10 Protein Folding

Since Anfinsen’s famous experiments in the 1960s, it has been known that the complex three‐ dimensional structure of protein molecules is encoded in their amino acid sequences, and the chains autonomously fold under proper conditions. Cracking this code, which is sometimes called ‘‘the second part of the genetic code,’’ has been one of the greatest challenges of molecular biology. Although a full understanding of how proteins fold remains elusive, theoretical and experimental studies of protein folding have come a long way since Anfinsen’s findings. In the living cell, folding occurs in a complex and crowded environment, often involving helper proteins, and in some cases it can go awry: the protein can misfold, aggregate, or form amyloid fibers. It is increasingly recognized that misfolded proteins and amyloid formation are the root cause of a number of serious illnesses including several neurodegenerative diseases. Therefore, the study of protein folding remains a key area of biomedical research. List of Abbreviations: AFM, atomic force microscopy; CCP, chaperonin‐containing TCP‐1; CIDNP, chemically induced nuclear polarization; DMD, discrete molecular dynamics; EM, electron microscopy; ESIMS, electrospray ionization mass spectrometry; FIS, factor for inversion stimulation; FMN, flavin mononucleotide; NOE, nuclear Overhauser effect; TF, trigger factor; TCP‐1, tailless complex polypeptide‐1 1 Protein Structure and Its Physical Basis The function of a protein can only be interpreted from its structure. The nervous system is a network of cells, and the peculiar functional properties of these cells can be derived from the properties and interactions of their proteins. Proteins are involved in all stages of neural activity. Those embedded wholly or partly in membranes regulate the transport of ions and molecules as a means of signal exchange with other cells and the external medium. Some of them have enzymatic functions to catalyze the chemical processes essential for function. The diverse and highly specific function of proteins is a consequence of their sophisticated, individual surface pattern regarding shape, charge, and hydrophobicity. The surface pattern is a consequence of the unique three‐dimensional structure of the polypeptide chain. Proteins are linear polymers with nonrepetitive, specific covalent structure. The covalent structure is determined by the order of amino acids in which they are linked together. Since Anfinsen’s famous experiments (1973) in the 1960s, it has been believed and today generally accepted that folding and the resulting native structure of proteins are autonomously governed and determined by the amino acid sequence of a particular protein and its natural solvent environment. 1.1 Physical Forces and Principles Underlying Protein Folding and Structure A linear polypeptide chain is autonomously organized into a space‐filling, compact, and well‐defined three‐ dimensional structure. In a globular protein, the internal core is mostly formed by hydrophobic amino acid residues, held together by van der Waals forces, and the surface of the globule is formed by mostly charged and polar side chains. Proteins exist in this state of condensed matter while the specific conformation is largely determined by the flexibility of the polypeptide backbone and by the specific, consistent intermolecular interactions of the side chains. The monomeric unit in a polypeptide chain is the peptide group. The sequence of amino acids is the primary structure of the protein. The C, O, N, and H atoms lie in the same plane; successive planes define angles f and c. The conformation of a chain of n amino acids can be defined by 2n parameters. The restricted flexibility of the polypeptide chain is a major factor among those determining protein structure and folding. The native conformation must be energetically stable. From a thermodynamic point of view, the free energy of a protein molecule is influenced by the following major contributions: (1) the hydrophobic effect, (2) the energy of hydrogen bonds, (3) the energy of electrostatic interactions, and (4) the conformational entropy due to the restricted motion of the main chain and the side chains. Protein folding 10 3