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Chapter written by Sylvain GERBER and Yoland SAVRIAMA.
2
Impact of a Point Mutation in a Protein Structure
2.1. Composition
Proteins are involved in most cellular functions at all levels, from DNA duplication to chemical metabolism, cell structuring and signal transmission. Despite their very varied activities, these molecules are quite homogeneous: proteins1 are polymers composed of 20 base units, the amino acids (or residues when polymerized). The latter are composed of a central carbon atom (Cα) linked to an amino group (NH2), a carboxylic group (COOH), a hydrogen atom and one of 20 different chemical groups called “side chains” (Figure 2.1). Residues and their different chemical functions allow the functional diversity of proteins. In the polypeptide chain, the α-carboxylic group of an amino acid is linked to the α-amino group of the next amino acid through an amide bond (peptide bond −CO−NH−, Figure 2.2). Most natural proteins contain between 50 and 2,000 amino acid residues. The unbranched chain of residues is oriented: it starts at the amino end (N-terminal) and ends at the carboxy end (C-terminal). The chain of atoms regularly repeating the peptide bonds is called the “peptide backbone”. The peptide bond is rigid and flat because of the partial double bond character of the −CO−NH− bond, but rotations are possible around the other bonds of the backbone.
Proteins can be roughly divided into four classes according to their morphology: globular proteins, which are in an aqueous environment, fibrous proteins, which form large aggregates and mostly constitute the cytoskeleton, membrane proteins and so-called “disordered” proteins, which are generally small and have no inherent fixed structure. Here, we will only discuss the first category of proteins, which are the globulars.
Figure 2.1. a) General structure of an amino acid; b) chemical formula of leucine
Figure 2.2. A polypeptide consisting of four amino acids (tetrapeptide)
2.2. Folding
Proteins adopt a specific spatial organization, most often called a “structure”. This structure is crucial for their function. This relationship between structure and function, established by Emil Fisher at the end of the 19th century, is the foundation of structural biology. Methods used for determining the structure of proteins have evolved considerably, but the method of choice remains as X-ray diffraction, which requires the protein to be crystallized. The data bank listing protein structures (as well as nucleic acids and some sugars) is the PDB (Protein Data Bank) (Berman et al. 2000). The number of resolved protein structures is growing rapidly from year to year. A protein could theoretically adopt a large number of three-dimensional conformations, but most of them spontaneously fold into a particular and unique stable form. This particular shape is due to the fact that the peptide backbone groups and side chains interact with each other and with water. Thus, some conformations have more stabilizing interactions than others and are therefore favored (Alberts et al. 1994). The paradigm of the relationship between the protein sequence and its three-dimensional (3D) structure comes from Christian Anfinsen’s studies on ribonuclease (Anfinsen 1973). Anfinsen showed that proteins isolated in solution can regain their original active conformation after denaturation. Therefore, the conclusion was that all the information needed to fold a protein must be inherent to its amino acid order (Alberts et al. 1994). Other studies have also drawn the same conclusions, leading to the general theory that the amino acid sequence of a protein specifies its conformation (Stryer 1994).
“Water-soluble” proteins fold into a compact globular form (unlike fibrous, membrane and “disordered” proteins). The hydrophobic nature of certain amino acids makes this compact folding necessary. Indeed, the side chains of the non-polar residues are hydrophobic and are grouped together within the globular structure of the protein – isolated from the surrounding water – while the