Latest
-
2015 Lab Holiday Party
On Friday the 18th we had our lab Holiday party! It was supposed to be ugly sweater attire, but only a few of us came dressed appropriately. Fortunately, more people were proactive when participating in the potluck aspect! We had homemade goodies galore, including a creme caramel that had rave reviews, many delicious cookies, an…
-
Jacob Bale’s Defense
On Thursday, December 17th, Jacob Bale defended and passed with flying colors! To celebrate, we had various kinds of ice cream floats; some of his family members who attended the defense even joined us in enjoying the sweet treats. We look forward to seeing what Jacob will do in the future. Congratulations! [envira-gallery id=”628″]
-
Halloween party pictures!
Back in October, the Baker lab threw a party to celebrate “All Hallows Eve”! Costume was encouraged, but not required, though a contest was held for best group outfit and best solo outfit. The gang from “Inside Out” made an awesome showing, and all five emotions were present. There was also a battle of good…
-
Large-scale determination of previously unsolved protein structures using evolutionary information
The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test…
-
Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces
We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the seventeen 2D layer groups, the degrees of freedom of the lattice are sampled to identify configurations with shape-complementary interacting surfaces, and the interaction energy is minimized using sequence design calculations. We…
-
Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement
We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced…
-
Trapping a transition state in a computationally designed protein bottle
The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed…
-
Computational protein design enables a novel one-carbon assimilation pathway
We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one–carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixation pathway, the formolase pathway, consisting of a small number of thermodynamically favorable chemical transformations that convert formate into a three-carbon sugar in central metabolism. The formolase pathway is predicted to use carbon more…