Water-mediated influence of a crowded environment on internal vibrations of a protein molecule - Publikacja - MOST Wiedzy

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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule

Abstrakt

The influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described. The cross-correlation function of the collective velocities of surface atoms of two proteins was decomposed into the Fourier series. The amplitude spectrum displays a peak at low frequencies. Also, the results of principal component analysis suggest that the close presence of an additional protein molecule influences the high-amplitude, low-frequency modes in the most prominent way. This part of the spectrum covers biologically important protein motions. The neighbor-induced changes in the inner dynamics of the protein may be connected with the changes in the velocity power spectrum of interfacial water. The additional protein molecule changes the properties of solvation water and in this way it can influence the dynamics of the second protein. It is suggested that this phenomenon may be described, at first approximation, by a damped oscillator driven by an external random force. This model was successfully applied to conformationally rigid Choristoneura fumiferana antifreeze protein molecules.

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Kategoria:
Publikacja w czasopiśmie
Typ:
artykuł w czasopiśmie wyróżnionym w JCR
Opublikowano w:
PHYSICAL CHEMISTRY CHEMICAL PHYSICS nr 18, wydanie 6, strony 4881 - 4890,
ISSN: 1463-9076
Język:
angielski
Rok wydania:
2016
Opis bibliograficzny:
Kuffel A., Zielkiewicz J.: Water-mediated influence of a crowded environment on internal vibrations of a protein molecule// PHYSICAL CHEMISTRY CHEMICAL PHYSICS. -Vol. 18, iss. 6 (2016), s.4881-4890
DOI:
Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1039/c5cp07628e
Weryfikacja:
Politechnika Gdańska

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