Up to now, proteins have essentially been studied with respect to their catalytic properties as well as to the general structure of each type. Imaging by, e.g. X-ray crystallography gives information about the three dimensional structure of a protein at a resolution which allows individual atoms to be distinguished. However, this image acquisition technique has limitations. Some proteins cannot be crystallised, or the crystallisation takes long time (weeks or months). Moreover, X-ray crystallography gives only one example how the subunits of a protein are related to each other, i.e. one example of all the existing conformations.
State of the art image acquisition techniques nowadays allows for imaging of individual proteins by using electron microscopes. The protein is imaged from several different angles and a three dimensional, so called cryo-electrontomography (cryo-ET), image is generated. Cryo-ET gives an image of the protein with lower resolution than if X-ray crystallography is used. Still the resolution is high enough to distinguish the subunits of the protein and to measure how the subunits are related to each other. Moreover, cryo-ET has the advantages that the protein does not need to by crystallised, i.e. a small amount of material is required for the analysis, and that individual proteins can be imaged. This opens up for a new and interesting research area where we can study the shape of individual proteins of a specific type and draw conclusions about its flexibility and how it effect its function. We can say that we study individual proteins from a structural point of view.
The amount of data which is generated by cryo-ET is large. To handle these data, advanced tools are required. One such a tool is computerised image analysis, which allows us to objectively and quantitatively extract measurements of the relations between the subunits of a specific protein. The measurements can then be used to create models on how flexible the protein is. The models can be related to the function of the protein and thereby give a better understanding of the biology behind.
In this lecture I will focus of my part of the above described research, i.e. how to extract quantitative measurements on protein flexibility from cryo-ET images. It is an interesting topic not only with respect to the specific application but also from an image analysis point of view. In cryo-ET images, the protein is represented by a rather small number of image points, which makes shape analysis difficult. The electron microscope images, used to generate a cryo-ET image, are collected by aiming an electron beam towards the sample and then using a detector which register the number of electrons which passes through the sample in the various points on the detector. This results in an image of the density in each point of the sample. Only a low dose of electrons can be used in order to not destroy the structure of the protein. For this reason, the contrast in cryo-ET images is low, which is something that also makes the analysis difficult.
Computerised image analysis is used in many applications. Often the same type of methods can be used for different problems. To point out this, I will round off the lecture by showing examples from a completely different application, namely quantitative measurement of the three dimensional structure of paper and wood fibre composite materials.
Comment: The docent lecture was held in swedish.