CHEM 3510 CHEM3510
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This 3 page Class Notes was uploaded by Amalachi Notetaker on Friday September 9, 2016. The Class Notes belongs to CHEM3510 at University of Toledo taught by Bellizzi,J in Fall 2016. Since its upload, it has received 63 views. For similar materials see Biochemistry I in Natural Sciences and Mathematics at University of Toledo.
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Date Created: 09/09/16
Lecture 8: Primary and Secondary Structure of Proteins Levels of Protein Structure 2 Primary – covalent linkage of polypeptide chain (sequence of amino acids) Secondary – specific stable conformations involving noncovalent interactions between amino acid residues close together in sequence Tertiary – 3D structure formed as secondary structural units pack together (overall “fold”) Quaternary –noncovalent association of multiple polypeptide chains (subunits) Primary Structure of a Protein The primary structure is the sequence of amino acids in a protein. • Fully describes the covalent linkages between atoms: which amino acids, in what order (plus disulfide bonds, if any) • The defining characteristic of a protein (different primary structure= different protein). • The final conformation of the protein (secondary, tertiary, quaternary structure) arises spontaneously from the primary structure! • Comparison of primary structures can help us understand/ predict structure, function and molecular evolution Protein Backbone Conformations • Conformation of polypeptide chain determined by rotation of these peptide planes about the N Cα bond and the Cα C bond Dihedral Angles Torsional angles of peptide backbone that describe the conformation. Values from 0° (anti) to ±180°(eclipsed) φ = NCα bond ψ= CαC bond ω = peptide bond Dihedral Angles Not all combinations of φ, ψ are possible due to steric repulsion 99.5% of peptide bonds are in the trans configuration (ω= ±180°) cispeptide (ω= 0°) sterically unfavorable (side chain steric clash). Almost never seen except Pro (~6% of the time) Ramachandran Plot • Not all dihedral angles are possible (steric repulsion) • G.N. Ramachandran predicted which combinations of φ, ψ are possible (without steric collisions) • Glycine has more accessible combinations of φ, ψ than the other amino acids (why?) Protein Secondary Structure Segment of polypeptide chain where consecutive peptide bonds have the same φ, ψ angles. Characteristics: • Sterically allowed combinations of φ, ψ • Stabilized by intramolecular Hbonds between backbone atoms (amide NH donor, carbonyl O acceptor). Proteins are mostly made up of two secondary structural elements: • αhelices • βstrands (which assemble into βsheets) The αhelix Right handed helix φ = 57°, ψ = 47° 3.6 residues/turn Pitch = 5.4 Å/turn Rise = 5.4/3.6 = 1.5 Å/residue Hbonds between carbonyl of residue i and amide NH of residue i+4. Overall helical dipole moment The αhelix Side chains project out and “down” (towards Nterminus). “Upsidedown Christmas tree” Side chains 34 residues away in sequence are close to each other in 3D space (helical wheel). Some sequences are more likely to form stable α helices than others Helical propensity (does side chain restrict φ, ψ angles?) Pro and Gly are helix breakers Consecutive residues with like charges or adjacent bulky/branched residues are not common Negatively charged side chains occur more often at the aminoterminal end of helix and vice versa. βStrands • Extended conformation of protein backbone = βstrand (close to a completely anti/staggered hydrocarbon chain) • Backbone Hbond donors and acceptors not pointing towards each other. • Instead, NH forms Hbonds with O on adjacent βstrand βSheets • βstrands organize into βsheets • Adjacent strands Hbond to each other • Side chains alternate projecting above and below plane of sheet • Sheet is pleated • Sheet may be all parallel, all antiparallel, or mixed. • Antiparallel βsheets • φ = 139°, ψ = 135° • 3.5 Å/residue • Parallel βsheets • φ = 119°, ψ = 113° • 3.25 Å/residue Coils and loops “Random coils” (aka coil, loop) • Region of chain without regular secondary structure. • Not actually random – has a specific conformation (but may be highly flexible). • Each residue has a φ, ψ different from its neighbors. Reverse turns • In between βstrands and αhelices, reverse turns change the direction of the chain. • γturns (only one residue involved in turn) • βturns (two residues involved in turn) • Most common, occur in several different varieties • Residues 2 and 3 do not participate in Hbonding. • Type I – residue 2 is usually Pro (sometimes cis) • Type II– residue 3 is Gly (notice φ, ψ angles!)
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