structural biology

The Scientific Activist

Category archives for structural biology

Last year, I wrote about a scientific controversy over the structure of the influenza M2 proton channel, particularly over the protein’s binding site for adamantane type anti-flu drugs. The Schnell/Chou model, based on solution NMR, had the drug binding to the outside of the channel, within the membrane (at a 4:1 drug:protein ratio). On the…

On Mimicking Phosphotyrosine

When doing science, there’s generally one totally optimal way of performing an experiment. But, there may also be several other less optimal means of gathering similar data, and one of those may be much more feasible than the totally optimal method. As a scientist, you have to determine whether this other method is sufficient, or…

Two New Papers on Integrin Activation

Just as I was in the process of finishing my doctorate in August, I found out that my first first-author paper had been accepted for publication by The EMBO Journal. This was good news, because we were reporting some pretty fundamental findings in a relatively saturated field, and one of our competitors had managed to…

Late last week, I received emails from two journals (The Journal of Biological Chemistry (JBC) and PLoS ONE) indicating that they are now incorporating interactive 3D images of molecular structures in their papers. The atomic coordinates of all published biomolecular structures have been available for some time at the Protein Data Bank. However, making sense…

The winners of this year’s Nobel Prize in Chemistry have been announced, and the prize will be shared equally between Venkatraman Ramakrishnan, Thomas Steitz, and Ada Yonath “for studies of the structure and function of the ribosome.” The information encoded in DNA is decoded to produce functional proteins in two stages: transcription (DNA –> RNA)…

On Wednesday, the CDC reported that influenza A H1N1 viruses from 13 patients with confirmed diagnoses of swine flu had been tested for resistance to a variety of antiviral drugs. The good news was that all of the isolates were susceptible to the antiviral drugs oseltamivir (Tamiflu) and zanamivir (Relenza). However, all 13 were resistant…

Fine-Tuning Cell Adhesiveness

Cells in higher organisms exist in a dynamic environment, requiring the ability to alternately grasp and disengage from the three-dimensional web of their surroundings. One family of proteins in particular, the integrins, plays a key role in this process by acting as the hands of the cell. Spanning the cell membrane, they link the extracellular…

An individual cell inside the human body is in a dynamic environment: it not only has to anchor itself to its surroundings but also be able to communicate with them and respond as appropriate. One group of proteins–the integrins–play a central role in all of these tasks. The integrins are large (about 200,000 Da) membrane-spanning…

The Structure of the Living Cell

One of the goals of modern structural biology is to integrate the two traditionally distinct subfields of structural molecular biology (determination of the structures of macromolecules at atomic resolution) and structural cell biology (general architecture of of the cell and the localization of subcellular structures within it). The end result–as my research advisor at Oxford,…