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What determines the three dimensional structure of a protein?
A protein is a polymer composed of a sequence of amino acids bonded by peptide bonds. These amino acids form peptide chains, with lengths varying from a few to thousands of monomer constituents; this is the basic protein subunit, called the primary structure. However, peptide chains do not remain linear unless so maintained chemically. Instead, there are several forces which determine in what way a particular sequence of amino acids will fold, although ultimately the vast majority of proteins take the form which minimises its free energy, i.e. the conformation which is the most thermodynamically stable. Peptide chains can fold a finite number of ways into secondary and tertiary structures, and peptide chains may come together to form a quaternary structure. Secondary structure is the name given to the initial protein folding pattern, where bonds and folds occur between residues near to each other in the primary sequence, resulting in a peptide chain repeatedly and regularly folded. There are three main elements of secondary structures: alpha helices, beta pleated sheets and loops. Alpha helices arise when there are certain angles of the covalent bonds in the amino acids, which twist the structure such that there exists a complete turn every 3.6 amino acids along with a rise of 1.5A, resulting in a helix 5 to 40 residues long. Sometimes a helices coil together to form a coiled-coil structure. Beta pleated sheets form from several strands of adjacent amino acid chains, running in parallel or antiparallel directions and held together by hydrogen bonds (discussed later). Loops are less uniformly structured segments of the peptide, which are found at the ends of a protein or which join two other elements, such as the portion between two a helices, and they also form the extremes of beta pleated sheets as strands double back on themselves. The tertiary structure of a protein can be defined as the spatial arrangement of all secondary elements, and thus is the shape of the whole peptide chain. The first factor determining the folding of a peptide into secondary and tertiary structures is the shape of the amino acids themselves. There are steric constrictions placed on the angles along which the chains can lie; obviously two atoms cannot occupy the same space. This has a huge effect on a helices, which are very rarely left-handed due to potential steric clashes of side groups. Every residue contains at least one double bond, that which joined the carbon to the oxygen in the acid terminus. Because of the electron arrangements in double bond, they are inflexible and no rotation can occur around them; the same in the case of the C-N peptide bonds. Some amino acids, such as tryptophan, contain aromatic rings as well as double bonds, and these rigid structures limit the shape that part of the peptide chain can assume. Weak non-covalent bonds, present in large amounts between many amino acids in a peptide, have a combined strength enough to also determine a protein's folded shape. These forces hold a helices, b sheets and tertiary structures together. They include ionic interactions, which arise between amino acids with charged side chains, such as histidine and glutamic acid. Also called electrostatic interactions, these can arise between two charged groups, a charge and a dipole, or two dipoles, and often aid tertiary and quaternary structures because they are strong over relatively long distances. equation Another bond type which reinforces structures is van der Waals' forces, or instantaneous dipole-dipole interactions. The dipoles arise from the mobile nature of electron clouds, and are stronger over shorter distances (provided atoms are not so close that their electron clouds repel each other) so this force tends to favour molecules which are of a regular or linear enough shape to pack closely together. Hydrogen bonds are also very important for maintaining protein structure as they are the main bonds between the turns in a helices (where every N-H and C=O of the peptide groups are usually hydrogen bonded), as well as stabilising back bones by linking R-groups together and forming beta sheets (where hydrogen bonds are present between the N-H and C=O
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