lecture 4 - 4-1MCB354Lecture 4Reading in Lehninger:Chapter...

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Unformatted text preview: 4-1MCB354Lecture 4Reading in Lehninger:Chapter 4Secondary Structure of Proteinsα-helicesβ-sheetsβ-turnsBiological macromolecules are stabilized by interactions:StrongWeakCovalent bondsIonic interactionsIon-dipole interactionsVan der Waals interactionsHydrogen bondsHydrophobic interactions4-24-3Particularly stable arrangementsof ααresidues giving rise toregular folding patternsof thepolypeptide backbone3-D foldingof a polypeptide:i) simple combinations of 2° structuralelements = “motifs”ii) combination of motifs into “domains” Secondary structure of proteinsPeptide bond has partial double bond character4-4is 6% ofbonds w. Pro.unable to rotatefreelybecause ofpartial double bond characterrotation permittedabout N-Cαand Cα-C bondsATOMS LIEIN PLANE4-5Peptide bond is rigid and planarThe Dihedral Angle4-6polypeptide in fully extended conformation with all peptide groups in the same plane:then, by convention, both φand ψare defined as 180°.N-Cαbond angle φCα-C bond angle ψ4-7φand ψanglesNot all φand ψangles are allowed 4-8eg. if we try to rotate the bonds flanking Cαsuch that both φand ψ= 0°, and the two peptidebonds flanking that α-carbon are in the sameplane, it won’t work, because of steric overlapbetween an αcarbonyl Oand an α-amino HRamachandran plot4-9Fully allowed conformations,no steric overlapIN DARKEST BLUEConformations allowed at limitsfor unfavorable atomic contactsConformations permissible if a...
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lecture 4 - 4-1MCB354Lecture 4Reading in Lehninger:Chapter...

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