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In some cases, both hydrophilic and hydrophobic properties occur in a single molecule. An example of these amphiphilic molecules is the lipids that comprise the cell membrane . Another example is soap , which has a hydrophilic head and a hydrophobic tail, allowing it to dissolve in both water and oil.
An ubiquitous example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. The simplest case is a pair of water molecules with one hydrogen bond between them, which is called the water dimer and is often used as a model system. When more molecules are present, as is ...
The beta sheet (β-sheet, also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino ...
The tertiary structure of a protein consists of the way a polypeptide is formed of a complex molecular shape. This is caused by R-group interactions such as ionic and hydrogen bonds, disulphide bridges, and hydrophobic & hydrophilic interactions. Protein tertiary structure is the three-dimensional shape of a protein.
The strand order in this barrel (GFP) is: 1 6 5 4 9 8 7 10 11 3 2. The inter-strand hydrogen bonds can be summarised in a table. Each column contains the residues in one strand (strand 1 is repeated in the last column). The arrows indicate the hydrogen bonds that were identified in the figures.
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).
In chemistry, a hydroxy or hydroxyl group is a functional group with the chemical formula −OH and composed of one oxygen atom covalently bonded to one hydrogen atom. In organic chemistry, alcohols and carboxylic acids contain one or more hydroxy groups. Both the negatively charged anion HO−, called hydroxide, and the neutral radical HO ...
A transmembrane domain (TMD) is a membrane-spanning protein domain. TMDs may consist of one or several alpha-helices or a transmembrane beta barrel. Because the interior of the lipid bilayer is hydrophobic, the amino acid residues in TMDs are often hydrophobic, although proteins such as membrane pumps and ion channels can contain polar residues.