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Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organization of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure ...
Knowledge of the relationship between a protein's structure and its dynamic behavior is essential for understanding protein function. The description of a protein three dimensional structure as a network of hydrogen bonding interactions (HB plot) [12] was introduced as a tool for exploring protein structure and function. By analyzing the ...
L-Ribose Fischer Projection. Ribose is a simple sugar and carbohydrate with molecular formula C 5 H 10 O 5 and the linear-form composition H−(C=O)−(CHOH) 4 −H. The naturally occurring form, d-ribose, is a component of the ribonucleotides from which RNA is built, and so this compound is necessary for coding, decoding, regulation and expression of genes.
The length of the carbonhydrogen bond varies slightly with the hybridisation of the carbon atom. A bond between a hydrogen atom and an sp 2 hybridised carbon atom is about 0.6% shorter than between hydrogen and sp 3 hybridised carbon. A bond between hydrogen and sp hybridised carbon is shorter still, about 3% shorter than sp 3 C-H.
The proximity of the terminal C α atoms often correlates with formation of an inter main chain hydrogen bond between the corresponding residues. Such hydrogen bonding is the basis for the original, perhaps better known, turn definition. In many cases, but not all, the hydrogen-bonding and C α-distance definitions are equivalent.
The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined).
The alpha helix is also commonly called a: Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure); 3.6 13-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen)
In aqueous solution, carbon dioxide forms carbonic acid. CO 2 + H 2 O ⇌ H 2 CO 3. This reaction is very slow in the absence of a catalyst, but quite fast in the presence of the hydroxide ion CO 2 + OH − ⇌ HCO − 3. A reaction similar to this is almost instantaneous with carbonic anhydrase. The structure of the active site in carbonic ...