Abstract
The propensity of many proteins to oligomerize and associate to form complex structures from their constituent monomers, is analyzed in terms of their hydrophobic (H), and electric pseudo-dipole (D) moment vectors. In both cases these vectors are defined as the product of the distance between their positive and negative centroids, times the total hydrophobicity or total positive charge of the protein. Changes in the magnitudes and directions of H and D are studied as monomers associate to form larger complexes. We use these descriptors to study similarities and differences in two groups of associations: a) open associations such as polymers with an undefined number of monomers (i.e. actin polymerization, amyloid and HIV capsid assemblies); b) closed symmetrical associations of finite size, like spherical virus capsids and protein cages. The tendency of the hydrophobic moments of the monomers in an association is to align in parallel arrangements following a pattern similar to those of phospholipids in a membrane. Conversely, electric dipole moments of monomers tend to align in antiparallel associations. The final conformation of a given assembly is a fine-tuned combination of these forces, limited by steric constraints. This determines whether the association will be open (indetermined number of monomers) or closed (fixed number of monomers). Any kinetic, binding or molecular peculiarities that characterize a protein assembly, comply with the vector rules laid down in this paper. These findings are also independent of protein size and shape.
Highlights
One of the most fundamental aspects of the knowledge of protein function is their ability to self-associate, constituting larger structures suitable for many cell structures and functions
These are both associative processes that are essential for cell life [6,7,8,9] or bring disease and death [10,11,12,13]. These processes may show different association kinetics among them but both may share common features that may yield some clues about necessary conditions for association. Which of these conditions are being shared by associations that end up with a definitive number of monomers, such as virus capsids, or protein cages? One of the fundamental questions is what can be common to all associative processes and what makes them different
Transmembrane Proteins In order to find an interpretation of protein hydrophobic moments we studied the behavior and disposition of H vectors of phospholipids within a membrane and their interaction with H vectors of transmebrane proteins. (Vector quantities are denoted by bold characters in this article)
Summary
One of the most fundamental aspects of the knowledge of protein function is their ability to self-associate, constituting larger structures suitable for many cell structures and functions. All those characteristics involved when certain proteins form any kind of association (from dimers to sizeable oligomers) have been of great interest from the earliest moments of protein research and continue to be the object of intense research in many areas [1,2,3,4,5] This interest covers the most basic knowledge in cell function from actin and tubulin polymerization, to those mechanisms that provoke serious diseases like Alzheimer’s, which imply large amyloid aggregations in the cytoskeleton, just to mention two conspicuous examples. This article is an attempt to find and use simple descriptors suitable in all protein assembly processes
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