The side chain gives the amino acid distinctive structural and chemical properties as side chains differ in size, shape, polarity, charge and hydrophobicity ( Figure 1). What is most interesting, is that for 19 of the 20 different amino acids, the C α group is also bonded to a different R group, giving every amino acid its unique ‘side chain’. Each amino acid has a common structure containing a central α carbon atom (C α) that is joined to an amino group (–NH 2) and a carboxylic acid group (–COOH) both of which are used to form peptide bonds. Proteins are polymers of typically hundreds of amino acids joined together by peptide bonds, whereas shorter polypeptides (less than 30 amino acids) are typically referred to as peptides. All of these large ‘macromolecules’ are carbon-based covalent compounds that use weak reversible non-covalent interactions to fold and interact with their targets, giving the molecules and their complexes distinct shapes and dynamics. Proteins are one of the four major molecules that direct life that includes nucleic acids (deoxyribonucleic acid (DNA), RNA), lipids (fats) and polysaccharides (sugars). Given the interdisciplinary nature of this topic, along the way, we have provided some stand-alone boxes to give more details about the fundamental science behind these concepts. We then discuss in detail the primary techniques used to study protein structure and dynamics that have provided these insights. In particular, although proteins usually exist in one dominant conformation, we discuss how proteins actually exist in a population (ensemble) of rapidly interconverting conformations that allow them to be flexible and adapt their shapes required for function. We also explore other universal properties of proteins that include their ability to change their shape known as conformational change. As such, we consider protein folding thermodynamics and also what happens when proteins misfold inside a cell. Proteins are biological molecules produced in living cells, and we must also consider how a long chain of amino acids that are produced from the ribosome can transition to a folded structure that is central to the protein’s function. We start by describing the four levels of protein structure and how a variety of protein domains and architectures exist. This topic is truly interdisciplinary and in addition to biochemistry, spans the fields of biophysics, structural biology and computational biology. Furthermore, to understand how we experimentally study protein structure, we explore fundamental concepts in physics and associated computational methods. We consider how interactions between amino acids help proteins fold and fluctuate as they adopt a variety of structures. To understand structure, we explore the chemical nature of amino acids which are the building blocks of proteins.
To fully understand their role, it is essential to explore both their structure and function and this review focuses on how we uncover protein structure.
Proteins are one of the most important classes of molecules for life and underpin the field of biochemistry. Protein structural biology is a relatively new and exciting field that promises to provide atomic-level detail to more and more of the molecules that are fundamental to life processes. In the second part of this review, we describe the variety of methods biochemists use to uncover the structure and properties of proteins that were described in the first part. We look at protein dynamics and how proteins can take on a range of conformations and states. We consider the thermodynamics of protein folding and why proteins misfold. We start with the chemistry of amino acids and how they interact within, and between proteins, we also explore the four levels of protein structure and how proteins fold into discrete domains. This article gives the reader an insight into protein structure and the underlying chemistry and physics that is used to uncover protein structure. The resulting structures are then used to help explain how proteins function. Structural biology is the study of the molecular arrangement and dynamics of biological macromolecules, particularly proteins.
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