scholarly journals Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

2021 ◽  
Author(s):  
Xinqiang Ding ◽  
Xingcheng Lin ◽  
Bin Zhang
Keyword(s):  
Free Energy ◽  
Energy Surface ◽  
Three Dimensional ◽  
Sampling Technique ◽  
Thermal Fluctuations ◽  
Open Chromatin ◽  
Free Energy Surface ◽  
Intermediate States ◽  
Folding Pathways

The three-dimensional organization of chromatin is expected to play critical roles in regulating genome functions. High-resolution characterization of its structure and dynamics could improve our understanding of gene regulation mechanisms but has remained challenging. Using a near-atomistic model that preserves the chemical specificity of protein-DNA interactions at residue and base-pair resolution, we studied the stability and folding pathways of a tetra-nucleosome. Dynamical simulations performed with an advanced sampling technique uncovered multiple pathways that connect open chromatin configurations with the zigzag crystal structure. Intermediate states along the simulated folding pathways resemble chromatin configurations reported from in situ experiments. We further determined a six-dimensional free energy surface as a function of the inter-nucleosome distances via a deep learning approach. The zigzag structure can indeed be seen as the global minimum of the surface. However, it is not favored by a significant amount relative to the partially unfolded, in situ configurations. Chemical perturbations such as histone H4 tail acetylation and thermal fluctuations can further tilt the energetic balance to stabilize intermediate states. Our study provides insight into the connection between various reported chromatin configurations and has implications on the in situ relevance of the 30nm fiber.

scholarly journals Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Xinqiang Ding ◽  
Xingcheng Lin ◽  
Bin Zhang
Keyword(s):  
Free Energy ◽  
Energy Surface ◽  
Sampling Technique ◽  
Thermal Fluctuations ◽  
Open Chromatin ◽  
Free Energy Surface ◽  
In Situ Experiments ◽  
Intermediate States ◽  
Folding Pathways

AbstractThe three-dimensional organization of chromatin is expected to play critical roles in regulating genome functions. High-resolution characterization of its structure and dynamics could improve our understanding of gene regulation mechanisms but has remained challenging. Using a near-atomistic model that preserves the chemical specificity of protein-DNA interactions at residue and base-pair resolution, we studied the stability and folding pathways of a tetra-nucleosome. Dynamical simulations performed with an advanced sampling technique uncovered multiple pathways that connect open chromatin configurations with the zigzag crystal structure. Intermediate states along the simulated folding pathways resemble chromatin configurations reported from in situ experiments. We further determined a six-dimensional free energy surface as a function of the inter-nucleosome distances via a deep learning approach. The zigzag structure can indeed be seen as the global minimum of the surface. However, it is not favored by a significant amount relative to the partially unfolded, in situ configurations. Chemical perturbations such as histone H4 tail acetylation and thermal fluctuations can further tilt the energetic balance to stabilize intermediate states. Our study provides insight into the connection between various reported chromatin configurations and has implications on the in situ relevance of the 30 nm fiber.

Free energy surface of two- and three-dimensional transitions of Au 12 nanoclusters obtained byab initiometadynamics

2010 ◽  
Vol 81 (17) ◽  
Author(s):  
Gianluca Santarossa ◽  
Angelo Vargas ◽  
Marcella Iannuzzi ◽  
Alfons Baiker
Keyword(s):  
Free Energy ◽  
Energy Surface ◽  
Three Dimensional ◽  
Free Energy Surface

scholarly journals Sampling the Folding Transition State Ensemble in a Tube-Like Model of Protein

10.29007/ml3c ◽  
2020 ◽  
Author(s):  
Ba Hung Nguyen ◽  
Hoang Trinh Xuan
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Energy Surface ◽  
Sampling Technique ◽  
Small Region ◽  
Umbrella Sampling ◽  
Free Energy Surface ◽  
State Ensemble ◽  
State Region ◽  
Transition State Ensemble

We used the tube model with Go-like potential for native contacts to study the folding transition of a designed three-helix bundle and a designed protein G-like structure. It is shown that both proteins in this model are two-state folders with a cooperative folding transition coincided with the collapse transition. We defined the transition states as protein conformations in a small region around the saddle point on a free energy surface with the energy and the conformational root-mean-square deviation (RMSD) from the native state as the coordinates. The transition state region on the free energy surface then was sampled by using the umbrella sampling technique. We show that the transition state ensemble is broad consisting of different conformations that have different folded and unfolded elements.

scholarly journals Sampling the Folding Transition State Ensemble in a Tube-like Model of Protein

2019 ◽  
Vol 29 (2) ◽  
pp. 129
Author(s):  
Nguyen Ba Hung ◽  
Trinh Xuan Hoang
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Energy Surface ◽  
Sampling Technique ◽  
Small Region ◽  
Umbrella Sampling ◽  
Free Energy Surface ◽  
State Ensemble ◽  
State Region ◽  
Transition State Ensemble

We used the tube model with Go-like potential for native contacts to study the folding transition of a designed three-helix bundle and a designed protein G-like structure. It is shown that both proteins in this model are two-state folders with a cooperative folding transition coincided with the collapse transition. We defined the transition states as protein conformations in a small region around the saddle point on a free energy surface with the energy and the conformationalroot mean square deviation (rmsd) from the native state as the coordinates. The transition state region on the free energy surface then was sampled by using umbrella sampling technique. We show that the transition state ensemble is broad consisting of different conformations that have different folded and unfolded elements.

scholarly journals Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11− Fluxional Cluster

Materials ◽  
2020 ◽  
Vol 14 (1) ◽  
pp. 112
Author(s):  
Carlos Emiliano Buelna-Garcia ◽  
José Luis Cabellos ◽  
Jesus Manuel Quiroz-Castillo ◽  
Gerardo Martinez-Guajardo ◽  
Cesar Castillo-Quevedo ◽  
...  
Keyword(s):  
Free Energy ◽  
Infrared Spectrum ◽  
Infrared Spectra ◽  
Thermal Effects ◽  
Global Minimum ◽  
Energy Surface ◽  
Weighted Sums ◽  
Free Energy Surface ◽  
Temperature Dependent ◽  
Relative Population

The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11− clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be6B11− clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations’ temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer’s infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the spectra of the lowest-energy structure and its isomers located at higher energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra.

scholarly journals The Influence of Starch Origin on the Properties of Starch Films: Packaging Performance

Materials ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 1146
Author(s):  
Zuzanna Żołek-Tryznowska ◽  
Alicja Kałuża
Keyword(s):  
Tensile Strength ◽  
Free Energy ◽  
Surface Free Energy ◽  
Food Packaging ◽  
Energy Surface ◽  
Free Energy Surface ◽  
Casting Method ◽  
Starch Solution ◽  
Film Properties ◽  
Starch Films

Starch films can be used as materials for food packaging purposes. The goal of this study is to compare how the starch origin influence the selected starch film properties. The films were made from various starches such as that from maize, potato, oat, rice, and tapioca using 50%w of glycerine as a plasticizer. The obtained starch-based films were made using the well-known casting method from a starch solution in water. The properties of the films that were evaluated were tensile strength, water vapour transition rate, moisture content, wettability, and their surface free energy. Surface free energy (SFE) and its polar and dispersive components were calculated using the Owens-Wendt-Rabel-Kaelbe approach. The values of SFE in the range of 51.64 to 70.81 mJ∙m−2 for the oat starch-based film and the maize starch-based film. The films revealed worse mechanical properties than those of conventional plastics for packaging purposes. The results indicated that the poorest tensile strength was exhibited by the starch-based films made from oat (0.36 MPa) and tapioca (0.78 MPa) and the greatest tensile strength (1.49 MPa) from potato.

Efficient approach to include molecular polarizations using charge and atom dipole response kernels to calculate free energy gradients in the QM/MM scheme

2015 ◽  
Vol 17 (40) ◽  
pp. 26955-26968 ◽  
Author(s):  
Toshio Asada ◽  
Kanta Ando ◽  
Koji Sakurai ◽  
Shiro Koseki ◽  
Masataka Nagaoka
Keyword(s):  
Free Energy ◽  
Energy Surface ◽  
Free Energy Surface ◽  
Efficient Approach ◽  
Reaction Processes ◽  
Dipole Response

An efficient approach to evaluate free energy gradients within the QM/MM framework has been proposed to clarify reaction processes on the free energy surface.

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