Atomic evidence: the foundations of structural molecular biology.

ABSTRACT Atomic structures of biomolecules have provided the experimental evidence for many of the major discoveries in molecular biology, including the basic principles of protein folding and function, modes of biological information and energy flow, and mechanisms of molecular evolution. These experimental data are freely available in online structural databases. Keywords: protein structure and function, structural molecular biology, Protein Data Bank, molecular evolution Introduction Structural molecular biology is one of the few fields of science where the primary scientific data is easily accessible to anyone who is interested. Techniques like X-ray crystallography, NMR spectroscopy and electron microscopy are used to determine the atomic structures of biological molecules. These structures are available in public databases such as the Protein Data Bank (PDB; www.pdb.org), the Nucleic Acids Database (ndbserver.mtgers.edu), and EM Databank (emdatabank.org), and many excellent tools are freely available for exploring these structures (1,2). Atomic structures provide the support for many of the basic functional principles of molecular biology. This support is particularly direct: the structures show the three-dimensional arrangement of atoms. Often, a structure will bring together decades of biochemical results, revealing the atomic basis of experimental observations and occasionally refuting theories based on more indirect results. Atomic structures are limited, however (3). Often, they capture only one of many conformational states of the molecule, so dynamic processes must be inferred. Structures are difficult to obtain for large and flexible molecules, so structures may be obtained for stable fragments or individual subunits of a larger complex. In the case of enzymes, structures are often obtained for stable substrate analogs and inhibitors rather than the actual substrates and products of the reaction. In spite of these limitations, many of the foundational concepts of molecular biology have been discovered through the determination of atomic structures. In this review, I will present some of the basic principles of biomolecular structure and function, and describe the structures that were instrumental in their discovery. Using resources like the Protein Data Bank, you can go directly to these structures and explore these atomic structures yourself. Protein folding and hierarchical structure The earliest atomic structures proved that proteins have a defined, hierarchical structure, and revealed how function is manifested in this structure. The first atomic structure of a protein was obtained for myoglobin, a protein that stores oxygen in cells (4). The structure revealed a hierarchical arrangement, with the primary sequence of amino acids adopting a collection of secondary structure elements (alpha helices), which then fold into a distinctive globular tertiary structure. The protein chain perfectly enclosed the heme cofactor, providing a chemically-matched collection of amino acids to hold the cofactor and to interact with the iron ion. This ground-breaking structure is available at the PDB in entry 1mbn (Figure 1). The subsequent structure of hemoglobin extended this hierarchy to the additional level of quaternary structure, where several protein chains assemble to form a larger complex (5). As discussed below, it also revealed the basis of allosteric regulation, where small changes in shape control the function of the complex. This structure of hemoglobin is available in PDB entry 2mhb (Figure 1). [FIGURE 1 OMITTED] As more structures were solved in the following years, the general principles of protein structure were defined. Based on thousands of protein structures, it was discovered that proteins are modular in structure, built of stable domains that are mixed and matched to form larger structures. …