Complex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model

Conformational fluctuation is usually the key characteristic of the bio-molecular system, and many kinds of elements from bio-molecules themselves and surroundings can affect this fluctuation. Flexibility is a typical feature of the bio-molecules, and it can also be easily affected by the surroundin...

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Autores principales:	Yue Zheng, Junjun Xu, Ke Tang
Formato:	article
Lenguaje:	EN
Publicado:	AIP Publishing LLC 2021
Materias:	Physics QC1-999
Acceso en línea:	https://doaj.org/article/00fb9127f9a648e1b30cec0b9b78156b
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spelling	oai:doaj.org-article:00fb9127f9a648e1b30cec0b9b78156b2021-12-01T18:52:06ZComplex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model2158-322610.1063/5.0072871https://doaj.org/article/00fb9127f9a648e1b30cec0b9b78156b2021-11-01T00:00:00Zhttp://dx.doi.org/10.1063/5.0072871https://doaj.org/toc/2158-3226Conformational fluctuation is usually the key characteristic of the bio-molecular system, and many kinds of elements from bio-molecules themselves and surroundings can affect this fluctuation. Flexibility is a typical feature of the bio-molecules, and it can also be easily affected by the surroundings. As flexibility is regarded to connect with the conformational fluctuation, it becomes an important entrance to analyze the behavior of the bio-molecules. It is known that the typical kinetic characteristics of bio-molecules are mainly controlled by the rate constant, and these properties are usually dominated by surrounding conditions and configuration features of bio-molecules. We have studied the migration rate of bio-molecules by using the two-dimensional (2D) free-energy landscape and the 2D model that includes the extension coordinate and conformational variable in this work. The 2D generalized Langevin equation with a fractional Gaussian noise or white noise matrix is adopted to reveal the key qualities of the bio-molecular system. The reaction temperature and its flexibility (∆k‡) have been particularly analyzed, and these factors can affect the mean waiting time significantly. Particular attention is paid to distinguish typical discrepancies between normal diffusion and dynamic disorder situations. Our results show that the important conditions from complex surroundings cannot be neglected, and they can be the important factors that affect the kinetic behavior of bio-molecules seriously.Yue ZhengJunjun XuKe TangAIP Publishing LLCarticlePhysicsQC1-999ENAIP Advances, Vol 11, Iss 11, Pp 115210-115210-6 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Physics QC1-999
spellingShingle	Physics QC1-999 Yue Zheng Junjun Xu Ke Tang Complex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model
description	Conformational fluctuation is usually the key characteristic of the bio-molecular system, and many kinds of elements from bio-molecules themselves and surroundings can affect this fluctuation. Flexibility is a typical feature of the bio-molecules, and it can also be easily affected by the surroundings. As flexibility is regarded to connect with the conformational fluctuation, it becomes an important entrance to analyze the behavior of the bio-molecules. It is known that the typical kinetic characteristics of bio-molecules are mainly controlled by the rate constant, and these properties are usually dominated by surrounding conditions and configuration features of bio-molecules. We have studied the migration rate of bio-molecules by using the two-dimensional (2D) free-energy landscape and the 2D model that includes the extension coordinate and conformational variable in this work. The 2D generalized Langevin equation with a fractional Gaussian noise or white noise matrix is adopted to reveal the key qualities of the bio-molecular system. The reaction temperature and its flexibility (∆k‡) have been particularly analyzed, and these factors can affect the mean waiting time significantly. Particular attention is paid to distinguish typical discrepancies between normal diffusion and dynamic disorder situations. Our results show that the important conditions from complex surroundings cannot be neglected, and they can be the important factors that affect the kinetic behavior of bio-molecules seriously.
format	article
author	Yue Zheng Junjun Xu Ke Tang
author_facet	Yue Zheng Junjun Xu Ke Tang
author_sort	Yue Zheng
title	Complex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model
title_short	Complex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model
title_full	Complex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model
title_fullStr	Complex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model
title_full_unstemmed	Complex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model
title_sort	complex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model
publisher	AIP Publishing LLC
publishDate	2021
url	https://doaj.org/article/00fb9127f9a648e1b30cec0b9b78156b
work_keys_str_mv	AT yuezheng complexsurroundingaffectionsforkineticspropertiesofbiomoleculesintwodimensionalfreeenergymodel AT junjunxu complexsurroundingaffectionsforkineticspropertiesofbiomoleculesintwodimensionalfreeenergymodel AT ketang complexsurroundingaffectionsforkineticspropertiesofbiomoleculesintwodimensionalfreeenergymodel
_version_	1718404671763120128

Complex surrounding affections for kinetics properties of bio-molecules in two-dimensional free-energy model

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