Expression of the transcription factor, TFII-I, in post
... interaction site, polyproline II domain and SH3 binding domain [1]. The helix-loop-helix motif within each I-repeat (R1-R6), by analogy to other transcription factors of similar structure, may be responsible for DNA binding or protein–protein interactions [2-4]. All repeats have similar folds, howev ...
... interaction site, polyproline II domain and SH3 binding domain [1]. The helix-loop-helix motif within each I-repeat (R1-R6), by analogy to other transcription factors of similar structure, may be responsible for DNA binding or protein–protein interactions [2-4]. All repeats have similar folds, howev ...
HMM_4
... A triplet of 3 nucleotides – called codon - codes for amino acids (see next slide). It is known that in parts of DNA which code for genes, the three codons positions has different statistics. Thus a Markov chain model for DNA should represent not only the Nucleotide (A, C, G or T), but also it ...
... A triplet of 3 nucleotides – called codon - codes for amino acids (see next slide). It is known that in parts of DNA which code for genes, the three codons positions has different statistics. Thus a Markov chain model for DNA should represent not only the Nucleotide (A, C, G or T), but also it ...
Libraries of Specific Assays Covering Whole
... specimens (typically serum or plasma). It is estimated that ELISA kits exist in some form for perhaps 2000 human proteins, but the quality of most of these is unlikely to approach that of the 200 highly-optimized clinical protein assays, which themselves have taken years to develop and occasionally ...
... specimens (typically serum or plasma). It is estimated that ELISA kits exist in some form for perhaps 2000 human proteins, but the quality of most of these is unlikely to approach that of the 200 highly-optimized clinical protein assays, which themselves have taken years to develop and occasionally ...
How to Spot Signs of Protein Deficiency
... Watch your muscles' growth, or lack thereof. If the body does not have a sufficient supply of protein, it cannot properly build and maintain muscle tissue. Additionally, protein is stored in the muscles and will be used by the body in case of deficiency. If your muscles appear more flabby than norma ...
... Watch your muscles' growth, or lack thereof. If the body does not have a sufficient supply of protein, it cannot properly build and maintain muscle tissue. Additionally, protein is stored in the muscles and will be used by the body in case of deficiency. If your muscles appear more flabby than norma ...
Protein Structure - E-Learning
... All proteins are made up of many amino acids joined by peptide bonds. Peptide bonds are strong bonds and are not easily disrupted. (dipeptide = two amino acids, polypeptide = several amino acids) Each protein has a complex and unique conformation, which is determined by the specific amino acids and ...
... All proteins are made up of many amino acids joined by peptide bonds. Peptide bonds are strong bonds and are not easily disrupted. (dipeptide = two amino acids, polypeptide = several amino acids) Each protein has a complex and unique conformation, which is determined by the specific amino acids and ...
Proteins
... polypeptides twisted, folded, and coiled into a unique shape • The sequence of amino acids determines a protein’s three-dimensional conformation • A protein’s conformation determines its function • Ribbon models and space-filling models can depict a protein’s conformation ...
... polypeptides twisted, folded, and coiled into a unique shape • The sequence of amino acids determines a protein’s three-dimensional conformation • A protein’s conformation determines its function • Ribbon models and space-filling models can depict a protein’s conformation ...
Exam 1
... D. ____________ In blue/white colony screening, white colonies are selected because they have intact galactosidase genes in their recombinant plasmids. E. ____________ Two peptides can form a disulfide bond with each other if they both contain the amino acid with the one letter abbreviation C. F. __ ...
... D. ____________ In blue/white colony screening, white colonies are selected because they have intact galactosidase genes in their recombinant plasmids. E. ____________ Two peptides can form a disulfide bond with each other if they both contain the amino acid with the one letter abbreviation C. F. __ ...
Automated Assignment of Backbone NMR Data
... linked chemical shift values which reflects the sequential linear arrangement of the individual residues in the protein sequence (Figure 2). This pattern is then matched with the protein sequence, by using the fact that certain residues have characteristic Cα and Cβ chemical shift ranges which uniqu ...
... linked chemical shift values which reflects the sequential linear arrangement of the individual residues in the protein sequence (Figure 2). This pattern is then matched with the protein sequence, by using the fact that certain residues have characteristic Cα and Cβ chemical shift ranges which uniqu ...
This exam has 8 pages, including this one.
... 6-residue long sequence was dropped on the floor, thus it was only possible to obtain the sequence of the 2 residue peptide: Leu-Leu. Determine as much of the sequence of this peptide as possible (Hint, you may not have enough information to completely determine the sequence). ...
... 6-residue long sequence was dropped on the floor, thus it was only possible to obtain the sequence of the 2 residue peptide: Leu-Leu. Determine as much of the sequence of this peptide as possible (Hint, you may not have enough information to completely determine the sequence). ...
A photoactivatable green-fluorescent protein from the phylum
... we cloned from cDNA prepared from ctenophore specimens. We therefore now believe that the green-fluorescent proteins reported in our study are not from ctenophores, and were due to incorporation of cnidarian prey into the ctenophore tissues. Although our genes were cloned from two independent sample ...
... we cloned from cDNA prepared from ctenophore specimens. We therefore now believe that the green-fluorescent proteins reported in our study are not from ctenophores, and were due to incorporation of cnidarian prey into the ctenophore tissues. Although our genes were cloned from two independent sample ...
Leukaemia Section t(8;20)(p11;q13) Atlas of Genetics and Cytogenetics
... has an open reading frame that may generate a functional chimeric protein. ...
... has an open reading frame that may generate a functional chimeric protein. ...
Expression and purification of huntingtin domain
... production, 3 mL samples (saved by the eukaryotic production team) of the original culture underwent testX purification as per BVES protocols. Elution of the sample from cobalt purification were analysed by SDS-PAGE. The protein is present in these elution samples. Unfortunately this implies that I ...
... production, 3 mL samples (saved by the eukaryotic production team) of the original culture underwent testX purification as per BVES protocols. Elution of the sample from cobalt purification were analysed by SDS-PAGE. The protein is present in these elution samples. Unfortunately this implies that I ...
biological process
... Many websites are available for the analysis of individual proteins. ExPASy and ISREC are two excellent resources. The accuracy of these programs is variable. Predictions based on primary amino acid sequence (such as molecular weight prediction) are likely to be more trustworthy. For many other prop ...
... Many websites are available for the analysis of individual proteins. ExPASy and ISREC are two excellent resources. The accuracy of these programs is variable. Predictions based on primary amino acid sequence (such as molecular weight prediction) are likely to be more trustworthy. For many other prop ...
Sander van Riet 13 June Reviewer Gene co
... IvIiev et al. uses this concept together with Protein Atlas project in order to identify new genes associated with motile cilia. Data from 3 different regions known to harbour motile cilia obtained from the GEO database were used. First they linked with already known motile cilia proteins together w ...
... IvIiev et al. uses this concept together with Protein Atlas project in order to identify new genes associated with motile cilia. Data from 3 different regions known to harbour motile cilia obtained from the GEO database were used. First they linked with already known motile cilia proteins together w ...
Modified Green Fluorescence Protein
... The green fluorescent protein (GFP) is a protein, comprised of 238 amino acids (26.9 kDa), originally isolated from the jellyfish Aequorea victoria that fluoresces green when exposed to blue light. The GFP from A. victoria has a major excitation peak at a wavelength of 395 nm and a minor one at 475 ...
... The green fluorescent protein (GFP) is a protein, comprised of 238 amino acids (26.9 kDa), originally isolated from the jellyfish Aequorea victoria that fluoresces green when exposed to blue light. The GFP from A. victoria has a major excitation peak at a wavelength of 395 nm and a minor one at 475 ...
Protein Requirements for Good Nutrition
... not supplemented in their food. This is why there is the old adage that dogs can eat cat food but cats cannot eat dog food. A deficiency in any of the amino acids can cause health-related problems. Protein quality Every protein source contains different levels of amino acids and each protein is diff ...
... not supplemented in their food. This is why there is the old adage that dogs can eat cat food but cats cannot eat dog food. A deficiency in any of the amino acids can cause health-related problems. Protein quality Every protein source contains different levels of amino acids and each protein is diff ...
Protein and its functional properties in food
... Amino acids Protein is made up of small units called amino acids. Amino acids are compounds which contain carbon, hydrogen, oxygen and nitrogen. A few also contain sulphur and phosphorous. There are around 20 different amino acids commonly found in plant and animal proteins. All amino acids have an ...
... Amino acids Protein is made up of small units called amino acids. Amino acids are compounds which contain carbon, hydrogen, oxygen and nitrogen. A few also contain sulphur and phosphorous. There are around 20 different amino acids commonly found in plant and animal proteins. All amino acids have an ...
Establish healthy, life-long habits, boost energy and
... Establish healthy, life-long habits, boost energy and immunity, slow the aging process and reduce disease risk. Take our fruit and veggie challenge for a chance to win a $100 ClubSport Rewards Card! ...
... Establish healthy, life-long habits, boost energy and immunity, slow the aging process and reduce disease risk. Take our fruit and veggie challenge for a chance to win a $100 ClubSport Rewards Card! ...
Nutrients - Food a fact of life
... Amino acids Protein is made up of small units called amino acids. Amino acids are compounds which contain carbon, hydrogen, oxygen and nitrogen. A few also contain sulphur and phosphorous. There are around 20 different amino acids commonly found in plant and animal proteins. All amino acids have an ...
... Amino acids Protein is made up of small units called amino acids. Amino acids are compounds which contain carbon, hydrogen, oxygen and nitrogen. A few also contain sulphur and phosphorous. There are around 20 different amino acids commonly found in plant and animal proteins. All amino acids have an ...
Genome Analysis and Genome Comparison
... algorithms for genomic analysis • Most algorithms were developed for comparing single protein sequences or DNA sequences containing a single gene • Most algorithms were based on assigning a score to all the possible alignments (usually by the sum of the similarity/identity values for each aligned re ...
... algorithms for genomic analysis • Most algorithms were developed for comparing single protein sequences or DNA sequences containing a single gene • Most algorithms were based on assigning a score to all the possible alignments (usually by the sum of the similarity/identity values for each aligned re ...
Week 3 lectures continued
... PAM units measure the amount of evolutionary distance between two amino acid sequences. Two strings S and T are said to be 1-PAM units diverged if a series of accepted substitutions (no indels) has converted S to T with an average of one accepted point-mutation per 100 amino acids. Accepted means th ...
... PAM units measure the amount of evolutionary distance between two amino acid sequences. Two strings S and T are said to be 1-PAM units diverged if a series of accepted substitutions (no indels) has converted S to T with an average of one accepted point-mutation per 100 amino acids. Accepted means th ...
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.