Deep architectures for protein contact map prediction
... Protein residue-residue contact prediction is the problem of predicting whether any two residues in a protein sequence are spatially close to each other in the folded 3D structure. For a protein of N amino acids, the contact map is an NxN matrix C whose elements are by: ...
... Protein residue-residue contact prediction is the problem of predicting whether any two residues in a protein sequence are spatially close to each other in the folded 3D structure. For a protein of N amino acids, the contact map is an NxN matrix C whose elements are by: ...
Hidden Markov models for detecting remote protein homologies
... where aij=Pr[entering state j at time t+1| in state i at time t] B=output probabilities={bj(k)}, where bj(k)=Pr[producing vk at time t | in state j at time t] ...
... where aij=Pr[entering state j at time t+1| in state i at time t] B=output probabilities={bj(k)}, where bj(k)=Pr[producing vk at time t | in state j at time t] ...
proteomics - Sigma
... of a potentially exposed, immunogenic internal sequence for antibody generation. Surface regions or regions of high accessibility often border helical or extended secondary structure regions. In addition, sequence regions with b-turn or amphipathic helix character have been found to be antigenic. Pe ...
... of a potentially exposed, immunogenic internal sequence for antibody generation. Surface regions or regions of high accessibility often border helical or extended secondary structure regions. In addition, sequence regions with b-turn or amphipathic helix character have been found to be antigenic. Pe ...
Seminar L11- Laboratorija za molekularno biologijo in
... This thermophoretic movement is determined by the entropy of the hydration shell around the molecules. Microscale Thermophoresis allows quantification of binding affinities of protein-, nucleic acid- and small molecule-interactions. The steep microscopic temperature gradient is generated by an IR-La ...
... This thermophoretic movement is determined by the entropy of the hydration shell around the molecules. Microscale Thermophoresis allows quantification of binding affinities of protein-, nucleic acid- and small molecule-interactions. The steep microscopic temperature gradient is generated by an IR-La ...
Protein Structure
... α-helix • R groups perpendicular to helix • To right is view down helix axis • AA close in primary sequence of protein not necessarily close in final structure • AA far away in primary often close in final structure ...
... α-helix • R groups perpendicular to helix • To right is view down helix axis • AA close in primary sequence of protein not necessarily close in final structure • AA far away in primary often close in final structure ...
Chapter 8: CELL MEMBRANE
... ● Phospholipids are amphipathic molecules, containing hydrophobic and hydrophilic regions ...
... ● Phospholipids are amphipathic molecules, containing hydrophobic and hydrophilic regions ...
Chapter 8: CELL MEMBRANE
... ● Phospholipids are amphipathic molecules, containing hydrophobic and hydrophilic regions ...
... ● Phospholipids are amphipathic molecules, containing hydrophobic and hydrophilic regions ...
Chemical reaction
... • Polar nature of water causes water molecules to be attracted to each other. • This attraction: hydrogen bond. ...
... • Polar nature of water causes water molecules to be attracted to each other. • This attraction: hydrogen bond. ...
Structural Studies of DsbA and its Putative Partner, VKOR, in
... be re-oxidized by its putative partner, vitamin K epoxide reductase (VKOR). The intent of this study is to further investigate the molecular determinants of the interactions between DsbA and VKOR by X-ray crystallography. In order to achieve this, DsbA crystals were grown in order to be soaked with ...
... be re-oxidized by its putative partner, vitamin K epoxide reductase (VKOR). The intent of this study is to further investigate the molecular determinants of the interactions between DsbA and VKOR by X-ray crystallography. In order to achieve this, DsbA crystals were grown in order to be soaked with ...
Structural Genomics - University of Houston
... Electrostatics, hydrogen bonds and van der Waals forces hold a protein together. Hydrophobic effects force global protein conformation. ...
... Electrostatics, hydrogen bonds and van der Waals forces hold a protein together. Hydrophobic effects force global protein conformation. ...
mcnair 2003 poster template
... suspended in a solution containing primary antibody (ligand). In our case this antibody recognizes the intermediate chain of dynein. The beads are coated with a specific protein to which the antibody tail binds. Next the beads are added to Xenopus egg extract, which contains the target protein. The ...
... suspended in a solution containing primary antibody (ligand). In our case this antibody recognizes the intermediate chain of dynein. The beads are coated with a specific protein to which the antibody tail binds. Next the beads are added to Xenopus egg extract, which contains the target protein. The ...
Escherichia coli
... Due to hydrophobic and amphiphilic nature Less than 1% of high resolution 3D structures known ...
... Due to hydrophobic and amphiphilic nature Less than 1% of high resolution 3D structures known ...
BCH 201 B
... - Combination of these elements : Variety of chemical structure & reactivity - Compound representing all three states of matters (gases, liquid and solids) are present in living cells : • Gas : Nitric Oxide (NO) in the brain – for biological regulation ...
... - Combination of these elements : Variety of chemical structure & reactivity - Compound representing all three states of matters (gases, liquid and solids) are present in living cells : • Gas : Nitric Oxide (NO) in the brain – for biological regulation ...
primary structure
... • If for some reason a protein’s shape is altered, it can no longer function – Denaturation will cause polypeptide chains to unravel and lose their shape and, thus, their function – Proteins can be denatured by changes in salt concentration and pH ...
... • If for some reason a protein’s shape is altered, it can no longer function – Denaturation will cause polypeptide chains to unravel and lose their shape and, thus, their function – Proteins can be denatured by changes in salt concentration and pH ...
blumberg-lab.bio.uci.edu
... comparing with an independent yeast two-hybrid project that used different strategies ...
... comparing with an independent yeast two-hybrid project that used different strategies ...
Techniques in Protein Biochemistry
... A density gradient is formed in a centrifuge tube, and a mixture of proteins in solution is placed on top of the gradient. To identify the estradiol receptor, the protein mixture is first incubated with radioactive estradiol, which is readily detected. Only the estradiol receptor will bind to t ...
... A density gradient is formed in a centrifuge tube, and a mixture of proteins in solution is placed on top of the gradient. To identify the estradiol receptor, the protein mixture is first incubated with radioactive estradiol, which is readily detected. Only the estradiol receptor will bind to t ...
21. Membranes
... increased motor proteins, and steroids to act as a fluidity buffer. ii. By the same token, warmer temperatures will encourage saturated hydrocarbons, etc… iii. The ultimate advantage in this evolutionary arms race is the ability to change the construction of the membrane seasonally. C. Proteins 1. P ...
... increased motor proteins, and steroids to act as a fluidity buffer. ii. By the same token, warmer temperatures will encourage saturated hydrocarbons, etc… iii. The ultimate advantage in this evolutionary arms race is the ability to change the construction of the membrane seasonally. C. Proteins 1. P ...
Chemistry of Life
... Unsaturated fatty acids have some single Covalent bonds but have double covalent bonds as well, like Linoleic acid Plant oils ...
... Unsaturated fatty acids have some single Covalent bonds but have double covalent bonds as well, like Linoleic acid Plant oils ...
FIGURE LEGENDS FIGURE 9.1 Overview of G
... FIGURE 9.4 (A) G proteins are held in an inactive state because of very high affinity binding of GDP to their α subunits. When activated by agonist, membrane-bound seven helical receptors (Fig. 9.4 right, glowing magenta) interact with heterotrimeric G proteins (α, amber; β, teal; γ, burgundy) and s ...
... FIGURE 9.4 (A) G proteins are held in an inactive state because of very high affinity binding of GDP to their α subunits. When activated by agonist, membrane-bound seven helical receptors (Fig. 9.4 right, glowing magenta) interact with heterotrimeric G proteins (α, amber; β, teal; γ, burgundy) and s ...
realburn
... The kinetics of protein denaturation is affected by so many different factors: density, solvent, bond strengths, interactions with surrounding molecules. ...
... The kinetics of protein denaturation is affected by so many different factors: density, solvent, bond strengths, interactions with surrounding molecules. ...
Proteins
... Protein Functions Signal transduction Transcription regulation Immune response Other vital cellular actions ...
... Protein Functions Signal transduction Transcription regulation Immune response Other vital cellular actions ...
Cyclol
The cyclol hypothesis is the first structural model of a folded, globular protein. It was developed by Dorothy Wrinch in the late 1930s, and was based on three assumptions. Firstly, the hypothesis assumes that two peptide groups can be crosslinked by a cyclol reaction (Figure 1); these crosslinks are covalent analogs of non-covalent hydrogen bonds between peptide groups. These reactions have been observed in the ergopeptides and other compounds. Secondly, it assumes that, under some conditions, amino acids will naturally make the maximum possible number of cyclol crosslinks, resulting in cyclol molecules (Figure 2) and cyclol fabrics (Figure 3). These cyclol molecules and fabrics have never been observed. Finally, the hypothesis assumes that globular proteins have a tertiary structure corresponding to Platonic solids and semiregular polyhedra formed of cyclol fabrics with no free edges. Such ""closed cyclol"" molecules have not been observed either.Although later data demonstrated that this original model for the structure of globular proteins needed to be amended, several elements of the cyclol model were verified, such as the cyclol reaction itself and the hypothesis that hydrophobic interactions are chiefly responsible for protein folding. The cyclol hypothesis stimulated many scientists to research questions in protein structure and chemistry, and was a precursor of the more accurate models hypothesized for the DNA double helix and protein secondary structure. The proposal and testing of the cyclol model also provides an excellent illustration of empirical falsifiability acting as part of the scientific method.