99. Contact map distance matrix of a protein provides a two-dimensional view of a three dimensional structure of a protein. How can you obtain a proper three-dimensional structure from the contact map?
(a) Directly from the contact map by mapping the distance on the sequence,
(b) The contact map and secondary structure prediction tools are simultaneously used to generate the 3D structure,
(c) Using contact map along with computational modelling techniques like simulated annealing,
(d) Using the contact map to generate Ramachandran plot for the protein which will provide the 3D structure

Detailed Explanation:

A contact map is a 2D representation of a protein’s 3D structure that displays whether two residues (amino acids) are in close proximity to each other in the folded structure. It helps in understanding the spatial arrangement of amino acids, and can be used as a starting point in predicting the full three-dimensional structure of the protein.

However, converting a contact map into an actual 3D structure is a complex task. While the contact map shows which amino acids are near each other, it does not provide the detailed spatial information required for a complete 3D structure. This is where computational techniques come in.

How to Obtain the 3D Structure:

The process of generating a 3D structure from a contact map typically involves advanced computational methods, including:

1. Simulated Annealing:

   • This is a popular computational technique used to model protein folding. Simulated annealing helps optimize the conformation of the protein by minimizing energy states based on the contact map.

   • The algorithm simulates the gradual cooling of the system (protein structure) to find a stable, low-energy conformation that fits the contact map.

2. Computational Modeling:

   • Techniques like molecular dynamics simulations, energy minimization, and other modeling approaches are used in conjunction with the contact map to predict the protein’s exact 3D structure.

3. Secondary Structure Prediction:

   • In some cases, secondary structure prediction tools (e.g., for helix, sheet, and loop structures) are combined with the contact map and used to refine the 3D structure.

Conclusion:

The most effective way to derive a 3D protein structure from a contact map is by using computational modeling techniques such as simulated annealing, which optimizes the folding process. Therefore, option (c) is the correct answer.