Highlighting membrane protein structure and function: A celebration of the Protein Data Bank (original) (raw)

Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact. As membranes were critical to the separation of chemistries essential to the origin of life, membrane proteins (MPs) are key players in some of the most important physiological processes in living organisms. Characterizing MPs structurally and functionally is still extremely challenging due to their frequent low abundance, and difficulties in purifying functional MPs intact from their native membrane, though it is going through an exciting revolution now due to several key factors. It took several decades to obtain the structural information that now allows pursuit of understanding MP function in health and disease, to manipulate them as drug targets, and to engineer them into new powerful tools to fuel discovery. We highlight some of the landmarks in this endeavor that drove or depended on the discovery of new technologies required specifically for structural studies of membrane, versus soluble proteins. Previously, handwritten letters delivered by post requested coordinate sets that were not always readily given. The vision of Hamilton, Myer, Koetzle, and the joint venture between the Cambridge Crystallographic Data Center in the United Kingdom and the Brookhaven National Laboratories at Stony Brook University led to the Protein Data Bank (PDB). Then for the first time, one could begin to ask questions with all the relevant structures at hand. In celebrating 50 years of the PDB, we focus on some of the ingeniously crafted inventions and discoveries that led the way for entire classes of MPs, and those new approaches that now promise structures of large and complex machines from their native cellular environments, in action. In the following Historical perspective, we provide a brief historical perspective of some MP insights (other than the crucial G-protein-coupled receptors (GPCRs) that are the subject of a dedicated review in this volume) and consider the value of the PDB in disseminating this information. Seemingly insurmountable difficulties were often overcome with invention of new technologies to reveal important structural features of classes of MPs that make the fabric of today's approaches. In How do membrane proteins accomplish key physiological functions?, we describe how the structures of several of the major MP classes were uncovered, which often required technological developments that are now woven into the fabric of structural biology. First, how are the α-helical, tail-anchored, and all β-sheet MP broad categories correctly targeted to and inserted into membranes and allowed to fold correctly? We progress to landmark discoveries involving the roles of MPs in physiology and some of the critical barriers that had to be overcome to realize these achievements. How do water channels conduct water at diffusion limited rates without allowing leakage of protons (H +) or hydronium ions (H 3 O +) or any other ions? How do potassium channels conduct K + ions, but ‡ These authors contributed equally.