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Pitt BIOSC 1000 - Secondary, Tertiary, and Quaternary Structure of Proteins
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BIOSC 1000 Lecture 4Outline of Last Lecture1. Amino Acids2. Peptides3. Characteristics of Primary Structures of Proteins Outline of Current Lecture1. Review of Peptides2. Properties of the Peptide Bond3. Secondary Structure of Proteins4. Tertiary Structure of Proteins5. Quaternary Structure of Proteins6. The Biological Protein Folding Problem Current Lecture1. Review of Peptides- Polypeptide “backbone”- Amino acids can be joined to form polypeptides – condensation reaction- Polypeptides can be cleaved to yield monomers – hydrolysis reaction- Free amino acids are zwitterions near neutral pH- Polypeptides have one N-terminus and one C-terminus and both termini will be charged near neutral pH – unless chemically modified or blocked- Polypeptide and protein sequences are written from N-terminus to C-terminus WITHOUT EXCEPTION- Peptide group contains 6 atoms –Ca1-CO-NH-Ca2-- Peptide group cannot be charged but forms H-bondso O and N are both electronegativeo O – acceptor; N –donor o Cis or trans peptide bonds Locate the two α C bonding the peptide bones  Trans – α Cs on opposite side of bonds – no steric hindrance Cis – steric clash – αCs on same side of peptide bonds  Trans predominates over cis conformation (2000:1) to avoid steric hindrance from bulky R-groups clashing into each other Trans is only slightly favored when Xxx-pro over cis (20:1) Peptide bond planarity means torsion angle ω is close to 180 degrees (meaning usually trans) or close to 0 degrees (meaning rarely cis) o2. Properties of the Peptide Bond – Example: Proline- To distinguish cis vs. trans peptide conformation, find both α-C next to one CO-NH bond. o If both α-C are on the same side – ciso If α-C are on opposite sides – trans- Φ and Ψ angles in the polypeptide backboneo Cα-C-N-Cα amide bond or torsion angle -- omega ωo Φ (phi bond)  C-N-Cα-C o Ψ (psi bond)  N-Cα-C-N When fully extended = 180°- Somewhat free rotation occurs about both Ψ and Φ (unlike ω) Consequently, 2 torsion angles define conformation of polypeptide backbone- Certain Φ and Ψ angle combinations are prohibited. o Two torsion angles define conformation of peptide bond-- Ramachandran Plots- Plot of observed Φ and Ψ angles showing sterically allowable conformationo Look where black dots lie – which quadrant3. Secondary Structures of Proteins- 1° structure  covalent arrangement of the amino acids in protein sequence plus disulfides- 2° structure  describes local spatial arrangements of groups of amino acidso some stable, recurring arrangements with regular phi and psi angles for each residue in the 2° structure α-helix β-conformation (or β-strand) β-turno Main goal: lowest free energy of conformation Maximize main-chain hydrogen bonding Maximize van der Waals contacts of main-chain atoms Minimize steric clashes between main-chain and side-chainatoms- Protein α-Helixo 3.6 resides/turno 5.4Å /turno α-helices are right-handedo right hand helix: follow the curl of your fingers of right hando N-terminus at topo Intrinsic electric dipole of magnitude proportional to α-helix lengtho Hydrogen Bonds: 2.8Å long, proton donor (amide grp, N-H) is the 4th residue from proton acceptor (carbonyl C=O)o Approx. parallel to helix axis, involves nearly all peptide bond NHand CO in H-bonds (except near helix ends) – confers exceptionalstability!o Backbone atoms in α helix core tightly packed to maximize van der Waals contacts and exclude free watero Side chain points away from a-helix and slightly toward N-terminus to avoid steric interference Pauling & Coreyo Alpha helix was first repetitive protein structure element recognized Makes up most of secondary structure o Exhibit electric dipole moment since all of the H-bonds have same polarityo The longer the helix, the greater the total dipole momento δ+ at the N-terminus; δ– at the C-Termins- Factors affecting stability of an α-helixo Amino acid sequence: Some AA adopt Ψ and Φ angles that increase propensity for adopting α-helical conformation- i.e. – Ala is good for a-helix; Pro & Gly are bado Relative side-chain position: Charged residues in same neighborhood of primary sequence affect α-helical propensity – spacing of 3 or 4 matter the most  Electrostatic attraction is good; repulsion is bad Amphipathic α-helices- Sometimes α-helices are hydrophilic on one face and hydrophobic on the other- Review: 5 constraints affect α-helix stabilityo 1. Electrostatic attraction or repulsion involving adjacent AAs with charged R group (repulsion is bad)o 2. Bulkiness of adjacent R groupso 3. Interactions between R groups ~ 3-4 residues aparto 4. Occurrence of Pro or Gly in sequence (usually excluded)o 5. Interaction between charges of AA R-groups at ends of an αhelical segment and the electric dipole inherent to the α-helix (acidic R groups favorable near N-terminus; basic R-groups favorable near C-terminus) 4-helix bundles- putting hydrophobic residues on the inside of helical bundle allows for great stability - β-conformation and β-sheetso β-conformation – extended zig-zag Align side by side Maximizes main-chain H-bonds and forms β-sheets Can be anti-parallel (MORE COMMON -- alternating NC & CN) or parallel(all NC) sometimes these are called β-pleated sheets: the H-bonds perpendicular and between strands AA-side chains alternate above and below the plane of the sheet, sheets often amphipathic (hydrophobic facing interior, hydrophilicon the surface) Anti-parallel sheets are more stable than parallel sheets, owing to stronger and more effective pattern of H-bonding between the strands (recall that straight H-bonds are stronger) Typically, sheets somewhat twisted in real proteins, usuallyin same right-handed sense sheets were second repetitive structure in proteins to be recognized, make of almost all of secondary structure in some proteins, and at least part of secondary structure in most o β-turns allow protein strands to reverse direction Type I Turn: Pro at 2nd position- (rigid backbone held in cis conformation conducive to reversing chain direction) Type II Turn: Gly at 3rd position- (smallest side chain, thus backbone conformation very flexible)- Turns were among first & most prevalent non-repetitive protein structure elements to be recognized and classified - Ramachandran


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Pitt BIOSC 1000 - Secondary, Tertiary, and Quaternary Structure of Proteins

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