Abstract
Protein self-assembling is studied under the light of the Biological Membrane model. To this purpose we define a simplified formulation of hydrophobic interaction energy in analogy with electrostatic energy stored in an electric dipole. Self-assembly is considered to be the result of the balanced influence of electrostatic and hydrophobic interactions, limited by steric hindrance as a consequence of the relative proximity of their components. Our analysis predicts the type of interaction that drives an assembly. We study the growth of both electrostatic and hydrophobic energies stored by a protein system as it self-assembles. Each type of assembly is studied by using two examples, PDBid 2OM3 (hydrophobic) and PDBid 3ZEE (electrostatic). Other systems are presented to show the application of our procedure. We also study the relative orientation of the monomers constituting the first dimer of a protein assembly to check whether their relative position provides the optimal interaction energy (energy minimum). It is shown that the inherent orientation of the dimers corresponds to the optimum energy (energy minimum) of assembly compatible with steric limitations. These results confirm and refine our Biological Membrane model of protein self-assembly valid for all open and closed systems.
Highlights
It has been proposed that the configuration adopted by protein monomers when they self assemble forming large and complex structures is analogous to that adopted by a double layer of phospholipids constituting a biological membrane under the hydrophobic effect [1,2,3]
We have derived a useful and simplified version of pseudo hydrophobic energy based on the use of hydrophobic moment vectors
Whether the energy holding the system together is attractive or repulsive depends on the type of interaction that the dipole moments exert on each other
Summary
It has been proposed that the configuration adopted by protein monomers when they self assemble forming large and complex structures is analogous to that adopted by a double layer of phospholipids constituting a biological membrane under the hydrophobic effect [1,2,3]. Charged amino acids exert attractions or repulsions on groups that are subject to hydrophobic attractions or repulsions In addition to these effects, spatial limitations on the monomers have an unavoidable influence on the particular configuration any given protein assembly may adopt [4, 5].
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