scholarly journals On the Role of Entropy in the Stabilization of α-Helixes

2020 ◽  
Author(s):  
Adolfo Bastida ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Beatriz Miguel ◽  
Javier Cerezo
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Nearest Neighbor ◽  
Conformational Space ◽  
Folded Structure ◽  
Enthalpy And Entropy Changes ◽  
Potential Energy Landscapes ◽  
Folded Structures ◽  
Dynamics Simulations

Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of the free energy upon reaching the folded structure. <br>A complete understanding of this process requires, therefore, a deep insight into both contributions to the free energy.<br>In this work, we clarify the role of entropy in favoring the stabilization of folded structures in polyalanine peptides with up to 12 residues . We use a novel method referred to as K2V that allows us to obtain the potential energy landscapes in terms of residue conformations extracted from molecular dynamics simulations at conformational equilibrium, and yields folding thermodynamic magnitudes in agreement with the experimental data available. <br>Our results demonstrate that the folded structures of the larger polyalanine chains are stabilized with respect to the folded structures of the shorter chains mostly by an increase of the entropic contribution of the solvent, which compensates the decrease of conformational entropy of the polypeptide, thus unveiling a key piece in the puzzle of protein folding.<br>In addition, the ability of the K2V method to provide the enthalpic and entropic contributions for individual residues along the peptide chain makes it clear that the entropic stabilization is basically governed by the nearest neighbor residues conformations, with the folding propensity being rationalized in terms of triads of residues.<br><br>

scholarly journals On the Role of Entropy in the Stabilization of α-Helixes

2020 ◽  
Author(s):  
Adolfo Bastida ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Beatriz Miguel ◽  
Javier Cerezo
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Nearest Neighbor ◽  
Conformational Space ◽  
Folded Structure ◽  
Enthalpy And Entropy Changes ◽  
Potential Energy Landscapes ◽  
Folded Structures ◽  
Dynamics Simulations

Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of the free energy upon reaching the folded structure. <br>A complete understanding of this process requires, therefore, a deep insight into both contributions to the free energy.<br>In this work, we clarify the role of entropy in favoring the stabilization of folded structures in polyalanine peptides with up to 12 residues . We use a novel method referred to as K2V that allows us to obtain the potential energy landscapes in terms of residue conformations extracted from molecular dynamics simulations at conformational equilibrium, and yields folding thermodynamic magnitudes in agreement with the experimental data available. <br>Our results demonstrate that the folded structures of the larger polyalanine chains are stabilized with respect to the folded structures of the shorter chains mostly by an increase of the entropic contribution of the solvent, which compensates the decrease of conformational entropy of the polypeptide, thus unveiling a key piece in the puzzle of protein folding.<br>In addition, the ability of the K2V method to provide the enthalpic and entropic contributions for individual residues along the peptide chain makes it clear that the entropic stabilization is basically governed by the nearest neighbor residues conformations, with the folding propensity being rationalized in terms of triads of residues.<br><br>

scholarly journals Intriguing Role of Water in Plant Hormone Perception

2021 ◽  
Author(s):  
Chuankai Zhao ◽  
Diego Eduardo Kleiman ◽  
Diwakar Shukla
Keyword(s):  
Free Energy ◽  
Plant Growth ◽  
Binding Site ◽  
Plant Hormones ◽  
Plant Hormone ◽  
Water Molecules ◽  
Water Displacement ◽  
Dynamics Simulations ◽  
Free Energy Of Binding

Plant hormones are small molecules that regulate plant growth, development, and responses to biotic and abiotic stresses. Plant hormones are specifically recognized by the binding site of their receptors. In this work, we investigated the role of water displacement and reorganization at the binding site of plant receptors on the binding of eight classes of phytohormones (auxin, jasmonate, gibberellin, strigolactone, brassinosteroid, cytokinin, salicylic acid, and abscisic acid) using extensive molecular dynamics simulations and inhomogeneous solvation theory. Our findings demonstrated that displacement of water molecules by phytohormones contributes to free energy of binding via entropy gain and is associated with free energy barriers. Also, our results have shown that displacement of unfavorable water molecules in the binding site can be exploited in rational agrochemical design. Overall, this study uncov- ers the role of water molecules in plant hormone perception, which creates new avenues for agrochemical design to target plant growth and development.

scholarly journals The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Renuka Kudva ◽  
Pengfei Tian ◽  
Fátima Pardo-Avila ◽  
Marta Carroni ◽  
Robert B Best ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Domain ◽  
Coarse Grained ◽  
E Coli ◽  
Folded Structure ◽  
Bacterial Ribosome ◽  
Folded Proteins ◽  
Exit Tunnel ◽  
Ribosome Exit Tunnel ◽  
Dynamics Simulations

The E. coli ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. It remains unclear, however, to what extent the geometry of the tunnel influences protein folding. Here, using E. coli ribosomes with deletions in loops in proteins uL23 and uL24 that protrude into the tunnel, we investigate how tunnel geometry determines where proteins of different sizes fold. We find that a 29-residue zinc-finger domain normally folding close to the uL23 loop folds deeper in the tunnel in uL23 Δloop ribosomes, while two ~ 100 residue proteins normally folding close to the uL24 loop near the tunnel exit port fold at deeper locations in uL24 Δloop ribosomes, in good agreement with results obtained by coarse-grained molecular dynamics simulations. This supports the idea that cotranslational folding commences once a protein domain reaches a location in the exit tunnel where there is sufficient space to house the folded structure.

scholarly journals Effects of lipid composition on membrane distribution and permeability of natural quinones

2019 ◽  
Author(s):  
Murilo Hoias Teixeira ◽  
Guilherme Menegon Arantes
Keyword(s):  
Free Energy ◽  
Lipid Composition ◽  
Proton Translocation ◽  
Acyl Chain ◽  
Free Energy Calculations ◽  
Free Energy Barrier ◽  
Water Penetration ◽  
Amphiphilic Molecules ◽  
Dynamics Simulations

ABSTRACTNatural quinones are amphiphilic molecules that function as mobile charge carriers in biological energy transduction. Their distribution and permeation across membranes are important for binding to enzymatic complexes and for proton translocation. Here, we employ molecular dynamics simulations and free energy calculations with a carefully calibrated classical force-field to probe quinone distribution and permeation in a multicomponent bilayer trying to mimic the composition of membranes involved in bioenergetic processes. Ubiquinone, ubiquinol, plastoquinone and menaquinone molecules with short and long isoprenoid tails are simulated. We find that water penetration increases considerably in the less ordered and porous bilayer formed by di-linoleoyl (18:2) phospholipids, resulting in a lower free energy barrier for quinone permeation and faster transversal diffusion. In equilibrium, quinone and quinol heads localize preferentially near lipid glycerol groups, but do not perform specific contacts with lipid polar heads. Quinone distribution is not altered significantly by the quinone head, tail and lipid composition in comparison to a single-component bilayer. This study highlights the role of acyl chain unsaturation for molecular permeation and transversal diffusion across biological membranes.

scholarly journals The Shape of the Bacterial Ribosome Exit Tunnel Affects Cotranslational Protein Folding

2018 ◽  
Author(s):  
Renuka Kudva ◽  
Pengfei Tian ◽  
Fatima Pardo Avila ◽  
Marta Carroni ◽  
Robert B. Best ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Domain ◽  
Coarse Grained ◽  
E Coli ◽  
Folded Structure ◽  
Bacterial Ribosome ◽  
Folded Proteins ◽  
Exit Tunnel ◽  
Ribosome Exit Tunnel ◽  
Dynamics Simulations

AbstractThe E.coli ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. It remains unclear, however, to what extent the geometry of the tunnel influences protein folding. Here, using E. coli ribosomes with deletions in loops in proteins uL23 and uL24 that protrude into the tunnel, we investigate how tunnel geometry determines where proteins of different sizes fold. We find that a 29-residue zinc-finger domain normally folding close to the uL23 loop folds deeper in the tunnel in uL23 Δloop ribosomes, while two ~100-residue protein normally folding close to the uL24 loop near the tunnel exit port fold at deeper locations in uL24 Δloop ribosomes, in good agreement with results obtained by coarse-grained molecular dynamics simulations. This supports the idea that cotranslational folding commences once a protein domain reaches a location in the exit tunnel where there is sufficient space to house the folded structure.

Using Data Mining Techniques to Probe the Role of Hydrophobic Residues in Protein Folding and Unfolding Simulations

2010 ◽  
pp. 258-276
Author(s):  
Cândida G. Silva ◽  
Pedro Gabriel Ferreira ◽  
Paulo J. Azevedo ◽  
Rui M.M. Brito
Keyword(s):  
Data Mining ◽  
Molecular Dynamics ◽  
Protein Folding ◽  
Protein Unfolding ◽  
Amino Acid Residues ◽  
Molecular Events ◽  
Accessible Surface ◽  
Using Data ◽  
Dynamics Simulations

The protein folding problem, i.e. the identification of the rules that determine the acquisition of the native, functional, three-dimensional structure of a protein from its linear sequence of amino-acids, still is a major challenge in structural molecular biology. Moreover, the identification of a series of neurodegenerative diseases as protein unfolding/misfolding disorders highlights the importance of a detailed characterisation of the molecular events driving the unfolding and misfolding processes in proteins. One way of exploring these processes is through the use of molecular dynamics simulations. The analysis and comparison of the enormous amount of data generated by multiple protein folding or unfolding simulations is not a trivial task, presenting many interesting challenges to the data mining community. Considering the central role of the hydrophobic effect in protein folding, we show here the application of two data mining methods – hierarchical clustering and association rules – for the analysis and comparison of the solvent accessible surface area (SASA) variation profiles of each one of the 127 amino-acid residues in the amyloidogenic protein Transthyretin, across multiple molecular dynamics protein unfolding simulations.

FOLDING FREE ENERGY LANDSCAPE OF THE DECAPEPTIDE CHIGNOLIN

2008 ◽  
Vol 22 (31) ◽  
pp. 3087-3098 ◽  
Author(s):  
XIANGHUA DOU ◽  
JIHUA WANG
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Force Fields ◽  
Energy Landscapes ◽  
Native Structure ◽  
Good Template ◽  
Free Energy Landscapes ◽  
Folded Structures ◽  
Dynamics Simulations ◽  
Folding Free Energy

Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

scholarly journals THE FOLDED STRUCTURE. PROSPECTS FOR THE DEVELOPMENT OF NEW FORMS

2016 ◽  
Vol 1 (12) ◽  
pp. 71-75
Author(s):  
Храбатина ◽  
Natalya Khrabatina ◽  
Ярмош ◽  
Tatyana Yarmosh ◽  
Мирошниченко ◽  
...  
Keyword(s):  
Folded Structure ◽  
Folded Structures

This article describes the function of folded structures, as well as the diversity of species, underlined studies relevant in the search for new forms that will be technically effective and economically jus-tified; it shows the growing role of aesthetic and artistic trends in contemporary design, to assess the prospects of their use in various fields of architecture and construction. Examples of Russian and foreign architects.

Sign in / Sign up

Export Citation Format

Share Document