What is a Protein? – Protein Data Bank/RCSB

Proteins are end products of the Central Dogma of biology. They are essential for cellular structure and function. Proteins have dizzyingly diverse structures. Since the invention of X-ray chrystallography by the Australian physicist William Lawrence Bragg structures of many complex molecules have been resolved including proteins. Solved structures of proteins are deposited in the Protein Data Bank (PDB), a free and curated structural data resource for thousands of biological molecules. These structures are stored in the form of Cartesian coordinates for each atom in the protein. Every structure registered in PDB has a unique four character code. For instance 3J07 is the retrieval code for the multi-subunit (24mer) beta chrystallin protein forming the refractive lens of the cow eye.

Proteins are made up of hundreds or thousands of smaller units called amino acids, which are attached to one another in long chains. There are 21 types of amino acids that can be combined naturally by living organisms. However with the inclusion of new synthetic nucleotide bases into the genetic code this is soon about to change. This means living bodies will not be limited to 21 amino acids and entirely different types of proteins can be synthesized. The sequence of amino acids determines each protein’s unique 3-dimensional structure and its specific function.

Just like everything else science also operates in most economical fashion. It is best to study the “low hanging fruits” first. For example once Central Dogma has been established abundant and easier to isolate mRNA fraction was studied first. As the DNA sequencing technology advanced small RNA species that are harder to detect took the center stage such as the microRNAs. Today we know quite a bit about microRNAs and RNA interference. A similar trend is now happening in the protein front. The attention is turning into previously ignored/unknown peptides called microProteins. These very short peptides lead to post-translational regulation through their short domains that facilitate protein-protein interactions. MicroProteins can disrupt the functions of larger protein complexes both in plant and animal systems.

A less known fact about proteins is the non-ribosomal peptide synthesis common among bacterial and fungal organisms. This way of peptide synthesis can incorporate more than 500 types of amino acids. In this respect non-ribosomal peptide synthesis adds a huge diversity to the repertoire of peptides compared to the ribosomal system limited to 21 amino acids. Check out an excellent review on the enzymes non-ribosomal synthetases facilitating this feat here.