Computational characterization of hybrid proteins containing ordered and intrinsically disordered regions
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| Year of publication | 2017 |
| Type | Conference abstract |
| MU Faculty or unit | |
| Citation | |
| Description | 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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