Study Notes on Non-Covalent Interactions in Proteins
Non-Covalent Interactions in Proteins
Overview of Protein Conformation
The unique properties of a protein are attributed to its specific three-dimensional (3D) conformation.
This conformation is stabilized by different types of non-covalent interactions.
Proteins have evolved such that one folded conformation is more stable than any other, known as the native state.
There exist some proteins without stable structures, referred to as intrinsically disordered proteins.
Certain diseases, such as Alzheimer's and Parkinson's, involve high molecular weight (MW) alternative low-energy folded states (e.g., amyloid fibers).
Main Classes of Non-Covalent Interactions
There are four principal classes of non-covalent interactions:
Salt Bridges
Hydrogen Bonds
Van der Waals Interactions
Hydrophobic Effect
Salt Bridges
Definition: Electrostatic interactions occurring between fully ionized negative and positive charges.
At neutral pH, proteins contain several charged groups:
Negatively Charged Groups:
$ ext{a-COOH}$ (C-terminus) with pKa = 3.5-4.3
Aspartate (Asp) and Glutamate (Glu) sidechains (carboxyl) with pKa = 3.9-4.5
Positively Charged Groups:
Histidine (His) sidechain (imidazole) with pKa = 6.0-7.0
$ ext{a-NH2}$ (N-terminus) with pKa = 6.8-8.0
Lysine (Lys) sidechain (amino) with pKa = 10.4-11.1
Arginine (Arg) sidechain (guanidinium) with pKa = 12.0
Characteristics of Salt Bridges
Salt bridge formation stabilizes the charges and modifies the individual pKa values of the interacting groups.
Charged groups do not remain buried in proteins unless they are 'neutralized' by forming a salt bridge.
The contribution of a salt bridge to overall protein stability depends on its burial or exposure on the surface.
A change in pH can cause charged groups to titrate, initiating or disrupting salt bridges, resulting in protein unfolding at extreme pH levels.
The dielectric constant of the solvent increases with the addition of salt, influencing salt bridge interaction strength.
Hydrogen Bonding
Definition: A hydrogen bond occurs when two electronegative atoms compete for the same hydrogen atom.
Structure of a hydrogen bond:
Donor Atom: Covalently bonded to the hydrogen atom.
Acceptor Atom: Interacts favorably with the hydrogen atom.
Notable properties:
The small size of the hydrogen atom allows for high polarization during bonding.
Strong hydrogen bonds exhibit near covalent characteristics due to notable electron redistribution.
Common Hydrogen Bonds in Proteins:
**Amine - Carbonyl
Amine - Hydroxyl
Amine - Imidazole
Hydroxyl - Carbonyl**
Backbone-to-backbone interactions are crucial for secondary structure formation.
Directionality of Hydrogen Bonds
Hydrogen bonds demonstrate unique directionality, with the interaction strength being maximum when the angle (q) between the atoms involved is 180 degrees; typically q is greater than 120 degrees.
The length of a hydrogen bond is approximately 3 Å, with specific distances (e.g., 2.9 Å for backbone-to-backbone H-bonds).
Hydrogen bonds are affected by the dielectric properties of the medium, resulting in varied strengths depending on the environment (e.g., presence of water).
Van der Waals Interactions
Definition: All atoms generate transient dipoles due to fluctuating electron clouds, inducing attractive forces in nearby atoms.
Characteristics:
The attractive forces diminish rapidly with increasing distance, following the relationship \( ext{attraction} \sim rac{1}{ ext{distance}^6} \$.
As atoms approach each other, repulsive forces increase steeply, represented by \( ext{repulsion} \sim rac{1}{ ext{distance}^{12}} \$.
Optimal attraction occurs when atoms are 0.3 to 0.5 Å apart (close to the sum of their van der Waals radii).
The Hydrophobic Effect
Definition: The hydrophobic effect refers to the entropic increase associated with non-polar molecules aggregating in aqueous solutions, resulting in a thermodynamically favorable state.
Water is a polar solvent that forms hydrogen bonds, creating a network that influences the solvation of polar and non-polar molecules:
Non-polar molecules do not form hydrogen bonds with water, causing them to be insoluble.
The energy change (ΔH) for transferring a non-polar molecule from the liquid to aqueous solution is approximately zero, while the process is unfavorable in terms of entropy (ΔS < 0).
Example: Cyclohexane at 25°C illustrates this effect, with Gibbs free energy (ΔG) calculations confirming entropy-driven hydrophobic interactions.
Water-Ordering Effect
When non-polar molecules are introduced into water, cavities form, and the resulting ordering of water molecules reduces system entropy.
The aqueous environment will exclude non-polar molecules, reducing their surface area to minimize the associated water-ordering effect.
Amino Acid Hydrophobicity Scale
Hydrophobicity varies among amino acid side chains, influencing protein folding and stability:
Trp: 2.25
Ile: 1.80
Phe: 1.79
Leu: 1.70
Cys: 1.54
Met: 1.22
Val: 0.96
Tyr: 0.72
Pro: 0.31
Ala: 0.26
His: 0.00
Gly: -0.04
Ser: -0.22
Gln: -0.60
Asn: -0.64
Glu: -0.77
Asp: -0.99
Lys: -1.01
Arg: -1.01
Note: Despite containing a polar group, Trp ranks as the most hydrophobic amino acid.
Implications of Non-Covalent Interactions
The collective strength of non-covalent interactions in proteins creates a robust network essential for maintaining protein structure.
Proteins are marginally stable, with conformational stability estimated to be only 20-60 kJ/mol, equivalent to a few hydrogen bonds.
Stability is contingent on a narrow range of external conditions, including pH, temperature, and solvent type. Deviations from these conditions can lead to loss of non-covalent interactions, resulting in protein unfolding or denaturation.