Methods in Molecular Biophysics Structure, Dynamics, Function for Biology and Medicine

The ideal biophysical method would be capable of measuring atomic positions in molecules in vivo. It would also permit visualization of the structures that form throughout the course of conformational changes or chemical reactions, regardless of the timescale involved. At present there is no single experimental technique that can yield this information.

A BRIEF HISTORY AND PERSPECTIVES

Molecular biology was born with the double-helix model for DNA, which provided a superbly elegant explanation for the storage and transmission mechanisms of genetic information (Fig. 1). The model by J. D. Watson and F. H. C. Crick and supporting fiber diffraction studies by M. H. F. Wilkins, A. R. Stokes, and H. R Wilson, and R. Franklin and R. G. Gosling, were published in a series of papers in the April 25, 1953 issue of Nature, and marked a major triumph of the physical approach to biology.

The Watson and Crick model was based only in part on data from X-ray fiber diffraction diagrams. The patterns, which demonstrated the presence of a helical structure of constant pitch and diameter, could not provide unequivocal proof for a more precise structural model. One of the “genius” aspects of the discovery was the realization that A–T and G–C base pairs have identical dimensions; as the rungs of the double-helix ladder, they give rise to a constant diameter and pitch. From a purely “diffraction physics” point of view, a variety of helical models was compatible with the fiber diffraction diagram, and other authors proposed an alternative model for DNA, the so-called “side-by-side model,” coupling two single DNA helices. This shows that if molecular biology were ever to be established, it was important to obtain the structure of biological molecules in more detail than was possible from fiber diffraction. Considering the dimensions involved, about 1 Å (0.1 nm) for the distance between atoms, X-ray crystallography appeared to be the only suitable method. Major obstacles remained to be overcome, such as obtaining suitable crystals, coping with the large quantity of data required to describe the positions of all the atoms in a macromolecule, and solving the phase problem.