PyMOL Modelling Workshop Outline of PyMOL usage
... • generate -> symmetry mates -> within 4 Å • note that several surrounding molecules are now present and we need to figure out which is the correct one ◦ take note of the contacts between them ◦ re-color the original structure red and turn on and off the symmetry related objects until you find the s ...
... • generate -> symmetry mates -> within 4 Å • note that several surrounding molecules are now present and we need to figure out which is the correct one ◦ take note of the contacts between them ◦ re-color the original structure red and turn on and off the symmetry related objects until you find the s ...
The DsbA Signal Sequence Directs Efficient
... protein folding pathway, assembles into its stable three-dimensional structure before it has a chance to be exported by the Sec pathway. However, Jonda et al. (11) reported that with an analogous fusion in which the signal sequence of DsbA (a periplasmic disulfide bond oxidoreductase) (DsbAss) is fu ...
... protein folding pathway, assembles into its stable three-dimensional structure before it has a chance to be exported by the Sec pathway. However, Jonda et al. (11) reported that with an analogous fusion in which the signal sequence of DsbA (a periplasmic disulfide bond oxidoreductase) (DsbAss) is fu ...
No Slide Title
... • Model applied to other cell types and conditions • These are predictions - No experimental data from the ‘test’ cell type is used (unless stated otherwise) • Model parameters are fixed unless stated otherwise ...
... • Model applied to other cell types and conditions • These are predictions - No experimental data from the ‘test’ cell type is used (unless stated otherwise) • Model parameters are fixed unless stated otherwise ...
Supplemental figure legends13092010HM
... both negative stain and cryo-EM maps using the fit-in-map module of the Chimera program (Goddard et al, 2007) starting from different initial positions. The best fits were then further refined within the cryo-EM map using simulated annealing rigidbody dynamics as implemented in the Flex-EM program ( ...
... both negative stain and cryo-EM maps using the fit-in-map module of the Chimera program (Goddard et al, 2007) starting from different initial positions. The best fits were then further refined within the cryo-EM map using simulated annealing rigidbody dynamics as implemented in the Flex-EM program ( ...
Engineering Tyrosine-Based Electron Flow Pathways in Proteins
... 1. INTRODUCTION In a recent article, Gray and Winkler have reviewed electron flow through metalloproteins pointing out the role played by certain aromatic amino acid residues (Tyr, Trp) that are capable of acting as redox intermediates.1 An important issue addressed by these authors is the mechanism ...
... 1. INTRODUCTION In a recent article, Gray and Winkler have reviewed electron flow through metalloproteins pointing out the role played by certain aromatic amino acid residues (Tyr, Trp) that are capable of acting as redox intermediates.1 An important issue addressed by these authors is the mechanism ...
Interplay of pH and Binding of Multivalent Metal Ions: Charge
... theory.21 The association of salt counterions with inversely charged side chains at the protein surface seems to be the dominant effect and is suggested as the basic model for ionprotein interaction.22 Ion association has been identified to occur mainly at hydrophilic sites surrounded by hydrophobic s ...
... theory.21 The association of salt counterions with inversely charged side chains at the protein surface seems to be the dominant effect and is suggested as the basic model for ionprotein interaction.22 Ion association has been identified to occur mainly at hydrophilic sites surrounded by hydrophobic s ...
Macromolecules in Biological System.doc
... - A good learning objective describes, when possible, the conditions under which a learner must perform a task. - A good learning objective, when possible, clarifies how well the student must perform a task, in order for the performance to be acceptable. Attached, is Bloom’s taxonomy (Annex 3). It p ...
... - A good learning objective describes, when possible, the conditions under which a learner must perform a task. - A good learning objective, when possible, clarifies how well the student must perform a task, in order for the performance to be acceptable. Attached, is Bloom’s taxonomy (Annex 3). It p ...
Drosophila ventral furrow morphogenesis: a
... obtain relatively pure populations of ventral and lateral cells, genetically ventralized and lateralized embryos were used (St. Johnston and Nüsslein-Volhard, 1992; Ferguson and Anderson, 1992). Females that were heterozygous for Tl10b (Tl10b/+) produced ventralized embryos. Females that were hetero ...
... obtain relatively pure populations of ventral and lateral cells, genetically ventralized and lateralized embryos were used (St. Johnston and Nüsslein-Volhard, 1992; Ferguson and Anderson, 1992). Females that were heterozygous for Tl10b (Tl10b/+) produced ventralized embryos. Females that were hetero ...
WAVE/Scars in platelets
... Ectopic expression of WAVEs and interacting proteins in Cos7 cells The full-length cDNA3,29 of human WAVE/Scars (WAVE1 [Genbank Accession no. D87459 as KIAA0269], WAVE2 [AB026542], and WAVE3 [AB026543]) was subcloned into FLAG-tagged pBluescript and then constructed in the pEF-BOS vector.29,30 Human ...
... Ectopic expression of WAVEs and interacting proteins in Cos7 cells The full-length cDNA3,29 of human WAVE/Scars (WAVE1 [Genbank Accession no. D87459 as KIAA0269], WAVE2 [AB026542], and WAVE3 [AB026543]) was subcloned into FLAG-tagged pBluescript and then constructed in the pEF-BOS vector.29,30 Human ...
INVESTIGATION INTO THE ALLOSTERIC REGULATION OF MITOTIC KINESIN EG5 Introduction Results
... are likely contingent upon the different modes of contact to the L5 pocket. The pathway of allosteric inhibition is conserved. The long distance allosteric network observed originally in Eg5 is conserved in Klp61F. The networks of amino acid residues involved in allosteric communication between the ...
... are likely contingent upon the different modes of contact to the L5 pocket. The pathway of allosteric inhibition is conserved. The long distance allosteric network observed originally in Eg5 is conserved in Klp61F. The networks of amino acid residues involved in allosteric communication between the ...
Glycoblocks: a schematic three-dimensional
... green, mannose; yellow, galactose; see Fig. 1) and identifies the different sugar types by altering each block’s shape (e.g. square, amino sugars; diamond, acidic sugars; or a white hexagon for unknown sugars; see Fig. 1), with and bonds being depicted as dashed and continuous lines respectively ...
... green, mannose; yellow, galactose; see Fig. 1) and identifies the different sugar types by altering each block’s shape (e.g. square, amino sugars; diamond, acidic sugars; or a white hexagon for unknown sugars; see Fig. 1), with and bonds being depicted as dashed and continuous lines respectively ...
e. Reference States are critical for the application of empirical
... for all types of residue pairs are given in the Appendix in Table IV.6.A1. Energy values throughout this section are given in dimensionless RT units, unless otherwise stated. For this reference state, the opposite charge interactions are the most favored pairs and the hydrophobic pairs exhibit quite ...
... for all types of residue pairs are given in the Appendix in Table IV.6.A1. Energy values throughout this section are given in dimensionless RT units, unless otherwise stated. For this reference state, the opposite charge interactions are the most favored pairs and the hydrophobic pairs exhibit quite ...
Enzymes: “Helper” Protein molecules
... sucrase breaks down sucrose Oh, I get it! They end in -ase ...
... sucrase breaks down sucrose Oh, I get it! They end in -ase ...
the chemistry of life: organic and biological chemistry
... as in acetylene (C 2H 2). In aromatic hydrocarbons the carbon atoms are connected in a planar ring structure, joined by both O" and 1T bonds between carbon atoms. Benzene (C 6H 6 ) is the best-known example of an aromatic hydrocarbon. Alkenes, alkynes, .and aromatic hydrocarbons are called unsaturat ...
... as in acetylene (C 2H 2). In aromatic hydrocarbons the carbon atoms are connected in a planar ring structure, joined by both O" and 1T bonds between carbon atoms. Benzene (C 6H 6 ) is the best-known example of an aromatic hydrocarbon. Alkenes, alkynes, .and aromatic hydrocarbons are called unsaturat ...
Noni Juice - Healthoracle.org
... This claim and the following are continually used to market noni juice: the claim that noni juice is pharmacologically inactive unless taken on an empty stomach because a proenzyme susceptible to pepsin is needed to convert proxeronine to xeronine; the claim that each body tissue has cells that cont ...
... This claim and the following are continually used to market noni juice: the claim that noni juice is pharmacologically inactive unless taken on an empty stomach because a proenzyme susceptible to pepsin is needed to convert proxeronine to xeronine; the claim that each body tissue has cells that cont ...
Robust circadian clocks from coupled protein
... of fully phosphorylated KaiC into the PPC. (B) PPC-in vitro model: Only the PPC is present, and the concentration of each Kai protein is constant. (C) PPCin vivo model: Only the PPC is present, but all Kai proteins are now continually synthesized and degraded, with rates that are constant in time. ( ...
... of fully phosphorylated KaiC into the PPC. (B) PPC-in vitro model: Only the PPC is present, and the concentration of each Kai protein is constant. (C) PPCin vivo model: Only the PPC is present, but all Kai proteins are now continually synthesized and degraded, with rates that are constant in time. ( ...
Protein translocation channel of mitochondrial inner
... We reasoned that if all important protein–protein interactions of Tim44 are mediated by its N-terminal domain and the only function of the C-terminal domain is to recruit Tim44 to the membrane, then a construct consisting of the N-terminal domain, extended to include the membrane-recruitment helices ...
... We reasoned that if all important protein–protein interactions of Tim44 are mediated by its N-terminal domain and the only function of the C-terminal domain is to recruit Tim44 to the membrane, then a construct consisting of the N-terminal domain, extended to include the membrane-recruitment helices ...
of Pseudomonas aeruginosa - BMC Microbiology
... challenge. The resistance of this opportunist pathogen to β-lactam antibiotics is determined mainly by production of the inactivating enzyme AmpC, a class C cephalosporinase with a regulation system more complex than those found in members of the Enterobacteriaceae family. This regulatory system als ...
... challenge. The resistance of this opportunist pathogen to β-lactam antibiotics is determined mainly by production of the inactivating enzyme AmpC, a class C cephalosporinase with a regulation system more complex than those found in members of the Enterobacteriaceae family. This regulatory system als ...
Small-Angle X-ray Scattering SAXS vs. X
... • RG is highly shape‐dependent and a poor measure of molecular weight (volume) measure of molecular weight (volume). • RG2 corresponds to the average square distance of each scatterer (electron) from the center of the molecule. • Sphere of radius r has ...
... • RG is highly shape‐dependent and a poor measure of molecular weight (volume) measure of molecular weight (volume). • RG2 corresponds to the average square distance of each scatterer (electron) from the center of the molecule. • Sphere of radius r has ...
Diapositiva 1
... Role of the hedgehog protein in the hedgehog signaling pathway > To become an active ligand requires: > > Autoprocessing reaction > > Palmitoylation of the most amino-terminal cysteine > Once released into the extracellular environment, interacts with different proteins in multimeric form > Targets ...
... Role of the hedgehog protein in the hedgehog signaling pathway > To become an active ligand requires: > > Autoprocessing reaction > > Palmitoylation of the most amino-terminal cysteine > Once released into the extracellular environment, interacts with different proteins in multimeric form > Targets ...
iii. acidic and basic properties of amino acids
... • At physiologic pH (≈7.4), the carboxyl group is dissociated, forming the negatively charged carboxylate ion (– COO–), and the amino group is protonated (– NH3+) • In proteins, almost all of these carboxyl and amino groups are combined through peptide linkage and, in general, are not available for ...
... • At physiologic pH (≈7.4), the carboxyl group is dissociated, forming the negatively charged carboxylate ion (– COO–), and the amino group is protonated (– NH3+) • In proteins, almost all of these carboxyl and amino groups are combined through peptide linkage and, in general, are not available for ...
collagen - MBBS Students Club
... acid content of collagen followed by hydroxyproline and proline account for another one-third of amino acid content of collagen. ...
... acid content of collagen followed by hydroxyproline and proline account for another one-third of amino acid content of collagen. ...
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.