Armed with a growing library of protein structures and decreasing costs of ever-
ID: 181606 • Letter: A
Question
Armed with a growing library of protein structures and decreasing costs of ever-more-powerful computers, biochemists can now attempt to solve protein structures computationally. This software takes the amino acid sequence and runs folding simulations. Each simulation calculates the free energy for that conformation. The process is repeated until the software fails to identify a conformation of a lower free energy. This final conformation is deemed the lowest free conformational energy for the given polypeptide. Using computational biochemistry software, you find a predicted structure for your protein of interest. Using this prediction, you identify a potential binding site for a drug that is known to bind your protein of interest. However, when you mutate the putative binding site in the protein, you find no effect on the binding of drug, indicating that the software has failed to find the native structure for your protein of interest. Identify whether each of the following statements is a likely or an unlikely reason for the failure of the software to determine the native structure. Drag the appropriate items to their respective bins.
The protein has many different The software identified an alternate The software was trapped in a local conformations of similar low free minimum, e.g. a folding biological conformation of the protein, only one of which binds the intermediate. energy, e.g. a misfolded aggregate. drug. The amino acid sequence alone is not The protein represents a new fold that sufficient to specify its native was previously unidentified. structure. Yes: Likely reason for the failure No: Unlikely reason for the failure reset helpExplanation / Answer
Answer:
MOST LIKELY REASON FOR FAILURE:
- The software was trapped in a local minimum i.e a folding intermediate
- The protein has many different confirmation of similar low free energy, only one of which binds to the drug
UNLIKELY REASON FOR FAILURE:
-The software identified an alternative biological confirmation of the protein i.e misfolded aggregation.
- The protein represents a new fold that was previously unidentified
- The aminoacid alone is not sufficient to specify its nature structure
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