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

Entropy (Basel). 2020 Apr 1;22(4):405. doi: 10.3390/e22040405.

Authors

Piotr Weber¹, Piotr Bełdowski², Krzysztof Domino³, Damian Ledziński⁴, Adam Gadomski²

Affiliations

¹ Atomic and Optical Physics Division, Department of Atomic, Molecular and Optical Physics, Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland.
² Institute of Mathematics and Physics, UTP University of Science and Technology, Kaliskiego 7, 85-796 Bydgoszcz, Poland.
³ Institute of Theoretical and Applied Informatics, Polish Academy of Sciences, Bałtycka 5, 44-100 Gliwice, Poland.
⁴ Faculty of Telecommunications, Computer Science and Technology, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland.

Abstract

This work presents the analysis of the conformation of albumin in the temperature range of 300 K - 312 K , 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 306 K - 309 K 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.

Keywords: Fisher’s test; Flory–De Gennes exponent; Kullback–Leibler divergence; albumin; conformation of protein; non-gaussian chain; non-isothermal characteristics.