Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study

0421903 - ÚOCHB 2014 RIV US eng J - Journal Article
Profantová, B. - Profant, V. - Zíma, V. - Kopecký, V. Jr. - Bednárová, Lucie - Zentz, Ch. - Baumruk, V. - Turpin, P. Y. - Štěpánek, J.
Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study.
Journal of Physical Chemistry B. Roč. 117, č. 50 (2013), s. 16086-16095. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR GA202/09/0193
Institutional support: RVO:61388963
Keywords : MADS box * protein secondary structure * tyrosine * pHtransition * Raman spectroscopy
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.377, year: 2013

The high sensitivity to pH of a short segment (an octamer) of serum response factor (SRF), an important member of the MADS box family of transcription factors, was investigated by Raman scattering, infrared and circular dichroism spectroscopies. Molecular dynamics (MD) and density functional theory (DFT) calculations enabled interpretation of spectral changes in close detail. Although there was a negligible difference between spectra in acidic and neutral environments, the spectrum in basic pH was substantially different. The major changes were attributed to the deprotonation of tyrosine. The secondary structure of the SRF octamer fragment was estimated experimentally as well as predicted theoretically by MD. All techniques proved that it exists in a dynamical equilibrium among several conformations mostly close to β turn, unordered conformations, and extended structure, in contrast to the stable secondary structure it possesses as a part of SRF. Generally, this approach represents a useful tool for the study of various short oligopeptides.
Permanent Link: http://hdl.handle.net/11104/0228153