(7) The smallest independently folding protein domain we know of is called the t
ID: 87706 • Letter: #
Question
(7) The smallest independently folding protein domain we know of is called the trp cage. Download structure 1L2Y into pymol. Use the intermolecular forces that you learned in class to tabulate all of the energies involved in its folding – the hydrophobic effect, hydrogen bonds, polar interactions, configurational entropy, etc – and predict the folding energy. Show your work. The more detail you use the higher your score will be.
(https://www.ncbi.nlm.nih.gov/Structure/pdb/1L2Y)
(http://isiknowledge.com/)
Explanation / Answer
Answer:
The three main questions which arise in computational simulations of protein folding processes are questions of structure, thermodynamics and kinetics.
The following equation represents the local electrostatic term, a hydrogen-bond term and an effective hydrophobic attraction:
E = Eev+ Eloc + Ehb+ Ehp
The simulation is carried out using protein folding and aggregation program PROFASI which works on the above mentioned equation.
The free energy landscape of IL2Y is characterized by a funnel-like topology around a dominating minimum. This indicates a broad native attractor basin. This topology indicates that there is synchronization between the collapse of the protein chain and helix formation. The first molecule is the -helical 1 L2Y with one extra turn of the -helix.
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