scholarly journals Comprehensive characterization of oligosaccharide conformational ensembles with conformer classification by free-energy landscape via reproductive kernel Hilbert space

2021 ◽  
Vol 23 (16) ◽  
pp. 9753-9760
Author(s):  
Tokio Watanabe ◽  
Hirokazu Yagi ◽  
Saeko Yanaka ◽  
Takumi Yamaguchi ◽  
Koichi Kato
Keyword(s):  
Hilbert Space ◽  
Free Energy ◽  
Kernel Method ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Conformational Ensembles ◽  
Conformational Free Energy ◽  
Comprehensive Characterization

A kernel method enables the comprehensive characterization of conformational ensembles of oligosaccharides in association with the conformational free-energy landscape.

scholarly journals On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units

2019 ◽  
Author(s):  
Loukas Kollias ◽  
David Cantu ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Metal Organic Framework ◽  
Energy Landscape ◽  
Ionic Species ◽  
Free Energy Landscape ◽  
Materials Synthesis ◽  
Factors Affecting ◽  
Enthalpy And Entropy ◽  
Conformational Free Energy

The thermostructural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of MOF structure defects during synthesis. In this paper, we evaluate factors affecting the flexibility of MIL-101(Cr) half – secondary building units (half-SBUs) in solution using enhanced sampling methods. In particular, we calculate entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs, in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). We find that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, we investigate the role of enthalpy and entropy in the conformational rearrangement of an SBU in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. Our analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units, as such effects can significantly impact the relative stability of structurally different conformers, which ultimately can be responsible for the formation of defects during materials synthesis.

scholarly journals On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units

2019 ◽  
Author(s):  
Loukas Kollias ◽  
David Cantu ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Metal Organic Framework ◽  
Energy Landscape ◽  
Ionic Species ◽  
Free Energy Landscape ◽  
Materials Synthesis ◽  
Factors Affecting ◽  
Enthalpy And Entropy ◽  
Conformational Free Energy

The thermostructural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of MOF structure defects during synthesis. In this paper, we evaluate factors affecting the flexibility of MIL-101(Cr) half – secondary building units (half-SBUs) in solution using enhanced sampling methods. In particular, we calculate entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs, in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). We find that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, we investigate the role of enthalpy and entropy in the conformational rearrangement of an SBU in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. Our analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units, as such effects can significantly impact the relative stability of structurally different conformers, which ultimately can be responsible for the formation of defects during materials synthesis.

scholarly journals Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Song-Ho Chong ◽  
Sihyun Ham
Keyword(s):  
Free Energy ◽  
Intrinsically Disordered Proteins ◽  
Energy Landscape ◽  
Disordered Proteins ◽  
Free Energy Landscape ◽  
Ww Domain ◽  
Intrinsically Disordered ◽  
Ca 50 ◽  
Folding Free Energy

Abstract Folding funnel is the essential concept of the free energy landscape for ordered proteins. How does this concept apply to intrinsically disordered proteins (IDPs)? Here, we address this fundamental question through the explicit characterization of the free energy landscapes of the representative α-helical (HP-35) and β-sheet (WW domain) proteins and of an IDP (pKID) that folds upon binding to its partner (KIX). We demonstrate that HP-35 and WW domain indeed exhibit the steep folding funnel: the landscape slope for these proteins is ca. −50 kcal/mol, meaning that the free energy decreases by ~5 kcal/mol upon the formation of 10% native contacts. On the other hand, the landscape of pKID is funneled but considerably shallower (slope of −24 kcal/mol), which explains why pKID is disordered in free environments. Upon binding to KIX, the landscape of pKID now becomes significantly steep (slope of −54 kcal/mol), which enables otherwise disordered pKID to fold. We also show that it is the pKID–KIX intermolecular interactions originating from hydrophobic residues that mainly confer the steep folding funnel. The present work not only provides the quantitative characterization of the protein folding free energy landscape, but also establishes the usefulness of the folding funnel concept to IDPs.

scholarly journals Free-energy landscape of a hyperstable RNA tetraloop

2016 ◽  
Vol 113 (24) ◽  
pp. 6665-6670 ◽  
Author(s):  
Jacob C. Miner ◽  
Alan A. Chen ◽  
Angel E. García
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
High Performance ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Left Handed ◽  
Rna Conformation ◽  
Dynamics Simulations ◽  
Secondary Structure Motif

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

scholarly journals On the Role of Enthalpic and Entropic Contributions to the Conformational Free Energy Landscape of MIL‐101(Cr) Secondary Building Units

2020 ◽  
Vol 3 (12) ◽  
pp. 2000092
Author(s):  
Loukas Kollias ◽  
David C. Cantu ◽  
Vassiliki‐Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Secondary Building Units ◽  
Conformational Free Energy

scholarly journals The Effect of Tensile Stress on the Conformational Free Energy Landscape of Disulfide Bonds

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e108812 ◽  
Author(s):  
Padmesh Anjukandi ◽  
Przemyslaw Dopieralski ◽  
Jordi Ribas–Arino ◽  
Dominik Marx
Keyword(s):  
Free Energy ◽  
Tensile Stress ◽  
Disulfide Bonds ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Conformational Free Energy
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