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lecture6.pdflecture6a.pdfLectures 6-8: Protein Architecture• Forces Influencing Protein Structure• Role of the Amino Acid Sequence in Protein Structure• Secondary Structure of Proteins• Protein Folding and Tertiary Structure• Subunit Interactions and Quaternary StructureThe Weak Forces• van der Waals: 0.4 - 4 kJ/mol• hydrogen bonds: 12-30 kJ/mol• ionic bonds: 20 kJ/mol• hydrophobic interactions: <40 kJ/molIonic InteractionsHydrophobic Interactions• Transfer free energy is about 0.7 kJ/mol per methylene group• Calculation of hydrophobic energy requires calculation of accessiblesurface area (ASA) of hydrophobic groupsThe Role of the Sequence in Protein StructureChristian Anfinsen (1957). All of the information necessary for folding thepeptide chain into its "native” structure is contained in the primary amino acidstructure of the peptide.Ribonuclease ASecondary Structure• Two rotational degrees of freedom per residuefor the peptide chain• Resonance stabilization energy of the planaramide structure is 88 kJ/mol (kT~2.5 kJ/mol)• Amide is locked planar and (usually) trans• Angle about the Ca-N bond is denoted phi (f)• Angle about the Ca-C bond is denoted psi (y)• The entire path of the peptide backbone isknown if all f and y angles are specified• Some values of f and y are more likely thanothers.The f,y Energy Landscape for Alanine (left) and Valine (right)yfEf -60°, y -45°,f -120°, y 120°yff,y Energy Difference Landscape: DE = E(val) - E(ala)yfDEf -60°, y -45°,f -120°, y 120°The a-helical f -60°, y -45° region is disfavored in val compared to ala, but the f -120°,y 120° region is OK. Valine has an intrinsic preference for b-strand structures.Steric Constraints on f & y• G. N. Ramachandran was the first to demonstrate the convenience of plotting f,ycombinations from known protein structures• The sterically favorable combinations are the basis for preferred secondarystructuresClasses of Secondary Structurelocal structures stabilized by hydrogen bonds"a-helix• other helices (eg p-helix, 310 helix)"b-sheet (composed of b-strands)• tight turns (aka b-turns or b-bends)The a-Helix• First proposed by Linus Pauling and Robert Corey in 1951• Identified in keratin by Max Perutz• A ubiquitous component of proteins• Stabilized by H-bonds• Intrahelical H-bonds are between amino acids 4 residues apart in the sequenceThe a-Helix (continued)• Residues per turn: 3.6• Rise per residue: 1.5 Å• Rise per turn (pitch): 3.6 x 1.5 Å = 5.4 Å• The backbone loop that is closed by any H-bond in an a-helix contains 13 atoms"f = -60°, y = -45°• The a-helix has a macrodipoleSome Globular Proteins are Predominantly a-HelicalThe b-Pleated Sheet• Composed of b-strands• Also first postulated by Pauling and Corey, 1951• Strands may be parallel or antiparallel• Rise per residue:– 3.47 Å for antiparallel strands– 3.25 Å for parallel strands• Interstrand H-bonds are usually between residues that are far apart in the sequenceThe Antiparallel b-Pleated SheetparallelantiparallelThe b-Turn (aka b-bend, tight turn)• allows the peptide chain to reverse direction• carbonyl C of one residue is H-bonded to the amide proton of a residue threeresidues away• proline and glycine are prevalent in b-turnsType I b-turn"f(R2) -60° y(R2) -30°"f(R3) -90° y(R3) 0°• pro strongly favored at R2• asp, asn favored at R3• R2 side chain can H-bondback onto NH (eg glu)Type II b-turn"f(R2) -60° y(R2) 120°"f(R3) 80° y(R3) 0°• pro strongly favored at R2• gly almost always at R3Secondary Structural Preferences of the Amino AcidsTertiary Structure Several important principles:• Secondary structures form wherever possible (due to formation of largenumbers of H-bonds)• Helices and sheets often pack close together• The backbone links between elements of secondary structure are usually short• Proteins fold to make the most stable structures (make H-bonds and minimizesolvent contact)Fibrous Proteins• Much or most of the polypeptide chain is organized approximately parallelto a single axis• Often mechanically strong• Usually insoluble• Usually play a structural role…a-Keratin• hair, fingernails, claws, horns and beaks• 311-314 residue a-helical rod segments capped with non-helical N- and C-termini• Primary structure of helical rods consists of 7-residue (heptad) repeats: (a-b-c-d-e-f-g)n, where a and d are nonpolar• Creates amphiphilic a-helices• Directs aggregation and formation of quarternary structureHeptad Repeat in Coiled-CoilsKSRQ I I IT ILVK R N KE M E KD Q AE R HStripe ofhydrophobic‘a’ and ‘d’amino acids-TKQEIAEINRMIQRLRSEIDHVKK-d e f g a b c d e f g a b c d e f g a b c d e fHigher Order Structuresb-KeratinProteins that form extensive beta sheets• Found in silk fibers• Alternating sequence: gly-ala/ser-gly-ala/ser....• Since residues of a beta sheet extend alternately above and below the plane ofthe sheet, this places all glycines on one side and all alanines and serines onother side!• This allows glys on one sheet to mesh with glys on an adjacent sheet (same forala/sers)Collagen - A Triple Helixprincipal component of connective tissue (tendons, cartilage, bones, teeth)• basic unit is tropocollagen:– three intertwined polypeptide chains (1000 residues each)– MW = 285,000– 300 nm long, 1.4 nm diameter– unique amino acid composition• Nearly one residue out of three is gly• pro content is unusually high• Unusual amino acids found:– 4-hydroxyproline (hyp)– 3-hydroxyproline and 5-hydroxylysine– pro and hyp together make 30%• Remember pro f is constrained -60 to -70°The Collagen Triple Helixa case of structure following composition• The high pro/gly composition of collagen is unsuited for a-helices OR b-sheets• A single strand adopts a polyproline type II helix (compare a-helices - tend to berandom coil as single strand)• Ideally suited for the collagen triple helix: three intertwined helical strands• Much more extended than a-helix, 2.9 Å rise per residue• 3.3 residues per turn• Long stretches of gly-pro-pro/hyp• PPII helices are staggered, and not in registerStructural basis of the collagen triple helix• Every third residue faces the crowded center of thehelix - only gly fits here• pro and hyp suit the constraints of f and y• Interchain H-bonds involving hyp stabilize helix• Fibrils are further strengthened by intrachain


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UVM CHEM 205 - Protein Architecture

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