Molecules that do the actual work in your body
Proteins are essential parts of all living organisms. They participate in every process within cells like metabolism, cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins can also have a structural or mechanical functions, such as the proteins in the cytoskeleton that that maintains cell shape. A protein consists of amino acids that are connected by peptide bonds into a long linear chain. The order of the amino acids is encoded in the DNA. After transcription in the nucleus of the cell into RNA the molecule is transported outside the nucleus. Here, the ribosome translates the RNA into protein. Often the protein is chemically altered in post-translational modification: either before the protein can function in the cell, or as part of control mechanisms. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.
The fuction of the protein depends on its structure. This structure can be described on 4 different levels.
- Primary structure: This is only the order of all amino acids in the protein, also known as the sequence of the protein.
- Secondary structure: The long chain of amino acids folds into small, recurring structures. These structures, known as the α-helix and β-sheet are connected by β-turns and coils. They are stabilized by hydrogen bonds.
- Tertiary structure: The overall fold of the protein is known as tertiary structure. The secondary structure elements fold into a complete protein, guided by hydrophopbic interactions, salt bridges and disulfide bonds.
- Quaternary structure: Very often the protein works in a complex with other proteins, this assembly if several proteins is known as the quaternary structure.
The structure defines the function of a protein. A mutation that changes the structure of a protein can also change the its function and this is why mutations often result in diseases.
Many proteins catalyse biochemical reactions. They provide a scaffold where the reaction can take place without be used themselves. Therefore, proteins contain a binding site, also known as the active site of the protein, where the substrate can bind. After substrate binding the reaction takes place, for instance cleavage or phosphorylation. To release the substrate to protein changes it conformation. Therefore, proteins are flexible structures.
Common experimental methods of structure determination include X-ray crystallography and NMR spectroscopy, both of which can produce information at atomic resolution. Solved structures are usually deposited in the Protein Data Bank (PDB), a freely available resource from which structural data about thousands of proteins can be obtained in the form of Cartesian coordinates for each atom in the protein.
There are many more known gene sequences than there are solved protein structures. Further, the set of solved structures is biased toward those proteins that can be easily subjected to the experimental conditions required by one of the major structure determination methods. In particular, globular proteins are comparatively easy to crystallize in preparation for X-ray crystallography, which remains the oldest and most common structure determination technique. Membrane proteins, by contrast, are difficult to crystallize and are underrepresented in the PDB. Structural genomics initiatives have attempted to remedy these deficiencies by systematically solving representative structures of major fold classes. Protein structure prediction methods attempt to provide a means of generating a plausible structure for proteins whose structures have not been experimentally determined.