Chapter 4
Macromolecular Machines | Proteins
Module 1 | How to Build a Molecular Machine | Hierarchal Levels of Protein Structure
Lesson 1 | Primary Protein Structure
If you've made it this far, you're ready to build a molecular machine, also known as a protein. Biological molecules are built from hierarchal levels of subatomic particles, atoms, and functional groups. Each level builds on the previous to give rise to the final cumulative structure. Similarly, the progression from amino acid chain to a fully functional folded protein also involves an ordered progression through different levels of molecular architecture. Specifically, there are four levels of protein structure referred to as primary, secondary, tertiary, and quaternary, each building upon the previous.
The primary structure of a protein is simply the sequence of residues within the polypeptide chain. Since we know that each type of protein has a unique amino acid sequence, we can say that the primary structure is what defines the protein.
Each polypeptide chain is composed of a molecular backbone and associated side chains. The backbone is formed by the peptide-bonded nitrogen and carbon atoms from adjacent amino acids and their associated oxygen and hydrogen atoms, as well as the central carbon atom from each amino acid. This "-N-C-C-" pattern backbone thus forms a continuous chain of atoms down the length of the polypeptide, with hydrogen and oxygen atoms protruding at regular intervals. The side chains, or "R" groups, are attached to the central carbon of each residue.
In linear, primary structure form, polypeptide chains are extremely flexible, with each residue being able to rotate not around the peptide bonds that join adjacent residues, but rather around the central carbon atom. This carbon atom is referred to as the α-carbon. The reason that a peptide bond cannot rotate is because although it is composed of a single covalent bond, the interactions between valence shell electrons in these atoms are similar to what we would normally see in a double bond.
Lesson 2 | Secondary Protein Structure
The primary structure of a polypeptide chain folds into a secondary structure via interactions between backbone atoms.
Regardless of the amino acid sequence, we learned in the last lesson that the pattern of backbone atoms within a polypeptide chain is the same for every protein. It should therefore come as no surprise to learn that due to limitations on how each bond can twist, there are only two main types of secondary structures. These two structures represent the only two ways in which a polypeptide chain can fold in order to maximize the interactions between backbone atoms.
Specifically, these interactions occur as hydrogen bonds between the N-H group of one residue and the C=O group of another.
Now with that said, it should be noted that certain side chain groups promote or restrict the formation of certain types of secondary structures because the side chains do have some influence on how each residue can bend and twist within the chain.
The two main types of secondary structures are called alpha helices and beta pleated sheets. They are highly ordered meaning that all alpha helices look very similar to each other, as do all beta sheets. There is also a third type of secondary structure which is called unordered. As you may have guessed, unordered secondary structures do not have any recognizable shape. Unlike alpha helices and beta sheets which are usually fairly rigid, unordered secondary structures are usually very flexible. Most proteins are composed mostly of alpha helices and/or beta sheets with only a small portion of the structure adopting unordered secondary structures.
Lesson 3 | Alpha Helices
Alpha helices are formed when the polypeptide chain spirals around itself with backbone atoms hydrogen-bonding with each other on the inside and side groups facing outwards. Alpha helices form right-handed spirals that turn 360 degrees every 3.6 residues. This spiral shape is maintained by hydrogen bonds that occur between a C=O group from one residue and the N-H group from a residue four units away.
Because alpha helices involve only backbone chain interactions, they can be composed of a variety of different amino acids and therefore can display a variety of side group patterns on their exterior. As we'll see later, these exposed side groups are involved in the formation of higher order structures such as tertiary and quaternary protein structures.
Multiple alpha helices can spiral around each other creating a coiled-coil. Coiled-coils are typically held together by interactions between hydrophobic side chains on each helix. These types of structures are rope-like in nature and as you can imagine, are used to provide mechanical strength at the molecular level. Technically speaking, coiled-coils are a type of tertiary structure.
Lesson 4 | Beta Sheets
The other main type of secondary structure we see in protein architecture is beta sheets, sometimes referred to as beta pleated sheets. Unlike alpha helices which involve only a single polypeptide chain twisting around itself, beta sheets involve backbone interactions between two different regions of a polypeptide chain. Beta sheets form flat, rigid, sheet-like
structures that are held together by hydrogen bonds between an N-H group from one chain and a C=O group from a distant region of the same polypeptide chain. The term "pleated" is sometimes used because this specific arrangement of atoms creates pleats or folds in the sheet. Because the N-C-C polypeptide backbone has directionality, beta sheets can be parallel or antiparallel, depending on the relative orientation of each chain.
The side groups in beta sheets extend outward from both sides of the sheet. Beta sheets can be formed between two sections of the same polypeptide chain or between two different polypeptide chains however we will address the latter when we learn about quaternary protein structure.
So far, the secondary structures that we've learned about are held together only by hydrogen bonds. Take a moment to remember that hydrogen bonds result from the partial charges carried by polar covalent bonds. Polar covalent bonds in turn exist because of the unequal sharing of valence shell electrons, with one atom pulling more than the other. All of this secondary structure architecture is therefore made possible by nothing more than a simple imbalance at the subatomic level. As we dive deeper into the next levels of protein structure try to make the connection between macromolecular machine and subatomic particle by imagining how they are connected through the multiple levels of atomic and molecular structure.
Lesson 5 | Tertiary Protein Structure
Some proteins consist of simply one secondary structure element, for example, one alpha helix. However most proteins contain multiple alpha helices, multiple beta sheets, or more commonly, both multiple alpha helices and multiple beta sheets. The interaction between multiple secondary structure elements forms the protein's tertiary structure.
Although we can usually predict the formation of secondary structure elements by looking at the primary amino acid sequence, it is much harder to predict the way in which secondary structure elements will fold and interact with each other to form a tertiary structure. For this reason, unlike secondary structures that are fairly uniform in structure, there is a high amount of morphological variation in a protein's tertiary structure.
Another important difference between secondary and tertiary structure is that secondary structure elements are held together via backbone chain interactions while tertiary structures are held together by side group interactions. This makes sense because in secondary structure elements, backbone atoms are concealed while side groups are exposed. The 20 different types of amino acids allow for different side chain groups to interact via hydrogen bonding, ionic bonding, or hydrophobic interactions.
Different tertiary structures within the same protein are usually referred to as different domains and different domains typically have different functions. In this way, the structure of a protein is tied to its function.
Lesson 6 | Quaternary Protein Structure
While many proteins are formed from only a single polypeptide chain, others are instead composed of multiple polypeptide chains. When multiple polypeptide chains interact to form a larger structure the overall structure is referred to as a protein's quaternary structure. Quaternary structure elements are held together in much the same was as tertiary structures, via hydrogen bonds, ionic bonds, and hydrophobic shunning. However whereas tertiary structure involves
interactions between secondary structure elements, quaternary structure involves interactions between tertiary structure elements. Many large, structurally complex proteins with multiple moving parts have quaternary structure.
Terminology is important here. A "protein" is the final structure. So for a protein with only tertiary structure elements, the single polypeptide chain is referred to as a protein. However for proteins with quaternary structure, the entire collection of polypeptide chains is collectively referred to as a protein while each individual polypeptide chain is referred to as a subunit.
For proteins with quaternary structure, the entire protein is sometimes referred to as a protein complex.
Proteins containing two or three subunits are called dimers or trimers respectively. This terminology can continue indefinitely with tetramers which are composed of four subunits, pentamers which are compsed of five subunits, and so on.
Moreover, when the subunits are identical, the word "homo", meaning the same, is added in front of the words dimer or trimer. When the subunits are different polypeptide chains, the word "hetero", which means different, is added instead.
For example, the terms homodimer and heterotrimer therefore describe quaternary-structured proteins with two identical subunits and three different subunits respectively. There is no real limit as to how many subunits a protein can possess and thus no limit to the size and complexity of protein machines. For example, the protein pyruvate dehydrogenase, which we'll learn about in the next unit, is composed of over 100 subunits!
Lesson 7 | RNA can form Similar Structures
Although RNA macromolecules are usually linear in shape, they are sometimes capable of folding onto themselves in a manner similar to the folding of primary-structured polypeptide chains into secondary structure elements. However instead of the backbone or side group interactions we see in proteins, RNA macromolecules adopt three dimensional shapes via interactions between different nucleotides within the same chain. Specifically, these interactions consist of hydrogen bonds that occur between nitrogenous bases from different nucleotides.
We'll talk more about this in the "Evolution" unit later on however suffice to say now that these three dimensional RNA structures can also function as molecular machines. Specifically, RNA macromolecules are found at the core of a huge molecular machine called a ribosome. Ribosomes are huge complexes composed of both RNA and proteins. They produce polypeptide chains by reading the corresponding copy of DNA code, which indecently is also composed of RNA. Moreover, it's actually the RNA macromolecules that are found at the business end of this machine while the proteins are simply present for helping and fine tuning.
Lesson 8 | Visualization of Molecular Machines
As we've transitioned from protein primary structure to quaternary structure we've gone through a dramatic change in scale. Showing every single atom in a protein is great for understanding all of the micro-interactions that are important for protein function however when we eventually transition to the cellular world we'll see that each individual atom becomes too small to notice.
For this reason, and for the sake of simplicity, we're going to slowly transition into a different way of visualizing these proteins. We're essentially going to cover the entire structure with a continuous skin so that we can still see the bumps and dimples of the individual atoms but at the same time allow our eyes to focus instead on the overall structure. The location of this skin is actually of biological significance. It represents the minimum distance from the center of each atom for which van Der Walls interactions, hydrogen bonds, and ionic bonds can occur. To put this another way, if the skins of two proteins are in contact, it means that the two proteins are interacting with each other in some non-covalent manner.
As we transition through the rest of this unit you'll notice that sometimes we do show each of the individual atoms whereas other times we'll only show the skin. As we get closer to the cellular world, you'll notice that we slowly transition to simply showing the protein skin.
Module 2 | Holding Proteins Together | Maintaining Protein Integrity
Lesson 1 | Hydrophobic Magnets
Hydrophobic interactions play a major role in holding most proteins together. This includes the hydrophobic interactions between secondary structure elements which hold tertiary structures together as well as the hydrophobic interactions between different protein subunits which hold together the quaternary structure of protein complexes. It is thus typical to find hydrophobic residues buried within the interior of the three dimensional protein while hydrophilic residues are typically exposed on the outside.
Remember that the term "hydrophobic interactions" does not mean that two hydrophobic side groups are attracted to each other, but rather that they are pushed together by hydrophilic molecules trying to maximize the number of hydrogen bonds that they make.
Therefore it's not that protein domains and subunits are held together by hydrophobic residues, but rather these hydrophobic regions are pushed together by the force generated by the surrounding water molecules attempting to maximize their hydrophilic interactions with each other. Any attempt to unfold the polypeptide chains in order to reveal the hidden hydrophobic residues would quickly be subdued by the strength of the hydrogen bonding network of water molecules all pulling each other around the exterior of the protein. This circumferential pulling force can be thought of as a type of tension that in turn creates a pushing force that compresses the hydrophobic residues against each other. As an observer, this phenomenon would appear as if the hydrophobic residues are acting as magnets that snap together.
Incidentally, this same phenomenon is what holds the lipids together within plasma membranes. The amphipathic lipids that form plasma membranes interact with each other not because they are attracted to each other, but because they are pushed together by the shunning of hydrophilic molecules around them as the hydrophilic molecules attempt to maximize their interactions with each other. Therefore every time you see a plasma membrane, remember that it's the hydrophilic interactions between water molecules on either side of the membrane that pushes the lipids together and generates the structure we call a plasma membrane.
Lesson 2 | Covalent Staples
Despite being held together by multiple non-covalent bonds and interactions, some proteins require further reinforcement in the form of covalent connections between different secondary, tertiary, or quaternary structure elements in order to maintain their overall three-dimensional structure. Such covalent connections don't usually change the shape of the
protein but rather re-enforce the existing shape. This type of reinforcement acts by strengthening the physical integrity of the protein and thereby limiting the flexibility that might otherwise occur between the different domains or subunits.
These reinforcing covalent connections are formed between the sulfur atoms of cysteine residues. This means that two cysteine residues from different secondary or tertiary structure elements must be located very close to each other in 3D space.
To make life more confusing, these covalent "staples" have many names: Disulfide bonds, disulfide bridges, S-S bonds, or even crosslinks, although the term crosslink is a more broad term that can also include other types of covalent bonds.
The acidity of the environment can affect the stability of disulfide bonds so these bonds are usually only found in the extracellular solution where the pH is such that disulfide bonds are favored.
Module 3 | How Proteins Work
Lesson 1 | Functional Moving Parts | Conformational Changes
Proteins work in much the same way that any machine works: by the movement of functional parts. Proteins therefore change their shape in order to function, a morphological transformation referred to as a conformational change.
Depending on the protein, this may involve movement between different secondary, tertiary, or quaternary structures, flexibility within the secondary structure elements themselves, or even the folding or unfolding of one hierarchal structural level into another.
To observe a conformational change is to observe a complex macromolecular transformation that is the manifestation of changes occurring between many of the covalent and non-covalent bonds and interactions that hold the protein together.
Trying to track every single change in inter-atomic interaction that occurs during a given conformational change would be much too complicated. What's more important is having a good conceptual understanding of why this occurs, so this is what we will explore in the next lesson.
Typically, proteins have different functions when adopting different conformations. This is because changing conformations changes the exposure and pattern of some of the amino acid side groups and it is through these side groups that proteins function.
Conformational changes can be physically small and subtle or dramatically elaborate. However the physical magnitude of the conformational change is not always proportional to the associated change in function. Sometimes a slight conformational change that is so small it's hard to detect by eye can result in major functional differences.
Lesson 2 | Inducing Conformational Change
Conformational changes in proteins can be induced by interaction with other proteins or molecules, a change in the aqueous environment (including changes in pH, temperature, or ion concentration), or even the covalent attachment of
molecules to certain exposed amino acid side chains. Whatever the cause, being able to adopt different conformations by undergoing conformational changes is what allows proteins to function as molecular machines.
All conformational changes occur in much the same way. First, the conformational change is induced by one of the previously mentioned external factors. This induction involves changes in attractive or repulsive forces at specific atomic locations that push and pull on different atoms and residues within the protein, thereby changing the location of these residues in three dimensional space. Remember that each amino acid in a polypeptide chain is directly connected to all other amino acids in a linear fashion via covalent connections down the backbone of the polypeptide chain as well as indirectly connected via the non-covalent interactions that hold the protein together. This means that the movement of one or a few amino acids can result in the shifting of secondary structure elements, which in turn may induce the shifting of tertiary and quaternary structure elements as well. The cumulative effect of all of these changes then leads to a macromolecular shift in position.
So because the entire protein is connected, small changes in the dynamics of valence shell electrons at the level of an individual atom can lead to huge macromolecular changes involving large scale shifting of positions between secondary, tertiary, and/or quaternary structures.
Lesson 3 | Specificity of Protein-Protein Interactions
Most proteins interact with other proteins as part of their function. The ability for two proteins to bind each other will depend on the compatibility between their unique surface distribution patterns of amino acid side groups. For example, patterns that facilitate the formation of ionic and hydrogen bonds between two proteins will promote their interaction.
When these surface patterns are compatible the proteins are said to have high affinity for each other and will thus most likely remain bound for a short period of time after colliding. When these patterns are not compatible, the proteins are said to have low affinity for each other and will thus most likely not remain bound after colliding.
Remember that all molecules and macromolecules are in constant motion. The same concepts of molecular interaction and binding affinity that we learned about for molecules also apply to all macromolecules, including proteins. Therefore when we say that protein A interacts with protein B, this actually means that when they bump into each other by chance, they will stay bound for a short amount of time versus not staying bound at all.
Lesson 4 | Simple Moving Parts | Tertiary Structure
For the remainder of this chapter we're going to look at some specific examples of molecular machines undergoing conformational changes. We're going to start simple and then increase in complexity. As we go through each example we'll make sure to compare the size of each of these proteins so we can appreciate the incredible difference in scale between the smaller machines and the large mega-complexes. Also, don't worry about understanding how ATP energy drives some of these conformational changes. We'll discuss that in the next unit.
Example: Phospholycerate kinase
Phosphoglycerate kinase (PGK) is a protein that removes a phosphate group from a 3-carbon molecule and adds the phosphate group to adenosine diphosphate (ADP) to form adenosine triphosphate (ATP). ATP can then be used as energy for the cell. We'll learn more about this in the next unit. In this scenario, ATP and this 3-carbon molecule are called
substrates. Substrates are small molecules or proteins that bind to a specific region of a protein which is usually called a binding pocket.
PGK is composed of one polypeptide chain with two tertiary-structured domains, each connected by a flexible linker. To get a feel for how proteins are folded, let's unfold the tertiary structure to reveal the secondary structure and then unfold these secondary structure elements to reveal the primary structure. Now upon refolding, we can see how the primary structure folds into secondary structure and then how secondary structure elements fold into the tertiary structure.
The linker connecting the two tertiary-structured domains acts as a hinge and the changing of covalent bonds within the small substrates is mediated by the opening and closing of the two domains. Only ADP and the specific 3-carbon sugar can bind to the binding pocket of PGK because only these molecules are complementary to the exposed amino acid side groups in the pocket.
Lesson 5 | Simple Moving Parts | Quaternary Structure | Part 1
Example: Sodium potassium pump
The sodium/potassium pump is a membrane-embedded protein that interacts with the hydrophobic interior of the membrane via exposed hydrophobic residues on the protein's surface. The sodium potassium pump exchanges Na+ ions for K+ ions by pumping Na+ ions out of the cell and at the same time pumping K+ ions into the cell. This direction goes against the normal concentration gradient for each of these ions, so this process requires energy, which is provided in the form of ATP. We'll learn exactly how this works in the next unit.
The sodium/potassium pump has quaternary structure. It is composed of one main subunit and two accessory subunits.
The binding pockets in the sodium/potassium pump are fine tuned to accept these specific ions based on ion size and charge. Remember that the elements in the first column of the periodic table can all carry a charge of plus one however they are all different sizes because of the different number of electron shells they each possess.
If we zoom in for a closer look at one of the ATP-binding pockets, we can see the changes in non-covalent interactions and the resulting repositioning of key atoms that occur as a result of the release of a phosphate group from ATP. Because the entire protein complex is connected by covalent and non-covalent bonds and interactions, we can see this small change propagate through the various domains, amplifying and manifesting as large scale movements throughout the entire protein machine.
Lesson 6 | Simple Moving Parts | Quaternary Structure | Part 2
Example: Calcium pump
Proteins are incredibly find-tuned to perform a specific function. This calcium pump looks and moves very similar to the sodium/potassium pump however it only pumps Ca2+ ions out of the cell. Although we can't tell just by looking at it, the specific residues that line its central membrane-spanning channel as well as the dimensions of the channel itself are fine- tuned to accept only Ca2+ ions.
Example: Clamp loader
The clamp loader loads a protein called the clamp around a double-stranded DNA helix during the process of DNA replication, a process that occurs when it's time for the cell to divide. The clamp loader is composed of five subunits which each use ATP-derived energy to move the subunits relative to each other. The clamp loader forms non-covalent bonds with the clamp and its movement thus causes the clamp to open and close. If we zoom in for a closer look at one of the ATP-binding pockets, just like in the sodium/potassium pump, we can see the changes in non-covalent interactions and the resulting repositioning of key atoms that occur as a result of the phosphate group release from the ATP molecule. Because the entire protein complex is connected by covalent and non-covalent bonds, we can see this small change amplify and manifest as large scale movements throughout the entire machine.
Lesson 7 | Complex Moving Parts
Example: Vinculin and α-catenin
In multicellular organisms, cells are connected to each other via rope-like junctions that span the cell membranes of both cells. These junctions are composed of many proteins. When tension forces attempt to pull the two cells apart, this mechanical tension is felt at the molecular level by one of the junction proteins, α-catenin. The physical stretching of α- catenin leads to the exposure of a previously concealed vinculin-binding domain. Vinculin can then bind, unfold itself, and make additional attachments to the cell skeleton for reinforcement.
Example: Pyruvate dehydrogenase
Although this beast may look intimidating, it's actually just a spherical array of repeating subunits, over 100 in total!
Pyruvate dehydrogenase is involved in the breakdown of glucose for energy. The part of the pathway that pyruvate dehydrogenase is involved in is a three step process and the arms that you see moving around are moving the substrates through each of the three stations. Notice that the flexible part of the arm is composed of an unordered secondary structure.
Example: ATP synthase
ATP synthase acts like a molecular turbine and it is a great example of a molecular machine with moving parts. As protons flow across a plasma membrane they spin the turbine domain of ATP synthase. This turbine domain is referred to as the F0 domain. This in turn spins a rotor that rotates inside of the stationary domains above. This stationary domain is referred to as the F1 domain. Because the rotor is asymmetrical, it pushes on different F1 subunits at different times causing each pair of F1 subunits to open and close sequentially. When opened, ADP and a free phosphate group can bind. Upon closing, these two substrates are pushed so close together that they covalently join to form ATP. ATP synthase thus converts mechanical energy into chemical energy through the production of ATP. We'll take a much closer look at this incredible machine when we learn about cellular energy in the next unit.
Lesson 8 | Mega-Protein Complexes
Some protein complexes are huge. Let's look at a few examples.
Example: Ribosome
Ribosomes make proteins. Ribosomes are machines that translate RNA code, which in turn was copied from the original DNA code, into a sequence of amino acids. Compared to most proteins, ribosomes are very large with dimensions of about 20 by 25 nm. As mentioned earlier, ribosomes are composed of both protein and RNA.
Example: Replisome
The replisome is technically a collection of different proteins that all come together when it comes time to replicate the cell's DNA. Each of the proteins within the replisome has a specific function. One of these proteins is the clamp loader, which we learned about earlier.
Example: Photosystems
Photosystems are huge complexes of plasma membrane-bound proteins that collectively act as large antennae dishes that capture sunlight energy in plants. Embedded within the many subunits are over 100 molecules called pigments which are responsible for capturing the photons of light.
Example: Nuclear pore complex (NPC)
Nuclear pore complexes (or NPCs) are gigantic, at approximately 120 nm in diameter. NPCs are embedded in the nuclear membrane and act as gateways between the nucleus and the cytosol. Although most of the complex is stationary, the central channel is filled with a network of many flexible arms that regulate which proteins enter and exit the nucleus.
Lesson 9 | Dynamic Mega-Protein Structures
Just as amino acids act as building blocks for proteins, proteins sometimes also act as building blocks for huge mega- protein structures, some of which are highly dynamic. Let's start with a simple example and then work our way up from there.
Example: COPII-coated vesicle budding
COPII proteins aggregate with each other at specific angles to ultimately form a sphere. Because they are bound to the plasma membrane via adaptor proteins, COPII proteins pull out spherical pieces of plasma membrane. This is a way to transport contents from one intracellular compartment to another. We'll learn more about this process in the next chapter.
Example: Filipodia extension
Migrating cells sense chemicals in their environment that orient their direction of migration. The antennae that detect these chemicals are called filipodia. Filipodia extend via polymerization of many protein monomers called actin. This polymerization is synchronized by dozens of polymerization complexes at the tip of the extending filipodium.
Example: Flagellum and Salmonella needle
Both bacterial flagella and the needle structure found in Salmonella are structurally very similar, suggesting that one may have evolved from the other. Both structures are huge. The flagellum can spin at over 100,000 rpm and is powered by continually changing positions of charged ions.
Example: Focal adhesion rearrangement
Migrating cells need to have their feet on the ground in order to be able to push the bulk of their mass forward. These feet are called focal adhesions. Focal adhesions are highly dynamic structures composed of many different types of proteins.
Notice that the growing and shrinking of focal adhesions is caused by proteins either joining or leaving the mega-complex.
Example: The lamellipodium treadmill
The lamellipodium is a network of polymerized actin filaments and accessory proteins that acts as a rigid skeleton that pushes the cell membrane forward during cell migration. Like focal adhesions, the lamellipodium is also highly dynamic.
Notice that the entire structure is not actually moving forward, but rather polymerizing at the front end and breaking down at the rear. Incidentally, focal adhesions anchor the lamellipodium to the ground providing the leverage needed to push the cell membrane forward.
Lesson 10 | The Structure/Function Relationship
Why is the structure/function relationship such an important concept in biology? Isn't it obvious that the structure of a machine is typically indicative of its function? After all, in our everyday world machines are built in a particular way for a particular function. For example, the engine and drive train of a car.
It turns out that this concept was not always so obvious in molecular biology. We are lucky to live in a time when we know the detailed molecular structure of over 150,000 proteins. Just two decades ago this number was less than 10,000 and in the mid 80's it was less than a few hundred. Before knowing what proteins looked like it was incredibly difficult to imagine how they might function.
As biologists discovered more structures they began to notice that proteins act as molecular machines. At this point in time the structure/function relationship in molecular biology was a new concept. Today however, although the structure/function relationship should be obvious to us, it's important to remember that this wasn't always the case.
Module 4 | Protein Diversity
Lesson 1 | How to Categorize Multi-Functional Machines
Every protein is different. Although we will try to categorize proteins based on common criteria keep in mind that there are no discrete borders between different categories because most proteins have multiple functions. The only reason we're introducing these categories is to cover some of the more common types of protein functions, but know that it is rare to find a protein that belongs to only one of these groups.
Also note that proteins can be classified in several ways. For example, we can classify proteins based on their physical shape. Some are more globular while others are more linear or fibrous. Of course, some proteins like the motor protein myosin involved in muscle contraction have both globular and fibrous domains. We can also classify proteins based on their solubility. For example, PGK is soluble while the sodium potassium pump is not, because of its exposed hydrophobic residues. However Protein Kinase C (PKC), which is involved in intracellular signal transduction, is sometimes soluble and sometimes not based on the type of exposed surface residues that change with the protein adopts different conformations.
Probably the most logical way to classify proteins is by function, so that's what we'll do. However keep in mind that the goal here is not to memorize which proteins belong to which functional group, or even to memorize the various groups themselves. But rather, the goal is to appreciate the diversity of protein function. Also remember that most proteins have more than one function so these categories are not mutually exclusive.
For the remainder of this module we'll examine three of the major categories of protein function: structural proteins, transport channels, and enzymes. However remember that there are of course many more categories.
Lesson 2 | Structural Proteins
Probably the easiest category to start with is structural proteins. This category includes proteins that provide mechanical support and shape to a cell. Three proteins that clearly belong in this group are actin filaments, microtubules, and intermediate filaments, the three proteins that together form the macromolecular skeleton of a cell, a dynamic cellular structure referred to as the cytoskeleton.
Actin is a globular protein that on its own is referred to as G-actin, where "G" stands for globular. When many G-actin proteins are polymerized into a long, filamentous chain, the entire structure is called F-actin, where "F" stands for filamentous. We've seen F-actin before when we learned about filipodia, lamellipodia, and focal adhesions. F-actin filaments are usually used to shape the cell membrane rather than to provide mechanical support to the cell.
Microtubules are long, stiff tubes that are about three times as wide as actin filaments. They are polymerized from subunits of the heterodimer tubulin, which in turn is composed of an α-tubulin and a β-tubulin subunit. Microtubules position the various intracellular compartments within a cell and also act as roadways upon which motor proteins travel.
Motor proteins use microtubule roadways to transport cargo to and from different parts of the cell.
Intermediate filaments are composed of homotetramer protein subunits. They are a bit wider than actin filaments and are very strong. Intermediate filaments provide mechanical support to a cell just like our bones provide mechanical support for our body.
Lesson 3 | Transport Channels
We've already learned about two transport channels: the sodium/potassium pump and the nuclear pore complex (or NPC).
As the name indicates, the sodium/potassium pump pumps Na+ and K+ ions in opposite directions across the cell membrane. The sodium/potassium pump works together with other membrane transport channels such as the sodium channel and potassium channel to regulate the flow of ions and charges that propagate down the cell membrane of nerve cells. This is how nerve cells in our nervous system communicate with each other.
The NPC is probably one of the largest transport channels in a cell. As we learned earlier, the NPC regulates the transport of proteins across the nuclear envelope. RNA copies of the DNA code must exit the nucleus to be translated into proteins by ribosomes in the cytosol while certain proteins like the clamp and clamp loader must enter the nucleus when it comes time for DNA replication.
In contrast to the huge NPC, many transport channels are actually quite small. For example, virtually all cells possess relatively small water channels in their cell membrane called aquaporins. Aquaporins are homotetramers that allow the hydrophilic water molecules to freely flow through in single file across the hydrophobic membrane. The amino acid side groups lining the inside of each channel are positioned in a way that only allows water molecules to pass.
Lesson 4 | Enzymes
Enzymes perform chemical reactions meaning that they make, break, or change covalent bonds within their substrates.
The protein phosphoglycerate kinase (or PGK) that we learned about earlier is an example of an enzyme. Enzymes function by binding to their substrates in a way that physically contorts the substrate molecule. This contortion induces stress on the covalent bonds that hold that molecule together which lead to the breaking and rearranging of these bonds. The situation is actually more complex than this, and because this process involves entering into a discussion of energy, we will save this explanation for the next unit.
Enzymes are usually given names that end with "ase" such as isomerase, kinase, phosphatase, and polymerase. Isomerases rearrange covalent bonds in their substrates, kinases covalently attach phosphate groups to their substrates, phosphatases remove such phosphate groups, and polymerases polymerize polymers from monomers through the formation of covalent bonds.
The huge protein complex pyruvate dehydrogenase is another example of an enzyme.
Lesson 5 | Motors
Some proteins use the chemical energy stored in ATP to power mechanical motors thereby creating movement. We'll learn exactly where this energy comes from and how this occurs in the next unit, but for now, let's take a look at some examples of these motor proteins.
Myosin is composed of a filamentous tail and a globular head. Through the energy released by breaking ATP into ADP and a free phosphate group, a process called ATP hydrolysis, the myosin head moves back and forth relative to its tail. The conformational changes associated with this movement are such that they allow myosin to bind and then unbind F-actin filaments, pulling the F-actin filaments towards them as they move. If we zoom into our muscle cells, we'll see that these cells are packed full of myosin and F-actin filaments that are arranged in a specific three dimensional configuration. The combined pulling force of all of the myosin-F-actin interactions is what makes our muscles contract.
Another motor protein called kinesin works in a similar way to myosin. Kinesin is composed of two fibrous legs twisted around each other with two globular feet at the ends. Just as the myosin head moves back and forth through the power released by ATP hydrolysis, the kinesin feet step sequentially one in front of the other in a walking motion. Kinesin literally walks along microtubule roadways carrying cargo across the cell.
