4 Structure Determination

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics. The main emphasis of this work is to provide a background on experimental techniques for protein structure determination. The focus is set on X-ray crystallography and Nuclear Magnetic Resonance spectroscopy (NMR), which are by far the main methods used to determine the structure of soluble proteins. We will also introduce cryogenic Electron Microscopy (cryo-EM) and electron diffraction which are more suited to analyze membrane proteins and larger protein complexes. At the end, more qualitative techniques are summarized that are used to obtain insight on the overall structure and dynamics of proteins. Note that this introduction to protein structure determination aims at familiarizing the reader to different experimental techniques, their benefits and bottlenecks, but that a thorough mathematical and technical description of the concept is beyond the scope of this work.