Macromolecular Crystallographic Computing

Macromolecular Crystallographic Computing

Kostas Bethanis (Agricultural University of Athens, Greece), Petros Giastas (Hellenic Pasteur Institute, Greece), Trias Thireou (Agricultural University of Athens, Greece) and Vassilis Atlamazoglou (Agricultural University of Athens, Greece)
DOI: 10.4018/978-1-60566-768-3.ch001
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Abstract

Structural genomics or structural proteomics can be defined as the quest to obtain the three-dimensional structures of all proteins. Single-crystal X-ray crystallography provides the most direct, accurate and in most of the cases the only way of forming images of macromolecules. Using crystallography, threedimensional images have been made of thousands of macromolecules, especially proteins and nucleic acids. These give detailed information about their activity, their mechanism for recognizing and binding substrates and effectors, and the conformational changes which they may undergo. This chapter presents the basic crystallographic procedure steps and a thorough survey of the computational software used most frequently by protein X-ray crystallographers. The determination of the structure of 2[4Fe-4S] ferredoxin from Escherichia coli. is examined as a case study of implementation of these steps and programs. Finally, some of the perspectives of the field of computational X-ray crystallography are noted showing the future developments in the ceaseless evolution of new methods and proliferation of new programs.
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Single Crystal X-Ray Crystallography: The Basic Steps

Crystallography provides the most direct way of forming three-dimensional images of molecules. The most common experimental means of obtaining a detailed model of a large molecule, allowing the resolution of individual atoms, is to interpret the diffraction of X-rays from many identical molecules in an ordered array like a crystal. This method is called single-crystal X-ray crystallography. The three-dimensional structures of macromolecules, especially proteins and nucleic acids, give detailed information about their activity, their mechanism for recognizing and binding substrates and effectors, and the conformational changes which they may undergo. They show graphically the evolutionary relationships between molecules from widely separated systems and they give a wide view of the resemblances between different proteins, showing strong links in three-dimensional structure where the relationship between amino-acid sequences has dwindled to insignificance (Blow D., 2002).

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