Download - Protein structural element
Protein structural Protein structural elementelement
Yun-Ru (Ruby) Chen 陳韻如 Ph.D.
The Genomics Research Center
(office at 7th floor)
2789-9930 ext 355
outline
1. Atom interaction and bonding
2. Amino acid and peptide bond
3. Secondary structure
4. Tertiary structure
5. Quantiary structure
6. Function
Bonding
Atom Interactions
Covalent interaction
Non-covalent interaction
Energy
300-400x
noncovalent interactions are 10-100 times weaker than covalent bonds.
Non-covalent interactions
Coulomb's law defines the force between a pair of charges (q1 and q2) separated by a vacuum by a distance, r asF = k*(q1q2)/r2, where k is a constant.E in vacuum=120kcal/M (very strong)
The dielectric constant arises from the fact that the dielectric medium shields the charges from each other. D water=79dE in solution is lower because of hydration
In non-vacuum, dielectric medium
F = k*(q1q2)/(D*r2)
Charge-charge interaction
Hydrogen bond
Hydrogen is shared between 2 electronegative atoms
Directional Stronger than van der waal Strength depends on donor and
Acceptor electronegativity (O>N>S)
Van der Waal radius of atoms
Van der Waal
pKa Peptide bondCarboxyl group(-COOH)=~2Amide (-NH3+)=~9.6
Charged residuesAcidic: Asp, D, pK1=~3.9, -carboxyl.Glu, E, pKa=~4.3, -carboxylBasic: Lys, K, pK1=~10.5, -carboxyl.Arg, R, pKa=~12.5, -carboxylHis, H, pKa=~6,
Hydroxyl residuesSer, pKa=~13.6Thr, pKa=~13.6Cys,pKa=~10.3
Protonation pKa<pH, deporto
nated pKa=pH, half-half pKa>pH, protonat
ed
Histidine
Hydroxyl residues
Aliphatic pKa=13.6
cis-trans Isomerization (trans:cis)
Non-proyl (1000:1)
X-proyl bond (4:1)
Disulfide bonds Cysteine v.s. Cystine
Glutathione (reduced form vs. oxidized form (GSSG))-Glu-Cys-Gly
Reducing agent
DTT(dithiothreitol)
TCEP(Tris[2-carboxyethyl] phosphine)
Aromatic residues
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
Reaction of a primary amine with an STP ester
Reaction of a primary amine with a sulfonyl chloride
Thiol group
Reaction of a thiol with a maleimide
Reaction of a thiol with a symmetric disulfide (e.g., didansyl-L-cystine, D146).
Reaction of a thiol with an alkyl halide
Steric constrains dictate the possible types of secondary structure
Ramachandran plot
phi
psi
Protein secondary structure
Turn: beta turn, reverse turn, hairpin turn
The simplest secondary structure element3 or 4 aa involved
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
Helical (macro)dipole (N-ter: positive; C-ter: negative)
Helical wheel
Lucine zipper
Alpha-helices can be amphipathic with one polar and one non-polar face (favored helix-helix interaction)
Special casesCollagen 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)
Beta sheets are extended structures that sometimes form barrels
Parallel strand must be joined by long connections
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 -carbon are often found in stand
Proline and glycine are disfavored in helix and sheet
Predication is based on empirical rules (Chou-Fasman)
None is completely accurate
Condensed multiple secondary elements leads to tertiary structure (all alpha, all beta, mixed alpha/beta)
Triosephosphate isomerase Dihydrofolate reductaseV domain of IG light chain
Bound water
In unfolded protein: backbond contacts with waterIn 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.
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
solubility
Proteins are flexible molecules
Quaternary structure
Protein interacting domains
Reading Assignment
Chapter1 of Protein Structure and Function (or any other protein structure text book)