Multiple choice

PDB is an important data archive for protein structures and their structural information. Majority of structures available are obtained from X-ray crystallography. PDB file contains the coordinate information of the atoms including their spatial organisation. The water molecules are represented as HETATM (heteroatoms to the primary structure), which denotes the atoms that are not primary to the structure of the protein, i.e. non-main chain atoms.

During molecular dynamics studies of biological proteins, these PDB files are used. The protein structures need to be normalised before subjecting them to actual simulation process, so non-required information is discarded from PDB files. Majority of water molecules are removed but at certain places, water is retained. Why are selective water molecules retained?

  1. Because water is life and it is required to stabilise the protein activity

  2. Because water molecules act as space fillers owing to their small size

  3. Because water molecules are used in crystallisation process to stabilise the protein structure

  4. Because water is very essential to protein function without which it cannot be simulated

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C Correct answer
Explanation

In a PDB file, the water atom is represented as ‘HOH’ that symbolises its arrangement of atoms. In crystallisation, water exists as water of crystallisation, where water is added to the protein to stabilise the crystal. Proteins are charged molecules and are localised in the cell where water is the solvent. So, in order to maintain its folded structure, water forms hydrogen bonds and therefore, water is added to stabilise the structure outside of the cell. During simulation process, the water which acts as a solvent can be removed but the water molecules present as water of crystallisation cannot be removed. 

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