Steven`s project - The University of Texas at Dallas
... Using the downloaded software The downloaded software is much more difficult to use and does not contain user friendly GU interfaces. Whenever possible a novice user should opt for the on line version as described above. However, if you intend to repack proteins quite regularly, or need to repack i ...
... Using the downloaded software The downloaded software is much more difficult to use and does not contain user friendly GU interfaces. Whenever possible a novice user should opt for the on line version as described above. However, if you intend to repack proteins quite regularly, or need to repack i ...
(EC 2.2.1.1) active in the Calvin cycle of spinach chloroplasts
... Wisconsin package [9]. Sequence alignments were created with CLUSTAL V [17] and refined by eye. Distance between sequences for phylogenetic inference with the neighbor-joining method [35] was measured as numbers of amino acid substitutions per site corrected for multiple substitutions with the Dayho ...
... Wisconsin package [9]. Sequence alignments were created with CLUSTAL V [17] and refined by eye. Distance between sequences for phylogenetic inference with the neighbor-joining method [35] was measured as numbers of amino acid substitutions per site corrected for multiple substitutions with the Dayho ...
1 Determinants of protein-protein interfaces
... The abundance of each amino acid in such pairings needs to be normalized by an appropriate measure. Here we have taken for simplicity the abundances published in [4] which are reproduced in the column entitled Total Abundance [4] in Table 3. We do not claim that this provides the optimal reference t ...
... The abundance of each amino acid in such pairings needs to be normalized by an appropriate measure. Here we have taken for simplicity the abundances published in [4] which are reproduced in the column entitled Total Abundance [4] in Table 3. We do not claim that this provides the optimal reference t ...
Cis-trans peptide variations in structurally similar proteins.
... found to be conserved in similar structures. A different view using Protein Block based description of backbone conformation, suggests that many of the local conformational changes are highly different from the general local structural variations observed among structurally similar proteins. Changes ...
... found to be conserved in similar structures. A different view using Protein Block based description of backbone conformation, suggests that many of the local conformational changes are highly different from the general local structural variations observed among structurally similar proteins. Changes ...
ST.25 - WIPO
... acids or as “Xaa” in the sequence itself if the modified amino acid is one of those listed in Appendix 2, Table 4, and the modification shall be further described in the feature section of the sequence listing, using the codes given in Appendix 2, Table 4. These codes may be used in the description ...
... acids or as “Xaa” in the sequence itself if the modified amino acid is one of those listed in Appendix 2, Table 4, and the modification shall be further described in the feature section of the sequence listing, using the codes given in Appendix 2, Table 4. These codes may be used in the description ...
Identification of a Protein with Antioxidant Activity that is Important for
... Free thiol-containing proteins in each of the beers were visualised using the free-thiol labelling reagent, MPB (N'-(3-maleidylpropionyl)) biotin and SDS-PAGE separation. Initial Coomassie Blue staining showed that each sample of beer contained 2 major protein bands at 43 kDa and 10 kDa and they wer ...
... Free thiol-containing proteins in each of the beers were visualised using the free-thiol labelling reagent, MPB (N'-(3-maleidylpropionyl)) biotin and SDS-PAGE separation. Initial Coomassie Blue staining showed that each sample of beer contained 2 major protein bands at 43 kDa and 10 kDa and they wer ...
Characterization and Cloning of the Chlorophyll
... Suzuki et al., 2002). As shown in Figure 1, one route consists of two reactions: first, enzymatic conversion of Pheid a to a precursor of PyroPheid a, identified as C-132-carboxylPyroPheid a, and, next, spontaneous conversion of the precursor to PyroPheid a (Shioi et al., 1996b; Watanabe et al., 199 ...
... Suzuki et al., 2002). As shown in Figure 1, one route consists of two reactions: first, enzymatic conversion of Pheid a to a precursor of PyroPheid a, identified as C-132-carboxylPyroPheid a, and, next, spontaneous conversion of the precursor to PyroPheid a (Shioi et al., 1996b; Watanabe et al., 199 ...
... Gibbs energy for the overall reaction is negative and also comment on the fidelity of the reaction, or why the polymerase is more likely to incorporate the correct base (Note: do not discuss removal of an incorrect base, see following question). Choice B: Describe the mechanism by which tRNA ...
Protein-RNA interactions: Structural analysis and functional classes
... excluding the binding site residues. The propensity function gives values centred around 1. A propensity value >1 indicates that a particular amino acid occurs more frequently in the RNA binding interface than on the surface of the protein. A propensity value <1 indicates that an amino acid occurs l ...
... excluding the binding site residues. The propensity function gives values centred around 1. A propensity value >1 indicates that a particular amino acid occurs more frequently in the RNA binding interface than on the surface of the protein. A propensity value <1 indicates that an amino acid occurs l ...
Cell-Free Protein Expression Systems
... Introduction Cell-free protein synthesis is an important tool for molecular biologists in basic and applied sciences. It is increasingly being used in high-throughput functional genomics and proteomics, with significant advantages compared to protein expression in live cells. Cell-free protein synt ...
... Introduction Cell-free protein synthesis is an important tool for molecular biologists in basic and applied sciences. It is increasingly being used in high-throughput functional genomics and proteomics, with significant advantages compared to protein expression in live cells. Cell-free protein synt ...
Supplemental Materials
... Ryan is married to the famous actress Joscelyn Dupee. They have a 6 year old boy Jameson. He already looks like an NFL quarterback! Will he have the same disease as his Dad? What if Denver wants to draft him for their team? Can he play there? Let’s find out what hemoglobin genes (alleles)/proteins y ...
... Ryan is married to the famous actress Joscelyn Dupee. They have a 6 year old boy Jameson. He already looks like an NFL quarterback! Will he have the same disease as his Dad? What if Denver wants to draft him for their team? Can he play there? Let’s find out what hemoglobin genes (alleles)/proteins y ...
Amino Acids and Proteins Amino Acid Compound
... forces involve the interactions that occur when uncharged non-bonded atoms come very close together but do not induce dipoles. The repulsion is the result of the electron-electron repulsion that occurs as two clouds of electrons begin to overlap. Although van der Waals forces are extremely weak, rel ...
... forces involve the interactions that occur when uncharged non-bonded atoms come very close together but do not induce dipoles. The repulsion is the result of the electron-electron repulsion that occurs as two clouds of electrons begin to overlap. Although van der Waals forces are extremely weak, rel ...
Profile TildeCRF: a new tool for protein homology detection
... [DARWIN, 1868], Gregory Mendel provided in parallel a logical explanation for the mechanism of heredity after his experiments on pea plant hybridization, which led him to formulate his laws of inheritance [MENDEL, 1866]. Nonetheless, it was not until 1953 that James D. Watson and Francis Crick first ...
... [DARWIN, 1868], Gregory Mendel provided in parallel a logical explanation for the mechanism of heredity after his experiments on pea plant hybridization, which led him to formulate his laws of inheritance [MENDEL, 1866]. Nonetheless, it was not until 1953 that James D. Watson and Francis Crick first ...
Preparing and Analyzing Expressed Sequence Tags (ESTs) Library
... and postnatal ESTs, respectively. According to the statistical results of PANTHER of high similarity prenatal and postnatal ESTs, 137 and 127 different putative genes were listed and classified, respectively, by GO terms. 39 prenatal ESTs and 37 postnatal EST were uncategorized. 9 different types of ...
... and postnatal ESTs, respectively. According to the statistical results of PANTHER of high similarity prenatal and postnatal ESTs, 137 and 127 different putative genes were listed and classified, respectively, by GO terms. 39 prenatal ESTs and 37 postnatal EST were uncategorized. 9 different types of ...
Dreze et al, Methods Enzymol 2010
... DB-X autoactivators, higher 3AT concentrations can be used to circumvent autoactivator-dependent activity of GAL1-HIS3. Interactions identified at higher 3AT concentrations should be accompanied by rigorous quality control and validation of every individual interaction using multiple assays. Y2H con ...
... DB-X autoactivators, higher 3AT concentrations can be used to circumvent autoactivator-dependent activity of GAL1-HIS3. Interactions identified at higher 3AT concentrations should be accompanied by rigorous quality control and validation of every individual interaction using multiple assays. Y2H con ...
The hnRNP C Proteins Contain a Nuclear Retention Sequence That
... its endogenous counterpart and shuttles between the heterologous nuclei (data not shown; Pifiol-Roma and Dreyfuss, 1992). The hnRNP proteins that are restricted to the nucleus may be retained because they lack an NES, or because they contain nuclear retention sequences. To distinguish between these ...
... its endogenous counterpart and shuttles between the heterologous nuclei (data not shown; Pifiol-Roma and Dreyfuss, 1992). The hnRNP proteins that are restricted to the nucleus may be retained because they lack an NES, or because they contain nuclear retention sequences. To distinguish between these ...
A study of archaeal enzymes involved in polar lipid
... into two groups, based on the sequence similarity. Members of the first group, including ASS from M. thermautotrophicus, were closely related to PSS. The rough agreement between PSS homologue distribution within Archaea and the experimentally identified distribution of archaetidylserine suggested th ...
... into two groups, based on the sequence similarity. Members of the first group, including ASS from M. thermautotrophicus, were closely related to PSS. The rough agreement between PSS homologue distribution within Archaea and the experimentally identified distribution of archaetidylserine suggested th ...
Molecular Docking
... three times (A, B, C). For each one, we have a set of potential solutions that can be generated. Each intermediate level is extended to the next one by adding a new next fragment in all possible configurations. Solutions with a bad score are ...
... three times (A, B, C). For each one, we have a set of potential solutions that can be generated. Each intermediate level is extended to the next one by adding a new next fragment in all possible configurations. Solutions with a bad score are ...
Dynamics of Protein Tyrosine Nitration and
... different N-terminal inserts and microtubule binding repeats [65]. Endogenous tyrosine residues prone to be nitrated in tau protein are at 18, 29, 197, 310, and 394 position (numbers correspond to the longest tau isoform, which contains441 amino acids). In vitro, selectively of ONOO- mediated tyrosi ...
... different N-terminal inserts and microtubule binding repeats [65]. Endogenous tyrosine residues prone to be nitrated in tau protein are at 18, 29, 197, 310, and 394 position (numbers correspond to the longest tau isoform, which contains441 amino acids). In vitro, selectively of ONOO- mediated tyrosi ...
Engineering of factors determining alpha-amylase and
... The starch-degrading enzymes A-amylase and cyclodextrin glycosyltransferase (CGTase) are functionally and structurally closely related, with CGTases containing two additional domains (called D and E) compared to the three domains of A-amylases (A, B and C). Amino acid residue 196 (Thermoanaerobacter ...
... The starch-degrading enzymes A-amylase and cyclodextrin glycosyltransferase (CGTase) are functionally and structurally closely related, with CGTases containing two additional domains (called D and E) compared to the three domains of A-amylases (A, B and C). Amino acid residue 196 (Thermoanaerobacter ...
Comparison of the Structure of the Extrinsic 33 kDa Protein from
... mature protein; they are located at positions 100 and 193, respectively. Among them, the ATG codon at nucleotide number 100 was assigned as the start codon, because this codon is similar to the start codon (AnnATGGC) for translation initiation in higher plants (Lutcke et al. 1987) (see also below). ...
... mature protein; they are located at positions 100 and 193, respectively. Among them, the ATG codon at nucleotide number 100 was assigned as the start codon, because this codon is similar to the start codon (AnnATGGC) for translation initiation in higher plants (Lutcke et al. 1987) (see also below). ...
Cysteine 230 Modulates Tumor Necrosis Factor
... exhibits much stronger apoptotic activity than other TNF family members and is able to kill many cell types without potentiating agents such as actinomycin D or cycloheximide (10, 18, 19). Second, TRAIL kills tumor cells more effectively than normal cells by virtue of differential expression of DcRs ...
... exhibits much stronger apoptotic activity than other TNF family members and is able to kill many cell types without potentiating agents such as actinomycin D or cycloheximide (10, 18, 19). Second, TRAIL kills tumor cells more effectively than normal cells by virtue of differential expression of DcRs ...
Nitrogen Balance With Sheep on Rations Containing Urea
... IabUe tOl'JDl of nttroaen 18 subject to even greater error and requires V1g1lant ...
... IabUe tOl'JDl of nttroaen 18 subject to even greater error and requires V1g1lant ...