Undergrads Being Scientists!

On Friday, May 20, 2016, three of our undergrads participated in the 19th annual Undergraduate Research Symposium. Tessa Howard, Kara Lau, and Vanessa Nguyen presented posters on projects/topics stemming from their work done in our labs. We’d like to recognize the excellent job they did on their presentations! Please see below for their titles and …

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De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity

General design principles for protein interaction specificity are challenging to extract. In DNA, specificity arises from a limited set of hydrogen-bonding interactions in the core of the double helix to design and build a wide range of shapes. In proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Protein-based materials …

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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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