Self-Assembly of Open Protein Systems: A Comprehensive View Based onthe Interactions between 3d Hydrophobic and Electric Dipole MomentVectors

Mozo-Villarías, Angel; Cedano, Juan; Querol, Enrique

doi:10.4172/jpb.1000449

Cited by 4 publications

(7 citation statements)

References 31 publications

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“…Hydrophobic moments have been a resourceful tool for describing the hydrophobic properties of proteins, since they are easy to compute and have been shown to provide a number of applications [1–3, 12, 17–21]. The present work is based on two main pillars: the use of hydrophobic moments of proteins, as described in Methods, and the analogy of interactions of these hydrophobic moments similar to those of electric dipole moments (although with different power laws).…”

Section: Discussionmentioning

confidence: 99%

“…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 [1–3]. This configuration appears in every type of structure ranging from actin filaments and microtubules to all types of viral capsids, amyloid fibers, protein cages, etc.…”

Section: Introductionmentioning

confidence: 99%

“…In previous articles [1–3], open and closed assembled systems were studied in terms of both electric dipole and hydrophobic moment vectors and their relative orientations. Some conclusions drawn for open systems in the present article are based on that previous work on closed systems.…”

Section: Introductionmentioning

confidence: 99%

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A protein self-assembly model guided by electrostatic and hydrophobic dipole moments

Mozo-Villarías

Querol

2019

PLoS ONE

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A protein self-assembly model guided by electrostatic and hydrophobic dipole moments

Mozo-Villarías

Querol

2019

PLoS ONE

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“…This method focuses on two concepts: the hydrophobic moment and the hydrophobic energy of interaction between molecules or complexes as described in the following sections. The interaction of these hydrophobic moments is modelled by using the so-called ‘biological membrane’ model (BM model, Mozo-Villarías et al ., 2014, 2016, 2017; Mozo-Villarías and Querol, 2019), according to which the hydrophobic moments of macromolecules tend to align like phospholipids in the double layer of a membrane. The hydrophobic tails of the phospholipids tend to hide from the aqueous medium while the hydrophilic heads are exposed to the aqueous medium, as is well known (Fig.…”

Section: Biological Membrane Modelmentioning

confidence: 99%

“…), are addressed in 3D. Hence, H and D directly indicate the direction and magnitude of the hydrophobic and electrical anisotropies (Mozo-Villarías et al ., 2014, 2017; Mozo-Villarías and Querol, 2019). This review shows examples of DNA and protein behaviour as well as protein self-assembly and interactions with DNA.…”

Section: Moment Vectors and Energiesmentioning

confidence: 99%

Use of vector formalism in the analysis of hydrophobic and electric driving forces in biological assemblies

Mozo-Villarías

Cedano

Querol

2022

Quart. Rev. Biophys.

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Hydrophobic forces are known to have a crucial part not only in the conformation of the three-dimensional structure of proteins, but also in the build-up of DNA–protein complexes. Electric forces also play an important role both in the tertiary as well in the quaternary structure of macromolecular associations. Sometimes both hydrophobic and electric interactions add up their strengths to accomplish these structures but in most cases they act in opposite directions. This fact, together with being overall interactions with different ranges, provides a nuanced equilibrium also modulated by the need to comply with steric hindrances and geometric frustration effects. This review focuses on the utility of using the hydrophobic and electrical dipole moment vectors to describe the interactions that give rise to the structures of biological macromolecules. Although different definitions of both electric dipole and hydrophobic moments have been described in the literature, results obtained in biological assemblies demonstrate the principle of the biological membrane model. According to this model, postulated by our group, biological macromolecules tend to associate by aligning their hydrophobic moments in a similar manner to phospholipids in a membrane. Examples of both closed and open structures are used to assess the predictability of our model. We seek agreement between our results with those described in the current literature. The review ends with possible future projections using this formalism.

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The importance of hydrophobic interactions in the structure of transcription systems

2021

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Self-Assembly of Open Protein Systems: A Comprehensive View Based onthe Interactions between 3d Hydrophobic and Electric Dipole MomentVectors

Cited by 4 publications

References 31 publications

A protein self-assembly model guided by electrostatic and hydrophobic dipole moments

A protein self-assembly model guided by electrostatic and hydrophobic dipole moments

Use of vector formalism in the analysis of hydrophobic and electric driving forces in biological assemblies

The importance of hydrophobic interactions in the structure of transcription systems

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