Protein structure

Protein structure is the three-dimensional arrangement of atoms in a protein. It is described at primary, secondary, tertiary, and, for multi-subunit proteins, quaternary levels.

Amino acid: An organic molecule containing amino and carboxyl groups; amino acids are the subunits linked in proteins. A protein’s primary structure is its ordered chain of amino acids.
Protein folding: The process by which a polypeptide adopts a defined three-dimensional structure. It describes how a sequence acquires the arrangement represented by protein structure.
X-ray crystallography: A method for determining atomic structures by analyzing X-ray diffraction from a crystal. It has provided many high-resolution protein structures from ordered crystals.
Protein dynamics: The motions and conformational changes that proteins undergo over time. A single structural model captures only part of proteins’ changing conformational behavior.
Peptide bond: A covalent bond linking the carboxyl group of one amino acid to the amino group of another. These bonds connect residues into the chain whose sequence defines primary structure.
Hydrogen bond: An attractive interaction involving a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom. Backbone hydrogen bonds stabilize helices and sheets, while other interactions shape folds.
Nuclear magnetic resonance spectroscopy: A method that uses nuclear magnetic properties to determine molecular structure and dynamics in solution. It can characterize protein structures and motions without requiring crystals.
Protein misfolding: The adoption of a non-native protein conformation that can impair function or promote aggregation. It shows how departures from a functional structure can damage cells or form aggregates.
Protein primary structure: The linear amino-acid sequence of a protein, including the positions of covalent links such as disulfide bonds. It is the first level in the structural hierarchy and constrains later folding.
Hydrophobic effect: The tendency of nonpolar groups in water to cluster, reducing their exposure to the surrounding solvent. It often drives nonpolar side chains toward the interior of soluble proteins.

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