Structure to Function

Protein Structure-Function Relationships


About Donald S. Berkholz

(you can call me Donnie)

My broad interest is using the intimate relationship between protein structure & function to impact scientific research and improve people’s lives.

Toward that end, I am now learning structure-based drug design at the Mayo Clinic, improving my skills in X-ray crystallography and in better understanding the medical relevance of my research.

My Ph.D. thesis work focused on understanding and leveraging protein structure at atomic resolution. I’ve used a combination of crystallography and computation to pursue this goal.

In one project, analysis of a vast database of nearly 20,000 residues uncovered significant conformation-dependent trends in the backbone’s covalent geometry for all bond angles and lengths. Conformation-dependent averages for the N-Ca-C angle, which varied most dramatically, range from 107°–114° in well-populated regions. Tests suggest that accounting for these systematic variations will improve the accuracy of protein modeling and crystallographic refinement.

In another project, a series of catalytically relevant, atomic-resolution “snapshots” of the flavoenzyme glutathione reductase enabled us to reach numerous insights into how radiation can affect active sites and how exquisitely detailed structural changes can drive catalytic power.

About this blog

Protein structure–function relationships underlie the machinery that drives our bodies, and all living things. My main focus is the intimate yet veiled connection between protein structure and its determination of how proteins function. I also post on related topics, such as the building blocks of protein structure, methods for determining protein structure, molecular biology, and protein biochemistry.


Written by Donnie Berkholz

June 12, 2010 at 3:02 am

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