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Proteins are highly complex molecules that are actively involved in the most basic and important aspects of life. These include metabolism, movement, defense, cellular communication, and molecular recognition. Accordingly, protein science is at the very center of biological research, and is applied to disciplines such as medicine, agriculture, biotechnology, and even unconventional warfare. In the last few decades, with the development of accurate and sophisticated means of molecular structure determination, it has become clear that the functions of macromolecules in general and of proteins in particular are direct results of structure and structural dynamics. It has similarly become evident that, to obtain a true understanding of protein function, structure and dynamics, it is necessary to both qualitatively and quantitatively characterize the dominant physical forces that act on proteins at the atomic level. These insights have prompted the emergence of a new field in biological sciences, termed ‘structural biophysics. This book aims to provide the reader with a detailed description of protein structure and dynamics, combined with an in-depth discussion of the relationship between these aspects and protein function. We approach these topics through the lens of structural biophysics, focusing on the molecular interactions and thermodynamic changes that transpire in highly complex biological systems. There are several types of textbooks describing protein structure and function. Biochemistry textbooks emphasize the functional aspects of proteins and provide rather general descriptions of structures and the structure-function relationships. Structural biology textbooks provide extensive descriptions of protein structures, and also refer to the structure-function relationships with varying degrees of detail. However, energy-related aspects are often avoided. Molecular biophysics textbooks focus on molecular interactions and thermodynamic aspects of protein structures, but tend not to delve deeply into structural and dynamic aspects or into the structure-function relationships. Our book refers to all of the aforementioned aspects, and attempts to provide a unified view. Our energy-oriented approach is manifested throughout the book, whether we discuss structure, dynamics, or specific functions of proteins, such as catalysis or signal transduction. An extensive discussion of the energetics of protein structure is also given in a chapter dedicated to this topic. Most textbooks that describe the structure-function relationships in proteins do so by using specific examples or protein types. This approach provides a broad view of protein activity, but may be insufficient to enable the reader to draw general conclusions. Here, when possible, we attempt to provide clear outlines of the principles of protein action (as we understand them). This is done throughout the book, but particularly in the last three chapters describing membrane-bound proteins, protein-ligand interactions, and enzyme-mediated catalysis. These topics, as well as any topic involving protein structure and function, are difficult to explain by using text and simple graphics.