A view on the dogma of hydrophobic imperialism in protein folding

Graziano, Giuseppe

doi:10.1080/07391102.2012.748545

Cited by 4 publications

(8 citation statements)

References 28 publications

(43 reference statements)

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“…The latter publication makes clear that water molecules in the interfacial setting with their dipole character, in combination with cytoplasm inorganic ions, interact with charged groups on the protein backbone, by which surface charges become masked and relatively hydrophobic domains are created that can lead to deformations (see Figure 2(C)) and creation of local pockets or cavities, that even may exclude acqueous solvent molecules. This adds up to the natural influence of both hydrophilic and hydrophobic portions of the particular protein chain that are involved in the initial folding process as well as protein stability [82]. Water molecules have typical resonances at Hertz frequencies, and a typical frequency can be expressed in 3-prime-limit tuning.…”

Section: The Essential Role Of Cell Water In the Protein Folding Procmentioning

confidence: 99%

“…In this respect, some innovative papers with designed and properly controlled experiments, suggested that electromagnetic fields may reflect macromolecular features of enzymes like DNA-polymerase in water, and that this provides structure specific information storage in aqueous solutions [82] [83] [84]. The electromagnetic radiative properties of DNA and enzyme macromolecules likely depend on the characterization of their electric dipoles.…”

Section: The Essential Role Of Cell Water In the Protein Folding Procmentioning

confidence: 99%

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Guided Folding of Life’s Proteins in Integrate Cells with Holographic Memory and GM-Biophysical Steering

Meijer¹,

Geesink²

2018

OJBIPHY

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The current geometric and thermodynamic approaches in protein folding studies do not provide a definite solution to understanding mechanisms of folding of biological proteins. A major problem is that the protein is first synthesized as a linear molecule that subsequently must reach its native configuration in an extremely short time. Hydrophobicity-hydrophilicity models and random search mechanism cannot explain folding to the 3-D functional form in less than 1 second, as it occurs in the intact cell. We propose an integral approach, based on the embedding of proteins in the whole cellular context under the postulate: a life protein is never alone. In this concept the protein molecule is influenced by various long and short distance force fields of nature such as coherent electromagnetic waves and zero-point energy. In particular, the role of solitons is reviewed in relation to a novel GM-scale biophysical principle, revealed by us. This recent finding of a set of discrete EM frequency bands, that either promote or endanger life conditions, could be a key in further studies directed at the morphogenetic aspects of protein folding in a biological evolutionary context. In addition, an alternative hypothesis is presented in which each individual cell may store integral 3-D information holographically at the virtual border of a 4-D hypersphere that surrounds each living cell, providing a field receptive memory structure that is instrumental in guiding the folding process towards coherently oscillating protein networks that are crucial for cell survival.(hydrophobic-hydrophilic) model, is extremely complex (i.e., generally requires an enormous number of steps [2]. Levinthal concluded rightfully that a random search can only be performed in an unrealistic timeframe of billions of years [1]. Thus two major questions remain: what are the actual folding mechanisms and how can this ultra-rapid process be realized in the whole, intact, cell structure?Martinez noted that the current folding models had weak predictive ability [3]. Natural proteins consist of 100 to 500 building blocks (alpha-amino-acids), but a random search mechanism cannot provide real-time folding on the order of 1 sec. for these proteins. In the framework of a funnel-like energy landscape, the author considers a simple kinetic model of protein folding. However, this kinetic model assumes that once a domain reaches the correct state, it stays there. However, it remains unclear how the domain "knows" that it reached the correct state. After all, an intermediate state is not the minimum energy a state-the minimum is only expected for the whole structure. In the current geometric and thermodynamic approaches in protein folding mechanisms, impressive progress was made, as for instance exemplified by recent papers [4] [5], yet such bottom up approaches fail to provide a satisfactory and generally predictive solution.Munoz and Cerminara recently reviewed current generation of thermodynamic methods to map ultrafast folding landscapes, interaction networks and var...

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Section: The Essential Role Of Cell Water In the Protein Folding Procmentioning

confidence: 99%

Section: The Essential Role Of Cell Water In the Protein Folding Procmentioning

confidence: 99%

Guided Folding of Life’s Proteins in Integrate Cells with Holographic Memory and GM-Biophysical Steering

Meijer¹,

Geesink²

2018

OJBIPHY

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“…To the best of our knowledge, a reliable rationalization of the D 2 O stabilizing effect has not yet been provided, even though it has been proposed that heavy water stabilizes the N‐state because it increases the strength of the hydrophobic effect (i.e., the latter is still considered to be the main stabilizing contribution in the overall Gibbs energy balance). This idea originated from the analysis of solubility data for α‐amino acids in H 2 O and D 2 O performed by Scheraga and coworkers in 1965 .…”

Section: Introductionmentioning

confidence: 99%

Effect of heavy water on the conformational stability of globular proteins

Pica

Graziano

2017

Biopolymers

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It is well established from the experimental point of view that the native state of globular proteins is more stable in heavy water than in water. No robust explanation, however, has been provided up to now. The application of the theoretical approach, originally devised to rationalize the general occurrence of cold denaturation, indicates that the magnitude of the solvent-excluded volume effect is slightly smaller in heavy water than in water and cannot explain the observed protein stabilization. The latter has to be due to the strength of protein-water van der Waals attractions which are weaker in heavy water due to the smaller molecular polarizability of D O compared with that of H O molecules. Since protein-water van der Waals attractions occur more in the denatured than in the native state, this contribution leads to a stabilization of the latter through a destabilization of the former.

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“…potential of mean force (the dependence of pairwise HI on the distance between the two molecules) at 25 • C and 1 atm, providing important information on the energetics of the contact-minimum configuration, the desolvation barrier, and the solvent-separated configuration. In addition, some computer simulation studies have been devoted to characterize the pairwise HI of methane at very high hydrostatic pressure, [12][13][14][15][16] with the aim to shed light on the effect of pressure on the strength of the association and so to gain a molecular understanding of the pressure-induced denaturation of globular proteins 17 (since the main stabilizing contribution of the native-folded conformation should be HI 18 ). A relative stabilization of the solvent-separated configuration with respect to the contact-minimum configuration on increasing hydrostatic pressure emerged and this simulation result has been used to construct a heuristic rationalization of the pressure effect on the stability of globular proteins.…”

Section: Introductionmentioning

confidence: 99%

Hydrostatic pressure effect on hydrophobic hydration and pairwise hydrophobic interaction of methane

Graziano

2014

The Journal of Chemical Physics

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At room temperature, the Ben-Naim standard hydration Gibbs energy of methane is a positive quantity that increases markedly with hydrostatic pressure [M. S. Moghaddam and H. S. Chan, J. Chem. Phys. 126, 114507 (2007)]. This finding is rationalized by showing that the magnitude of the reversible work to create a suitable cavity in water increases with pressure due to both the increase in the volume packing density of water and the contribution of the pressure-volume work. According to the present approach, at room temperature, the Gibbs energy of the contact-minimum configuration of two methane molecules is a negative quantity that increases in magnitude with hydrostatic pressure. This result is not in line with the results of several computer simulation studies [T. Ghosh, A. E. Garcia, and S. Garde, J. Am. Chem. Soc. 123, 10997-11003 (2001)], and emerges because pairwise association causes a decrease in solvent-excluded volume that produces a gain of configurational/translational entropy of water molecules, whose magnitude increases with the volume packing density of the liquid phase.

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A view on the dogma of hydrophobic imperialism in protein folding

Cited by 4 publications

References 28 publications

Guided Folding of Life’s Proteins in Integrate Cells with Holographic Memory and GM-Biophysical Steering

Guided Folding of Life’s Proteins in Integrate Cells with Holographic Memory and GM-Biophysical Steering

Effect of heavy water on the conformational stability of globular proteins

Hydrostatic pressure effect on hydrophobic hydration and pairwise hydrophobic interaction of methane

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