Paper Citing NAMD - Abstract
Profantova, Barbora; Profant, Vaclav; Zima, Vlastimil; Kopecky, Vladimir, Jr.; Bednarova, Lucie; Zentz, Christian; Baumruk, Vladimir; Turpin, Pierre-Yves; Stepanek, Josef
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, 117:16086-16095, DEC 19 2013
The high sensitivity to pH of a short segment (an octamer) of serum response factor (SRF), an important member of the MAPS 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 beta 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.
