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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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Ebola virus capsid assembly.Front (a) and side (b) views of the eight monomers that compose the Ebola virus matrix protein VP40. Blue arrows represent the individual H vectors of the ensemble. Red arrows are the individual D vectors. The green arrow in the centre is the net H vector. The net D vector is virtually zero.
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pone-0110352-g009: Ebola virus capsid assembly.Front (a) and side (b) views of the eight monomers that compose the Ebola virus matrix protein VP40. Blue arrows represent the individual H vectors of the ensemble. Red arrows are the individual D vectors. The green arrow in the centre is the net H vector. The net D vector is virtually zero.

Mentions: This membrane-associated complex (PDBid: 1H2C) is the structural constituent of the Ebola virion [29], facilitating virus budding and it comprises a ring of eight monomers, each interacting with RNA. The peculiarity of this assembly is that it is built in such a way that the projections of the H and D vectors on the axis of the ring, point alternatively in opposite directions, leaving a residual component on the axis of the ring. The components of the H vectors on the plane of the ring radiate outwards with no net resultant in this plane. The alternating (antiparallel) disposition of the individual electric dipole moments confers sound stability to this complex (Figure 9).


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

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

Ebola virus capsid assembly.Front (a) and side (b) views of the eight monomers that compose the Ebola virus matrix protein VP40. Blue arrows represent the individual H vectors of the ensemble. Red arrows are the individual D vectors. The green arrow in the centre is the net H vector. The net D vector is virtually zero.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110352-g009: Ebola virus capsid assembly.Front (a) and side (b) views of the eight monomers that compose the Ebola virus matrix protein VP40. Blue arrows represent the individual H vectors of the ensemble. Red arrows are the individual D vectors. The green arrow in the centre is the net H vector. The net D vector is virtually zero.
Mentions: This membrane-associated complex (PDBid: 1H2C) is the structural constituent of the Ebola virion [29], facilitating virus budding and it comprises a ring of eight monomers, each interacting with RNA. The peculiarity of this assembly is that it is built in such a way that the projections of the H and D vectors on the axis of the ring, point alternatively in opposite directions, leaving a residual component on the axis of the ring. The components of the H vectors on the plane of the ring radiate outwards with no net resultant in this plane. The alternating (antiparallel) disposition of the individual electric dipole moments confers sound stability to this complex (Figure 9).

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