Mountains: Faith and Hope

Dale E. Tronrud

Member of the Coronavirus Structural Task Force
Contact me at

X-ray crystallography is a technique where a crystal of a material is illuminated by a beam of x-rays. The scattering of those x-rays are measured and used to determine the arrangement of atoms in that crystal. The methods for determining the structure of large molecules, such as proteins and DNA, are of particular interest to me.I have developed a number of novel methods, written papers describing them, and incorporated these ideas into the TNT refinement package. Unfortunately quite a few of my ideas have been implemented in TNT without ever having been written up in papers. It's my own fault, of course.


I have worked on a number of crystal structures myself. Not many, but they are good ones. Using data collected by Roger Fenna and Mike Schmid, I refined a model for the FMO protein from the Green Sulfur Bacteria formerly known as Prosthecochloris aestuarii 2K. This 1.9 Å model stood as the highest resolution model of a chlorophyll containing protein until 2004. In 2009 I published and deposited a 1.3 Å model of this same protein (PDB code: 3EOJ) and regained the title of highest resolution chlorophyll containing protein.


Since none of the refinement programs available in the 1980's could handle the complexities of a bacteriochlorophyll-a molecule I needed to use Lynn Ten Eyck's TNT refinement program, which is how I got into that business.


I have also worked on a number of inhibitor complexes with the endopeptidase Thermolysin. Thermolysin was a great system to work with because one could soak in rather large inhibitors (the equivalent of four amino acids in size). We worked with a variety of inhibitors to probe various ideas for the design of better inhibitors, and by analogy, better drugs.


While I had been working in Brian Matthews' lab for many years, that lab shut down in 2009. I worked for Andy Karplus at Oregon State University for the next seven years. The main thrust of my work there was the exploration of the practical consequences of using his new library of standard values for bond lengths and angles in the peptide backbone.


I'm currently working on projects of my own. I have collected a lot of ideas over the years and now seems a good time to work through them and get them published (if they end up making sense!). The list includes quite a number of ideas for improving the crystallographic part of refinement, but I intend to contine some of the conformation-dependent stereochemical restraint work I started in the Karplus Lab.

Near the start of the pandemic in 2020 I signed up with the Coronavirus Structural Task Force. This is a group of structural biologists who are organizing, assessing, correcting, and distributing information about the SARS-CoV-2 virus. I have done some work on various parts of NSP3 but also pontificate on the ugly and dark history of protein crystallography.

I am maintaining connections to labs both at the University of Oregon and Oregon State University, despite the general animosity felt by the alumni of those two institutions.



TNT is a package of programs used to optimize the fit of a model of a protein/nucleic acid to X-ray diffraction data while maintaining quality bond lengths, angles, and other good things.

Method Papers

Structure Papers

PhD Thesis

PowerPoint Presentations

Copyright 2021 by Dale E. Tronrud.