Proteins: Why They're Cool

BACKGROUND

The purpose of this post is not to provide specific information of a vast array of proteins but rather to give you an overview of what a protein is, and why they are important. It is to act as a reference point for later posts which will refer to terms like amino acid, enzyme, and protein structure, and to give an appreciation for the complexity of these molecules. As cool and interesting as the study of DNA, genes and genetic disorders is, the study of protein biochemistry is much more fascinating. Just as there are diseases associated with mutations in DNA, there are diseases that result from the poor organization of protein molecules. You will have heard them in the form of BSE, CJD, and Alzheimer's. I plan to discuss these in more detail in later posts, but for now, here is an introduction to proteins, and why you should care what they are.

PROTEINS

Proteins, along with lipids, sugars, and nucleotides, are one of four macromolecules of life responsible for many vital functions within a cell. There are three major classifications of proteins, structural, enzymatic and cell signalling/receptor proteins. These are distinguished by both their structure and their function, and both structure and function are intertwined. That is, the shape and composition of a protein really matters, and determines how it behaves in the cell. 

COMPOSITION

Proteins are composed of small chemical compounds called amino acids. There are a total of twenty amino acids, all similar in size and composition, but each of them unique. Amino acids combine to form complex and unique three-dimensional protein structures. When two amino acids combine they form what is called a dipeptide. When many amino acids combine they are called a polypeptide. Proteins are composed of polypeptide chains which fold into three dimensional shapes. The image below shows the chemical structure of each of the twenty amino acids. The point of this is not to confuse you with chemical structures, but instead to get an appreciation for the complexity and variety of these compounds. If you look at each of these compounds you will notice they all share the same chemical structure, except for the parts highlighted in red, these are called side chains.

Image taken from http://amit1b.wordpress.com/the-molecules-of-life/about/amino-acids/

The amino acid side chains are partially responsible for providing a protein with its shape, and function. Like DNA, each compound is given a one letter code so that it can be referred to quickly and easily, and proteins can be depicted as long sequences of letters. For example, the amino acid Isoleucine is "I", Tyrosine is "T", Alanine is "A", Serine is "S", Valine is "V", Asparagine is "N" Cysteine is "C", Lysine is "V" and Aspartate is "D". A peptide composed of these amino acids would be depicted as ITASVNCAKKIVSD. You'll notice the same amino acid can be present more than once in the same polypeptide sequence.

STRUCTURE

Biologists love to identify and classify things, and this extends all the way down to the molecular level. This linear arrangement of amino acids depicted in the previous paragraph is called the primary protein structure. The primary structure folds in on top of itself to form one of two new structures called (i) the alpha-helix, or (ii) the beta-sheet. Sheets and helices are often linked together by smaller segments of the protein which do not assume any three dimensional shape.

Three dimensional structure of a helix (left) and sheet (right). Image was made from the data on a small protein called hen egg white lysozyme, using the rendering program YASARA.

Within a single protein molecule there could be numerous helix and sheet structures linked together by small unstructured regions. These helix and sheet structures are called secondary structures, and the primary amino acid sequence determines which one is formed since certain amino acids have a propensity for helix formation, while others favour sheet formation. The combination of secondary structures linked together by small unstructured regions of protein is called tertiary structure, and is generally what is being referred to when biologists talk about proteins. The process of going from primary to tertiary structure is referred to as protein folding, and it's a fascinating aspect of protein biochemistry. See here for an excellent video of how proteins assemble from their component parts.

FUNCTIONS

Like many other aspects of biology, there is a structure/function relationship with proteins, by which I mean the function of a protein is dependent on the structure and composition of the protein. Proteins are roughly separated into enzymes and structural proteins. They both have vital but distinct roles in the body. Enzymes modify and change things in the body, whereas structural proteins provide physical support to the shape of a cell.

PROTEINS IN THE CELL MEMBRANE

Proteins are present within every part of the cell in addition to the cell surface. Proteins on the cell surface are typically involved in cellular communication, as well as transport of materials in and out of cells. Below is the structure of a cholesterol transporter (shown in yellow), imbedded in the cell surface, a region referred to as the lipid bilayer, or cell membrane. Even without knowing anything about the structure of cells in general you can see how this protein carves out a space in the lipid bilayer and provides a channel that allows the passage of small chemical compounds. While some compounds would be able to make their way through the lipid bilayer without a protein channel others would never stand a chance.

Image taken from Ukasz Jaremko, M. Jaremko, K. Giller, S. Becker, M. Zweckstetter. Structure of the Mitochondrial Translocator Protein in Complex with a Diagnostic Ligand.Science, 2014; 343 (6177): 1363 DOI: 10.1126/science.1248725

PROTEINS INSIDE CELLS

Proteins inside cells perform a massive array of functions. For example, the conversion of food to cellular energy involves ten proteins (enzymes), in addition to a transporter protein located on the surface of the cell. Each one of these enzymes performs a small but necessary part in the conversion of sugar to ATP, and this is just one small metabolic pathway in the body. There are proteins for carrying oxygen around the blood, proteins for regulating the formation and release of dopamine, and serotonin in the brain, proteins for clotting your blood and proteins for regulating how and when your DNA is used.

Actin is one of the most abundant proteins in our cells, and forms what is referred to as the cytoskeleton. In the same way that we have skeletons made of bone that allow us to move, cells have cytoskeletons make of long filaments of actin protein that allow them to move. The structure of actin is shown below. As you can see, The actin protein is long, and thin, exactly what you need for providing structural support to a cell. Multiple actin molecules bundle together in close proximity to provide additional tensile strength.

Actin filament, image was made from X-ray crystal structure data found in the protein data bank, PDB ID 1M8Q.

Compare this to the structure of some other non-structural proteins shown in images (a) to (d) below. These proteins are enzymes, or transporters, and they do not need to be mechanically tough. They move around the cell, or bind to substrates which often induce a change in structure. You can immediately see the difference between these proteins and the actin filament protein.

The structure of four proteins not involved in structural stability of the cell, (a) hen egg white lysozyme, an anti-baterial protein, (b) hexokinase, a protein involved in glucose metabolism, (c) calmodulin, a protein involved in calcium transport, and (d) haemoglobin, a protein involved in oxygen transport. All images made using YASARA.

SO - THERE ARE DIFFERENT PROTEINS, SO WHAT?

Well, my point here is that when people come across the word protein they tend to think of something pretty uninteresting, a block of cheese, or some milk, or maybe some beige coloured protein powder. It's true, these are foodstuffs that contain proteins, but what I have a attempted to show you is that proteins are far from boring to look at, and far from uninteresting. They are complex three dimensional structures made of smaller simpler components. The can assume a vast array of shapes, and the shape and function are linked.

It's worth noting, cells exist as a collective, they need to share information about their surroundings. Cells need to know when to divide, when to stop dividing, when to signal for an immune response, and when to metabolise sugar to energy. All of these functions are performed by protein molecules on the surface of the cell, or embedded in the cell membrane. You can think of them as a mixture of radio transmitters/receivers controlling a set of locked gates. Nothing gets past unless it has the correct chemistry to do so.

If you think of DNA as the instruction booklet for the manufacture of a human being, proteins are the machines that create and destroy all the components, they ferry raw materials around, they make sure there is a constant supply of raw material around, they regulate production to meet demand, and they work together to fight infection, heal wounds, and keep us breathing. They really are the cogs in the machine that is our body. 

REFERENCES/EXTRA STUFF

• YASARA, short for Yet Another Scientific Artificial Reality Application, this is a free application for downloading and viewing protein molecules called PDB structures.

• Check out this cool video from the PDB on protein structure 

• The protein data bank, a website for downloading PDB files, crystal structures, of proteins for viewing on your own computer.