The composition and structure of proteins. Types of bonds in molecules of proteins.

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Protein structure is the biomolecular structure of a protein molecule. Each protein is a polymer – specifically a polypeptide – that is a sequence formed from various L-α-amino acids (also referred to as residues). By convention, a chain under 40 residues is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations, driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is the topic of the scientific field of structural biology, which employs techniques such as X-ray crystallography, NMR spectroscopy, and dual polarisation interferometry to determine the structure of proteins.

Protein structures range in size from tens to several thousand residues ^[1] Proteins are classified by their physical size asnanoparticles (definition: 1–100 nm). Very large aggregates can be formed from protein subunits: for example, many thousand actinmolecules assemble into a microfilament.

Proteins are composed of a linear (not branched and not forming rings) polymer of amino acids. The twenty genetically encoded amino acids are molecules that share a central core: The α-carbon is bonded to a primary amino (-NH₂) terminus, a carboxylic acid (-COOH) terminus, a hydrogen atom, and the amino acid side chain, also called the "R-group". The R-group determines the identity of the amino acid. In an aqueous solution, at physiological pH (~6.8), the amino group will be in the protonated -NH₃⁺ form, and the carboxylic acid will be in the deprotonated -COO^-form, forming a zwitterion. Most amino acids that make up proteins are L-isomers, although a few exotic creatures use D-isomers in their proteins. It is important to note that levorotatory (L) and dextrorotatory (D) are not specific to rectus (R) and sinister (S) configurations. A levorotatory form of a protein can be either R or S configuration. Levorotatory and dextrorotatory refer to how the proteins bend light in a polarimeter.

A. Ionic Bonds - Salt Bridges
Ionic bonds are formed as amino acids bearing opposite electrical charges are juxtaposed in the hydrophobic core of proteins. Ionic bonding in the interior is rare because most charged amino acids lie on the protein surface. Although rare, ionic bonds can be important to protein structure because they are potent electrostatic attractions that can approach the strength of covalent bonds. In the model peptide, a negatively charged O on the sidechain of asp¹⁹⁴ lies 2.8 Å from the positively charged N on the amino terminus of chain B (ile¹⁶).

B. Water Shells and Charged Surface Residues
Electrically charged amino acids, mostly found on protein surfaces, promote appropriate folding by interacting with the water solvent. Polar water molecules can form shells around charged surface residue sidechains, helping to stabilize and solubilize the protein. Here, electrostatic interactions between electronegative oxygens of two H₂O's and the positively charged NH3's on the sidechains of lys²⁰² and lys²⁰³ are shown:.

C. Hydrogen Bonds
When two atoms bearing partial negative charges share a partially positively charged hydrogen, the atoms are engaged in a hydrogen bond (H-bond). The correct 3-D structure of a protein is often dependent on an intricate network of H-bonds. These can occur between a variety of atoms, involving:

atoms on two different amino acid sidechains
atoms on amino acid sidechains and water molecules at the protein surface
atoms on amino acid sidechains and protein backbone atoms
backbone atoms and water molecules at the protein surface
backbone atoms on two different amino acids

Examples of several of these types of H-bonds may be illustrated using amino acids of the model peptide (hydrogens not shown).

Ser¹⁹⁵ in the model peptide is positioned to interact with his⁵⁷ through a hydrogen bond, its sidechain -O sharing a hydrogen with a nitrogen (N) on the sidechain ring of his⁵⁷.

Gly¹⁹³ provides an H-bond acceptor (its backbone carboxy oxygen) and his⁴⁰'s sidechain provides an -NH donor, forming a hydrogen bond.

Asp²⁰⁴ contains a sidechain C=O (-) group that can accept a hydrogen from a solvent H₂O at the protein surface.

Most of the H-bonds in a protein are between backbone N-H and C=O groups in either alpha helices or beta sheets. The model peptide (residues 193-204) is a beta strand that is extensively H-bonded to an adjacent, antiparallel beta strand (residues 205-214). Here, two H-bonds between backbone atoms in leu¹⁹⁹ and gly²¹¹ are shown.

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