Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Piotr Weber; Piotr Bełdowski; Krzysztof Domino; Damian Ledziński; Adam Gadomski

doi:10.3390/e22040405

Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Abstract

This work presents the analysis of the conformation of albumin in the temperature range of 300K – 312K, i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from two angles that reflect global dynamics in the conformational space. A thorough rationalization, based on the scaling theory, for the subdiffusion Flory–De Gennes type exponent of 0.4 unfolds in conjunction with picking up the most appreciable fluctuations of the corresponding statistical-test parameter. These fluctuations coincide adequately with entropy fluctuations, namely the oscillations out of thermodynamic equilibrium. Using Fisher’s test, we investigate the conformational entropy over time and suggest its oscillatory properties in the corresponding time domain. Using the Kruscal–Wallis test, we also analyze differences between the root mean square displacement of a molecule at various temperatures. Here we show that its values in the range of 306K – 309K are different than in another temperature. Using the Kullback–Leibler theory, we investigate differences between the distribution of the root mean square displacement for each temperature and time window.

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Category:: Articles
Type:: artykuły w czasopismach
Published in:: ENTROPY no. 22, pages 1 - 21,
ISSN: 1099-4300
Language:: English
Publication year:: 2020
Bibliographic description:: Weber P., Bełdowski P., Domino K., Ledziński D., Gadomski A.: Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations// ENTROPY-SWITZ -Vol. 22,iss. 4 (2020), s.1-21
DOI:: Digital Object Identifier (open in new tab) 10.3390/e22040405
Verified by:: Gdańsk University of Technology