Lesson 4: Protein Architecture
Describe how intermolecular forces are involved in determining the secondary structure of a protein
1. A segment of a polypeptide adopts an alpha-helical conformation because of the hydrogen bonding between the backbone amide groups in nearby residues along with the polypeptide chain 2. Meanwhile, the segment of the adopts a beta-sheet conformation because of the hydrogen bonding between amide groups on the adjacent chain segments
collagen
A structural protein found in connective tissues such as tendons, ligaments, as well as in cartilage and corneas
Globular protein
Aqueous -catalysts -form due to how alpha and beta are arranged with each other in one protein -characteristically have a hydrophobic interior and hydrophilic surface
Disulfide bonds within proteins
Disulfide bonds are not generally found in intermolecular proteins but are sometimes found in intercellular proteins but are sometimes found in proteins that are secreted from cells, but they are often stabilized by these disulfide bonds -Does not drive protein folding; instead, the bonds form where two cystein residues are appropriately located once the protein is folded -the formation of a disulfide bond requires oxidation of the thiol groups of the cysteine residues -complete denaturation of proteins containing disulfide bonds requires cleavage of these bonds in addition to disruption of hydrophobic interactions and hydrogen bonds
Alpha helix
Proteins that are coiled together -Side chains point outward from an alpha helix *often a hydrophobic and hydrophilic side of the helix ^due to side chain that sick off of either sides of the helix ^often seen on tertiary structures -a region of alpha-helical secondary structure has N-terminus at the bottom and the C-terminus at the top . -Each carbonyl oxygen forms a hydrogen bond with the amide hydrogen of the fourth residue further toward the C-terminus of the polypeptide chain. -The hydrogen bonds are approximately parallel to the long axis of the helix ^Note that all the carbonyl groups point toward the c-terminus. -in an ideal alpha-helix, equivalent positions recur every 0.54nm (the pitch of the helix), each amino acid residue advances the helix by 0.15 nm along the long axis of the helix (the rise), and there are 3.6 amino acids residues per turn. ^ In a right-handed helix the backbone turns in a clockwise direction when viewed along the axis from its N-terminus. ^If you imagine that the right handed helix is a spiral staircase, you will be turning to the right as you walk down the staircase
The hydrophobic effect
Proteins are more stable in water when their hydrophobic side chains are aggregated in the protein interior rather than exposed on the surface to the aqueous medium
Secondary structure
Refers to whether a segment of a protein chain is coiled into an alpha helix or whether the chains are stacked into sheets -Refers to the regularities in local conformations maintained by hydrogen bonds between amid hydrogens and carbonyl oxygens of the peptide backbone *The short range conformation of the backbone chain -stabilized by hydrogen bonding between amide hydrogen's and carbonyl oxygen's of the polypeptide backbone
Interleukin-29 is a protein involved in the body's immune system, and it has an alpha-helical conformation. Is this an example of a primary, secondary, tertiary, or quaternary structure?
Secondary because there is only one alpha-helix
Myoglobin
Stores oxygen in the muscles
A lactase enzyme molecule can catalyze the breakdown of lactose because several helical segments of the lactase enzyme molecule are arranged to make a molecule that has a cavity shaped like a lactose molecule in which the lactose molecule can easily fit. Which is this structure most like?
Tertiary because these are helical segments of the same polypeptide bonds
Tertiary structure
The arrangement in 3D shape of segments of the same polypeptide chain relative to each other -This refers to how several helical segments or sheet segments of the same polypeptide chain are arranged in space relative to each other -Stabilized by the interactions of amino acid side chains in non-neighboring regions of the polypeptide chain *The formation of tertiary structures bring distant portions of primary and secondary structures close -tertiary structure results from the folding of a polypeptide into the closely packed three-dimensional structure ^primary structures are brought together through the interactions of among their side chains *stabilized primarily by noncovalent interactions (mostly hydrophobic effect) between the side chains of amino acid residues
Quaternary structure
The arrangement in 3D space of multiple polypeptide chains in proteins that have multiple polypeptide chain -Some proteins are made up of more than one polypeptide chain ^refers to how the separate chains are arranged in space relative to each other -When there is more than one polypeptide feeding into it ^work together for motion etc... -The association of two or more polypeptide chains into a multisubunit or oligomeric protein -refers to the organization and arrangement of subunits in a protein with multiple subunits ^each subunit is a separate polypeptide chain
Energy well of protein folding
The funnels represent the free-energy potential of folding proteins -a simplified funnel showing two possible pathways to the low energy native protein -In path B, the polypeptide enters a local low energy minimum as it folds -a more realistic version of the possible free-energy forms of a folding protein with many local peaks and dips
Do you think a leucine residue in hemoglobin would be more likely to be on the exterior of the protein, or at the interface between two of the polypeptide molecules that make up the hemoglobin when the protein is dissolved in water? (hint: think about which location is more exposed to water molecules)
The interface because less water is able to get in between the two polypeptides
k-casein also contains alanine residues. Do you think the alanine residues would be on the outside or inside of the globule protein when it is dissolved in water?
The interior because it has a hydrophobic side chain (CH3)
casein
The main protein in milk, provides dietary protein to mammalian young
Conformations
The spatial arrangement of atoms that depends on the rotation of a bond or bonds -can change without breaking the covalent bonds of a protein
reverse turns
the most common type of tight turn -also called beta-turns because they often connect different antiparallel beta strands -there are type I and type II of these turns ^both types of turn contain four amino acid residues and are stabilized by hydrogen bonding between the carbonyl oxygen and the hydrogen of the amide group of the fourth residue -both turns produce an abrupt (usually 180 degree) change in the direction of a polypeptide chain
Types of Alpha helices
3.6₁₃: The two residues are about 4 residues apart -go all the way around in a circle -3.6 residues per turns -13 backbone atoms per turn 3₁₀: -3 residues per turn -10 backbone atoms per turn ^Proline residues often disrupt alpha helices **Form from hydrogen bonding between amide groups ***There are other types of secondary structure
Describe what a "leucine zipper" is and explain why they are found in different proteins
A leucine zipper is a structure made of 2 parallel alpha-helical segments of a protein, which associate with each other because of the interactions between hydrophobic side chains of amino acid residues (often leucine residues) in 2 helices -leucine zippers bind DNA so many proteins involved in gene-expression feature of leucine zippers
What role does a molecular chaperone play in the body?
A molecular chaperone helps other proteins correctly fold into their proper tertiarry structures
Planar peptide groups in a polypeptide chain
A peptide group consists of the N-H and C double bond O groups involved in the formation of the peptide bond, as well as the alpha-carbons on each side of the peptide bond. -Two peptide groups are highlighted in this diagram
pepsin
Catalyzes the breakdown of food into smaller peptides in the stomach during digestion
trypsin
Catalyzes the breakdown of peptides (previously produced by food protein by the action of pepsin) in amino acids
Van der Waals
Contacts between nonpolar side chains also contribute to the stability of proteins -The extent of stabilization due to the optimized van der waals interactions is difficult to determine -the effects probably makes a significant contribution to stability because nonpolar side chains in the interior of a protein are densely packed -charge-charge interactions between oppositely charged side chains may make a small contribution to the stability of proteins but most ionic side chains are found on the surfaces where they are solvated and can contribute only minimally to the overall stabilization of the protein
Soap Micelle
Dissociates in water -proteins are similar ^hydrophilic face inside the globular protein ^hydrophobic face outside the globular *hydrophilic and hydrophobic groups are attracted to each other but are more attracted to like groups
amylase
catalyzes the breakdown of amylose and amylopectin (starch)
lactase
catalyzes the breakdown of lactose from milk into glucose and galactose
sucrase
catalyzes the breakdown of sucrose into glucose and fructose
alcohol dehydrogenase
catalyzes the conversion of ethanol to acetaldehyde during ethanol metabolism
Resonance structure of peptide bonds
- the peptide bond can be shown as a single C-N bond -the peptide bond can be shown as a double bond -The actual structure is best represented as a hybrid of the two resonance forms in which the electrons are delocalized over the carbonyl oxygen, the carbonyl carbon, and the amide nitrogen -Rotation around the C-N bond is restricted due to the double bond nature of the resonance hybrid form
Levels of protein structures
-The types of proteins build off of one another ^primary->secondary-> tertiary -relative to how proteins are arranged with each other
Describe how the intermolecular forces are involved in determining the tertiary structure of a protein
1. In an alpha-helical segment of a polypeptide, the hydrophobic side chain chains tend to fall on one side of the helix a. meanwhile, the hydrophilic side chains tend to fall on the other side 2. For this reason, when the protein is dissolved in water, the side of the helix with hydrophilic side chains will orient toward the exterior of the protein globule a. it is drawn by the attractions between the hydrophilic side chains and water molecules 3. Likewise, the side of the helix with the hydrophobic side chains will point toward the interior of the protein globule to minimize interactions between H2 molecules and the hydrophobic side chains 4. At the same time, the sides of the alpha-helices with hydrophobic side chains, or the sides of the beta-sheets that have hydrophobic side chains will associate with each other fixing alpha helices and beta-sheet segments in specific orientations relative to each other
On page 9 of the notes, which residues will have side chains that are pointing toward the interior of the protein? which residues would be pointed toward the exterior of the protein?
1. The alanine, valine, leucine, and isoleucine residues will have side chains that are pointing toward the interior of the protein because they have hydrophobic side chains 2. The asparate, arginine, serine, glutamate, asparagine, and glutamine residues will have side chains that are pointing toward the exterior of the protein
Determining protein structure
1. X-ray crystallization -has difficulty determining the three-dimensional structure of an entire protein 2. Nuclear magnetic resonance (NMR) spectroscopy -permits the study of proteins in a solution and doesn't require the preparation of crystals -The sample of the protein is placed in a magnetic field
Types of beta-strands
1. antiparallel: running opposite direction to N- to C- terminal direction 2. parallel: running in the same N- to C- terminal direction *less stable than antiparallel beta-sheets 3. a lot of strands make sheets *proteins can be BOTH alpha and beta
Name at least 2 human diseases which involve misshapen proteins
Individual answers may vary, but some well-known examples include 1. Alzheimer's disease, 2. Huntington's disease, 3.Rheumatoid arthritis, 4. Multiple Myeloma
Turns
Loops containing only a few (up to 5) residues -have to cause an abrupt change in the direction of the polypeptide chain
Will the reaction of acetic acid and k-casein be more hydrophobic or hydrophilic?
More hydrophobic because the ionic charge of the residue's side chain is cleaved
Lock and key mechanism
Most proteins must be in the correct 3-D conformation to work ex./ enzyme mechanism of lock and key -The active site of an enzyme must have the correct shape to work Application: Drug design -Build a molecule shapes like an enzyme active site -That molecule binds to the active site and blocks the substrate from entering e./ 6-mercapto purine: an anti-leukemia drug -blocks enzymes that help DNA production
Trans and cis conformations of a peptide group
Nearly all peptide groups in proteins are in the trans conformation -this minimizes steric interference between adjacent side chains -The arrows indicate the direction from the N to C terminus
Teprotide is component of the venom of a snake. The molecule is a modified peptide containing the sequence of amino acid residue WPRPQIPP. Do you think teprotide would have an alpha-helical conformation?
No because proline side chain is not able to hydrogen bond and would disrupt the hydrophilicity of other residues
Suppose you prepared a polypeptide made from a random mixture of amino acids. Would this peptide be considered a protein?
No because proteins require a specific arrangement/sequence of amino acid to have a function in the body
Suppose a synthetic polymer were prepared, with the repeat unit on page 5. Do you think this polymer would adopt a conformation similar to a beta sheet?
No because there is a methyl group on the nitrogen, so there is no possibility for hydrogen bonding
The protein k-casein has a globular shape and contains aspartate residues. Do you think the aspartate residues would be on the outside of a globular protein or the inside when the protein is dissolved in water?
On the outside because its side chain is hydrophilic
Primary structure
This is simply the sequence of amino acid residues in a protein - The linear sequence of amino acid residues in a protein ex./ fibroin in the main protein in silk (Gly-Ser-Gly-Ala-Gly-Ala)n
beta-sheets
When multiple beta strands are arranged side-by-side -stabilize by hydrogen bonds between the carbonyl oxygen's and the amide hydrogen on the adjacent beta-strands *sometimes called a beta-pleated sheet since the planar peptide groups meet each other at angles, like folds of an accordion
aggregation during folding in the absence of chaperones
due to the temporary formation of hydrophobic surfaces on folding intermediates ^The intermediates bind to the each other and the result is that they are taken out of the solution and are no longer able to explore the conformations represented by the energy funnel *chaperones isolate the polypeptide chains in the folding cavity and thus prevent the folding intermediates from aggregating
Configurations
a molecule can be changed only by breaking and reforming covalent bonds ex./ L and D forms of amino acids
kertatin
a structural protein that makes up hair skin and nails
denaturation
environmental changes or chemical treatments may disrupt the native conformation of a protein loss of biological activity - the amount of energy needed to cause denaturation is often small, perhaps equivalent to that needed for the disruption of three or four hydrogen bonds -some proteins can unfold completely when denatures to form a random coil (a fluctuating chain considered to be totally disorders) but most denatured proteins retain considerable internal structure -it is sometimes possible to find conditions under which small denatures proteins can spontaneously renature, or refold, following denaturation -proteins are commonly denatures by heating; under the appropriate conditions, a modest increase in temperature will result in unfolding and loss of secondary and tertiary structure -denaturation takes place over a relatively small range of temperature ^ this indicates that unfolding is cooperative process where the destabilization of just a few weak interactions leads to almost complete loss of native conformation -proteins can also be denatured by two types of chemicals- chaotropic agents and detergents
myosin
facilitates muscle contraction
hemoglobin
found in red blood cells, transports oxygen from the lungs to the body's cells
Domains
may consist of combinations of motifs. -The size of the domain varies from as a few 25-30 amino acid residues to more than 300 -ever domain is distinct compact units of the secondary structure -connected by loops of weak interactions *categorized as beta or alpha categories
Molecular chaperones
small molecules that help proteins fold into their correct tertiary structures 1. tertiary structures are often stabilized by disulfide bridges -increase the rate of correct folding of some proteins by binding newly synthesized polypeptides before they are completely folded. ^they prevent the formation of incorrectly folded intermediates that may trap the polypeptide in an aberrant for, -can also bind to unassembled protein subunits to prevent them from aggregating incorrectly and precipitating before they are assembles intoa somlete multisubunite protein
Fibrous protein
solids -form due to how alpha and beta are arranged with each other in one protein -provide mechanical support to cells or organisms
Oligomer
multisubunit protein -the subunits may be identical or different *when they are identical: dimers and tetramers predominate *when the subunits differ: each type often have a different function ^have a defined stereochemistry -determine composition with gel-filtration chromatography, or SDS polyacrlyamide gel electrophoresis 1. oligomers are usually more stable than their dissociated subunits suggesting that quaternary structure prolongs the life of a protein in vivo 2. The active sites of some oligomeric enzymes are formed by residues from adjacent polypeptide chains 3. The three-dimensional structures of many oligomeric proteins change when the proteins bind ligands. -both the tertiary structures of the subunits and the quaternary structures (i.e. the contacts between the subunits) may be altered -such changes are key elements in the regulation of the biological activity of certain oligomeric proteins 4. different proteins can share the same subunits. -since many subunits have a defined function (e.g. ligand bonding), evolution have favored selection for different combos of subunits to carry out related functions -this more efficient than selection for an entirely new monomeric protein that duplicates part of the function 5. A multisubunit protein may bring together two sequential enzymatic steps where the product of the first reaction becomes the substrate of the second reaction -This gives rise to the effect known as channeling
Loops
often contain hydrophilic residues and are usually found on the surfaces of proteins where they are exposed to solvent and formed hydrogen bonds with water -some loops consist of many residues of extended non-repetitive structure
part of k-casein protein has the amino acid residue sequence Pyr-Glu-Gln-Glu-Glu-Pro-Ile-Arg. Is this sequence the example of primary, secondary, tertiary, or quaternary.
primary because it is in the simplest form/sequence
Beta-strands
protein chains go straight for a while and then bends back -The ribbon shape hi-lights the backbone of the chain conformation -Proteins that are solids are usually beta-sheets -AKA portions of a polypeptide chain that are almost fully extended ^accounts for 0.32-0.34 nm of the overall length of the polypeptide chain, as opposed to the tight coil of the alpha-helix *proteins rarely consist of isolated beta strands because the structure by itself is not significantly more stable than other conformations **not just particular to the secondary structure; can be seen in tertiary even Quaternary structures -side chains orient above or below the strands ^hydrophilic side chains interact with the solvent and hydrophobic side chains interact with the hydrophobic core of the protein
In hemoglobin, four separate polypeptide chains associate together to form a ring shaped structure. Which structure is this?
quaternary because they are separate polypeptide chains associated with one another but not together
motifs
recognizable combos of alpha helices and beta strands, and loops that appear in a number of different proteins -sometimes associated with a particular function although structurally similar motifs may have different functions in different proteins 1. the simplest motif is the helix-loop-helix ^occurs in a number of calcium-binding proteins 2. The beta-meander motif: is an antiparallel beta sheet composed of sequential beta strands connected by loops or turns ^the same order as the order in the sequence of the polypeptide chain 3. The greek key: is a beta-sheet motif linking four antiparallel beta strands such as strands 3 and 4 from the outer edges of the sheet and strands 1 and 2 in the middle of the sheet 4. beta-sandwiches: the beta strands are connected by short loops and turns, but beta sandwiches cane also be forms by the interaction of two beta-sheets in different regions of the polypeptide chain
