!"#$%&' (#%) /&'(2+"( /&3&4,, ! " #$% - &'()!% *-sheet -(!-Helix - &'(&') +,(-. - &'()&+) /&%.(0&+(! - &'(1&2%( Basic amino acids

Transcription

1 Basic amino acids pk ~ 10.5 pk ~ 12.5 pk ~ 6.0 Polar 25!"#$%&' (#%)! " #$% - &'()!% *-sheet -(!-Helix - &'(&') +,(-. - &'()&+) /&%.(0&+(! - &'(1&2%( /&'(2+"( /&3&4,, :++55 ('&.! 6($.(" 40 > 3&4,, ('&.! 6($.(" 40 < (7(2+") 3&4,,&+(, 26 :%(58+ &!35) 6(3(-' 9.5 /&.(8(2&% +1 /&86'(:. /&3&4,,9 +5!+ * /&%2(". &+&:-(2%-9( &'&.!9 9$-9 - /&&+-&$ /&3&4,, *

2 A proteins primary (1 ) structure is its sequence A tetrapeptide (or oligopeptide): A polypeptide GluGlyAlaLys EGAK (DNA) 709 #$%. 6(%&)& 12(' 7(2+"9 #$% #$%6(&'(&') 6(.!69( 3(2&1 )& +2! +2! (DNA) 709 #$%. 6(%&)& 12(' 7(2+"9 6(&'(&') 6(.!69( 3(2&1 )& /&8(8&+!.0(3+ - (Cleavage);(6&" * 7&+(:'&!!.0(3+ - S-S %)- * 7"%8 6$(2-6,:(9-9&$+&%(,:(, * /&%"! /&%5(: 6,:(9( 9&$+&8(-&+0 * 9&$+&6. * Adenylation and ADP-ribosylation * 6(%"! * /(0%6 %"!+ 3(2&15 ;(6&" /&8(8&+ KVFGRCELAAAMKRHGLDNYRGYSLGNW VCAAKFESNFNTQATNRNTDGSTDYGIL QINSRWWCNDGRTPGSRNLCNIPCSALL SSDITASVNCAKKIVSDGNGMNAWVAWR NRCKGTDVQAWIRGCRL - /&&'(&') /&'2.!) /&:-&+9 *-sheet-( (/&%"!( ATGAGGTCTTTGCTAATCTTGGTGCTTTGCTTCCTGCCCCTGGCTGCTCTG MetArgSerLeuLeuIleLeuValLeuCysPheLeuPheLeuAlaAlaLeu M R S L L I L V L C F L P L A A L AAAGTCTTTGGACGATGTGAGCTGGCAGCGGCTATGAAGCGTCAC... GlyLysValPheGlyArgCysGluLeuAlaAlaAlaMetLysArgHis... G K V F G R C E L A A A M K R H ATCAGAGGCTGCCGGCTGTGA... IleArgGlyCysArgLeuStop... I R G C R L Stop 31

3 The peptide bond does not freely rotate Peptide bonds highly prefer to be trans, with one exception R 1 R 2 C N C N H H +&0% N-C %)-+ 3(0&'2 HC! 1 HC! 2 C N HC! 1 R 1 C N H HC! 2 H R 2 ci s tran s K eq = [trans] / [cis] All but Pro*: " K eq! 1000 Pro*: " K eq! 4 * When Pro contributes N- Torsion Angles of the polypeptide backbone - Phi and Psi Steric clash between the carbonyl- and the amide-h C!3 Amide H 1950s - Linus Pauling Model Building Allow on only " and # to vary Look for conformations that " maximize H-bonding C!2 C!1 Carbonyl

4 !"*+"&( ",$* Helix type Turn (aa) Phi Psi " /&%"! /&:-&+9(!-helix ( Pi ! >> 3 10 >> Pi :6("&5)?1(3.! "-helix * the phi and psi angles lie in the center of an allowed, minimum energy region of the Ramachandran map. * the dipoles of hydrogen bonding backbone atoms are in near perfect alignment. * the radius of the helix allows for favorable van der Waals interactions across the helical axis. * side chains are well staggered minimizing steric interference helix! * the phi and psi angles lie at the edge of an allowed minimum energy region. * the dipoles of hydrogen bonding backbone atoms are not well aligned with the carbonyl oxygens splayed out away from the helical axis (~30 degrees) * van der Waals contact across the helical axis may cause repulsion. * side chains are in identical azimuthal positions leading to potential steric interference. A Ramachandran Diagram 3.10 Pi -74, -4-57,-69.7 Pi helix * the phi and psi angles of the lie at the very edge of an allowed, minimum energy region. * requires that the angle tau (N-CA-C') be larger (114.9 ) than the standard tetrahedral angle of * the large radius of the pi helix means the polypeptide backbone is no longer in van der Waals contact across the helical axis forming an axial hole too small for solvent water to 38fill. * side chains are more staggered than the ideal 3.10 helix but not as well as the alpha helix.

5 Protein 2 Structure: the!-helix Amino acid side chains are on outside of the!-helix Most common structural feature Right handed helix 0.15 nm/residue rise in hight 3.6 residues/turn Stabelised by H-bonds between C of residue i and NH of residue i+3/i+4; also by Van-der-vals bonds Side view End view Side view Special problems at helix ends - no hidrogen bonds pairing 12 residue alpha helix = 12 backbone NH (donors) and 12 backbone C (acceptors) but only 8 hydrogen bonds "capping box" from cytochrome 351

6 Protein 2 Structure: the $-sheet GFP Second most common structural feature 2 residues/turn Stabelised by H- bonds and Van-dervals bonds 2 beta strands can be from far away parts of the protein *-sheet twisted *-sheet Protein 2 Structure: the Turns From: pancreatic trypsin inhibitor

7 Two basic classes of proteins &'()&+) 9'2. &'(&')9( &'()!%9 9'2.9 +) +(,&- 48 Fibrous " Elongated " Mostly play structural roles in cells and tissues " 1 structure (sequence) tends to be simple and " display repeating patterns of amino acids Globular " Much larger general class of proteins " Compact structures - no real systematic patterns of " repeating amino acids " Generally have a well defined inside and outside, with hydrophobic amino acids inside and hydrophilic " amino acids outside. An!-helical fibrous protein:!-keratins!-keratin coiled-coils assemble into higher order fibers A heptad repeat: a b c d e f g H y X X H y X X X A two-stranded coiled-coil Hair, wool, nails, hoofs and horns

8 A $-strand fibrous protein: Silk Fibroin A different repeat pattern: S-G-A-G-A-G Tropocollagen - a helical fibrous protein, but not!-helical! And another repeat pattern: " (G-X-Y) Gly is invariant; X is frequently P and Y is often P or HydroxyP Forms a left-handed helix (3.3 res/turn) Helices wrap around each other to form a right-handed superhelix Collagen Hydrophobic amino acids on inside, hydrophilic amino acids on outside globular protein interior is tightly packed!

9 Globular proteins show enormous structural diversity Protein family members share common domain structures lactate dehydrogenase malate dehydrogenase C- C- C- C- C + NADH CH 3 H CH CH3 + NAD + C H 2 C C- + NADH H CH CH 2 C- + NAD + Some 3-D arrangements are used over and over again Motifs!/$ barrels are often used to form enzyme active sites $!$ $ hairpin!! $ barrel $ barrel!/$ barrel using very different amino acid sequences to achieve the same 3-D structure! RuBisC

10 The EF Hand - a Ca ++ binding motif The Zinc Finger (C 2 H 2 ) - a DNA and RNA binding motif that requires Zn ++ Calmodulin The Rossman Fold - an NAD + binding motif /&%.(0&+(! - /&&'(1&2% /&'2. Many large globular proteins are composed of smaller domains Glyceraldehyde-3-phosphate dehydrogenase GroEL

11 Can have homo-multimers or hetero-multimers Highly sophisticated protein 4 structures can be assembled from simpler parts! 2 $ 2! 2 $% Copyright 2001 DeLano Scientific.