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 …

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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!

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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 …

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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 …

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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 …

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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 …

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Control of repeat-protein curvature by computational protein design

Shape complementarity is an important component of molecular recognition, and the ability to precisely adjust the shape of a binding scaffold to match a target of interest would greatly facilitate the creation of high-affinity protein reagents and therapeutics. Here we describe a general approach to control the shape of the binding surface on repeat-protein scaffolds …

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