A collaborative effort between scientists in the Baker lab and the laboratory of Peter Schultz (The Scripps Research Institute) resulted in a computationally designed protein that was able to kinetically stabilize the conformational transition state of the unnatural amino acid biphenylalanine. This work was published in the journal Science in a manuscript titled “Trapping a transition state in a computationally designed protein bottle“. IPD postdoctoral fellow Dr. Jeremy Mills and Scripps postdoctoral fellow Dr. Aaron Pearson used both computational and experimental approaches to arrive at a protein with high complementarity to the planar, high energy conformation of biphenylalanine. This work will improve efforts to design new enzymes with novel functions.

A trapped transition state of bond rotation about the central bond of biphenyl is illustrated. Computationally designed packing interactions (yellow spheres) between the core of a protein and biphenylalanine (blue spheres) are shown (left). The right panel shows electron density surrounding the planarized biphenyl side chain and surrounding residues.

IPD scientists also published two back-to-back papers in Nature Methods this month – one from the DiMaio lab and one from the Baker lab.

Dr. DiMaio, Baker lab researchers, and collaborators published a manuscript entitled “Atomic-accuracy models from 4.5-A cryo-electron microcopy data with density-guided iterative local refinement“. The authors describe a general approach to refine protein structure models based on cryo-EM data. Cryo-EM is a technique that allows for the observation of proteins in their native environment at extremely low temperatures. This work should significantly improve determination of atomic models from cryo-EM reconstructions.

Graduate student Yu-Ruei Wang and collaborators in the DiMaio lab published a paper “De novo protein structure determination from near-atomic-resolution cryo-EM maps“. Here, the authors describe a de novo model building approach using cryo-EM maps with 3 to 5 angstrom resolution.


IPD Director Dr. David Baker was the plenary speaker and the 2015 AAAS meeting in San Francisco this month. A video of his talk, ‘Evolutionary Biology: Design of Novel Protein Structures, Functions, and Assemblies’ covers a breadth of information on ongoing IPD research and can be viewed here: http://www.aaas.org/annual-meeting/2015/plenaries/post-evolutionary-biology-design-novel-protein-structures-functions-assemblies

Watch a Biophysical Society TV interview with IPD Assistant Professor Dr. Frank DiMaio at the 2015 New & Notable Symposium on his work studying a virus that infects hyperthermophilic archaea by encapsidating A-form DNA:


In line with the IPD Mini Symposia series, several visiting scientists came to the institute to speak about their research and discuss potential collaborations. This month we heard talks from:

Rogier Sanders (University of Amsterdam) – Inducing neutralizing HIV antibodies by soluble cleaved envelope trimers
Jim De Yoreo (Pacific Northwest National Laboratory)- What proteins like to do when they get together (protein interactions and self-assembly, biomineralization)
Sangamo Biosciences – Genome editing with zinc finger nucleases


We have several exciting opportunities for anyone interested in joining the IPD.

We are looking to hire a Senior Computer Specialist to help maintain the reliable, secure, and robust operation of the institute’s UNIX computing servers and networks. This role is crucial for the IPD’s cutting-edge scientific research! For more information please visit www.uw.edu/jobs and search for Requisition number 114020.

The IPD is offering an opportunity for a Practicum Independent Study for a Foster MBA student. An MBA Student is needed to work with IPD leadership to collect market data on  “Small Molecule Binder” applications. The data will be used to build valuation models that will help us to better understand the commercial opportunities for these applications (or others).

More information about both positions can be found on our Employment page.