Structure

The amino acid sequence of a protein determines its three-dimensional shape.

The structure of a protein can be described in several levels. The summaries below are based on definitions found in:

• Primary structure - the linear sequence of residues (amino acids) in a polypeptide chain.
• Secondary structure - the arrangement of a polypeptide chain into more or less regular hydrogen-bonded structures -- has two basic elements --
  • Alpha helix - spiral configuration of a polypeptide chain with 3.6 residues (amino acids) per turn. The helix may be left-handed or right-handed, and the latter is more common.
  • Beta strand - two adjacent polypeptide strands that are bonded together. Two or more strands may interact to form a beta sheet.
• Tertiary structure - the level of protein structure at which an entire polypeptide chain has folded into a three-dimensional structure. In multi-chain proteins, the term tertiary structure applies to the individual chains.
• Quaternary structure - the fourth order of complexity of structural organization exhibited by protein molecules, and refers to the arrangement in space of the complete protein, without regard to the internal geometry of the subunits. Quaternary structure is possessed only when the molecule is made of at least two subunits that are separable.

The three-dimensional structure of a protein is determined by techniques such as X-ray crystallography and nuclear magnetic resonance (NMR).

Scientists who determine the structure of a proteins deposit their data into a database such as Protein Data Bank (PDB). A structure record shows the three-dimensional coordinates of every atom in the molecule.

The Molecular Modeling Database (MMDB) at NCBI is derived from PDB, and includes the three-dimensional coordinates of every atom, as well as an explicit chemical graph showing which atom is bonded to which. The stucture records can be imported into a three-dimensional structure viewing program, such as Cn3D, Rasmol, or Kinemage, where the molecule can be turned and viewed in various renderings.

Sources:  image from the National Human Genome Research Institute (NHGRI) Talking Glossary of Genetic Terms; definitions from the Oxford Dictionary of Biochemistry and Molecular Biology (1997) by Smith, A.D., et al., eds.