Protein Structure

• Stryer 2nd or 3rd Edition provides Text Readings for all of Chapter 4.
• The objectives are to:
  • Characterize the nature of the peptide bond.
  • Define the different levels of protein structure.
  • Examine the characteristics of the different types of secondary structure.
  • Examine the forces involved in protein folding and stability.
  • Investigate the structure/function relationship of select proteins.

Peptide Bonds - General

• Peptide bonds are covalent linkages between amino acids.
• Peptide bonds form by condensation reactions involving the loss of a water molecule.
• Formation of peptide bonds eliminates the α-carboxyl and α-amino charged groups.
  • This is important for protein folding.
• Peptide bonds are the same, regardless of the amino acids that are joined.

Peptide Bonds - Polypeptide Main Chains

• Constant patterns repeat within the main chain because peptides bonds are conserved,
• The main chain is constant portion of the polypeptide, with variable side chains.
• The main-chain has a repeating pattern of NCCNCC.

Peptide Bonds - Partial Double Bond Characteristic

• Rotation is restricted around the C-N peptide bond due to its partial double-bond characteristic.
• Six atoms of the peptide group are rigid and planar because of the double bond characteristic.

Peptide Bonds - Configuration

• The partial double bond of the peptide bond creates cis-trans isomers.
• The oxygen of the carbonyl group and the hydrogen of the amide nitrogen are usually trans to each other.
• The trans configuration is favored because the cis configuration is more likely to cause steric interference between side chain groups.
• Steric exclusion means that two groups cannot occupy the same space at the same time.

Proteins - Four Levels of Protein Structure

• Primary Structure refers to the linear sequence of amino acids.
• Secondary Structure refers to localized interactions within a polypeptide.
• Tertiary Structure refers to the final folding pattern of a single polypeptide.
• Quaternary Structure refers to the folding pattern when multiple polypeptides are involved.

Primary Structure - General

• Defines the linear arrangement of amino acids in a polypeptide.
• Primary structure is presented from the N (amino) terminus to the C (carboxyl) terminus.
• An example of this is: Tyr-Gly-Gly-Phe-Leu or YGGFL.
• The information specifying correct folding is contained within the primary structure.
• Reliably predicting a three-dimensional structure based on the primary structure is not possible.
• Primary structure is often determined by investigation of the corresponding gene.

Secondary Structure - General

• Represents localized patterns of folding in a polypeptide.
• Maintained by hydrogen bonds between main-chain amide and carbonyl groups.
• Examples include α-Helicies and β-Sheets.
• Elements of secondary structure are found in different proteins.
• They retain the same characteristics regardless of protein context.
• Optimization must occur in the hydrogen bonding potential of main-chain carbonyl and amide groups for viable forms of secondary structure.
• There must be a favored representation of conformation of the polypeptide chain.
• Each peptide bond has a hydrogen bond donor and acceptor group.
• Number of hydrogen bond donors and acceptors are equal within the polypeptide main-chain.
  • This is important for optimizing hydrogen bonds.

Secondary Structure - Conformation of the Polypeptide Chain

• Each α-carbon is held within the main-chain through single bonds, about which there is complete freedom of rotation.
• Bonds are defined as Phi (Φ) Ca-N and Psi (ψ) Ca-C.
• The phi and psi can each theoretically range from -180 to 180.
• Steric interference prevents the formation of most conformations.
• Ramachandran plots illustrate the possible combinations of phi and psi.
• Highlighted are combinations of phi and psi actually observed in proteins.
• These favored conformations correspond to the common elements of secondary structures.

α-Helix - Discovery

• The first type of secondary structure.
• In 1948 Linus Pauling spent a day sick in bed reading detective stories.
• Linus then began to doodle.
• For this he received the Nobel Prize in Chemistry in 1954.

α-Helix - Hydrogen Bonds

• Right-handed helix with 3.6 residues/turn is created.
• Stabilized by hydrogen bonds, which run parallel to the axis of the helix.
• Carbonyl groups point toward the C-terminus and amide groups point to the N-terminus.
• Each carbonyl of residue "n" hydrogen bonds with amide group of residue "n+4".

α-Helix - Amino Acid Sequence Affect Stability

• Most sequences form an α-helix following certain guidelines and trends.
• Proline, because of its rigidity, is not usually found in α-helicies.
• Glycine, because of its flexibility, is also uncommon in α-helicies.
• Amino acids with side chain branches (Val, Thr, Ile) are less common because of interference.
• Amino acids with hydrogen bonding groups near the main-chain (Ser, Asp, Asn) are also less common.
• Charged residues tend to be positioned to form favorable ion pairs (residues of opposite charge separated by 3-4 positions).

α-Helix - The Helix Dipole

• Every peptide bond has a small electrical dipole.
• Hydrogen bonding communicates each dipole through the helix giving a net dipole.
  • N terminus has partial positive dipole charge.
  • C terminus has partial negative dipole charge.
• Dipole is stabilized by resides at each termini whose charge opposes the helix dipole.
  • Negatively charged residues (Asp, Glu) at the N terminus
  • Positively charged residues (Lys, Arg, His) at the C terminus

α-Helix - Amphipathic Helicies

• Residue is separated by three to four position in the primary sequence will be be on the same side of an α-helix with both polar and nonpolar faces.
• Residue is separated by two residues in the primary structure on opposite sides of the helix.
• Positioning of hydrophilic and hydrophobic residues within the primary structure generates am amphipathic helix with polar and non-polar faces.

β Sheets - General

• Discovered after alpha-sheets.
• Sheets involve multiple β strands arranged side-by-side
• β sheets are made up of β stands that are individual components, assembled within sheets.
• Number of β sheets often involves 4 or 5 β strands.
• Conformation of β Sheets are made of fully extended polypeptide chains.
• Stabilized by hydrogen bonds between C=O and -NH on adjacent strands.

β Sheets - Parallel and Anti-parallel

• Sheets are either parallel or antiparallel
• Strands run in the the same direction in parallel β sheets.
• Strands run in opposite direction in anti-parallel ẞ sheets.
• Anti-parallel ẞ sheets are more stable due to better geometry of hydrogen bonding.

β Sheets - Mixed -β-sheets

• β sheets can be parallel, anti-parallel, or mixed.
• Mixed β sheets contain both parallel and antiparallel β strands.

ẞ Sheets - Amphipathic ẞ Sheets-

• Side chains tend to alternate above and below the polypeptide chain.
• Alternating polar and non-polar residues within the primary structure of a beta sheet will result in an amphipathic beta sheet.

Proteins - Tertiary Structure

• Represents the final folding pattern of a single polypeptide.
• The biological active folding pattern is called the native conformation.
• The amino acid sequence determines tertiary structure.
• Describes the long range aspects of sequence interactions within a polypeptide.
• Residues separated by great distances in primary structure may be in close proximity.
• Different proteins have different structures which relate to their functions.
• Structures of different proteins vary in their content of alpha helicies and beta sheets.

Proteins - Conformation is Stabilized by Weak Interactions-

• Proteins are only marginally stable (stability is defined as the tendency to maintain a native conformation).
• Stabilizing protein structure predominates in weak interactions, not covalent interactions.
• The protein conformation with the lowest free energy (the most stable) is usually the one with the maximum number of weak interactions.
• The stability of protein reflects the difference in free energies of the folded and unfolded states.

Proteins - Folding

• Folded proteins occupy a low-energy state of great stability.
  • This low-energy state may be only marginally stable.
• Protein folding happens rapidly, and don't sample all folding patterns.
• Folding is funnel-shaped, where unstable conformations collapse to a single, stable folding pattern.
• Some proteins spontaneously fold to their native conformations:
  • Other proteins require the help of chaperones.

Proteins - Denaturation

• Protein denaturation is the disruption of native conformation with loss of biological activity.
  • The energy required is often small: perhaps only a few hydrogen bonds.
• Protein folding and denaturation is a cooperative.
• Denaturation is reversible for many proteins.

Proteins -Quaternary Structure

• Multiple subunits in which each subunit is a separate polypeptide.
• May involve multiple subunits of the same polypeptide or different polypeptides.
• Subunits usually associate through non-covalent interactions.
• Reserved for proteins of more complex biological function.

Proteins -Quaternary Structure

• Stabilizes subunits, and prolongs life of protein.
• Creates unique active sites as produced at the interfaces between subunits.
• Facilitates unique and dynamic combinations of structure/function through physiological changes in tertiary and quaternary structure(Hemoglobin).
• Conserves functional subunits, more efficient than selecting a new protein with the ideal function.

Proteins -Structure and Function

• Biological roles of proteins that:
  • Act as Enzymes
  • Are for storage and transport
  • Give physical cell shape and structure
  • Create mechanical movement
  • Act as Decoding cell information
  • Can be Hormones, enzymes, or Hormone receptors
  • Many more are also possible
• Diversity of function is enabled by the diversity of the structure.
• Proteins show extreme structural and functional diversity.

Proteins -Numbers and Diversity

• Varying organisms have differing amounts of proteins:
  • Bacteria have ~ 5,000 proteins
  • Fruit flies have ~ 16,000 proteins
  • Humans have ~25,000 proteins
• Additional isoforms are generated through post-translational modification which this represents the minimum number of proteins.
• There could be up to one million different protein isoforms for humans.

Proteins - Size

• Proteins are typically 100 to 1,000 amino acids.
• At 51 amino acids, it marks when a polypeptide becomes a protein.
• The largest protein discovered is Titin, containing 34,350 amino acids.
• Amino acids of a protein are estimated by dividing the proteins molecular weight by 110.

Proteins - Five Important Facts-

• Protein function depends on its structure.
• Structure of a protein is determined by its amino acid sequence.
• Stabilizing protein structure depends on weak interactions.
• There are common structural patterns among all proteins.
• An isolated protein usually exists in one, or a small number, of structural forms.

Questions cover peptide bonds, cis/trans configurations, proline's role, and primary, secondary, tertiary, and quaternary protein structures. Also addresses steric exclusion, denaturation, and hydrogen bonds.