Protein Crystallography from the Perspective of Technology Developments

Abstract

Early on, crystallography was a domain of mineralogy and mathematics and dealt mostly with symmetry properties and imaginary crystal lattices. This changed when Wilhelm Conrad Röntgen discovered X-rays in 1895, and in 1912 Max von Laue and his associates discovered X-ray irradiated salt crystals would produce diffraction patterns that could reveal the internal atomic periodicity of the crystals. In the same year the father-and-son team, Henry and Lawrence Bragg successfully solved the first crystal structure of sodium chloride and the era of modern crystallography began. Protein crystallography (PX) started some 20 years later with the pioneering work of British crystallographers. In the past 50-60 years, the achievements of modern crystallography and particularly those in protein crystallography have been due to breakthroughs in theoretical and technical advancements such as phasing and direct methods; to more powerful X-ray sources such as synchrotron radiation (SR); to more sensitive and efficient X-ray detectors; to ever faster computers and to improvements in software. The exponential development of protein crystallography has been accelerated by the invention and applications of recombinant DNA technology that can yield nearly any protein of interest in large amounts and with relative ease. Novel methods, informatics platforms, and technologies for automation and high-throughput have allowed the development of large-scale, high efficiency macromolecular crystallography efforts in the field of structural genomics (SG). Very recently, the X-ray free-electron laser (XFEL) sources and its applications in protein crystallography have shown great potential for revolutionizing the whole field again in the near future.

Keywords: X-ray crystallography; X-ray free-electron laser (XFEL); computer programs and graphics; protein crystallization; recombinant DNA techniques; structural genomics (SG); synchrotron radiation (SR).

Figure 1

A description of the development of protein crystallography with time, showing rapid exponential growth of protein crystallography since 1840s, the exponential growth of both proteins crystallized and protein crystal structures solved is well underway in the recent 20 years, block lettered events represent some of the most important milestones for protein crystallography.

Figure 2

The three representative technology fields with most rapidly increasing rates. All three have directly contributed to structural biology. In fact, among the three, electronics governed by the famous Moore's law has had the slowest but most stable exponential growth since 1970s. It has increased more than 10 orders of magnitude over the last 40 plus years and is responsible for the explosive growth of computers, IT and telecommunications industry. The red line represents the recent rapid growth of the so-call next generation sequencing (NGS) which has increased about 10 orders of magnitude just over the last 10 years. DNA (gene) sequences direct protein synthesis that is indispensible in recombinant DNA technology and therefore in solving protein structures. NGS makes it possible to get an overall estimation of how many proteins are in biological systems and that we might need to crystallize and visualize crystal structures. X-ray source intensities have increased more than 20 orders of magnitude since 1980s from the dedicated X-ray production source of 2nd generation SR to current XFEL sources.

Figure 3

Structure determination pipeline from the Joint Center for Structural Genomics (JCSG), USA. (Figure courtesy of I. A. Wilson).

Figure 4

Over the last several years, the Su laboratory at Peking University has built up technological platforms of high-throughput (HTP) methods for structural biology studies, including target selection; HTP and semi-robotic gene cloning; protein expression; protein purification; crystallization and crystal structure determinations.