Srivatsan Raman from University of Wisconsin-Madison lectured on the developments of protein science and new computational techniques. Protein science is entering an exciting new phase enabled by major advances in computational and experimental methods. Computational protein modeling has achieved unprecedented accuracy in predicting protein structures at atomic-level accuracy, and designing proteins as biocatalysts, with new binding partners (protein-protein, protein-DNA, protein-ligand) and self-assembling materials.

On the experimental side, with next generation technologies to synthesize and sequence DNA, we can evaluate millions of protein designs in a single tube, and quantify function by high-throughput sequencing. By combining computational modeling and high-throughput experiments, we can design, build and test a large number of candidates, and select the best performing design.

Biosensors are genetically encoded sensors that are specific to the target molecule and report concentration in each cell, allowing us to select the highest producer by high-throughput sorting or genetic selection.

Run Rosetta protein structure prediction simulations and analyze the results

The homework for this week is to run an ab initio folding algorithm in Rosetta software suite and compare the resulting models to native structure.

  • 1) Plot the score (or energy) vs rms plot. Rms stands for root mean square deviation. These are two columns in the score.fsc file. Compare that with the energy vs rms plots I showed in my slides.

  • 2) Pick the lowest energy model and structurally compare it to the native. How close is it to the native? If its different, what parts did the computer program get wrong? You'll have to compare the structures using a Viewer like pymol or chimera or rasmol.

  • 3) Pick the lowest rms model and structurally compare it to the native. How close is it to the native? If its different, how is it different? Remember that in a blind case, we will not have the benefit of an rms column.

    Selecting a protein to perform ab initio folding

    Generate models using AbInitio folding in Rosetta

    Native conformation of the protein in PyMol viewer.

    Energy vs RMS plot of 100 generated models.

    Comparison of minimum energy structure to native.

    Comparison of minimum rms structure to native.