Proteomics/Protein - Protein Interactions/Factors

Page Edited and Updated by: Dan Surdyk E-mail: dfs6389@rit.edu

This Section:

Factors Affecting Protein Protein Interactions
The analysis of protein protein interactions can be of two kinds :
 * 1) Qualitative
 * 2) Quantitative

In both the cases we have factors related to the interactions Factors affecting the qualitative analysis are discussed before. In this section we would mainly try to concentrate on the quantitative analysis.

Factors Affecting the Quantitative protein protein interactions
With regards to binding factors we mean whether the interaction is one-to-one or one-to-many binding. The one-to-one binding interactions can be quantified very easily but the problems lies when one protein has more than one binding sites. For one-to-many binding sites, there can be again two possibilities. If all these many binding are not associated with each other or in other words independent of each other we can just treat each binding as one-to-one and then sum them up all together. But if all these interactions are dependent on each other then we have to deal with its allosteric affects.

So the factors affecting the binding properties are :
 * 1) Affinity
 * 2) Kinetics
 * 3) Thermodynamics Properties

Affinity

 * 1) Ka (affinity constant) or Kd(dissociation Constant)
 * 2) Kd=1/Ka

Kinetics

 * 1) k(ass) or k(on) association rate constant or on rate
 * 2) K(diss) or K(off) dissociation rate constant or off rate

Thermodynamics properties

 * 1) Enthalpy Change
 * 2) Entropy Change
 * 3) Heat Capacity change
 * 4) Gibbs free energy change
 * 5) Role of Water

Role of Water
Since most of the protein protein interactions take place in acqueous phase we should also consider the affect of water in an interaction. Water makes the environment quite hydrophobic and considerably favourable for protein interactions as they are also hydrophobic molecules.Due to the abundance of water molecules, most of the bonds need to be broken to make the protein interactions favorable.Water can also act as a cementing material in the hydrophobic gaps between two proteins.

References (Open Access)
[http://www.biology.ucsd.edu/classes/bggn220.FA06/ProtProtinteractions.pdf Factors Affecting Protein-Protein Interaction