Using Crystallographic Data To Facilitate Students’ Discovery of How Protein Models Are Produced—An Activity Illustrating the Effect of Resolution on Model Quality

Abstract

X-ray crystallography is a core technique underpinning many important results in the field of biochemistry. Although most biochemists will not become experts in this technique, many will use the structural models deposited in the protein data bank for designing and interpreting other experiments. Since there are a number of limitations to these models, it is important that undergraduate biochemists, as potential end-users of this technique, have some understanding of how these models are produced. A computer activity is described in which the program WinCoot is used to build part of a protein model to interpret an electron density map. This activity allows students to experience the nature of crystallographic data first-hand and discover how protein structural models are produced.

Understanding Structure: A Computer-Based Macromolecular Biochemistry Lab Activity

“…Another lab activity intended to introduce students to model building using Coot focuses on the effect of map resolution on rebuilding. 7 As map resolution is not addressed in the lab activity presented in this paper, the resolution-focused activity could be used complementarily if attention to resolution is desired as well. The other available model building lab activities are designed to be completed over multiple lab periods, taking several weeks to complete.…”

“…Lysozyme has long been used as a model to give students an introduction to the process of protein purification, structure investigation, and crystallization with protocols available in the literature − and in some textbooks. Exercises for undergraduates exploring the final stages of model building and refinement, − which are equally as important, are not as ubiquitous. Of the few available, most are intended to take several weeks to complete. , …”

An All‐Inclusive and Straightway Laboratory Activity to Solve the Three‐Dimensional Crystal Structure of a Protein

“…Several articles can be found in the educational literature on protein crystallization [2][3][4][5][6], X-ray diffraction [7,8], and structure resolution [9,10]. Usually, these reports deal only with the individual steps, leaving incomplete the workflow performed by protein crystallographers.…”