Structural Cell Biology

We are a research team that is trying to understand the molecular details that determine how, where, and when motor proteins transport intracellular cargo. The past thirty years of cell biology research have set the stage for us to determine the general principles that underlie the complex process of intracellular transport. 

Overaching questions that we are trying to answer (and that keep us up at night):

  • How is specificity determined between motor proteins and cargo?
  • How are the activities of multi-motor complexes regulated? 
  • What are the molecular consequences of neurodegenerative disease-causing mutations? 

We are approaching these questions from a number of different angles, using cryo-electron microscopy, single molecule TIRF, and biochemistry to relate protein structure to its activity in a cell. 

Tool Development for Cryo-Electron Microscopy

As a fast-growing part of structural biology, cryo-electron microscopy (cryo-EM) is determining new and exciting macromolecular structures on a seeminly daily basis. Despite its power, cryo-EM is a field that needs to undergo rapid maturation to allow for new users to come into the fold to solve structures. 

Unlike other structural biology tools, cryo-EM necessarily requires access to high-performance computing capabilites. The large computational workload will limit the throughput and spread of cryo-EM due to users 1) waiting for cluster time or 2) being unable to find a cluster amenable for cryo-EM.

To address these problems, we are building cloud computing resources at Amazon Web Services and the San Diego Supercomputer Center to help give users access to cryo-EM so they can focus on understanding biology instead of dealing with Linux.

In addition to these new software tools, we are also considering new methods that will give un-supervised assessment of single particle electron microscopy data quality, given the large computing resources of the cloud.

The 'cloud' has become an integral part of big data processing across many disciplines. Due to the ever-increasing computational demand of cryo-EM, turning to cloud resources can allow for many users to solve structures as-fast-as-possible without any queueing / wait times.

This website will serve as the central location that will document and update cloud-computing resources available to the cryo-EM community.

The COSMIC² science gateway is a public resource for determining cryo-EM structures that provides a simple web interface to access National Science Foundation XSEDE supercomputing resources.