ZAPLETAL, Vojtěch, Arnošt MLÁDEK, Jozef HRITZ and Lukáš ŽÍDEK. Computational characterization of hybrid proteins containing ordered and intrinsically disordered regions. In 42nd Congress of the Federation-of-European-Biochemical-Societies (FEBS) on From Molecules to Cells and Back. 2017. ISSN 1742-464X.
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Basic information
Original name Computational characterization of hybrid proteins containing ordered and intrinsically disordered regions
Authors ZAPLETAL, Vojtěch (203 Czech Republic, belonging to the institution), Arnošt MLÁDEK (203 Czech Republic, belonging to the institution), Jozef HRITZ (703 Slovakia, belonging to the institution) and Lukáš ŽÍDEK (203 Czech Republic, guarantor, belonging to the institution).
Edition 42nd Congress of the Federation-of-European-Biochemical-Societies (FEBS) on From Molecules to Cells and Back, 2017.
Other information
Original language English
Type of outcome Conference abstract
Field of Study 10608 Biochemistry and molecular biology
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 4.530
RIV identification code RIV/00216224:14740/17:00095560
Organization unit Central European Institute of Technology
ISSN 1742-464X
UT WoS 000409918904041
Keywords in English NMR; hybrid proteins
Tags rivok
Changed by Changed by: Mgr. Pavla Foltynová, Ph.D., učo 106624. Changed: 9/3/2018 15:10.
Abstract
Intrinsically disordered proteins (IDPs) characterized by polypeptide chains that fail to fold into stable and well defined tertiary structure in an isolated state have been under our interest. IDPs play key roles in processes such as molecular recognition, regulation of transcription and they are related to neurodegenerative diseases. Most of IDPs are in fact intrinsically disordered regions (IDRs) that are tethered to ordered domains (ODs). It is imperative that the biophysical properties of these regions be studied in their naturally occurring contexts, which is tethered to ODs. It is difficult to cope with such systems for the experimental techniques and for computational methods. Typical experimental methods for study of IDPs are nuclear magnetic resonance (NMR) and small angle X-ray scattering (SAXS). The obtained data were used for verification of predicted values from the computational simulations. In our study, we generated structural ensembles of the -subunit of RNA polymerase and regulatory domain of human tyrosine hydroxylase using molecular dynamics simulations. The reliability of the obtained ensembles generated under different force field parameters (AMBER99SB-ILDN/CHARMM22 + TIP3P/TIP4P-D) was checked by the comparison of the corresponding calculated properties with their experimental values. Namely we monitored: NMR chemical shifts, residual dipolar couplings, paramagnetic relaxation enhancement, relaxation rates, and SAXS data. The best agreement was obtained for the AMBER99SB-ILDN/TIP4P-D force field parameters.
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EF16_013/0001776, research and development projectName: Česká infrastruktura pro integrativní strukturní biologii pro lidské zdraví
GA13-16842S, research and development projectName: PODJEDNOTKY URČUJÍCÍ DNA SPECIFICITU BAKTERIÁLNÍ RNA POLYMERÁZY S FLEXIBILNÍMI DOMÉNAMI: FUNKCE A DYNAMIKA
Investor: Czech Science Foundation
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