Protein Folding: Part I—Basic Principles

Abstract

By the early 1900s proteins had been studied for more than a hundred years. Chemists had begun to extract proteins such as albumin and wheat gluten from animals and plants at the beginning of the previous century. The Dutch chemist Gerardus Johannes Mulder (1802–1880) had found that each one of these proteins had nearly the same composition. He thought that all were variations on a single primordial substance composed of carbon, nitrogen, hydrogen, and oxygen with variable amounts of sulfur and phosphorus. In 1838, the Swedish chemist Jöns Jacob Berzelius (1779–1848) coined the name “protein” for this universal substance. These events were followed by groundbreaking investigations carried out in the later 1850s and 1860s by August Kekulé (1829–1896) that helped lay the foundations for structural chemistry and protein science. In his studies, Kekulé uncovered the tetravalent character of carbon, proposed its ability to bond to other carbons in long chains, and discovered the ring structure of benzene.

Appendix 1. X-Ray Crystallography

In their work, the Bragg’s noted that a three-dimensional crystal could be viewed as a set of equidistant parallel planes. In these situations, the conditions for maximal constructive interference are twofold. First the scattering from each plane must be a specular, or mirror, that is, reflection in which the angle of incidence equals the angle of reflection. This situation is depicted in Fig. 2.13. Second the X-ray wavelength λ, distance between parallel planes d, and angle of reflection θ obey the relationship known as Bragg’s law:

Fig. 2.13

The arrangement of crystal planes and the geometry in Bragg’s law

$$ 2d \sin \theta =n\lambda $$

(2.7)

In Eq. (2.7), n is an integer that can take on the values 1, 2, 3, and so on. When n = 1, the spots of light are known as first order reflections, and when n = 2, they are called second order reflections. First order reflections are more intense than second order reflections, and similarly for third and higher order contributions.

In more detail, x-rays are produced whenever swiftly moving electrons strike a solid target. In an X-ray tube, a beam of electrons is generated that strikes a metallic anode (typically copper) to produce an X-ray beam. The X-rays in the beam are scattered by the electron clouds of atoms, particularly by tightly bound electrons near the center of the atoms. Light scattered from single atoms is too weak to observe, but the amount of light can be amplified using purified crystals. In a crystal, large numbers of identical molecules are arranged in a regular lattice. Light passing through a crystal will be scattered in a variety of directions. Spherical wavelets scattered by different atoms will interfere, some constructively and some destructively. For certain wavelengths and scattering directions, the wavelets will be in phase to produce strong constructive interference. Constructive interference taking place between light waves scattered off of the atoms serves to amplify the light, producing a characteristic pattern of light spots and dark areas, a diffraction pattern that can be seen and analyzed to yield information on how the atoms are arranged.

The light spots are produced when the light waves arrive at the detector in phase with one another and thus constructively interfere. In an X-ray diffraction experiment, the intensities and positions of the light spots are recorded. The diffraction patterns are converted into electron density maps through application of a mathematical operation known as a Fourier transform. Several tens of thousands of reflections are collected in a typical X-ray diffraction experiment. Computer programs, taking as input the resulting electron density map and knowledge of the primary sequence, are used to deduce the three-dimensional arrangement of atoms in the protein (Fig. 2.14).

Fig. 2.14

Schematic depictions of the steps in X-ray crystallography in which an incident X-ray beam is directed at a crystal containing an array of unit cells, each cell containing the protein of interest. The two-dimensional diffraction pattern (here shown in 1D form with its peaks and valleys) is then Fourier-transformed (once the phase problem is solved). The resulting electron density map is further analyzed to produce the 3D protein structure

Today, once they are discovered, the three-dimensional coordinates (x, y, z) for each atom in a protein are routinely deposited in the Protein Data Bank (PDB) and made available to the research community. The PDB repository was established at Brookhaven National Laboratory in Long Island, and at several mirror sites throughout the world. Of the more than 84,000 structures for proteins and peptides that have been deposited in the PDB to-date, 75,000 were determined using X-ray crystallography and 9000 using nuclear magnetic resonance (NMR) spectroscopy (to be discussed in Chap. 3).