List of protein families currently covered by SVMProt
... Appendix S2 Method for computing the feature vector of a protein sequence A protein sequence is represented by specific feature vector assembled from encoded representations of tabulated residue properties including amino acid composition, hydrophobicity, normalized Van der Waals volume, polarity, p ...
... Appendix S2 Method for computing the feature vector of a protein sequence A protein sequence is represented by specific feature vector assembled from encoded representations of tabulated residue properties including amino acid composition, hydrophobicity, normalized Van der Waals volume, polarity, p ...
Functional and quantitative proteomics using SILAC
... spectrometric responses. Stable-isotope analogues of the molecule to be quantified have therefore been used for many years for accurate quantitation in small-molecule mass spectrometry. To differentially quantify two proteomes, a stable isotope can be introduced in various ways, most commonly by che ...
... spectrometric responses. Stable-isotope analogues of the molecule to be quantified have therefore been used for many years for accurate quantitation in small-molecule mass spectrometry. To differentially quantify two proteomes, a stable isotope can be introduced in various ways, most commonly by che ...
Lecture 2
... centre of the strip and current is passed through it. The colorless amino acid solution can be detected by spraying the strip with ninhydrin, which gives it a purple color. Migration of the spot towards the negatively charged cathode confirms the net positive charge of the amino acid. All amino acid ...
... centre of the strip and current is passed through it. The colorless amino acid solution can be detected by spraying the strip with ninhydrin, which gives it a purple color. Migration of the spot towards the negatively charged cathode confirms the net positive charge of the amino acid. All amino acid ...
... Activators and inhibitors binding away from the active site, changing the shape of the enzyme. Inhibitors shift the equilibrium to the tense form/decreasing the activity Activators shift the equilibrium to the relaxed form/increasing the activity. a) oxygen transport – oxygen is an allosteric activa ...
DNA intro There is a famous quip by Jacques Monod that “what is
... number of different combinations of hydrogen bonds through which nucleic acid bases can interact. Many of these possible arrangements, 28 to be precise, result in exactly the same kind of mutually stabilizing hydrogen bonds we see for the classic Watson-Crick base pairs GC and AT with similar energe ...
... number of different combinations of hydrogen bonds through which nucleic acid bases can interact. Many of these possible arrangements, 28 to be precise, result in exactly the same kind of mutually stabilizing hydrogen bonds we see for the classic Watson-Crick base pairs GC and AT with similar energe ...
Phosphoproteomics reveals extensive in vivo phosphorylation of
... by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited. ...
... by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited. ...
GEFs: master regulators of G
... control for most G-protein-regulated pathways. The array of cellular activities regulated by GEFs reflects the functional diversity of G proteins themselves; hence, various GEFs are involved in transcriptional regulation (by modulating the activity of Ras, Rap and Ral G proteins), cytoskeletal rearr ...
... control for most G-protein-regulated pathways. The array of cellular activities regulated by GEFs reflects the functional diversity of G proteins themselves; hence, various GEFs are involved in transcriptional regulation (by modulating the activity of Ras, Rap and Ral G proteins), cytoskeletal rearr ...
Tumor Necrosis Factor- alpha (human, recombinant) CATALOG NO
... SUPPLIED AS: Sterile, filtered white lyophilized powder. The protein was lyophilized after extensive dialysis against 5mM Tris buffer pH 8.0. 10mg of HSA was added per mg TNF-alpha. RECONSTITUTION: Reconstitute the lyophilized TNF-alpha in sterile water to a concentration of 100µg/ml or higher, whic ...
... SUPPLIED AS: Sterile, filtered white lyophilized powder. The protein was lyophilized after extensive dialysis against 5mM Tris buffer pH 8.0. 10mg of HSA was added per mg TNF-alpha. RECONSTITUTION: Reconstitute the lyophilized TNF-alpha in sterile water to a concentration of 100µg/ml or higher, whic ...
proteins: three-dimensional structure
... than the 3.6 residues per turn of a standard a helix, the two keratin helices are inclined about 18° relative to one another, resulting in the coiled coil arrangement. This conformation allows the contacting side chains to interdigitate (Fig. 6-14b). The higher order structure of a keratin is not we ...
... than the 3.6 residues per turn of a standard a helix, the two keratin helices are inclined about 18° relative to one another, resulting in the coiled coil arrangement. This conformation allows the contacting side chains to interdigitate (Fig. 6-14b). The higher order structure of a keratin is not we ...
Side chains are negatively charged
... due to ionization of COOH group to COO- -- need to put them in an acid solution to shift equilibrium and balance this charge (side chain is charged +) Basic (Arg, Lys and His) has pI >7 (charged -) All others have uncharged side chains (pl. in 5-6) ...
... due to ionization of COOH group to COO- -- need to put them in an acid solution to shift equilibrium and balance this charge (side chain is charged +) Basic (Arg, Lys and His) has pI >7 (charged -) All others have uncharged side chains (pl. in 5-6) ...
Bioinformatics of proteins: Sequence, structure and the `symbiosis
... E.g. the biological process hexose biosynthetic process has two parents, hexose metabolic process and monosaccharide biosynthetic process. biosynthetic process is a type of metabolic process and a hexose is a type of monosaccharide. When any gene is involved in hexose biosynthetic process, it is aut ...
... E.g. the biological process hexose biosynthetic process has two parents, hexose metabolic process and monosaccharide biosynthetic process. biosynthetic process is a type of metabolic process and a hexose is a type of monosaccharide. When any gene is involved in hexose biosynthetic process, it is aut ...
Protein Analysis - GRiSP Research Solutions
... Western blotting is a widely-used analytical technique for the study of proteins. This method, first described by Towbin, et. al1, allows for the detection of a single protein within a mixture of proteins derived from a biological sample. The specificity of Western blotting is achieved by using an a ...
... Western blotting is a widely-used analytical technique for the study of proteins. This method, first described by Towbin, et. al1, allows for the detection of a single protein within a mixture of proteins derived from a biological sample. The specificity of Western blotting is achieved by using an a ...
The Illinois Bio-Grid: A Software Framework for Industry
... The Purpose of Mass Spectrometry in Proteomics • Identify and sequence all proteins involved in an organism’s biology. • Use this knowledge to identify proteins (or peptides) that can be used to study and understand different biological states. • Correlate protein expression levels to biological fun ...
... The Purpose of Mass Spectrometry in Proteomics • Identify and sequence all proteins involved in an organism’s biology. • Use this knowledge to identify proteins (or peptides) that can be used to study and understand different biological states. • Correlate protein expression levels to biological fun ...
7. Lipidic metabolism in parasitic platyhelminthes
... Lipids are a highly diverse and heterogeneous group of compounds, with crucial roles in cellular structure and metabolism. They are major components of cell membranes and important energy reserves. Lipids also play important roles in enzyme regulation, cell surface recognition, cell interaction, sur ...
... Lipids are a highly diverse and heterogeneous group of compounds, with crucial roles in cellular structure and metabolism. They are major components of cell membranes and important energy reserves. Lipids also play important roles in enzyme regulation, cell surface recognition, cell interaction, sur ...
02_Murray - Sbkb.org
... Discriminate whether START domains bind cholesterol or PC (PI) or other ligands Provide leads for chemical library studies for function-interfering compounds Detailed computational analysis and function annotation Fine-grain structure analysis in the absence and presence of potential ligand Experime ...
... Discriminate whether START domains bind cholesterol or PC (PI) or other ligands Provide leads for chemical library studies for function-interfering compounds Detailed computational analysis and function annotation Fine-grain structure analysis in the absence and presence of potential ligand Experime ...
The Pros and Cons of Electrostatic Interactions
... and repulsive forces such as: • ion-ion • ion-dipole • dipole-dipole • H-bonding (= special case of dipole dipole) • cation- and anion--interactions • --stacking interaction • hydrophobic contacts • dispersion interactions Each of these interactions has ist unique properties, e.g.: • H-bonds are ...
... and repulsive forces such as: • ion-ion • ion-dipole • dipole-dipole • H-bonding (= special case of dipole dipole) • cation- and anion--interactions • --stacking interaction • hydrophobic contacts • dispersion interactions Each of these interactions has ist unique properties, e.g.: • H-bonds are ...
Protein Sorting to the Storage Vacuoles of Plants: A Critical Appraisal
... Proteins targeted to the LV of plant cells require sequence-specific vacuolar sorting determinants (ssVSD), most commonly of the NPIR type which are usually (but not always) located toward the N-terminus (10). These are recognized by members of the BP-80 family of VSRs (11). The lumenal domain of pe ...
... Proteins targeted to the LV of plant cells require sequence-specific vacuolar sorting determinants (ssVSD), most commonly of the NPIR type which are usually (but not always) located toward the N-terminus (10). These are recognized by members of the BP-80 family of VSRs (11). The lumenal domain of pe ...
Electrophoretic Properties of Native Proteins
... Proteins exhibit many different three-dimensional shapes and complex folding patterns which are determined by their amino acid sequence and post translational processing such as adding carbohydrate residues or prosthetic groups. The precise three-dimensional configuration of a protein is critical to ...
... Proteins exhibit many different three-dimensional shapes and complex folding patterns which are determined by their amino acid sequence and post translational processing such as adding carbohydrate residues or prosthetic groups. The precise three-dimensional configuration of a protein is critical to ...
1 Chapter 3: Chemistry of Water Polar covalent bonds within water
... -Always around a C = C bond -A cis isomer has the same atoms attached to double-bonded carbons on the same side of the double bond (see figure 4.7 in the book) -A trans isomer has these atoms on opposite sides of the double bond. Enantiomers are isomers that are mirror images of each other around an ...
... -Always around a C = C bond -A cis isomer has the same atoms attached to double-bonded carbons on the same side of the double bond (see figure 4.7 in the book) -A trans isomer has these atoms on opposite sides of the double bond. Enantiomers are isomers that are mirror images of each other around an ...
An operon encoding a novel ABC-type transport
... three ORFs (orfl, orf2 and orf3), probably organized in a single transcriptional unit, were found. The nucleotide sequence of or-7, or--2 and orf3 is given in Fig. 2. The 804 bp long orfl potentially codes for a protein of 268 amino acids whereas orf2 is 702 bp in length (protein of 234 amino acids) ...
... three ORFs (orfl, orf2 and orf3), probably organized in a single transcriptional unit, were found. The nucleotide sequence of or-7, or--2 and orf3 is given in Fig. 2. The 804 bp long orfl potentially codes for a protein of 268 amino acids whereas orf2 is 702 bp in length (protein of 234 amino acids) ...
Unit 1.1 Building Blocks of Life The student knows the significance of
... The student knows the significance of various molecules involved in metabolic processes and energy conversions that occur in living organisms. The student is expected to: ...
... The student knows the significance of various molecules involved in metabolic processes and energy conversions that occur in living organisms. The student is expected to: ...
Bchm2000_P1 - U of L Class Index
... the column. Thus, smaller solutes are retarded relative to larger solutes which do not enter the pores. (27) The unknown protein must be exposed to conditions that (1) disrupt quaternary structure and (2) maintain quaternary structure. SDS-PAGE in the presence of reducing agent (2-mercaptoethanol) w ...
... the column. Thus, smaller solutes are retarded relative to larger solutes which do not enter the pores. (27) The unknown protein must be exposed to conditions that (1) disrupt quaternary structure and (2) maintain quaternary structure. SDS-PAGE in the presence of reducing agent (2-mercaptoethanol) w ...
Chemistry: Biological Molecules (GPC)
... system may contain thousands of dierent proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence. The functions of proteins are very diverse because the ...
... system may contain thousands of dierent proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence. The functions of proteins are very diverse because the ...
Degradation signals within both terminal domains of the cauliflower
... Protein degradation plays an important role in many cellular processes: it allows much faster alteration of the amount of regulatory proteins than transcriptional or translational regulation, and is important for the relocation of biochemical resources. Although protein degradation has not been exte ...
... Protein degradation plays an important role in many cellular processes: it allows much faster alteration of the amount of regulatory proteins than transcriptional or translational regulation, and is important for the relocation of biochemical resources. Although protein degradation has not been exte ...
Document
... • Discontinuous buffer system – different buffer is used in the electrode chambers from that in the gel ...
... • Discontinuous buffer system – different buffer is used in the electrode chambers from that in the gel ...
Protein–protein interaction
Protein–protein interactions (PPIs) refer to physical contacts established between two or more proteins as a result of biochemical events and/or electrostatic forces.In fact, proteins are vital macromolecules, at both cellular and systemic levels, but they rarely act alone. Diverse essential molecular processes within a cell are carried out by molecular machines that are built from a large number of protein components organized by their PPIs. Indeed, these interactions are at the core of the entire interactomics system of any living cell and so, unsurprisingly, aberrant PPIs are on the basis of multiple diseases, such as Creutzfeld-Jacob, Alzheimer's disease, and cancer.PPIs have been studied from different perspectives: biochemistry, quantum chemistry, molecular dynamics, signal transduction, among others. All this information enables the creation of large protein interaction networks – similar to metabolic or genetic/epigenetic networks – that empower the current knowledge on biochemical cascades and disease pathogenesis, as well as provide putative new therapeutic targets.