Protein 3D Structure PDF

Protein 3D Structure (Secondary Structure) Chapter 4  Protein 3D Structure 1. Describe the four levels of protein structure. 2. Draw the resonance structures that contribute to the peptide bond and describe its properties – including conformational flexibility. 3. Identify c...

Protein 3D Structure (Secondary Structure) Chapter 4  Protein 3D Structure 1. Describe the four levels of protein structure. 2. Draw the resonance structures that contribute to the peptide bond and describe its properties – including conformational flexibility. 3. Identify cis and trans peptide bonds. State the configuration that is most stable and common in proteins and provide an explanation for its prevalence. 4. Define psi and phi angles. 5. Interpret a Ramachandran diagram and describe the information it conveys. 6. Identify and describe common secondary structures (α-helix, β-sheet, β- turn, etc.). List the non-covalent interactions that stabilize these secondary structure. State the H-bonding patterns that are characteristic in each structure. 7. State how different helical structures can be distinguished from one another. 8. Define secondary structure propensity for an amino acid. Explain the impact of Gly and Pro on helix structure. 9. Describe the basic structure of a β-turn including the number of amino acids involved and the interactions that stabilize the structure. 10. Compare and contrast different types of β-turns. Describe the structural differences and predict the impact of amino acid composition in these structures. Levels of Protein Structure Protein = polypeptide chain / chain of amino acids linked by peptide bonds Primary structure: sequence of a.a in a protein Secondary structure: Local folding/arrangement of backbone atoms Tertiary structure: 3D structure of entire polypeptide chain Combination of secondary structures Packing of side chains 3D structure - proteins fold When folding, proteins aim to: Minimize steric repulsions Maximize favorable non-covalent interactions, e.g - Ex: H-bonds, ionic interactions, dipole interaction, van der waals Properties of bonds in the peptide backbone: The peptide bond rotation restricted rotation possible Resonance causes peptide bonds to Have partial double bond character (NO free rotation) be quite rigid and nearly planar Exhibit a dipole moment Configuration of peptide bonds Cis: α-carbons on adjoining amino acids are on the same side of the peptide bond Trans: α-carbons on adjoining amino acids are on opposite sides of the peptide bond Trans vs cis peptide bond configuration The trans configuration is more favored/stable than cis H Cα Minimizes potential steric N clashes between R-groups C Cα O > 99% of peptide bonds not Trans Cis involving Pro are in the trans config. Look at orientation of alpha-carbons on either side of peptide bond to determine if it is a cis or trans Why is Pro the exception? peptide bond. 50% cis & 50% trans *Side chains covalently linked to backbone Extended Conformation of Polypeptide: R groups tend to alternate extending above and below the polypeptide chain Properties of bonds in the peptide backbone: The other bonds in the backbone can rotate freely The other two bonds are connected to the alpha carbon φ (phi): angle around the C𝝰- N bond ψ (psi): angle around C𝝰- C bond Favorable phi angles minimize repulsion between the R-group & C=O (n - 1 AA) Favorable psi angles minimize repulsion Animation: between the R-group & C=O http://www.umass.edu/molvis/workshop/imgs/phipsi an.htm Distribution of ϕ and ψ Dihedral Angles Some ϕ and ψ combinations are unfavorable because of steric crowding between atoms Some ϕ and ψ combinations are more favorable because they allow H-bonding interactions along the backbone Ramachandran plot shows the POSSIBLE distribution of ALLOWED ϕ and ψ dihedral angles for a particular peptide Ramachandran Diagram common secondary structure elements will map to a certain location on the Ramachandran Plot Beta sheets blue-shaded regions indicate favorable Collagen helix (sterically allowed) phi & psi angles Left-handed helix green-shaded regions indicate permitted phi & psi angles Alpha helix tan space indicates forbidden phi & psi angles yellow circles represent conformational angles of several common secondary structures ⇈ Parallel Applies to all residues except proline ⇅ Not parallel Examples of Regular Secondary Structures All have characteristic Phi and psi angles Hydrogen bond patterns Examples Alpha Helix β sheets (parallel and antiparallel) Left handed helix The α Helix Right Handed Backbone proceeds up/to the right One turn: 3.6 residues (5.4 angstroms) Pitch (height per turn): 5.4 Å Rise (height per aa): 1.5 Å The carbonyl oxygen from the backbone of the nth residue hydrogen bonds with the Side chains project outward and downward from helix Net dipole exists Helical Wheel Shows 3D arrangement between side chains in an alpha helix allows you to see which amino acids H bond are on the same “face” of a helix. sidechain of i aa is next to sidechains at i + 3 & i + 4 positions ionic hydrophobic interaction residue They can often have complementary properties, E.g. Hbond donor+acceptor Positive + negative charge The α Helix: Space Filling Model The outer diameter of the helix (with side chains) is 10 – 12 Å Happens to fit well into the major groove of DNA the core of the alpha helix is tightly packed Backbone atoms are in van der Waals contact Favorable dispersion forces Oxy-Myoglobin PDBid 1A6M β Sheets β Strand: stretch of polypeptide in an extended conformation β sheet: formed from H bonding between β Strands Like alpha helices, hydrogen bonding use backbone atoms Unlike alpha helices, hydrogen bonding is between neighboring strands Two β sheet conformations Parallel Antiparallel Which of these is more stable? Anti-parallel β Sheets  3 - 10 helix Other helical structures 𝛼-helix 𝜋-helix Sequence Affects 2º Structure Not all polypeptide sequences can adopt stable α-helical or β sheet structures. Small hydrophobic residues such as Ala are strong helix formers Proline not favored in alpha helix or beta sheet structure (known as helix breaker) Gly also not favored in helix Large conformational flexibility Incorporation into helix is entropically unfavorable  Proline can’t donate H-bond in an 𝞪-helix (helix breaker!) NAPL Turns and loops loops Bovine Carboxypeptidase A Protein tertiary structure is the combination of different secondary structures -includes helices, β strands, and their connecting turns & loops turns β turns Simplest turn in a polypeptide Comprised of 4 amino acids Result in a 180 degree turn in direction of the polypeptide Also known as reverse turns Different types exist Each is defined by the arrangement of the atoms in the 4AAs Certain positions are enriched in certain amino acids Type I and Type II β turns AA2 is often a proline – this causes a kink (first part of turn). Turn is stabilized by H bond between C=O of AA1 & NH of AA4 Difference between Type I and II turns: orientation of carbonyl Type 1 Type 2 of AA2 Type I and Type II β turns In Type II turns, the oxygen atom of residue 2 of the turn AA would crowd the Cβ atom of 4 f residue 3. Therefore residue 3 AA is often a glycine 3 e d b c a Which atoms are we talking about in AA the description above? 2 AA 1