By Shuchi Giridha
Proteins, ‘the building blocks of life’, are made up of amino acids which is in turn made up of nitrogen,
carbon, hydrogen, and oxygen. To carry out its biological functions, proteins twist and turn into
complete 3D figures. Only 20 of the 500 types of amino acids that have been identified in nature are
present in the proteins in our body, but these 20 types of amino acids form thousands of different
types of proteins, some short and some long in terms of their structure.
What are protein structures?
A primary protein structure is the linear sequence of amino acids in a protein. It is the 3D
arrangement of atoms in an amino acid chain. Proteins are polypeptides which are formed from
sequences of amino acids, which are the monomers of polymer. Peptides are short chains of amino
acid chained together by peptide bonds. Polypeptides are a longer, continuous peptide chain. Poly
peptides containing more than 50 amino acids are classified as proteins. A monomer is a molecule
that can interact with other monomer molecules. The secondary structure is a sub structure on the
actual polypeptide backbone chain. Then comes the tertiary structure which is the 3D structure
created by a single protein molecule. A quaternary structure is one consisting of the aggregation of
two or more individual polypeptide chains.
Why is studying protein structures important?
Knowing the structures of proteins can help scientists have a better understanding of the proteins
in our body. This allows to create conclusions on how to affect, modify and even control it. The
function of a protein is defined by the order of atoms in the structure of a protein. With the knowledge
of a structure, you could predict molecules that bind to a protein.
Why is studying protein structures difficult?
For studying a protein structure in detail, you need money, expertise, a lot of time and a lot more luck. The cost of solving a new protein structure can sum up to a whopping $100,000, and that’s just the tip of the iceberg. It can take years to solve a protein structure and even a small mistake can make you start over and set you back by years of research. Now let’s talk about the method. There are three experimental methods, namely, X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy, that are currently used to define the structure of a protein. X-ray crystallography is the method used to determine the atomic and Molecular structure of a crystal. Protein X-ray crystallography is a method used to define the 3D structure of a particular protein. NMR spectroscopy can be used to obtain knowledge about the structure and dynamics of proteins, it can also be used on nucleic acid and its complexes. Electron microscopy can be used to obtain high resolution images of specimens.
What has AI achieved?
Whenever we talk of AI, we think of a robot making things easier for us, but AI has also sped up
things that took years for scientists to infer earlier – the structures of proteins in this case. Google’s
Deep Mind has predicted the 3D structures of proteins. In a protein-structure prediction challenge
called Critical Assessment of Structure Prediction (CASP) Alpha fold, one of Deep Mind’s programs
outperformed 100 other teams in the event.
How does this achievement help scientists?
With this achievement the process of protein structure prediction can be done without having to
spend all your money and time on this. Scientists can spend more time on other important things.
The difficulties in the process are also lessened. This achievement helps in many fields including
drug discovery, since 80% of drugs work on proteins.