BCHM 3010 Protein Structure Part I
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This 5 page Class Notes was uploaded by Morgan Dimery on Wednesday January 20, 2016. The Class Notes belongs to 3010 at a university taught by Dr. Cheryl Ingram-Smith in Spring 2016. Since its upload, it has received 29 views.
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Date Created: 01/20/16
Protein Structure Reminder of the six themes of protein biochemistry we learned in class: 1. Primary sequence dictates protein folding and structure-‐ constraints from angles within the amino acid limit the way the protein can fold 2. Structure influences function 3. Non-‐covalent forces stabilize protein structures 4. Most proteins have one or a few stable structures 5. Proteins that have common structural characteristics are called families 6. Protein structures are not static Some vocabulary words: • Configuration-‐ spatial arrangement of an organic molecule lacking rotational freedom due to double bonds or specific arrangement of chiral centers. o Changing the configuration requires breaking bonds o Thinking back to organic chemistry and isomers-‐ cis/trans structures are an example of configurational isomers (this might help you remember). • Conformation-‐ spatial arrangement of substituent groups that are free to assume different positions in space. o Changing conformation occurs by simply rotating the bonds to give them a different orientation. o Thinking back to organic chemistry and isomers again-‐ Newman projections (see image below-‐ commons.wikimedia.org) are commonly used to show the different conformations of organic molecules. Different Newman projections of the same molecule are conformational isomers. • Dimer-‐ two subunits coming together • Residue-‐ specific amino acid in a chain • Protein domains-‐ areas of a protein that fold on its on no matter if the other parts of the protein are there. They also may have separate functions from one another-‐ they still must interact with each other in order to get to the final tertiary structure. They are driven by the hydrophobic core which allows for their stable formation • Protein structural motifs-‐ secondary structures that come together in the same way in different proteins • Protein families-‐ proteins that have a similar function and fold in the same manner-‐ have the same primary and tertiary sequence • Protein superfamilies-‐ proteins that have a similar structure but their primary sequences do not look alike and they do not have the same function Levels of Protein Structure 1. Primary structure • Amino acid sequence 2. Secondary structure • Structures that form due to hydrogen bonds (α-‐helices & β sheets) • These will be very important in the following sections!! 3. Tertiary structure • 3D shape • Single polypeptide chain • Secondary structures come together 4. Quaternary structure • Subunit organization • Basically multiple polypeptide chains coming together • Contain symmetry • Has many benefits o Increases functionality & stability o Decreases surface-‐to-‐volume ratio o Genetic economy and efficiency o Catalytic sites can come together o Once one subunit works, it helps the other subunits to work also Side note-‐ sometimes the tertiary structure does not need to join with anything to make the final protein product, in which case the tertiary and quaternary structure are the same structure • There are many different forces that help stabilize protein structures, but don’t let the strength of the force alone fool you! • Ionic interactions may be strong, but they DO NOT greatly stabilize proteins • Van der Waals interactions may be weak, but they DO greatly stabilize proteins • Hydrogen bonds are the main force that stabilizes the secondary structure of proteins, but they do not stabilize the tertiary structure very much. Hydrogen bonds are found pretty much everywhere in a protein. • Hydrophobic interactions also contribute to the stability of secondary protein structure. • Disulfide bonds (they are found in cysteine, YOU NEED TO KNOW THIS!) strongly stabilize the tertiary structure. • Covalent bonds hold amino acids together. Hydrophobic Interactions • Nonpolar side chains are not able to form hydrogen bonds, so they from hydrophobic interactions with each other instead. • Hydrogen bonding of water molecules causes clusters of hydrophobic regions to form Proteins will fold themselves so that the hydrophobic regions are hidden as much as possible, and the polar, charged parts of the chain are exposed to the aqueous environment. If you can’t remember anything else, at the very least remember this!!! Electrostatic Interactions • These include the attraction between opposite charges and the repulsion between like charges • These charged parts of the protein are located on the surface-‐ they do not fold as well on the inside of the protein The Alpha Helix • Helix arrangement that is stabilized by many hydrogen bonds. • Very compact, simple 3D arrangement • Put together so that the polypeptide backbone is on the inside and the side chains are on the outside • Right-‐handed and left-‐handed helices (right is more common) • HYDROGEN BONDS ARE EVERYWHERE! Specifically between every fourth amino acid and in most peptide bonds Different sides of the α helix may have different characteristics depending on whether they are polar or nonpolar. The Beta Sheet • Extended into a zigzag • Arranged side by side into sheets • Side chains extend from opposite sides-‐ alternate pointing up and down • Adjacent chains can either be parallel or antiparallel (they are hydrogen bonded to each other of course) • The hydrogen bonds between antiparallel strands are actually stronger than the hydrogen bonds between parallel strands. • Beta-‐turns are basically U-‐turns in the protein structure-‐ they connect the antiparallel strands by the 1 amino acid to the 4 Classification of Proteins Proteins are classified by structure and solubility • Structure o Fibrous o Globular • Solubility o Cytosolic o Membrane Fibrous Proteins • Insoluble because of the large amounts of hydrophobic amino acids • Have strength and give form • Can be α helix or β sheet, but never both at the same time • Examples include: α-‐ keratin, collagen, & silk fibroin α-‐keratin • Right-‐handed helix, left-‐handed coiled coil • Tend to have hydrophobic sides that hide by wrapping into other hydrophobic sides-‐ this also makes it stronger Collagen • More elongated than α-‐keratin • Found in many connective tissues • Left-‐handed helices-‐ 3 chains intertwine to make a triple helix • Contains a lot of glycine and proline (Gly-‐Pro-‐4Hyp repeats) • Stronger than steel of the same diameter • Proline is rigid and has a big R group, glycine is flexible and has a small R group-‐ this allows for chains to wrap more tightly together Silk Fibroin • Fibroin is the main protein in silk from moths and spiders • Antiparallel β sheet • Contains a lot of alanine and glycine-‐ they both have small R groups which allows for them to pack closer together (kind of like layering paper) • HYDROGEN BONDING is found within and between the sheets which gives it added strength • Even though it is not rigid at all, it is stronger than steel Globular Proteins • Ball-‐like • Contain both α helices and β sheets at the same time • The polar side chains that face the outside of the protein and the hydrophobic parts that face the interior of the protein interact with each other • As folding goes on, a hydrophobic core develops-‐ the tight packing makes it so that water cannot get into the hydrophobic region • Helices and sheets are able to interact with one another to sandwich in the hydrophobic layers between them Myoglobin • Protein that binds oxygen • Mostly consists of α helices, but does contain a few β sheets • Hydrophobic regions are hidden on the inside of the protein • Very compact so few waters can get inside After the secondary structure is made, the hydrophobic regions must be hidden as much as possible!!! Other Forces that Stabilize Proteins • Disulfide bonds-‐ cysteine contains these bonds that add stability to the protein • Metal-‐ any metals that are present in proteins add stability to it Some Key Points • Protein folding is not random-‐ secondary structures form whenever hydrogen bonds make it possible • There are usually no long stretches of unfolded proteins • Proteins always fold to make the most stable structure-‐ certain things (heat being an example) can cause the protein to be unstable again TO BE CONTINUED…