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JBB2026 Fall 2018 Gil Privé Protein Structure • Peptide Conformations

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JBB2026 Fall 2018 Gil Privé Protein Structure • Peptide Conformations JBB2026 Fall 2018 Gil Privé Protein Structure • peptide conformations and residue preferences • elements of secondary structure • supersecondary structure and motifs • packing of helices and sheets • chain topologies • internal packing • protein interfaces • membrane proteins • multimeric proteins • domain motions The Machinery of Life David S. Goodsell http://mgl.scripps.edu/people/goodsell Figure 1. Transcription and RNA processing in the nucleus. Figure 2. Transport through the nuclear pore. Figure 3. Endoplasmic reticulum. Figure 4. Transport from the endoplasmic reticulum. Figure 5. Protein sorting in the Golgi. Plasma cell - IgG secretion Figure 6. Transport from the Golgi. Figure 7. Transport of a vesicle through the cytoplasm. David Goodsell The Machinery of Life Figure 8. Export of proteins across the cell membrane. http://www.3dmoleculardesigns.com/Teacher-Resources/Tour-of-a-Human-Cell.htm Eukaryotic cell panorama 1. Transcription and RNA processing in the nucleus. 2. Transport through the nuclear pore. Biochemistry and Molecular Biology Education Yellow: DNA, proteins Volume 39, Issue 2, pages 91-101, 28 MAR 2011 DOI: 10.1002/bmb.20494 Pink: RNA, proteins http://onlinelibrary.wiley.com/doi/10.1002/bmb.20494/full#fig2 Blue: Cytoplasmic proteins http://www.3dmoleculardesigns.com/Teacher-Resources/Tour-of-a-Human-Cell.htm Purple: Ribosomes Green: Membranes,proteins 1. Transcription and RNA 2. Transport through the 3. Endoplasmic reticulum. processing in the nucleus. nuclear pore. 4. Transport from the endoplasmic reticulum. 5. Protein sorting in the golgi. 6. Transport from the golgi. 7. Transport of a vesicle 8. Export of proteins across the through the cytoplasm. cell membrane. Tyr Thr Gly Cys Ile Ile Ala Gly The structure (conformer) defined by the dihedral angles main chain (φ,ψ) side chains (!1, !2, …) φ =180 ; ψ=180 φ =-60 ; ψ=-45 φ ψ ω φ ψ Note: unsaturated C-N bond length is 1.45 Å -Peptide bond has ~40% double bond character - dihedral is constrained. ω is constrained to ~180° (trans peptide - we will revisit this). Bond lengths Bond angles Dihedrals sp2-hybridized atoms Shorter 120° (flat) More restrained (trans) sp3-hybridized atoms longer 109° (tetrahedral, Less restrained often chiral) (gauche-, gauche+, trans) One way of categorizing the 20 amino acids - each amino acid has particular characteristics Amino acid hydrophobicity Relevant amino acid properties Size (number of atoms) Shape (torsion angles) Flexibility (how many degrees of freedom?) Charge (N , O ; pKa values) Polarity (electronic structure) Hydrophobicity Aromaticity (F, Y) Protein conformations The conformation is the arrangement of the atoms in 3D space. The most stable conformation is at a potential energy minimum Proper treatment is quantum mechanical - but this is intractable with proteins (too many atoms). We use Newtonian mechanics and describe the system as a set of potential energy terms, each with a particular form. The overall potential energy can be broken down into a set of energy functions: LOCAL bond length (1,2) (strong) bond angle (1,3) (strong) dihedral angle (1,4) (medium) NON-LOCAL solvation / hydrophobic effect van der Waals (packing, steric clashes) electrostatics (incl. hydrogen bonds) conformational entropy These are additive: calculate the overall potential energy as the sum of these individual functions LOCAL bond length (1,2) bond angle (1,3) dihedral angle (1,4) NON-LOCAL van der Waals (packing, steric clashes) electrostatics (incl. hydrogen bonds) hydrophobic effect … E = f(bonds, angles, dihedrals, vdW, electrostatics, hydrophobic effect, ...) E = f(x,y,z) Can describe the energy of the system from the positions of the atoms! (need to consider the structure of the entire system, including waters) The structure (conformer) defined by the dihedral angles main chain (φ,ψ) side chains (!1, !2, …) The minimum energy conformer of the polymer is determined largely by the non-local interactions between the side chains. D. Goodsell Non-local molecular interactions attractive or distance Type repulsive? dependance Basis for van der Short Range Pauli exclusion Repulsive 1/r12 Waals radii of atoms * Electrostatic either; depends on Coulomb’s law 1/r (charge-charge) q1q2 either; depends of the involves polar Dipole-dipole Keesom interactions 1/r3 directions of the dipole molecules/groups moments polarization: Dipole-induced dipole Debye interactions attractive 1/r4 change in a dipole due to an external electronic field. Charge-dipole attractive London dispersive resonant induced Fluctuating dipoles attractive 1/r6 interactions dipoles * often treated as Hydrogen bond attractive electrostatic similar to charge- Cation-pi attractive induced dipole Hydrophobic effect Loren Williams website http://ww2.chemistry.gatech.edu/~lw26/structure/molecular_interactions/mol_int.html *Lennard-Jones “6-12” potential Lennard-Jones “6-12” potential ro: sum of the van der Waals radii of the two atoms vdW contact H-bonded 1.5 1.6 1.5 1.6 1.0 1.0 1.0 1.0 O H N O H N 3.5 Å 2.6 Å r(oxygen) 1.5 Å r(hydrogen) 1.0 Å closer contact than sum of radii r(nitrogen) 1.6 Å http://ww2.chemistry.gatech.edu/~lw26/structure/molecular_interactions/mol_int.html http://ww2.chemistry.gatech.edu/~lw26/structure/molecular_interactions/mol_int.html Hydrogen bonds - often high cooperative; zipper effect Figure 25. Self assembly of biological macromolecules is driven by complementary hydrogen-bonding interactions. (Left) Base pairing between complementary hydrogen bond donors and acceptors on the sidechains of nucleic acids. (Center) Backbone assembly between self-complementary hydrogen bond donors and acceptors of the protein backbone to form anti-parallel β-strands in a β-sheet, and (Right) Self-complementary hydrogen bond donors and acceptors in carbohydrate, between glucose moieties within cellulose. http://ww2.chemistry.gatech.edu/~lw26/structure/molecular_interactions/mol_int.html Partial charges in peptide produces dipoles bond dipoles 3.7 Debye (10-18 esu*cm) peptide group dipoles These are additive and can produce a macroscopic C dipole (esp. in α-helices). Alpha helix Hydrogen bond between carbonyl of residue i with amide-H of residue i + 4 i i+1 i+2 i+3 i+4 i+5 i+6 i+7 N N C Milner-White, Protein Science 6, 2477 (1997) The hydrophobic effect water molecules adjacent to a hydrocarbon molecule maintain their molecular interactions by sacrificing rotational and translational freedom. fewer low entropy waters Figure 32 shows how aggregation of hydrocarbon molecules causes the release of interfacial water molecules. Therefore the system gains entropy (positive TΔS) upon hydrocarbon aggregation. Release of low entropy interfacial water molecules into the bulk solution drives hydrocarbon aggregation. The bottom panel illustrates that there is more interfacial water on the left hand side of the equation than on the right hand side. http://ww2.chemistry.gatech.edu/~lw26/structure/molecular_interactions/mol_int.html Dihedrals revisited Main Chain Calculated energy surface “Classic” Ramachandran Plot (theoretical) Based on hard sphere potentials (sum off vdw radii; simple form of the L-J potential) Conformational energy of butane as a function of the central torsion angle Boltzman distribution: Populate according to energies 4 0 3 9 3 8 3 7 3 6 potential energy (kcal/mol) 35 0 90 180 270 360 e g+ t g- e Torsion angle (°) Population: 0% 15% 70% 15% 0% Potential surfaces for side chain dihedral angles This defines the major rotamers for each amino acid. E.g. χ 1 χ 2 plot for Phenylalanine gauche- χ 2 χ2 χ1 gauche+ φ ψ χ 1 Why can’t Phe χ 2 be trans? gauche- gauche+ trans Ch1 - Chi2 plots φ ψ omega From: Introduction to Protein Structure (Branden and Tooze) Potential energy curve for the peptide omega dihedral angle : Barriers for dihedral angle rotation can be attributed to the electronic structure of the amide bond (delocalized). Energy difference between cis and trans can be attributed to: -the exchange interaction of electrons in adjacent bonds -repulsive interactions between overlapping bond orbitals - steric clashes between atoms (Clash between groups 1 and 4 in the 1,4 bond disfavors cis). Note : only two minima here- why? Xaa-Pro is an exception (peptide bond preceding a proline) - lower barrier to interconversion - only ~2 kcal/mol energy difference between cis and trans omega bond - but slow interconversion (usu. needs to be catalyzed to equilibrate) - ~6% of Xaa-Pro have cis omega angles, otherwise v. rare (<0.5%) The only kind of of symmetric three dimensional structure for a linear polymer is a helix Helix: combination of a rotation and a translation (screw) n: residues per turn d: rise per residue (Å) (other parameters include pitch, twist, …) In this example, n = 8 d Snake toy Features: • Fixed bond lengths and angles • 8-fold torsional potential minima at φ = 0, 45, 90, 135, 180, 225, 270, 315, 360° • Linear polymer of 11 units 811 = 8.6 X 109 conformers! (not all are accessible) • Torsion dihedral is not colinear with the chain This makes it interesting… the toy would be pretty boring otherwise. But note that the angles are not the same as in a peptide Twist/step 0° 45° 90° 180° Name Frequency* φ (°) ψ (°) n d (Å) H-bonding 310 helix ~4% -74 -4 +3.0 2 i,i+3 α helix ~35% -57 -47 +3.6 1.5 i,i+4 αL helix - +57 +47 -3.6 1.5 i,i+4 Π helix - -57 -70 +4.3 1.1 i,i+5 Collagen (PP type II) Fibres -78 +149 -3.3 2.9 planar β-sheet (para) - -115 +115 2 3.2 twisted β- sheet parallel ~25% -120 +135 -2.3 3.3 interstrand twisted β- sheet antiparallel ~8 -139 +135 -2.3 3.3 interstrand B-DNA - - 10 3.4 interchain *Crude estimate in globular proteins β α Three rules for secondary structure 1) Local “bonded” potentials must be minimized - bond lengths (1,2) - bond angles (1,3) - dihedrals (1,4) (Ramachandran) regular: all (phi,psi) the same 2) Satisfy main chain hydrogen bonding - Typically, >90% of the potential backbone hydrogen bond donors and acceptors are involved in hydrogen bonds 3) No unfavourable steric interactions - Ramachandran Observed (φ,ψ) distributions from over 500 high quality experimental structures (97,368 residues) From: Lovell et al.
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