Download Protein Structure: Amino Acids, Conformations, and Interactions (Ch 2) and more Study notes Chemistry in PDF only on Docsity! Protein Structure (Ch 2) Mon 2/2-Wed 2/4/09 Amino acids defined Sidechain properties: range of size, shape, reactivity, nonpolar/polar (Hydrophobicity, H bonding) charged (+/-, pK) - acid/base chemistry, buffer, pI geometry of Gly & Pro (steric constraints) aromatic - UV absorbance Peptide backbone Peptide bond planar ( , ) conformational space; Ramachandran plot Alpha Helix 3.6 residues/turn; COi to NHi+4 H bonds 1.5Å/residue -- compact Helical wheels, sidechains out Beta Sheet Parallel or antiparallel 3.5Å/residue -- nearly extended Sidechains alternate above/below sheet Tertiary structure Hydrophobic core Quaternary structure Protein Folding Cooperative Hmwk Ch1: 1,3,4,6,8,9,10 Ch2:1,3,5,6,7,9,10 27 mas (AV 0CAbIE ack
Tae
A 1
180 -120 -60 0 60 120 +180 (@ = 90°, = -90°)
Disfavored
+180
wewel
: | 4
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Figure 2-28
Biochemistry, Sixth Edition
© 2007 W.H. Freeman and Company
| H R\ 0 yy = +85°
COi to NHi+4 H bonding Ends have unsatisfied H bonds, at protein surface, polar COi to NHi+4 H bonding Alpha helix Predicted by Linus Pauling & Robert Corey 1951 Verified by x-ray diffraction of myoglobin 1958 Protein Structure (Ch 2) Mon 2/2-Wed 2/4/09 Amino acids defined Sidechain properties: range of size, shape, reactivity, nonpolar/polar (Hydrophobicity, H bonding) charged (+/-, pK) - acid/base chemistry, buffer, pI geometry of Gly & Pro (steric constraints) aromatic - UV absorbance Peptide backbone Peptide bond planar ( , ) conformational space; Ramachandran plot Alpha Helix 3.6 residues/turn; COi to NHi+4 H bonds 1.5Å/residue -- compact Helical wheels, sidechains out Beta Sheet Parallel or antiparallel 3.5Å/residue -- nearly extended Sidechains alternate above/below sheet Tertiary structure Hydrophobic core Quaternary structure Protein Folding Cooperative Hmwk Ch1: 1,3,4,6,8,9,10 Ch2:1,3,5,6,7,9,10
Primary Secondary Tertiary
structure structure structure
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howd CO
Human insulin
Quarternary
structure
Globular proteins are compact! 585 residues x 3.5 Å/residue 2000 Å x 1.5 Å/residue 900 Å globular (human serum albumin) 100Å longest dimension Even better… RNAse A in Proteopedia http://www.proteopedia.org/wiki/index.php/1rta Explore Jmol menu: Select -> All Style -> Scheme -> try each one! What’s inside proteins?
Vmpaer BRS — hy drop lee bic core.
RIL Aloands satished > od 8
What’s on the surface?
polex aa’s
loops Thins a ap
ol
8
(A) (B) Heme group
Heme group
Figure 2-48
Biochemistry, Sixth Edition
© 2007 W.H. Freeman and Company
. Hydrophobic - blue
Charged - red
Figure 4-13 Principles of Biochemistry, 4/e
© 2006 Pearson Prentice Hall, In
Helical wheels: 3.6 residues per turn Repeats after 5 turns = 18 residues (blue offset to see repeat) a b c d e f g a b c d e f g coiled-coils parallel antiparallel interactions: a/d hydrophobic a/a & d/d e/g ionic e/e & g/g How could you predict anti- or parallel based on sequence? a b c d e f g a b c d e f g 3.5 residues per turn (LH supercoil) - “heptad repeat” = abcdefg Hydrophobic groups at interface = a & d Bordered by charged groups -> salt bridges = e & g
