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A model of protein association based on their hydrophobic and electric interactions.

Mozo-Villarías A, Cedano J, Querol E - PLoS ONE (2014)

Bottom Line: The final conformation of a given assembly is a fine-tuned combination of these forces, limited by steric constraints.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.

View Article: PubMed Central - PubMed

Affiliation: Institut de Recerca Biomèdica de Lleida & Departament de Medicina Experimental, Universitat de Lleida, Lleida, Spain.

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.

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Membrane model of hydrophobic moments.Left: Cartoon representation of the hydrophobic moment vector, H (yellow arrow) formed in a single phospholipid within a membrane. Its modulus is defined as the product of the total hydrophobicity of the phospholipid tail, times the distance between the hydrophobic centroid (somewhere in the tail) and the hydrophilic centroid (in the polar head). Right: Schematic representation of the transmembrane protein Chloroplast ATP synthase c-ring (PDBid 3V3C) inserted in a membrane. Blue and red arrows represent hydrophobic (H) and electric dipole moment (D) vectors respectively. Small yellow arrows represent the hydrophobic moment of each layer constituting the membrane. All hydrophobic moments of the phospholipids are quasi-parallel and perpendicular to the plane of the membrane.
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pone-0110352-g001: Membrane model of hydrophobic moments.Left: Cartoon representation of the hydrophobic moment vector, H (yellow arrow) formed in a single phospholipid within a membrane. Its modulus is defined as the product of the total hydrophobicity of the phospholipid tail, times the distance between the hydrophobic centroid (somewhere in the tail) and the hydrophilic centroid (in the polar head). Right: Schematic representation of the transmembrane protein Chloroplast ATP synthase c-ring (PDBid 3V3C) inserted in a membrane. Blue and red arrows represent hydrophobic (H) and electric dipole moment (D) vectors respectively. Small yellow arrows represent the hydrophobic moment of each layer constituting the membrane. All hydrophobic moments of the phospholipids are quasi-parallel and perpendicular to the plane of the membrane.

Mentions: 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). Each phospholipid constituting a membrane has a hydrophobic centroid in its hydrophobic tail and a hydrophilic centroid in its polar head. This defines a hydrophobic moment vector approximately perpendicular to the membrane surface (see Figure 1a). The parallel alignment of phospholipids in a membrane determines the parallel alignment of their hydrophobic moments in the most energetically stable configuration. In order to compare the orientation of hydrophobic moment vectors of phospholipids in a membrane with those of transmembrane proteins, we computed the H and D vectors for a set of 40 TM proteins as well as the angles they form. Several remarkable features are worth observing.


A model of protein association based on their hydrophobic and electric interactions.

Mozo-Villarías A, Cedano J, Querol E - PLoS ONE (2014)

Membrane model of hydrophobic moments.Left: Cartoon representation of the hydrophobic moment vector, H (yellow arrow) formed in a single phospholipid within a membrane. Its modulus is defined as the product of the total hydrophobicity of the phospholipid tail, times the distance between the hydrophobic centroid (somewhere in the tail) and the hydrophilic centroid (in the polar head). Right: Schematic representation of the transmembrane protein Chloroplast ATP synthase c-ring (PDBid 3V3C) inserted in a membrane. Blue and red arrows represent hydrophobic (H) and electric dipole moment (D) vectors respectively. Small yellow arrows represent the hydrophobic moment of each layer constituting the membrane. All hydrophobic moments of the phospholipids are quasi-parallel and perpendicular to the plane of the membrane.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4201486&req=5

pone-0110352-g001: Membrane model of hydrophobic moments.Left: Cartoon representation of the hydrophobic moment vector, H (yellow arrow) formed in a single phospholipid within a membrane. Its modulus is defined as the product of the total hydrophobicity of the phospholipid tail, times the distance between the hydrophobic centroid (somewhere in the tail) and the hydrophilic centroid (in the polar head). Right: Schematic representation of the transmembrane protein Chloroplast ATP synthase c-ring (PDBid 3V3C) inserted in a membrane. Blue and red arrows represent hydrophobic (H) and electric dipole moment (D) vectors respectively. Small yellow arrows represent the hydrophobic moment of each layer constituting the membrane. All hydrophobic moments of the phospholipids are quasi-parallel and perpendicular to the plane of the membrane.
Mentions: 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). Each phospholipid constituting a membrane has a hydrophobic centroid in its hydrophobic tail and a hydrophilic centroid in its polar head. This defines a hydrophobic moment vector approximately perpendicular to the membrane surface (see Figure 1a). The parallel alignment of phospholipids in a membrane determines the parallel alignment of their hydrophobic moments in the most energetically stable configuration. In order to compare the orientation of hydrophobic moment vectors of phospholipids in a membrane with those of transmembrane proteins, we computed the H and D vectors for a set of 40 TM proteins as well as the angles they form. Several remarkable features are worth observing.

Bottom Line: The final conformation of a given assembly is a fine-tuned combination of these forces, limited by steric constraints.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.

View Article: PubMed Central - PubMed

Affiliation: Institut de Recerca Biomèdica de Lleida & Departament de Medicina Experimental, Universitat de Lleida, Lleida, Spain.

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.

Show MeSH
Related in: MedlinePlus