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@article{1655320,
author = {Zapletal, Vojtěch and Mládek, Arnošt and Bendová, Kateřina and Louša, Petr and Nomilner, Erik and Jaseňáková, Zuzana and Kubáň, Vojtěch and Makovická, Markéta and Laníková, Alice and Žídek, Lukáš and Hritz, Jozef},
article_location = {Bethesda, USA},
article_number = {7},
doi = {http://dx.doi.org/10.1016/j.bpj.2020.02.019},
keywords = {MOLECULAR-DYNAMICS; TYROSINE-HYDROXYLASE; NMR RELAXATION; RNA-POLYMERASE; DELTA-SUBUNIT; PREDICTION; PHOSPHORYLATION; RECOGNITION; ALIGNMENT; BIOLOGY},
language = {eng},
issn = {0006-3495},
journal = {Biophysical Journal},
title = {Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions},
url = {https://www.sciencedirect.com/science/article/pii/S0006349520301685?via%3Dihub},
volume = {118},
year = {2020}
}
TY - JOUR
ID - 1655320
AU - Zapletal, Vojtěch - Mládek, Arnošt - Bendová, Kateřina - Louša, Petr - Nomilner, Erik - Jaseňáková, Zuzana - Kubáň, Vojtěch - Makovická, Markéta - Laníková, Alice - Žídek, Lukáš - Hritz, Jozef
PY - 2020
TI - Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions
JF - Biophysical Journal
VL - 118
IS - 7
SP - 1621-1633
EP - 1621-1633
PB - Biophysical Society
SN - 00063495
KW - MOLECULAR-DYNAMICS
KW - TYROSINE-HYDROXYLASE
KW - NMR RELAXATION
KW - RNA-POLYMERASE
KW - DELTA-SUBUNIT
KW - PREDICTION
KW - PHOSPHORYLATION
KW - RECOGNITION
KW - ALIGNMENT
KW - BIOLOGY
UR - https://www.sciencedirect.com/science/article/pii/S0006349520301685?via%3Dihub
L2 - https://www.sciencedirect.com/science/article/pii/S0006349520301685?via%3Dihub
N2 - Biomolecular force fields optimized for globular proteins fail to properly reproduce properties of intrinsically disordered proteins. In particular, parameters of the water model need to be modified to improve applicability of the force fields to both ordered and disordered proteins. Here, we compared performance of force fields recommended for intrinsically disordered proteins in molecular dynamics simulations of three proteins differing in the content of ordered and disordered regions (two proteins consisting of a well-structured domain and of a disordered region with and without a transient helical motif and one disordered protein containing a region of increased helical propensity). The obtained molecular dynamics trajectories were used to predict measurable parameters, including radii of gyration of the proteins and chemical shifts, residual dipolar couplings, paramagnetic relaxation enhancement, and NMR relaxation data of their individual residues. The predicted quantities were compared with experimental data obtained within this study or published previously. The results showed that the NMR relaxation parameters, rarely used for benchmarking, are particularly sensitive to the choice of force-field parameters, especially those defining the water model. Interestingly, the TIP3P water model, leading to an artificial structural collapse, also resulted in unrealistic relaxation properties. The TIP4P-D water model, combined with three biomolecular force-field parameters for the protein part, significantly improved reliability of the simulations. Additional analysis revealed only one particular force field capable of retaining the transient helical motif observed in NMR experiments. The benchmarking protocol used in our study, being more sensitive to imperfections than the commonly used tests, is well suited to evaluate the performance of newly developed force fields.
ER -
ZAPLETAL, Vojtěch, Arnošt MLÁDEK, Kateřina BENDOVÁ, Petr LOUŠA, Erik NOMILNER, Zuzana JASEŇÁKOVÁ, Vojtěch KUBÁŇ, Markéta MAKOVICKÁ, Alice LANÍKOVÁ, Lukáš ŽÍDEK and Jozef HRITZ. Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions. \textit{Biophysical Journal}. Bethesda, USA: Biophysical Society, 2020, vol.~118, No~7, p.~1621-1633. ISSN~0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2020.02.019.
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