About: Conformational flexibility of peptides in solution

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rdf:type	http://linked.opendata.cz/ontology/domain/vavai/Projekt
rdfs:seeAlso	http://www.isvav.cz/projectDetail.do?rowId=GA202/07/0732
Description	The project aims at the dynamic aspects of peptide conformation in aqueous solution where peptide structural properties are most relevant to their biological role. In order to obtain solid physical knowledge about peptide structure and dynamics, we will proceed from simple model dipeptides to more complex systems. Experimentally the project is based mainly on Raman Optical Activity (ROA) and Raman scattering that can sense equilibrium distributions of rapidly fluctuating structures with parallel NMR experiments. Interpretation of Raman and ROA spectra will be based on advanced spectral simulations taking into account conformational flexibility of the studied systems as well as solvent effects. Potential energy surface will be mapped for simple models to get realistic estimates of their flexibility. Force fields and polarizability tensors of longer peptides will be constructed from short fragments by means of atomic tensor transfer. The ultimate goal is to fill the gap between knowledge about (en) Podstatou projektu je studium dynamických aspektů konformace peptidů ve vodném prostředí, jehož vliv na strukturní vlastnosti je z hlediska biologické role nejdůležitější. Abychom získali spolehlivé fyzikální poznatky, navrhujeme směřovat od jednoduchéhoke složitějšímu, od jednoduchých modelových dipeptidů ke komplexnějším systémům. Experimentálně je projekt založen na využití Ramanovy optické aktivity (ROA) a Ramanova rozptylu, které umožňují získat informaci o rovnovážné distribuci rychle fluktuujících struktur. Doplňující informace bude získána i z NMR experimentů. Pro interpretaci naměřených dat budou vyvinuty nové nebo adaptovány existující metody zahrnujících jak konformační flexibilitu studovaných systémů tak i vliv rozpouštědla. Provětší oligopeptidy budou silová pole a tenzory polarizovatelnosti určující jejich spektrální vlastnosti konstruovány pomocí přenosu atomových tenzorů. Hlavním cílem je zaplnit mezeru ve znalostech chování jednoduchých dipeptidů a proteinů, a hlouběji
Title	Conformational flexibility of peptides in solution (en) Konformační flexibilita peptidů v roztoku
skos:notation	GA202/07/0732
http://linked.open...avai/cep/aktivita	Standard projects
http://linked.open...kovaStatniPodpora	http://linked.opendata.cz/resource/domain/vavai/projekt/GA202%2F07%2F0732/celkovaStatniPodpora
http://linked.open...ep/celkoveNaklady	http://linked.opendata.cz/resource/domain/vavai/projekt/GA202%2F07%2F0732/celkoveNaklady
http://linked.open...datumDodatniDoRIV	2015-01-22 (xsd:date)
http://linked.open...i/cep/druhSouteze	VS - Veřejná soutěž ve výzkumu a vývoji
http://linked.open...ep/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open.../cep/fazeProjektu	65674358
http://linked.open...ai/cep/hlavniObor	BO - Biofyzika
http://linked.open...hodnoceniProjektu	V - Vynikající výsledky (s mezinárodním významem apod.). Zároveň byly splněny cíle a předpokládané výsledky uvedené ve smlouvě / rozhodnutí o poskytnutí podpory.
http://linked.open...vai/cep/kategorie	ZV - Základní výzkum
http://linked.open.../cep/klicovaSlova	Raman optical activity; peptides; structure; flexibility; QM/MM calculations; potential energy surfaces (en)
http://linked.open...ep/partnetrHlavni	Matematicko-fyzikální fakulta
http://linked.open...inujicichPrijemcu	0 (xsd:int)
http://linked.open...cep/pocetPrijemcu	1 (xsd:int)
http://linked.open...ocetSpoluPrijemcu	1 (xsd:int)
http://linked.open.../pocetVysledkuRIV	38 (xsd:int)
http://linked.open...enychVysledkuVRIV	38 (xsd:int)
http://linked.open...lneniVMinulemRoce	2009-04-22 (xsd:date)
http://linked.open.../prideleniPodpory	http://linked.opendata.cz/resource/domain/vavai/cep/prideleniPodpory/202%2F07%2F0732
http://linked.open...iciPoslednihoRoku	2009
http://linked.open...atUdajeProjZameru	2010
http://linked.open.../vavai/cep/soutez	SGA02007GA-ST
http://linked.open...usZobrazovaneFaze	DUU
http://linked.open...ai/cep/typPojektu	P - Projekt výzkumu a vývoje financovaný ze státního rozpočtu
http://linked.open...ep/ukonceniReseni	2009-12-31 (xsd:date)
http://linked.open.../cep/vedlejsiObor	CF - Fyzikální chemie a teoretická chemie
http://linked.open...ep/zahajeniReseni	2007-01-01 (xsd:date)
http://linked.open...jektu+dodavatelem	. (en) Výsledky projektu přispěly k rozšíření aplikace Ramanovy optické aktivity do fyziky biomolekul především ve vysokofrekvenční oblasti, kde leží valeční vibrace vodíku. Tímto se dosud nikdo systematicky nezabýval. Projekt zároveň přispěl k rozvoji metod sim (cs)
http://linked.open...tniCyklusProjektu	ZBKU
http://linked.open.../cep/klicoveSlovo	Raman optical activity QM/MM calculations flexibility peptides structure
is http://linked.open...vavai/riv/projekt of	Raman optical activity of biomolecules: from simple models to complex systems 2D correlation spectroscopy and its application in vibrational spectroscopy using Matlab Conformational properties of the Pro-Gly motif in the D-Ala-L-Pro-Gly-D-Ala model peptide explored by a statistical analysis of the NMR, Raman, and Raman optical activity spectra Ab initio modeling of the electronic circular dichroism induced in porphyrin chromophores Raman spectral evidence of methyl rotation in liquid toluene Dependence ofthe L-alanyl-L-alanine conformation on molecular charge determined from ab initio computations and NMR spectra Comparison of quantitative conformer analyses by nuclear magnetic resonance and raman optical activity spectra for model dipeptides Circular Dichroism Enhancement in Large DNA Aggregates Simulated by a generalized oscillator model Vibrational circulardichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide Dynamics and magnetic resonance properties of Sc3C2@C80 and its monoanion Raman optical activity of biomolecules: From simple models to complex systems Molecular dynamics with restrictions derived from optical spectra Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging Infrared absorption detection of metal ion-deoxyguanosine monophosphate binding: Experimental and theoretical study Simulation of vibrational spectra of large molecules by arbitrary time propagation Interpretation of Raman and Raman Optical Activity Spectra of a Flexible Sugar Derivative, the Gluconic Acid Anion L-Alanyl-L-alanine Conformational Changes Induced by pH As Monitored by the Raman Optical Activity Spectra Characteristic spin - orbit induced 1H(CH2) chemical shifts upon deprotonation of group 9 polyamine aqua and alcohol complexes Solvent dependence of the N-methylacetamide structure and force field Structure of the Alanine Hydration Shell as Probed by NMR Chemical Shifts and Indirect Spin-Spin Coupling Modeling of a Tröger’s tweezer and its complexation properties TD-DFT Modeling of the Circular Dichroism for a Tryptophan Zipper Peptide with Coupled Aromatic Residues Theoretical Study of Vibrationally Averaged Dipole Moments for the Ground and Excited C=O Stretching States of trans-Formic Acid Theoretical Modeling of Magnesium Ion Imprints in the Raman Scattering of Water Vibrational and Electronic optical Activity of the Chiral Disulphide Group: Implications for Disulphide Bridge Conformation Intramolecular Proton Transfer in Calixphyrin Derivatives Side Chain and Flexibility Contributions to the Raman Optical Activity Spectra of a Model Cyclic Hexapeptide Raman optical activity study of poly-L-proline chains of various lengths PROBLEMS WITH A CONFORMATION ASSIGNMENT OF ARYL-SUBSTITUTED RESORC[4]ARENES Spectroscopic properties of the nonplanar amide group: A computational study DNA oligonucleotide-cis-platin Binding: Ab initio interpretation of the vibrational spectra Simulations of vibrational spectra from classical trajectories: Calibration with ab initio force fields Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions Matrix formulation of the surface-enhanced Raman optical activity theory Computational analysis of solvent effects in NMR spectroscopy A Fourier Transform Method for Generation of Anharmonic Vibrational Molecular Spectra A spectroscopic method to estimate the binding potency of amphiphile assemblies Applications of the Cartesian Coordinate Tensor Transfer Technique in the Simulations of Vibrational Circular Dichroism Spectra of Oligonucleotides
is http://linked.open...vavai/cep/projekt of	http://linked.opendata.cz/resource/domain/vavai/cep/ucast/GA202%2F07%2F0732/2007/ico%3A61388963 http://linked.opendata.cz/resource/domain/vavai/cep/ucast/GA202%2F07%2F0732/2007/orjk%3A11320 http://linked.opendata.cz/resource/domain/vavai/cep/ucast/GA202%2F07%2F0732/2008/ico%3A61388963 http://linked.opendata.cz/resource/domain/vavai/cep/ucast/GA202%2F07%2F0732/2008/orjk%3A11320 http://linked.opendata.cz/resource/domain/vavai/cep/ucast/GA202%2F07%2F0732/2009/ico%3A61388963 http://linked.opendata.cz/resource/domain/vavai/cep/ucast/GA202%2F07%2F0732/2009/orjk%3A11320 http://linked.opendata.cz/resource/domain/vavai/cep/ucast/GA202%2F07%2F0732/2010/orjk%3A11320

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