Monte Carlo Simulations of HIV Capsid Protein
... Specifically, we define the bound and unbound states based on the contact strength introduced earlier. For each frame in the simulation trajectory, we sum up the contact strengths of all residue pairs between the two proteins and classify it as a bound state if the total strength is larger than 1 or o ...
... Specifically, we define the bound and unbound states based on the contact strength introduced earlier. For each frame in the simulation trajectory, we sum up the contact strengths of all residue pairs between the two proteins and classify it as a bound state if the total strength is larger than 1 or o ...
T-cell regulator RNF125/TRAC-1 belongs to a novel family of
... isolation. COS-7, HeLa and HEK-293T (human embryonic kidney) cells were grown in DMEM (Dulbecco’s modified Eagle’s medium) (Cambrex), 10 % (v/v) FCS, 100 units/ml penicillin and 0.1 mg/ml streptomycin. For transfection, 107 Jurkat T-cells were electroporated in 250 µl of RPMI 1640 medium containing ...
... isolation. COS-7, HeLa and HEK-293T (human embryonic kidney) cells were grown in DMEM (Dulbecco’s modified Eagle’s medium) (Cambrex), 10 % (v/v) FCS, 100 units/ml penicillin and 0.1 mg/ml streptomycin. For transfection, 107 Jurkat T-cells were electroporated in 250 µl of RPMI 1640 medium containing ...
Chapter 20 – Proteins
... Just like the parent amino acids, peptides and proteins exist as zwitterions. And just like amino acids, proteins have isoelectric points. However, there is an important difference. While amino acids are not infinitely water soluble, under standard biological conditions they do not become insoluble. ...
... Just like the parent amino acids, peptides and proteins exist as zwitterions. And just like amino acids, proteins have isoelectric points. However, there is an important difference. While amino acids are not infinitely water soluble, under standard biological conditions they do not become insoluble. ...
Day 2 Western blotting
... dithiothreitol /DTT). Proteins solubilised in SDS bind the detergent uniformly along their length to a level of 1.4g SDS/g protein. This creates a charge/mass ratio which is consistent between proteins. For this reason, separation on a polyacrylamide gel in the presence of SDS occurs by mass alone, ...
... dithiothreitol /DTT). Proteins solubilised in SDS bind the detergent uniformly along their length to a level of 1.4g SDS/g protein. This creates a charge/mass ratio which is consistent between proteins. For this reason, separation on a polyacrylamide gel in the presence of SDS occurs by mass alone, ...
Using storage organelles for the accumulation and encapsulation of
... adapted for the storage of proteins in a stable and accessible form, a phenomenon that can be exploited to accumulate recombinant proteins [10]. Factors that influence protein expression and stability in seeds include genotype selection, transgene copy number and zygosity, construct design, and prot ...
... adapted for the storage of proteins in a stable and accessible form, a phenomenon that can be exploited to accumulate recombinant proteins [10]. Factors that influence protein expression and stability in seeds include genotype selection, transgene copy number and zygosity, construct design, and prot ...
A quantitative atlas of mitotic phosphorylation
... identification of >14,000 different phosphorylation events, more than half of which, to our knowledge, have not been described in the literature, along with relative quantitative data for the majority of these sites. We observed >1,000 proteins with increased phosphorylation in mitosis including man ...
... identification of >14,000 different phosphorylation events, more than half of which, to our knowledge, have not been described in the literature, along with relative quantitative data for the majority of these sites. We observed >1,000 proteins with increased phosphorylation in mitosis including man ...
Modulator of Diabetes and MetabolicSyndrome: Silent Proteins
... on loops, families and function from conserved regions. The Cn3D software gives a consensus view of the related sequence, which is the best indicator of conservation. In addition, the amino acids also exhibit certain properties like conservation and hydrophobicity, which are indicative of active sit ...
... on loops, families and function from conserved regions. The Cn3D software gives a consensus view of the related sequence, which is the best indicator of conservation. In addition, the amino acids also exhibit certain properties like conservation and hydrophobicity, which are indicative of active sit ...
occasional article intracellular protein degradation: from a vague
... The discovery of the lysosome along with independent experiments that were carried out at the same time and that have further strengthened the notion that cellular proteins are indeed in a constant state of synthesis and degradation (see, for example, Ref. 10), led scientists to feel, for the first ...
... The discovery of the lysosome along with independent experiments that were carried out at the same time and that have further strengthened the notion that cellular proteins are indeed in a constant state of synthesis and degradation (see, for example, Ref. 10), led scientists to feel, for the first ...
Chapter 17
... • Some introns contain sequences that may regulate gene expression • Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing • This is called alternative RNA splicing • Consequently, the number of different proteins an organism can pr ...
... • Some introns contain sequences that may regulate gene expression • Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing • This is called alternative RNA splicing • Consequently, the number of different proteins an organism can pr ...
Abiotic stress response in plants: When post
... transcripts, and ultimately of proteins [13]. RNA-mediated silencing is also emerging as an alternative mechanism to control the amount of specific transcripts by their degradation [14]. Subsequent steps of RNA processing, like the mRNAs transport through the nuclear envelope and the association of ...
... transcripts, and ultimately of proteins [13]. RNA-mediated silencing is also emerging as an alternative mechanism to control the amount of specific transcripts by their degradation [14]. Subsequent steps of RNA processing, like the mRNAs transport through the nuclear envelope and the association of ...
Translation - clemson.edu
... 6. What do the ribosomes link together? Amino acids 7. The ribosome reads the mRNA… how many nucleotides at a time? 3 8. What is a codon? Each group of 3 nucleotides 9. What is the start codon that the ribosome looks for? AUG 10. What brings the amino acids to the mRNA strand and ribosome? A tRNA 11 ...
... 6. What do the ribosomes link together? Amino acids 7. The ribosome reads the mRNA… how many nucleotides at a time? 3 8. What is a codon? Each group of 3 nucleotides 9. What is the start codon that the ribosome looks for? AUG 10. What brings the amino acids to the mRNA strand and ribosome? A tRNA 11 ...
Post-translational Modification Learning Objective Post
... directing the newly synthesized polypeptide ...
... directing the newly synthesized polypeptide ...
the RbDe web service - Oxford Academic
... the lack of better structural information, the term snake-like diagram has been coined, inspired by the layout of the sequence that spans the membrane several times. The automation of the rendering of snake-like diagrams, for proteins whose topology was similar to that of G proteincoupled receptors ...
... the lack of better structural information, the term snake-like diagram has been coined, inspired by the layout of the sequence that spans the membrane several times. The automation of the rendering of snake-like diagrams, for proteins whose topology was similar to that of G proteincoupled receptors ...
ch 17 from gene to protein
... • Some introns contain sequences that may regulate gene expression • Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing • This is called alternative RNA splicing • Consequently, the number of different proteins an organism can pr ...
... • Some introns contain sequences that may regulate gene expression • Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing • This is called alternative RNA splicing • Consequently, the number of different proteins an organism can pr ...
Tertiary and Quaternary Structure
... such supersecondary structures as coiled coils of α-helices, stacked β-sheets, βαβ elements, β-barrels, and β saddles. Define the terms domain and subunit as they relate to protein structure. Be able to recognize different domains in a ribbon diagram of a single polypeptide chain with 2 or more doma ...
... such supersecondary structures as coiled coils of α-helices, stacked β-sheets, βαβ elements, β-barrels, and β saddles. Define the terms domain and subunit as they relate to protein structure. Be able to recognize different domains in a ribbon diagram of a single polypeptide chain with 2 or more doma ...
Protein-RNA interactions: Structural analysis and functional classes
... the analysis of hydrogen bond and van der Waal contacts showed that in general proteins complexed with messenger RNA, transfer RNA and viral RNA have more base specific contacts and less backbone contacts than expected, while proteins complexed with ribosomal RNA have less base-specific contacts tha ...
... the analysis of hydrogen bond and van der Waal contacts showed that in general proteins complexed with messenger RNA, transfer RNA and viral RNA have more base specific contacts and less backbone contacts than expected, while proteins complexed with ribosomal RNA have less base-specific contacts tha ...
Heavy Metals and Metalloids As a Cause for Protein Misfolding and
... structure in a highly motile molten globule state) while the rest of the polypeptide chain is still being synthesized on the ribosome [38,39]. Experiments on in vitro refolding are usually performed with a purified protein at low concentration, i.e., under conditions that maximize the yield of refol ...
... structure in a highly motile molten globule state) while the rest of the polypeptide chain is still being synthesized on the ribosome [38,39]. Experiments on in vitro refolding are usually performed with a purified protein at low concentration, i.e., under conditions that maximize the yield of refol ...
Proteins
... an excellent food for the very young, but humans have also adapted milk, specifically cow’s milk, as a food substance for persons of all ages. ...
... an excellent food for the very young, but humans have also adapted milk, specifically cow’s milk, as a food substance for persons of all ages. ...
Sugar Transport in (Hyper-)Thermophilic Archaea
... the nanomolar range are usually observed only for substrates such as vitamins and iron which are found in very low concentrations in the environment. Uptake of substrates by hyperthermophilic archaea is usually optimal around the growth temperature. ...
... the nanomolar range are usually observed only for substrates such as vitamins and iron which are found in very low concentrations in the environment. Uptake of substrates by hyperthermophilic archaea is usually optimal around the growth temperature. ...
ER, Golgi and Vesicles :
... which has eukaryotic homologues (e.g. Oxa1 in mitochondria), is a 61 kDa transmembrane protein that is placed in the membrane through an SRP-Sec translocase mechanism. Once there, YidC interacts with nascent polypeptides (once they reach ~70 amino acids long) that have begun to interact with the lip ...
... which has eukaryotic homologues (e.g. Oxa1 in mitochondria), is a 61 kDa transmembrane protein that is placed in the membrane through an SRP-Sec translocase mechanism. Once there, YidC interacts with nascent polypeptides (once they reach ~70 amino acids long) that have begun to interact with the lip ...
ADP-ribosyltransferases: plastic tools for inactivating protein and
... domains have become associated with diverse regulatory domains (Bazan and Koch-Nolte, 1997). Some ADPRTs exhibit constitutive activity, others require proteolytic cleavage, reduction of a disulphide bond, or association with other proteins for activation. For example, diphtheria toxin is made as an ...
... domains have become associated with diverse regulatory domains (Bazan and Koch-Nolte, 1997). Some ADPRTs exhibit constitutive activity, others require proteolytic cleavage, reduction of a disulphide bond, or association with other proteins for activation. For example, diphtheria toxin is made as an ...
Gene Section RMRP (RNA component of mitochondrial RNA processing endoribonuclease)
... Expression: RMRP is strongly and ubiquitously expressed in mouse embryos (as an example an E15.5 mouse embryo is shown). In bone Rmrp is more strongly expressed in hypertrophic chondrocytes and pericondrium than in the zone of proliferating chondrocytes. There is also very strong expression in the e ...
... Expression: RMRP is strongly and ubiquitously expressed in mouse embryos (as an example an E15.5 mouse embryo is shown). In bone Rmrp is more strongly expressed in hypertrophic chondrocytes and pericondrium than in the zone of proliferating chondrocytes. There is also very strong expression in the e ...
Electrophoresis Western blotting
... • Due to high density of binding of SDS to proteins, the ratio size/charge is nearly the same for many SDS denatured proteins ...
... • Due to high density of binding of SDS to proteins, the ratio size/charge is nearly the same for many SDS denatured proteins ...
Biochemistry
... 3. active translation occurs on polyribosomes (also termed polysomes). This means that more than one ribosome can be bound to and translate a given mRNA at any one time. 4. chain elongation occurs by sequential addition of amino acids to the C-terminal end of the ribosome bound polypeptide. Translat ...
... 3. active translation occurs on polyribosomes (also termed polysomes). This means that more than one ribosome can be bound to and translate a given mRNA at any one time. 4. chain elongation occurs by sequential addition of amino acids to the C-terminal end of the ribosome bound polypeptide. Translat ...
Proteomics and Mass Spectroscopy
... there are far fewer protein-coding genes in the human genome than proteins in the human proteome – 20,000 to 25,000 genes coding for proteins. – about 1,000,000 proteins. • The human body may contain more than 2 million proteins, each having different functions. • The discrepancy implies that protei ...
... there are far fewer protein-coding genes in the human genome than proteins in the human proteome – 20,000 to 25,000 genes coding for proteins. – about 1,000,000 proteins. • The human body may contain more than 2 million proteins, each having different functions. • The discrepancy implies that protei ...
SR protein
SR proteins are a conserved family of proteins involved in RNA splicing. SR proteins are named because they contain a protein domain with long repeats of serine and arginine amino acid residues, whose standard abbreviations are ""S"" and ""R"" respectively. SR proteins are 50-300 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS binding domain. SR proteins are more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm.SR proteins were discovered in the 1990s in Drosophila and in amphibian oocytes, and later in humans. In general, metazoans appear to have SR proteins and unicellular organisms lack SR proteins.SR proteins are important in constitutive and alternative pre-mRNA splicing, mRNA export, genome stabilization, nonsense-mediated decay, and translation. SR proteins alternatively splice pre-mRNA by preferentially selecting different splice sites on the pre-mRNA strands to create multiple mRNA transcripts from one pre-mRNA transcript. Once splicing is complete the SR protein may or may not remain attached to help shuttle the mRNA strand out of the nucleus. As RNA Polymerase II is transcribing DNA into RNA, SR proteins attach to newly made pre-mRNA to prevent the pre-mRNA from binding to the coding DNA strand to increase genome stabilization. Topoisomerase I and SR proteins also interact to increase genome stabilization. SR proteins can control the concentrations of specific mRNA that is successfully translated into protein by selecting for nonsense-mediated decay codons during alternative splicing. SR proteins can alternatively splice NMD codons into its own mRNA transcript to auto-regulate the concentration of SR proteins. Through the mTOR pathway and interactions with polyribosomes, SR proteins can increase translation of mRNA.Ataxia telangiectasia, neurofibromatosis type 1, several cancers, HIV-1, and spinal muscular atrophy have all been linked to alternative splicing by SR proteins.