Protein structural Protein structural elementelement

Yun-Ru (Ruby) Chen 陳韻如 Ph.D.

The Genomics Research Center

(office at 7th floor)

yrchen@gate.sinica.edu.tw

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)