Identification of Domains using Structural Data
... • Neighboring residues within radius r are connected by dashed lines. • Connections between i and i + 2 have been omitted for clarity. • Label evolution is done without inverse distance weighting. ...
... • Neighboring residues within radius r are connected by dashed lines. • Connections between i and i + 2 have been omitted for clarity. • Label evolution is done without inverse distance weighting. ...
A. Collagen
... hydroxylysine Triple-helical structure Collagen doesn't fold into a compact structure- It has an elongated triple-helical structure , the amino acid side chains are placed outside of the molecule. This allow the interaction between triple-helical molecules that lead to aggregation of collagen monome ...
... hydroxylysine Triple-helical structure Collagen doesn't fold into a compact structure- It has an elongated triple-helical structure , the amino acid side chains are placed outside of the molecule. This allow the interaction between triple-helical molecules that lead to aggregation of collagen monome ...
PPT
... • Use Seq 1 as query sequence • What happens? E-value of both of these hits may be very high if domain A and B are long and well conserved. • Seq1 is homologous to Seq2&3, but remember Seq1 is not homlogous over the entire length to Seq2&3 • Just don’t depend on the E-value • “BLAST hits are not tra ...
... • Use Seq 1 as query sequence • What happens? E-value of both of these hits may be very high if domain A and B are long and well conserved. • Seq1 is homologous to Seq2&3, but remember Seq1 is not homlogous over the entire length to Seq2&3 • Just don’t depend on the E-value • “BLAST hits are not tra ...
nerve agents - 20 Years of OPCW
... of the protein leading to its three dimensional structure. Helical substructures and so called beta-sheets (thick arrows) can be identified. The catalytic active site is buried deep inside the enzyme. It contains three amino acids crucial for catalytic activity: Serine 200, Histidine 440 and Glutama ...
... of the protein leading to its three dimensional structure. Helical substructures and so called beta-sheets (thick arrows) can be identified. The catalytic active site is buried deep inside the enzyme. It contains three amino acids crucial for catalytic activity: Serine 200, Histidine 440 and Glutama ...
All About Proteins Proteins are highly folded polymers constructed
... memorize them. You DO need to recognize and be able to draw the general structure of an amino acid shown at left. The R groups are important because they may make an amino acid nonpolar, or polar, and some of the polar ones may become charged in water or act as acids or bases. These properties will ...
... memorize them. You DO need to recognize and be able to draw the general structure of an amino acid shown at left. The R groups are important because they may make an amino acid nonpolar, or polar, and some of the polar ones may become charged in water or act as acids or bases. These properties will ...
Recent advances in plant cell wall proteomics
... describe the arrangement of their components into dense interwoven networks of polysaccharides and proteins [2, 3]. Cellulose microfibrils and hemicelluloses constitute a network, another one is formed by structural proteins, e.g. extensins, both embedded in a pectin matrix. Plant cell walls are dyn ...
... describe the arrangement of their components into dense interwoven networks of polysaccharides and proteins [2, 3]. Cellulose microfibrils and hemicelluloses constitute a network, another one is formed by structural proteins, e.g. extensins, both embedded in a pectin matrix. Plant cell walls are dyn ...
1-Structure of Heme
... a histidine imidazole (known as proximal His). – One with O2 (the sixth coordinate) • Oxidation of iron to the Fe3+, ferric, state makes the molecule incapable of normal O2 binding ...
... a histidine imidazole (known as proximal His). – One with O2 (the sixth coordinate) • Oxidation of iron to the Fe3+, ferric, state makes the molecule incapable of normal O2 binding ...
Protein synthesis
... • 1) Ternary complex formation (IF2.GTP.initiator tRNA) • This complex binds to mRNA to form 30S initiation complex • The intereacting components are(mRNA+30S subunit+fMet tRNAf+GTP+Initiation factors) • The fmet-tRNAf is located to the AUG (initiator)codon • 50S subunit joins to 30S initiation comp ...
... • 1) Ternary complex formation (IF2.GTP.initiator tRNA) • This complex binds to mRNA to form 30S initiation complex • The intereacting components are(mRNA+30S subunit+fMet tRNAf+GTP+Initiation factors) • The fmet-tRNAf is located to the AUG (initiator)codon • 50S subunit joins to 30S initiation comp ...
Protein synthesis
... • 1) Ternary complex formation (IF2.GTP.initiator tRNA) • This complex binds to mRNA to form 30S initiation complex • The intereacting components are(mRNA+30S subunit+fMet tRNAf+GTP+Initiation factors) • The fmet-tRNAf is located to the AUG (initiator)codon • 50S subunit joins to 30S initiation comp ...
... • 1) Ternary complex formation (IF2.GTP.initiator tRNA) • This complex binds to mRNA to form 30S initiation complex • The intereacting components are(mRNA+30S subunit+fMet tRNAf+GTP+Initiation factors) • The fmet-tRNAf is located to the AUG (initiator)codon • 50S subunit joins to 30S initiation comp ...
Teaching Notes
... 2. Function: a. The RT enzyme has 2 active sites (in P66) – polymerase and RNase H. b. The polymerase active site can work with both RNA and DNA templates, while the RNase H domain functions to cleave RNA strands in an RNA-DNA duplex. Polymerase ...
... 2. Function: a. The RT enzyme has 2 active sites (in P66) – polymerase and RNase H. b. The polymerase active site can work with both RNA and DNA templates, while the RNase H domain functions to cleave RNA strands in an RNA-DNA duplex. Polymerase ...
Proteomic analysis of nipple aspirate fluid from women with early
... proteins in gels [16-18]. This is mainly because profiling experiments such as SELDI in which MS-1 only is performed, and not MS/MS, is not an inherently quantitative technique [16,19-22] and does not allow for the specific identification of individual peptides. The development of methods and instru ...
... proteins in gels [16-18]. This is mainly because profiling experiments such as SELDI in which MS-1 only is performed, and not MS/MS, is not an inherently quantitative technique [16,19-22] and does not allow for the specific identification of individual peptides. The development of methods and instru ...
Gene Section SS18 (synovial sarcoma translocation, chromosome 18) Atlas of Genetics and Cytogenetics
... The last 8 amino acid residues of the SS18 (SYT) protein are replaced by 78 amino acids from the Cterminal part of SSX proteins. ...
... The last 8 amino acid residues of the SS18 (SYT) protein are replaced by 78 amino acids from the Cterminal part of SSX proteins. ...
Protein Formation 3.3.3.2 Protein Formation 3.3.3.2 Upon successful
... copy and carry the code from the nucleus to the cytoplasm. In the cytoplasm, the messenger RNA is attached to a ribosome, an organelle that helps assemble proteins. The ribosomes are made partly of ribosomal RNA. So the job of rRNA is to make ribosomes. The RNA binds to the ribosomes. The ribosome r ...
... copy and carry the code from the nucleus to the cytoplasm. In the cytoplasm, the messenger RNA is attached to a ribosome, an organelle that helps assemble proteins. The ribosomes are made partly of ribosomal RNA. So the job of rRNA is to make ribosomes. The RNA binds to the ribosomes. The ribosome r ...
Characterizing the O-glycosylation landscape of human plasma
... by highly abundant proteins, we compared the dynamic range of the platelet O-glycoproteome to the published quantitative proteome36 to better understand the depth of coverage achieved. Even in the absence of extensive precolumn separation, we found the range of glycoprotein detection to recapitulate ...
... by highly abundant proteins, we compared the dynamic range of the platelet O-glycoproteome to the published quantitative proteome36 to better understand the depth of coverage achieved. Even in the absence of extensive precolumn separation, we found the range of glycoprotein detection to recapitulate ...
mitochondria
... Two signal sequences direct proteins to the thylakoid membrane in chloroplasts precursor proteins have a hydrophobic thylakoid signal sequence followed the N-terminal chloroplast signal sequence 1. proteins pass across the double membrane into the stroma ...
... Two signal sequences direct proteins to the thylakoid membrane in chloroplasts precursor proteins have a hydrophobic thylakoid signal sequence followed the N-terminal chloroplast signal sequence 1. proteins pass across the double membrane into the stroma ...
Overview of Rule Curation
... Define features for annotation using controlled vocabulary with evidence attribution ...
... Define features for annotation using controlled vocabulary with evidence attribution ...
Facts and Fallacies
... 5. My protein sequence is confirmed with two unique peptide hits. True False ...
... 5. My protein sequence is confirmed with two unique peptide hits. True False ...
Poster
... the development of a novel therapy for Hutchinson-Guilford Progeria. Farnesyltransferase inhibitors (FTIs) were originally designed as anti-cancer drugs, but recently have been shown to slow premature aging resulting from Progeria . This premature aging syndrome is caused by a mutation that affects ...
... the development of a novel therapy for Hutchinson-Guilford Progeria. Farnesyltransferase inhibitors (FTIs) were originally designed as anti-cancer drugs, but recently have been shown to slow premature aging resulting from Progeria . This premature aging syndrome is caused by a mutation that affects ...
PROTEINS:
... In the solid state amino acids exist entirely in the dipolar form callled zwitterion. Amino acids are internally neutralized molecule. Since amino acids has its own proton donating group, NH3+and has its own proton accepting group, COO- so these dipolar ions can neutralize acids or bases of sufficie ...
... In the solid state amino acids exist entirely in the dipolar form callled zwitterion. Amino acids are internally neutralized molecule. Since amino acids has its own proton donating group, NH3+and has its own proton accepting group, COO- so these dipolar ions can neutralize acids or bases of sufficie ...
Gene Section ENAH (enabled homolog (Drosophila)) Atlas of Genetics and Cytogenetics
... sequence conserved the two serine phosphorylation sites of murine Mena, whereas the tyrosine residue, site of phosphorylation in mouse Mena (Tani et al., 2003), is substituted by a glutamine residue in the human ...
... sequence conserved the two serine phosphorylation sites of murine Mena, whereas the tyrosine residue, site of phosphorylation in mouse Mena (Tani et al., 2003), is substituted by a glutamine residue in the human ...
Sato Talk
... while the origin of mitochondria is likely to be an ancestor of alpha proteobacteria. This inference is mainly supported by the comparison of genomic sequences of the organelles and various bacteria. However, we recently pointed out that, based on accumulating database information and analytical dat ...
... while the origin of mitochondria is likely to be an ancestor of alpha proteobacteria. This inference is mainly supported by the comparison of genomic sequences of the organelles and various bacteria. However, we recently pointed out that, based on accumulating database information and analytical dat ...
Supplementary Methods and References
... minutes at 30°C. Equal aliquots (15 μl) from the kinase assays were loaded on 10% SDSPAGE and, following electrophoresis the gels were exposed to X-ray film for 15 min to detect the phosphorylated kinase substrates. Expression and purification of recombinant SnRK1 substrate protein TRX-KD, carrying ...
... minutes at 30°C. Equal aliquots (15 μl) from the kinase assays were loaded on 10% SDSPAGE and, following electrophoresis the gels were exposed to X-ray film for 15 min to detect the phosphorylated kinase substrates. Expression and purification of recombinant SnRK1 substrate protein TRX-KD, carrying ...
Identification and Modeling of Conserved Secondary Structures of
... • Low symmetry between H3 and H2. The structural overlay of the H3 and H2 structures showed a torsional twist between the two proteins. ...
... • Low symmetry between H3 and H2. The structural overlay of the H3 and H2 structures showed a torsional twist between the two proteins. ...
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term proteomics was first coined in 1997 to make an analogy with genomics, the study of the genome. The word proteome is a portmanteau of protein and genome, and was coined by Marc Wilkins in 1994 while working on the concept as a PhD student.The proteome is the entire set of proteins, produced or modified by an organism or system. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes. Proteomics is an interdisciplinary domain formed on the basis of the research and development of the Human Genome Project; it is also emerging scientific research and exploration of proteomes from the overall level of intracellular protein composition, structure, and its own unique activity patterns. It is an important component of functional genomics.While proteomics generally refers to the large-scale experimental analysis of proteins, it is often specifically used for protein purification and mass spectrometry.