Recent Advances in Structural Bioinformatics 2007

From the Preface
The first mention of the word protein was from a letter sent by Jöns Jakob Berzelius to Gerhardus Johannes Mulder on 10 July 1838, where he wrote: "The name protein that I propose for the organic oxide of fibrin and albumin, I wanted to derive from p??te???, [protas meaning "of primary importance"] because it appears to be the primitive or principal substance of animal nutrition."

A protein is a complex, high-molecular-mass, organic compound that consists of amino acids joined by peptide bonds. Proteins are essential to the structure and function of all living cells and viruses. Different proteins perform a wide variety of biological functions. Some proteins are enzymes, which catalyze chemical reactions. Other proteins play structural or mechanical roles, such as those that form the struts and joints of the cytoskeleton, which is like a system of scaffolding within a cell. Still more functions filled by proteins include immune response and the storage and transport of various ligands.

Proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids. Thus, proteins are their own polymers, with amino acids being the monomers. We can refer to four distinct aspects of a protein's structure: (i) Primary structure: the amino acid sequence, (ii) Secondary structure: highly patterned sub-structures, (iii) Tertiary structure: the overall shape of a single protein molecule, (iv) Quaternary structure: the shape or structure that results from the interaction of more than one protein molecule, usually called protein subunits in this context, which function as part of the larger assembly or protein complex. The knowledge of protein structures can help in numerous cases, e.g. to annotate unknown function, to understand the function mechanism and so their dysfunctions, to design drugs, to propose new evolutionary prospects... This book is dedicated to the memory of Pr. Serge Hazout. He was an excellent scientist who had worked on numerous subjects such as human genetics, image pattern, sequence alignments, protein docking, protein side chain prediction, and recently developed numerous new approaches dedicated to structural alphabets and microarray data analysis, but more important, he was greatly human. . .