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Beta Structures • Anti-parallel b strands are usually arranged in two b-sheets that pack against each other and form a distorted barrel structure, the core of the structure. • Depending on the way the bstrands around the barrel are connected along the polypeptide chain, they can be divided into four major groups: Up-and-down barrel superoxide dismutase (SOD) Greek Key barrel Jelly roll barrel b-helix Up-and-down Barrel • The eight b strands are all antiparallel to each other and are connected by hairpin loops. • Beta strands that are adjacent in the amino acid sequence are also adjacent in the threedimensional structure of up-and-down barrels. Green Fluorescent Protein from Aequorea victoria (jellyfish) 11-stranded b-barrel with central -helix chromophore formed during folding (from residues S65, Y66, G67) is contained in the middle of the barrel contains 1 Trp, 10 Tyr Many current uses as reporters of gene expression and biosensors. Excitation 395 nm and 475 nm Emission 506 nm http://www.plantsci.cam.ac.uk/Haseloff/GFP/GFPbackgrnd.html Retinol-binding Protein (RBP) • • • • The structure of human plasma retinol-binding protein (RBP) is an upand-down b barrel. Plasma RBP is a temporary protein that binds and transports a retinol molecule (vitamin A) from the liver to dependent tissues Retinol is bound inside the barrel, between the two b sheets, such that its only hydrophilic part (an OH tail) is at the surface of the molecule. Exhibits only minimal conformational changes in both apo- (open) and holo- (bound) forms. Amino Acid Sequence Reflects b Structure • Amino acid sequence of b strands 2, 3, and 4 in human plasma retinol-binding protein. • The sequences are listed in such a way that residues which point into the barrel are aligned. • These hydrophobic residues form the barrel core, while the remaining residues are exposed to the solvent. Beta Structures Greek Key Motifs• This motif is formed when one of the connections of four antiparallel b strands is not a hairpin connection. • The motif occurs when strand number n is connected to strand n + 3 (a) or n - 3 (b) instead of n + 1 or n - 1 in an eight-stranded antiparallel b sheet or barrel. The two different possible connections give two different hands of the Greek key motif. • In all protein structures known so far, only the hand shown in (a) has been observed. The Fold of IgG Domains • • IgG (immunoglobulin) domains, found in antibodies, incorporate Greek Key motifs. Beta strands labeled A-G of the constant and variable domains of immunoglobulins have the same topology and similar structures. There are two extra b strands, C' and C'' (red) in the variable domain. The loop between these strands contains the hyper-variable region CDR2, which is modified for antigen specificity. The remaining CDR regions are at the same end of the barrel in the loops connecting b strands B and C and strands F and G. Gamma Crystallin Domain • The domain structure of g-crystallin is built up from two b sheets of four antiparallel b strands, sheet 1 from b strands 1, 2, 4, and 7, and sheet 2 from strands 3, 5, 6, and 8. • The b strands are arranged in two Greek key motifs, one (red) formed by strands 1 - 4 and the other (green) by strands 5 - 8. Complete g-crystallin Molecule • The two domains of the complete molecule have the same topology; each is composed of two Greek key motifs that are joined by a short loop region. • There is a greater amino acid sequence identity between the domains than the motifs within each domain, suggesting that the four Greek Key motifs in gcrystallin are evolutionarily related by gene duplication and fusion. Jelly Roll Motifs • The eight b strands are drawn as arrows along two edges of a strip of paper. The strands are arranged such that strand 1 is opposite strand 8, etc.. • These are archael proviruses from the PRD1-Adenovirus lineage. • Usually arranged in 2 sheets. • Can be more than 8 strands, as long as even number. Two-sheet b helix. • Antiparallel sheets. • Each structural unit is composed of 18 residues with a 9 residue consensus sequence Gly-Gly-XGly-X-Asp-X-U-X forming a bloop-b-loop structure, where U is a large hydrophobic residue, often Leu. • Each loop region contains six residues of sequence Gly-Gly-XGly-X-Asp where X is any residue. • Calcium ions are bound to both loop regions by D residues. • G residues provide loop flexibility. X X U U X X Extracellular bacterial proteinase Three-sheet b Helix • As shown in (a), two of the b sheets (blue and yellow) are parallel to each other and are perpendicular to the third (green). In (b), each structural unit is composed of three b strands connected by three loop regions (labeled a, b and c). • Loop a (red) is invariably composed of only two residues, whereas the other two loop regions vary in length. Beta Structures Visualization using Chimera PDBfile 2kfb • “Structure of the cataract causing P23T mutant of human gamma-D Crystallin.” Jung, J. (2009) Biochemistry 48: 2597-2609. PDBfile 4jgf, 1h4a. PDB Species WT / mutant Method 1h4a Human WT Xray 1.15A 2kfb Human P23T NMR 4jgf Human P23T Xray 2.5 A