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

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

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/pdf/10.1021/jp4099864
Description	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. 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. (en)
Title	Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study (en)
skos:prefLabel	Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study (en)
skos:notation	RIV/00216208:11320/13:10189617!RIV14-GA0-11320___
http://linked.open...avai/predkladatel	Matematicko-fyzikální fakulta
http://linked.open...avai/riv/aktivita	I P S
http://linked.open...avai/riv/aktivity	I, P(GA202/09/0193), S
http://linked.open...iv/cisloPeriodika	50
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Zíma, Vlastimil Štěpánek, Josef Profant, Václav Kopecký, Vladimír Baumruk, Vladimír Profantová, Barbora
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Univerzita Karlova v Praze / Matematicko-fyzikální fakulta
http://linked.open...dnocenehoVysledku	100572
http://linked.open...ai/riv/idVysledku	RIV/00216208:11320/13:10189617
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	frequencies; dna; model; spectra; time-scale; amino-acids; scale factors; benzene molecule; protein secondary structure; serum response factor (en)
http://linked.open.../riv/klicoveSlovo	benzene molecule serum response factor time-scale amino-acids model scale factors dna protein secondary structure spectra frequencies
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[448FC9DC32DD]
http://linked.open...i/riv/nazevZdroje	Journal of Physical Chemistry B
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	6 (xsd:int)
http://linked.open...cetTvurcuVysledku	9 (xsd:int)
http://linked.open...vavai/riv/projekt	Formation and dynamics of nucleic acid motifs involved in regulation of gene expression
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	117
http://linked.open...iv/tvurceVysledku	Bednárová, Lucie Turpin, Pierre-Yves Štěpánek, Josef Kopecký, Vladimír Baumruk, Vladimír Profantová, Barbora Zentz, Christian Profant, Václav Zíma, Vlastimil
http://linked.open...ain/vavai/riv/wos	000328920600017
issn	1520-6106
number of pages	10 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp4099864
http://localhost/t...ganizacniJednotka	11320

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