Computational characterization of hybrid proteins containing
ordered and intrinsically disordered regions

a 2017

Computational characterization of hybrid proteins containing ordered and intrinsically disordered regions

ZAPLETAL, Vojtěch, Arnošt MLÁDEK, Jozef HRITZ and Lukáš ŽÍDEK

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

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.530

RIV identification code

RIV/00216224:14740/17:00095560

Organization unit

Central European Institute of Technology

ISSN

UT WoS

000409918904041

Keywords in English

NMR; hybrid proteins

Abstract

V originále

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.

Links

EF16_013/0001776, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii pro lidské zdraví

GA13-16842S, research and development project

Name: PODJEDNOTKY URČUJÍCÍ DNA SPECIFICITU BAKTERIÁLNÍ RNA POLYMERÁZY S FLEXIBILNÍMI DOMÉNAMI: FUNKCE A DYNAMIKA

Investor: Czech Science Foundation

Citovat

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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   author = {Zapletal, Vojtěch and Mládek, Arnošt and Hritz, Jozef and Žídek, Lukáš},
   booktitle = {42nd Congress of the Federation-of-European-Biochemical-Societies (FEBS) on From Molecules to Cells and Back},
   keywords = {NMR; hybrid proteins},
   language = {eng},
   title = {Computational characterization of hybrid proteins containing ordered and intrinsically disordered regions},
   url = {https://2017.febscongress.org/abstract_preview.aspx?idAbstractEnc=4424170092093093093097424170},
   year = {2017}
}

TY  - CONF
ID  - 1410473
AU  - Zapletal, Vojtěch - Mládek, Arnošt - Hritz, Jozef - Žídek, Lukáš
PY  - 2017
TI  - Computational characterization of hybrid proteins containing ordered and intrinsically disordered regions
KW  - NMR
KW  - hybrid proteins
UR  - https://2017.febscongress.org/abstract_preview.aspx?idAbstractEnc=4424170092093093093097424170
L2  - https://2017.febscongress.org/abstract_preview.aspx?idAbstractEnc=4424170092093093093097424170
N2  - 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.
ER  -

ZAPLETAL, Vojtěch, Arnošt MLÁDEK, Jozef HRITZ and Lukáš ŽÍDEK. Computational characterization of hybrid proteins containing ordered and intrinsically disordered regions. In \textit{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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