Homology Modeling via Protein Threading
... NP-Hard (if include interactions of multiple residues) Build a score function based on energies in order to correctly recognize arrangements of residues ...
... NP-Hard (if include interactions of multiple residues) Build a score function based on energies in order to correctly recognize arrangements of residues ...
Methods to Make Homogenous Antibody Drug Conjugates
... engineered an optimized E.coli based cell-free system for predictable high-yield protein synthesis and folding that showed scalability over multiple orders of magnitude. E. coli strains and their extracts were engineered to contain all of the necessary components for transcription, translation and e ...
... engineered an optimized E.coli based cell-free system for predictable high-yield protein synthesis and folding that showed scalability over multiple orders of magnitude. E. coli strains and their extracts were engineered to contain all of the necessary components for transcription, translation and e ...
Characterization of Escherichia coZi adenylate cyclase mutants with
... The 4.3 kb EcoRI-Sd fragment of pDIAl00, a derivative of pBR322 containing the cya gene (Roy & Danchin, 1982),was inserted into EcoRI Sari-digested pSa206, a low-copy-number plasmid (Close et al., 1984), to give pDIA1900 (Fig. 2). When the Acya strain TP2010 was transformed with derivatives of pDIA1 ...
... The 4.3 kb EcoRI-Sd fragment of pDIAl00, a derivative of pBR322 containing the cya gene (Roy & Danchin, 1982),was inserted into EcoRI Sari-digested pSa206, a low-copy-number plasmid (Close et al., 1984), to give pDIA1900 (Fig. 2). When the Acya strain TP2010 was transformed with derivatives of pDIA1 ...
Intrinsic Protein Disorder and Protein
... number of highly connected proteins, called hubs, are observed, while most proteins have only a few connections [1, 2]. We proposed that hubs often use disordered regions to bind to multiple partners (one-to-many signaling), and we also proposed that structured hubs often bind to many partners via t ...
... number of highly connected proteins, called hubs, are observed, while most proteins have only a few connections [1, 2]. We proposed that hubs often use disordered regions to bind to multiple partners (one-to-many signaling), and we also proposed that structured hubs often bind to many partners via t ...
Flavin adenine dinucleotide as a chromophore of the Xenopus (6
... Previously we have shown that in Drosophila DNA photolyase genes are expressed at a very high level in the ovary and its translated products are stored in eggs (9,17). This suggests that ovary is a good candidate for testing (6-4)photolyase activity to screen mRNA in X.laevis. We tested binding acti ...
... Previously we have shown that in Drosophila DNA photolyase genes are expressed at a very high level in the ovary and its translated products are stored in eggs (9,17). This suggests that ovary is a good candidate for testing (6-4)photolyase activity to screen mRNA in X.laevis. We tested binding acti ...
birkbeck college - Principles of Protein Structure
... Each question must start on a new page and the question number written at the top of each sheet. ...
... Each question must start on a new page and the question number written at the top of each sheet. ...
pDsRed-Monomer Vector Information
... pDsRed-Monomer is primarily intended to serve as a source of DsRed-Monomer cDNA. The flanking MCS regions make it possible to excise the DsRed-Monomer coding sequence and insert it into other vector systems of choice. The vector can also be used in bacteria to produce DsRed-Monomer protein. For West ...
... pDsRed-Monomer is primarily intended to serve as a source of DsRed-Monomer cDNA. The flanking MCS regions make it possible to excise the DsRed-Monomer coding sequence and insert it into other vector systems of choice. The vector can also be used in bacteria to produce DsRed-Monomer protein. For West ...
Parallel Analysis of Gene Expression: Microarrays
... has been drawn (Churchill 2002). Technical replicates are repeated samples of the same biological material, for example RNA preparations, labeling reactions, hybridizations, and duplicate spots of the same probe on each array. Biological replicates are independent samples of similar material, for e ...
... has been drawn (Churchill 2002). Technical replicates are repeated samples of the same biological material, for example RNA preparations, labeling reactions, hybridizations, and duplicate spots of the same probe on each array. Biological replicates are independent samples of similar material, for e ...
Protein Secondary Structure
... Statistically, a very high percentage (~60%) of helices are terminated by a single amino acid, Proline: ...
... Statistically, a very high percentage (~60%) of helices are terminated by a single amino acid, Proline: ...
Systems-wide Chicken DNA Microarrays, Gene Expression Profiling
... (Smith et al., 2001) and pigs (Fahrenkrug et al., 2002). Incidentally, the number of EST sequences now available for the chicken greatly exceeds that of any other species of domestic animal, including pigs and cattle. The first assembly was made only on 40,935 EST from the UD collection (Table 2). A ...
... (Smith et al., 2001) and pigs (Fahrenkrug et al., 2002). Incidentally, the number of EST sequences now available for the chicken greatly exceeds that of any other species of domestic animal, including pigs and cattle. The first assembly was made only on 40,935 EST from the UD collection (Table 2). A ...
Sporopollenin Biosynthetic Enzymes Interact and
... produced fusions to either the GALACTOSE4 (GAL4) DNA-binding domain (BD) or activation domain (AD). After yeast transformation with different couples of AD and BD constructs, mating mixtures were plated on yeast media lacking Leu, Trp, and His to select transformed colonies wherein protein interacti ...
... produced fusions to either the GALACTOSE4 (GAL4) DNA-binding domain (BD) or activation domain (AD). After yeast transformation with different couples of AD and BD constructs, mating mixtures were plated on yeast media lacking Leu, Trp, and His to select transformed colonies wherein protein interacti ...
Precise Gene Disruption in Saccharomyces cerevisiae by Double Fusion Polymerase Chain Reaction.
... Figure 1. Strategy for constructing gene disruption cassettes by PCR. Step 1: the three primary PCR reactions. The regions flanking the site of selectable marker insertion (‘A’ and ‘C’) are amplified with oligonucleotide primers specific for the target sequence. The primers distal from the selectabl ...
... Figure 1. Strategy for constructing gene disruption cassettes by PCR. Step 1: the three primary PCR reactions. The regions flanking the site of selectable marker insertion (‘A’ and ‘C’) are amplified with oligonucleotide primers specific for the target sequence. The primers distal from the selectabl ...
to the reprint.
... Department of Anatomy and Cell Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, 2Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, NIH, Bethesda, MD , 1,3Department of Ophthalmology and Visual Sciences and Department of Cell Biology and Physiology, ...
... Department of Anatomy and Cell Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, 2Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, NIH, Bethesda, MD , 1,3Department of Ophthalmology and Visual Sciences and Department of Cell Biology and Physiology, ...
Two fatty acid ∆9-desaturase genes, ole1 and ole2
... strains of the oleaginous fungus Mortierella alpina. Two genomic sequences, ∆9-1 and ∆9-2, each containing a single intron, were cloned from strain CBS 528.72 while one cDNA clone, LM9, was isolated from strain CBS 210.32. The ∆9-1 gene encoded a protein of 445 aa which shared 99 % identity with the ...
... strains of the oleaginous fungus Mortierella alpina. Two genomic sequences, ∆9-1 and ∆9-2, each containing a single intron, were cloned from strain CBS 528.72 while one cDNA clone, LM9, was isolated from strain CBS 210.32. The ∆9-1 gene encoded a protein of 445 aa which shared 99 % identity with the ...
Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence
... a new Cys252 residue became responsible for this function. Our hypothesis was based on the similarity between the position of Cys252 and chromphore-binding Cys residues in the GAF domains of plant and cyanobacterial phytochromes, which utilize reduced tetrapyrrole bilins such as phytochromobilin and ...
... a new Cys252 residue became responsible for this function. Our hypothesis was based on the similarity between the position of Cys252 and chromphore-binding Cys residues in the GAF domains of plant and cyanobacterial phytochromes, which utilize reduced tetrapyrrole bilins such as phytochromobilin and ...
Conformational flexibility may explain multiple cellular roles of PEST
... where U2i is the mean square displacement of the atom i. Careful analysis of these B- factors available in the PDB files provides the measure of flexibility and dynamics of the atoms of interest in the protein. B-factors have already been used to evaluate the flexibility of regions of interest in the p ...
... where U2i is the mean square displacement of the atom i. Careful analysis of these B- factors available in the PDB files provides the measure of flexibility and dynamics of the atoms of interest in the protein. B-factors have already been used to evaluate the flexibility of regions of interest in the p ...
Bacterial Transformation with Green Fluorescent Protein
... In this lab, you will use a plasmid that encodes the gene for the Green Fluorescent Protein (GFP) and a gene for resistance to the antibiotic ampicillin. GFP comes from the bioluminescent jellyfish Aequorea victoria. This protein causes the jellyfish to fluoresce and glow in the dark. Following t ...
... In this lab, you will use a plasmid that encodes the gene for the Green Fluorescent Protein (GFP) and a gene for resistance to the antibiotic ampicillin. GFP comes from the bioluminescent jellyfish Aequorea victoria. This protein causes the jellyfish to fluoresce and glow in the dark. Following t ...
RNA Polymerase II Subunit Rpb9 Regulates Transcription
... elongation factor TFIIS. In general, these studies revealed a role for Rpb9 in transcription elongation. The parts of Rpb9 that contributed to the elongation activity were determined using a set of Rpb9 deletion and alanine-scanning mutants (18). These studies showed that the C-terminal zinc ribbon ...
... elongation factor TFIIS. In general, these studies revealed a role for Rpb9 in transcription elongation. The parts of Rpb9 that contributed to the elongation activity were determined using a set of Rpb9 deletion and alanine-scanning mutants (18). These studies showed that the C-terminal zinc ribbon ...
Cloning and characterization of the
... phenotype of the S.cerevisiae los1∆ pus1∆ strain as well its sequence homology to scPus1p indicate that spPus1p may have pseudouridine synthase activity. To show this experimentally, we tested whether recombinant spPus1p exhibits a similar enzymatic activity to recombinant scPus1p. The spPUS1 ORF wa ...
... phenotype of the S.cerevisiae los1∆ pus1∆ strain as well its sequence homology to scPus1p indicate that spPus1p may have pseudouridine synthase activity. To show this experimentally, we tested whether recombinant spPus1p exhibits a similar enzymatic activity to recombinant scPus1p. The spPUS1 ORF wa ...
lecture08_11
... – Detect similar function where sequence differs (only ~50% remote homologies can be detected based on sequence) ...
... – Detect similar function where sequence differs (only ~50% remote homologies can be detected based on sequence) ...
Binding Protein HU has a Regulatory Role in the Acid Stress
... each of the HU proteins used in this study. Cross-linking assays performed with these protein samples showed that the wild-type (HUwt) and the two mutant proteins (HUm2 and HUm3) form dimers in solution. To a lesser extent, we also observed formation of tetramers, all this in a pH-independent manner ...
... each of the HU proteins used in this study. Cross-linking assays performed with these protein samples showed that the wild-type (HUwt) and the two mutant proteins (HUm2 and HUm3) form dimers in solution. To a lesser extent, we also observed formation of tetramers, all this in a pH-independent manner ...
440-kD Ankyrins: Structure of the Major
... Circular dichroism was measured with a Jobin-Yvon Dichrograph Mark V instrument which was interfaced with an Apple IIC computer. Data was taken at 0.5-nm intervals with one second response time. Spectra were taken at 40C with protein concentration at 50/~g/ml in 1 mM Tris and 0.4 M NaE pH 7.4. This ...
... Circular dichroism was measured with a Jobin-Yvon Dichrograph Mark V instrument which was interfaced with an Apple IIC computer. Data was taken at 0.5-nm intervals with one second response time. Spectra were taken at 40C with protein concentration at 50/~g/ml in 1 mM Tris and 0.4 M NaE pH 7.4. This ...
Protein-protein interaction networks (I): data preprocessing
... 3. Some kinds of proteins, such as transcription factors, cannot be studied with this technique since their hybrids could activate the transcription even in absence of any interaction. 4. The extensive use of artificially made hybrids could lead to conformational changes in the bait and prey protein ...
... 3. Some kinds of proteins, such as transcription factors, cannot be studied with this technique since their hybrids could activate the transcription even in absence of any interaction. 4. The extensive use of artificially made hybrids could lead to conformational changes in the bait and prey protein ...
search1
... 3. Decrease the Expect value to 1.0 or lower eliminates many hits and concentrate on results which are more likely to contain large coding regions and genomic fragments. 4. Processing multiple query sequences in one run can be much faster than processing them with separate runs because the databas ...
... 3. Decrease the Expect value to 1.0 or lower eliminates many hits and concentrate on results which are more likely to contain large coding regions and genomic fragments. 4. Processing multiple query sequences in one run can be much faster than processing them with separate runs because the databas ...
report on HMM
... In humans, as in other higher organisms, a DNA molecule consists of two strands that wrap around each other to resemble a twisted ladder whose sides, made of sugar and phosphate molecules, are connected by rungs of nitrogen containing chemicals called bases. Four different bases are present in DNA: ...
... In humans, as in other higher organisms, a DNA molecule consists of two strands that wrap around each other to resemble a twisted ladder whose sides, made of sugar and phosphate molecules, are connected by rungs of nitrogen containing chemicals called bases. Four different bases are present in DNA: ...