Structure and Function in Proteins

Proteins exist in every living cell and serve a huge variety of purposes. They are involved in almost every process in the cell, from forming structural components to catalyzing reactions to cell signalling and interactions. Proteins are made of amino acids, which each have their own size, charge and hydrophobicity properties. These wide range of properties allow cells to build proteins with a wide range of functions, binding capabilities and reactivities. Because of this flexibility, proteins can be built that function in many ways

The amino acids that form proteins have a wide range of properties that determine the folding pattern for the larger structure. They generally fall into 4 categories:

Charged (Hydrophilic) – These amino acids feature a positive or negative charge that makes them important for the exterior of proteins that interact with water. They are also critical in salt bridges, which can provide some stability to protein structure and interactions.

Hydrophobic – These nonpolar amino acids drive the protein to fold in such a way as to remove these amino acids from the interior of a protein.

Polar – These residues are often involved in interactions with water and other proteins. They are also important in hydrogen bonding, which is critical for stabilizing key secondary structures.

Proteins, in general, can be categorized into a fairly small subset of major folds. These folds are composed of a handful of general protein secondary structures, which are listed below. The function of proteins are directly related to their folding and structure. The first major structural motif is helices. The most common type of helix is the alpha helix, which consists of a right-handed coil of protein in which the N=O group of a particular amino acid forms a hydrogen bond with the carboxyl group of the amino acid four residues earlier. This stabilities the structure of these helices. Helices often pack together in bundles or fold against beta sheets.

The second structural motif is the beta sheet. Beta sheets are composed of beta strands, where the amino acid strands are fully extended, exposing hydrogen bonding partners to other beta strands. These strands line up in either parallel or anti-parallel conformations to form these sheets.

Lastly is random coil. While often ordered in some way, the random coil does not fit neatly into other secondary structure motifs. The loops on the ends of helices, for instance, form random coil as they weave their way into the next helix.

Below is a general list of all the different functions of proteins in cells.

1) Reaction catalysis. Enzymes are proteins that are instrumental in controlling the rates of chemical reactions in the cell. Without this control, reactions would occur spontaneously and without limit, eating up vital ene
 rgy and destroying the organism. Enzymes are generally specific to just one or a few reactions in larger pathways and have very tight control. Many have allosteric or feedback regulators that control the enzyme’s activity based on cell conditions.

2) Cell signalling. A number of proteins exist to function as cell signalling components. Many of these are embedded into the membrane of the cell to allow for cell-cell signalling. They also may function as ligand binders, like antibodies. These proteins interact with a ligand, then in turn cause some form of signalling cascade that allows the cell to make a response to that exterior signal.

3) Transport within the cell. Connected to cell signalling is the role of proteins in small molecule transport. There are a number of proteins that exist to bind to molecules and move them from area of the cell to another or for export out of the cell. A whole class of proteins exist that move ions in and out of the cell through pores and ion transporters.

4) Structural support and movement. Many proteins are involved in protein structure, including cytoskeleton proteins like actin and tubulin. Some proteins are involved in cell motility, like myosin, which allows the cell to contract and stretch to move and expand. This is critical for cell replication, when the cell has to divide evenly so that daughter cells are fully functional. It is also important for muscle contractions in higher level organisms, where muscle cells must contract and expand to allow for whole organism movement. Other proteins are used by cells to form extracellular connective or structural tissue, such as collagen, elastin and keratin which forms ligaments, cartilage, and other connective and filamentous structures.