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Summary for each chapter
 

Chapter 1, Introduction, includes three parts. The first provides an overview of proteins' main functions and their importance to various fields, e.g., medicine and the drug industry. The second explains the central 'structure-dynamics-function' paradigm in proteins, thus providing the general rationale of the book. The third part describes the non-covalent forces acting on macromolecules, an overview that provides the reader with the necessary background to understand the notions presented later on in the book. Finally, the general layout of the book is presented.

Chapter 2, Protein Structure, describes in detail the different levels of protein structure. The physicochemical properties of amino acids are described at length. The description of secondary, tertiary, and quaternary structure that follows emphasizes the structural principles achieved by the observed architectures. Other factors affecting both protein structure and function—i.e., non-natural amino acids, enzymatic cofactors, prosthetic groups, and post-translational modifications—are also described, with emphasis on the structure-function relationship. All of these topics are exemplified using specific proteins. For instance, protein kinase A (PKA), a central enzyme in cellular communication, is used to demonstrate some of the main advantages of quaternary structure. Pyruvate dehydrogenase, a large enzyme complex involved in carbohydrate metabolism, is used to demonstrate the role of cofactors and prosthetic groups in protein function. The end of the chapter discusses a group of proteins that play relatively simple roles inside and outside cells, forming large fibrous structures. We discuss some well-studied examples, such as collagen, the principal protein of connective tissues, and keratin, a protein that provides toughness to horns, nails and claws.

Chapter 3, Methods for Determination and Prediction of Protein Structure, describes the main methods used today for structure determination, and their applications. First, methods based on particle/wave diffraction or scattering are described. These include X-ray crystallography, neutron scattering, electron scattering, and electron microscopy. We then discuss spectroscopic methods, including nuclear magnetic resonance (NMR) spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and circular dichroism (CD). This discussion is followed by a description of computational methods for predicting protein structure, which can be classified into two main groups, or approaches. The first, 'physical' approach relies on mathematical descriptions of the physical forces acting on the protein's atoms. We elaborate on several well-known methods corresponding to this approach, including molecular dynamics and simulated annealing. The second, 'comparative' approach, the most prominent of which is homology modeling, relies on sequence comparisons and statistical data. In covering this topic, we dedicate a great deal of the discussion to analyzing the advantages and disadvantages of each method, and the cases in which a given method is most applicable. Finally, we present the current tools for comparing the different methods and evaluating their efficiency.

Chapter 4, Protein Energetics and Stability, discusses the thermodynamic aspects of protein structure. It begins with an overview of the basic thermodynamic variables, the means by which they can be measured or calculated, and their interpretation in molecular systems. In discussing the latter, we refer to biological processes that can be characterized using thermodynamic variables. These include metabolic processes, protein folding, and protein-ligand interactions. The second section of the chapter discusses the main physical forces in the system with respect to their influence on protein structure. In the third and fourth sections we examine two cases in which the theoretical principles discussed are applied. The first is the adaptation of unicellular organisms to extreme environments, and the second is the use of protein engineering to enhance the industrial uses of enzymes.

Chapter 5, Protein Dynamics, expands the structure-function paradigm by incorporating structural dynamics. Two aspects of protein dynamics are discussed: protein folding, and folded (native) state dynamics. In addressing protein folding, we present the current views on how proteins acquire their three-dimensional structures. This field has been studied extensively, and we present the main conclusions. In addition, we discuss some well-known pathologies involving protein misfolding, such as cystic fibrosis, Parkinson's disease, and mad cow disease. Next, we discuss changes that can occur in a protein's native structure over time, and illustrate their functional importance on different levels. In this context, we elaborate on allostery as a key cellular approach for regulating protein function through manipulation of the protein’s dynamic properties. We discuss different models and mechanisms of allostery and use specific proteins to demonstrate them. For example, we refer to the medically-important enzyme dihydrofolate reductase (DFHR), which has been shown to be subject to long-distance allosteric effects. The oxygen-carrying protein hemoglobin is used to provide a detailed example of multi-level changes in protein dynamics, induced by allosteric regulators.

Chapter 6, Unstructured Proteins, focuses on a group of proteins that seem to deviate from the 'globular' behavior presented in the previous chapters. These proteins, called intrinsically unstructured proteins (IUPs), are characterized by the absence of a regular tertiary structure. IUPs have evolved to fulfill many different functions that do not require a permanent structure, and that even benefit from the lack thereof. As in Chapter 2, we discuss the principal properties of IUPs, with emphasis on the structure-function relationship.

Chapter 7, Membrane-Bound Proteins, focuses on a subtype of globular proteins that are located near and inside cellular membranes. These proteins constitute 20%–30% of the genome and play numerous roles in cellular physiology. Unlike water-soluble globular proteins, membrane-bound proteins are surrounded by a lipid environment and are therefore subjected to different forces, and consequently behave differently. The first part of this chapter overviews the structure, organization, and function of biological membranes. In particular, it discusses membrane asymmetry and the variability of membrane composition (and hence, the variability of the membrane’s properties) among different organisms. The second part analyzes membrane proteins, emphasizing common sequence- and structure-related themes, as well as folding energetics. The third part discusses the important issue of protein-membrane interactions, which has implications for both structure and function of membrane proteins. Finally, to illustrate the structure-function relationship in membrane proteins, we focus on G-protein coupled receptors (GPCRs), a group of receptors that serve as targets of most pharmacological drugs. We discuss in detail the β adrenergic receptor, the structure of which has recently been determined in its active state. Membrane proteins are notoriously difficult to crystallize, and are therefore desirable targets for structure prediction. Throughout this chapter, we mention key computational approaches developed for locating membrane proteins within genomes, for predicting their topology, and for predicting their full three-dimensional structures.

Chapter 8, Protein-Ligand Interactions, demonstrates the structure-function relationship in proteins by addressing proteins’ most important ability, i.e., binding to other molecules. After a short overview of the functional aspects of this ability, we discuss past and present theories on binding, and their thermodynamic implications. We then analyze protein binding on a molecular level, by focusing on the properties of protein binding sites. One such property is electrostatic potential, which we discuss using the example of acetylcholine esterase (AChE). AChE is a major enzyme responsible for the correct functioning of the nervous system and is, therefore, also a major target of various nerve agents and toxins. Its action is extremely fast, in part because of the mechanism of 'electrostatic steering', which the enzyme uses to draw its natural substrate into the catalytic site. The chapter subsequently illustrates the principles discussed above of protein-ligand binding by addressing the example of protein-protein interactions. Finally, we discuss the rational design of pharmaceutical drugs, which is a key practical application of protein-ligand interactions.

Chapter 9, Enzymatic Catalysis, discusses enzymes, which are probably the most sophisticated proteins in terms of function and molecular mechanism. In contrast to most biochemistry and protein structure/function books, this chapter provides a wide-angle, yet detailed description of various topics related to enzymes, including types of enzymes and reactions in their biochemical and metabolic contexts, molecular mechanisms, thermodynamics and kinetics, specificity, regulation, and ‘real-world’ applications, both medical and industrial. In accordance with the central theme of the book, Chapter 9 emphasizes structure-function relationships in enzyme catalysis, including some aspects that are usually ignored in other books, e.g., quantum tunneling and vibrational effects. Finally, the reader is provided with animations of the numerous chemical reactions and enzymatic mechanisms described in this chapter. These animations, which are expected to be particularly helpful for students of biochemistry and metabolism, are easily accessible via in-text QR codes that can be scanned using a smartphone.

The George S. Wise Faculty
of Life Sciences
Edmond J. Safra Center for Bioinformatics