Protein structural element

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Protein structural element

• Yun-Ru (Ruby) Chen ??? Ph.D.
• The Genomics Research Center
• (office at 7th floor)
• yrchen_at_gate.sinica.edu.tw
• 2789-9930 ext 355

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outline

1. Atom interaction and bonding
2. Amino acid and peptide bond
3. Secondary structure
4. Tertiary structure
5. Quantiary structure
6. Function

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Bonding
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Atom Interactions
Energy
Covalent interaction
300-400x
Non-covalent interaction
noncovalent interactions are 10-100 times weaker
than covalent bonds.
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Non-covalent interactions
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Charge-charge interaction
Coulomb's law defines the force between a pair
of charges (q1 and q2) separated by a vacuum by a
distance, r as F k(q1q2)/r2, where
k is a constant. DE in vacuum120kcal/M (very
strong)
In non-vacuum, dielectric medium
F k(q1q2)/(Dr2)
The dielectric constant arises from the fact that
the dielectric medium shields the charges from
each other. D water79 dE in solution is lower
because of hydration
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Hydrogen bond

• Hydrogen is shared between 2 electronegative
  atoms
• Directional
• Stronger than van der waal
• Strength depends on donor and Acceptor
  electronegativity
• (OgtNgtS)

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Van der Waal
Van der Waal radius of atoms
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pKa

• Peptide bond
• Carboxyl group(-COOH)2
• Amide (-NH3)9.6
• Charged residues
• Acidic
• Asp, D, pK13.9, b-carboxyl.
• Glu, E, pKa4.3, g-carboxyl
• Basic
• Lys, K, pK110.5, b-carboxyl.
• Arg, R, pKa12.5, g-carboxyl
• His, H, pKa6,
• Hydroxyl residues
• Ser, pKa13.6
• Thr, pKa13.6
• Cys,pKa10.3

• Protonation
• pKaltpH, deportonated
• pKapH, half-half
• pKagtpH, protonated

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Histidine
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Hydroxyl residues

• Aliphatic
• pKa13.6

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cis-trans Isomerization (transcis)

• Non-proyl (10001)

• X-proyl bond (41)

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Disulfide bonds

• Cysteine v.s. Cystine

• Reducing agent

DTT(dithiothreitol)
TCEP (Tris2-carboxyethyl phosphine)
Glutathione (reduced form vs. oxidized form
(GSSG)) g-Glu-Cys-Gly
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Aromatic residues
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labeling

• Amine-reacting group

Reaction of a primary amine with an
isothiocyanate
Reaction of a primary amine with a succinimidyl
ester or a tetrafluorophenyl (TFP) ester
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Reaction of a primary amine with an STP ester
Reaction of a primary amine with a sulfonyl
chloride
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Thiol group
Reaction of a thiol with an alkyl halide
Reaction of a thiol with a maleimide
Reaction of a thiol with a symmetric disulfide
(e.g., didansyl-L-cystine, D146).
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Steric constrains dictate the possible types of
secondary structure
Ramachandran plot
psi
phi
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Protein secondary structure
Turn beta turn, reverse turn, hairpin turn
The simplest secondary structure element 3 or 4
aa involved
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Helix

• Alpha-helices are versatile cylindrical
  structures stabilized by a network of backbone
  hydrogen bonds
• Helices can be right-handed (favored) or
  left-handed
• 3.6aa per turn (a rotation of 100A)
• 7aa for a helical wheel

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Helical (macro)dipole (N-ter positive C-ter
negative)
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Helical wheel
Alpha-helices can be amphipathic with one polar
and one non-polar face (favored helix-helix
interaction)
Lucine zipper
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Special cases
Collagen triple helix proline found in left
handed helices, three helices coil around each
other
Polyproline when the peptide bonds are all trans
it forms a left-handed helix with three residues
per turn. Often serve as a docking sites for
protein recognition modules such as SH3 domains
in signal transduction pathways (exist in
unfolded protein)
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Beta sheets are extended structures that
sometimes form barrels
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Parallel strand must be joined by long connections
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Certain aa are more usually found in alpha
helices, others in beta sheets

• Long side chains are often found in helices
• Side chain branched at b-carbon are often found
  in b stand
• Proline and glycine are disfavored in helix and
  sheet
• Predication is based on empirical rules
  (Chou-Fasman)
• None is completely accurate

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Condensed multiple secondary elements leads to
tertiary structure (all alpha, all beta, mixed
alpha/beta)
V domain of IG light chain
Triosephosphate isomerase
Dihydrofolate reductase
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Bound water
In unfolded protein backbond contacts with
water In folded protein water release from
backbond contacts to bulk water, but water still
interact with polar group on the surface either
peptide bond and side-chains.
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Hydrophobic effect

• The tendency of nonpolar groups in water to
  self-associated and thereby minimize their
  contact surface are with the polar solvent
• Exclusion of water
• A driving force for folding

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solubility
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Proteins are flexible molecules
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Quaternary structure
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Protein interacting domains
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Reading Assignment

• Chapter1 of Protein Structure and Function (or
  any other protein structure text book)