{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T09:58:01Z","timestamp":1775642281117,"version":"3.50.1"},"reference-count":35,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2020,4,1]],"date-time":"2020-04-01T00:00:00Z","timestamp":1585699200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Entropy"],"abstract":"<jats:p>This work presents the analysis of the conformation of albumin in the temperature range of     300 K    \u2013    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\u2013De 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\u2019s test, we investigate the conformational entropy over time and suggest its oscillatory properties in the corresponding time domain. Using the Kruscal\u2013Wallis 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    \u2013    309 K     are different than in another temperature. Using the Kullback\u2013Leibler theory, we investigate differences between the distribution of the root mean square displacement for each temperature and time window.<\/jats:p>","DOI":"10.3390\/e22040405","type":"journal-article","created":{"date-parts":[[2020,4,1]],"date-time":"2020-04-01T15:37:21Z","timestamp":1585755441000},"page":"405","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations"],"prefix":"10.3390","volume":"22","author":[{"given":"Piotr","family":"Weber","sequence":"first","affiliation":[{"name":"Atomic and Optical Physics Division, Department of Atomic, Molecular and Optical Physics, Faculty of Applied Physics and Mathematics, Gda\u0144sk University of Technology, ul. G. Narutowicza 11\/12, 80-233 Gda\u0144sk, Poland"}]},{"given":"Piotr","family":"Be\u0142dowski","sequence":"additional","affiliation":[{"name":"Institute of Mathematics and Physics, UTP University of Science and Technology, Kaliskiego 7, 85-796 Bydgoszcz, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7386-5441","authenticated-orcid":false,"given":"Krzysztof","family":"Domino","sequence":"additional","affiliation":[{"name":"Institute of Theoretical and Applied Informatics, Polish Academy of Sciences, Ba\u0142tycka 5, 44-100 Gliwice, Poland"}]},{"given":"Damian","family":"Ledzi\u0144ski","sequence":"additional","affiliation":[{"name":"Faculty of Telecommunications, Computer Science and Technology, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8201-1736","authenticated-orcid":false,"given":"Adam","family":"Gadomski","sequence":"additional","affiliation":[{"name":"Institute of Mathematics and Physics, UTP University of Science and Technology, Kaliskiego 7, 85-796 Bydgoszcz, Poland"}]}],"member":"1968","published-online":{"date-parts":[[2020,4,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e7","DOI":"10.1017\/S0033583519000027","article-title":"Dynamics of proteins in solution","volume":"52","author":"Grimaldo","year":"2019","journal-title":"Quarter. Rev. Biophys."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Rubinstein, M., and Colby, R.H. (2003). Polymer Physics, Oxford University Press.","DOI":"10.1093\/oso\/9780198520597.001.0001"},{"key":"ref_3","unstructured":"De Gennes, P.G. (1979). Scaling Concepts in Polymer Physics, Cornell University Press."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.biosystems.2019.01.002","article-title":"On (sub) mesoscopic scale peculiarities of diffusion driven growth in an active matter confined space, and related (bio) material realizations","volume":"176","author":"Gadomski","year":"2019","journal-title":"Biosystems"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"24128","DOI":"10.1039\/C4CP03465A","article-title":"Anomalous diffusion models and their properties: Non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking","volume":"16","author":"Metzler","year":"2014","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Weber, P., Be\u0142dowski, P., Bier, M., and Gadomski, A. (2018). Entropy Production Associated with Aggregation into Granules in a Subdiffusive Environment. Entropy, 20.","DOI":"10.3390\/e20090651"},{"key":"ref_7","unstructured":"Flory, P. (1953). Principles of Polymer Chemistry, Cornell University Press."},{"key":"ref_8","unstructured":"Doi, M., and Edwards, S.F. (1986). The Theory of The Polymer Dynamics. The International Series of Monographs on Physics, Oxford University Press."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"38731","DOI":"10.1074\/jbc.M005460200","article-title":"Binding of the General Anesthetics Propofol and Halothane to Human Serum Albumin","volume":"275","author":"Bhattacharya","year":"2000","journal-title":"J. Biol. Chem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1098\/rsif.2005.0086","article-title":"Rheopexy of synovial fluid and protein aggregation","volume":"3","author":"Oates","year":"2006","journal-title":"J. R. Soc. Interface"},{"key":"ref_11","first-page":"709","article-title":"Effect of hyaluronic acid on friction of articular cartilage","volume":"24","author":"Rebenda","year":"2018","journal-title":"Eng. Mech."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"6497","DOI":"10.1038\/ncomms7497","article-title":"Supramolecular synergy in the boundary lubrication of synovial joints","volume":"6","author":"Seror","year":"2015","journal-title":"Nat. Commun."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1016\/j.medengphy.2008.09.004","article-title":"Biotribology of articular cartilage\u2014A review of the recent advances","volume":"30","author":"Katta","year":"2000","journal-title":"Med. Eng. Phys."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/j.jbiomech.2014.11.008","article-title":"Impact of synovial fluid flow on temperature regulation in knee cartilage","volume":"48","author":"Moghadam","year":"2015","journal-title":"J. Biomech."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"527","DOI":"10.18388\/abp.1997_4402","article-title":"Design of a knowledge-based force field for off-latice simulations of protein structure","volume":"44","author":"Liwo","year":"1997","journal-title":"Acta Biochim. Pol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1080\/00018730110116353","article-title":"Diffusion in disordered media","volume":"51","author":"Havlin","year":"2002","journal-title":"Adv. Phys."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"503101","DOI":"10.1088\/0953-8984\/25\/50\/503101","article-title":"Flory theory for polymers","volume":"25","author":"Bhattacharjee","year":"2013","journal-title":"J. Phys. Condens. Matter"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"15396","DOI":"10.1073\/pnas.1407768111","article-title":"Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations","volume":"111","author":"Baxa","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Ahdesmaki, M., Lahdesmaki, H., and Yli-Harja, O. (2007, January 10\u201312). Robust Fisher\u2019s test for periodicity detection in noisy biological time series. Proceedings of the IEEE International Workshop on Genomic Signal Processing and Statistics, Tuusula, Finland.","DOI":"10.1109\/GENSIPS.2007.4365817"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1093\/bioinformatics\/btg364","article-title":"Identifying periodically expressed transcripts in microarray time series data","volume":"20","author":"Wichert","year":"2004","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Kanji, G.K. (2006). 100 Statiatical Tests, SAGE Publications Ltd.","DOI":"10.4135\/9781849208499"},{"key":"ref_22","unstructured":"Conover, W.J. (1980). Practical Nonparametric Statistics, John Wiley & Sons. [2nd ed.]."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Gupta, A., Parameswaran, S., and Lee, C.-H. (2009, January 19\u201324). Classification of electroencephalography signals for different mental activities using Kullback-Leibler divergence. Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing, Taipei, Taiwan.","DOI":"10.1109\/ICASSP.2009.4959929"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1016\/j.physa.2014.07.020","article-title":"The use of copula functions for predictive analysis of correlations between extreme storm tides","volume":"413","author":"Domino","year":"2014","journal-title":"Physica A"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1107\/S2059798316013218","article-title":"Empirical power laws for the radii of gyration of protein oligomers","volume":"72","author":"Tanner","year":"2016","journal-title":"Acta Crystallogr. D Struct. Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1002\/pro.3376","article-title":"Determination of protein oligomeric structure from small-angle X-ray scattering","volume":"27","author":"Korasick","year":"2018","journal-title":"Protein Sci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1016\/j.bpj.2019.03.015","article-title":"Thermodynamic Stability of the Transcription Regulator PaaR2 from Escherichia coli O157:H7","volume":"116","author":"Vandervelde","year":"2019","journal-title":"Biophys. J."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e23020","DOI":"10.1002\/bip.23020","article-title":"Hydrophobic-Hydrophilic Forces in Protein Folding","volume":"107","author":"Durell","year":"2017","journal-title":"Biopolymers"},{"key":"ref_29","first-page":"530","article-title":"Conformational Study of Human Serum Albumin in Pre-denaturation Temperatures by Differential Scanning Calorimetry, Circular Dichroism and UV Spectroscopy","volume":"39","author":"Moghaddamnia","year":"2006","journal-title":"J. Biochem. Mol. Biol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"L-469","DOI":"10.1051\/jphyslet:019800041019046900","article-title":"Flory exponents for generalized polymer problems","volume":"41","author":"Isaacson","year":"1980","journal-title":"J. Phys. Lett."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1002\/jcc.23899","article-title":"New ways to boost molecular dynamics simulations","volume":"36","author":"Krieger","year":"2015","journal-title":"J. Comput. Chem."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"9954","DOI":"10.1021\/jp003020w","article-title":"Structure and Dynamics of the TIP3P, SPC, and SPC\/E Water Models at 298 K","volume":"105","author":"Mark","year":"2001","journal-title":"J. Phys. Chem. A"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1002\/jcc.10349","article-title":"A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations","volume":"24","author":"Duan","year":"2003","journal-title":"J. Comput. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"11740","DOI":"10.1038\/srep11740","article-title":"Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads","volume":"5","author":"Baruah","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_35","unstructured":"(2017, April 30). SciLab. Available online: https:\/\/www.scilab.org."}],"container-title":["Entropy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1099-4300\/22\/4\/405\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:14:26Z","timestamp":1760174066000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1099-4300\/22\/4\/405"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,1]]},"references-count":35,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2020,4]]}},"alternative-id":["e22040405"],"URL":"https:\/\/doi.org\/10.3390\/e22040405","relation":{},"ISSN":["1099-4300"],"issn-type":[{"value":"1099-4300","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,1]]}}}