dysregulation of complex IV and nicotinamide adenine dinucleotide homeostasis in cortical neurons. J. Immunol. 178: 869 – 876. Throughout the article, NAD(P)H should have been used in place of NADPH to signif ...
... transcription protein elicits mitochondrial hyperpolarization and respiratory deficit, with dysregulation of complex IV and nicotinamide adenine dinucleotide homeostasis in cortical neurons. J. Immunol. 178: 869 – 876. Throughout the article, NAD(P)H should have been used in place of NADPH to signif ...
Technical Writing Workshop
... There are two common formats for units. The most common is to use superscripts (nmol min-1 mg-1), and occasionally the dividing symbol is used (nmol/min/mg). ...
... There are two common formats for units. The most common is to use superscripts (nmol min-1 mg-1), and occasionally the dividing symbol is used (nmol/min/mg). ...
Model Worksheet Student Handout
... Despite the complexity of life on Earth, the most important large molecules found in all living things (biomolecules) can be classified into only four main categories: carbohydrates, lipids, proteins and nucleic acids. Three of these four classes of biomolecules – carbohydrates, proteins and nucleic ...
... Despite the complexity of life on Earth, the most important large molecules found in all living things (biomolecules) can be classified into only four main categories: carbohydrates, lipids, proteins and nucleic acids. Three of these four classes of biomolecules – carbohydrates, proteins and nucleic ...
Michal Sharon received her BSc in Chemistry from the Hebrew
... Ph.D. studies at the Weizmann Institute of Science focused on studying the three-dimensional structure of proteins by NMR. She conducted postdoctoral research in the Department of Chemistry at the University of Cambridge, UK in the lab of Prof. Carol Robinson until 2007, when she joined the faculty ...
... Ph.D. studies at the Weizmann Institute of Science focused on studying the three-dimensional structure of proteins by NMR. She conducted postdoctoral research in the Department of Chemistry at the University of Cambridge, UK in the lab of Prof. Carol Robinson until 2007, when she joined the faculty ...
Knowledge-Based Integration of Neuroscience Data Sources
... • recursively traverse the has_a paths under brain_region collect all anatomical_entities ...
... • recursively traverse the has_a paths under brain_region collect all anatomical_entities ...
Questions
... A. Suggest the chemical-structural features of these drugs, which you believe are required for their activity. B. Are there other features you would consider as important? ...
... A. Suggest the chemical-structural features of these drugs, which you believe are required for their activity. B. Are there other features you would consider as important? ...
Name of Student: Dominik Sommerfeld
... In the last 5 years there have been several attempts to predict kinase specificities for protein substrate recognition. At Kinexus Bioinformatics, we developed an algorithm to predict the specificities of all typical protein kinases (Kinase Specificity Predictor 1.0). This algorithm utilizes mutual ...
... In the last 5 years there have been several attempts to predict kinase specificities for protein substrate recognition. At Kinexus Bioinformatics, we developed an algorithm to predict the specificities of all typical protein kinases (Kinase Specificity Predictor 1.0). This algorithm utilizes mutual ...
Homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the ""target"" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the ""template""). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure.It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone.The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity usually imply significant structural similarity.The quality of the homology model is dependent on the quality of the sequence alignment and template structure. The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. Model quality declines with decreasing sequence identity; a typical model has ~1–2 Å root mean square deviation between the matched Cα atoms at 70% sequence identity but only 2–4 Å agreement at 25% sequence identity. However, the errors are significantly higher in the loop regions, where the amino acid sequences of the target and template proteins may be completely different.Regions of the model that were constructed without a template, usually by loop modeling, are generally much less accurate than the rest of the model. Errors in side chain packing and position also increase with decreasing identity, and variations in these packing configurations have been suggested as a major reason for poor model quality at low identity. Taken together, these various atomic-position errors are significant and impede the use of homology models for purposes that require atomic-resolution data, such as drug design and protein–protein interaction predictions; even the quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid. Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds. The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection. Like other methods of structure prediction, current practice in homology modeling is assessed in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP.