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:
Smith, A.D., et al., eds. 1997. Oxford Dictionary of Biochemistry and
Molecular Biology. New York: Oxford University Press.
- 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. Quatenary 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 structure
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.
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