Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P‐D Water Model and the Representativeness of Protein Disorder Models

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

Abstract

Here, we first present a follow-up to a previous work by our group on the problematic of molecular dynamics simulations of intrinsically disordered proteins (IDPs) [Henriques et al. J. Chem. Theory Comput. 2015, 11, 3420−3431], using the recently developed TIP4P-D water model. When used in conjunction with the standard AMBER ff99SB-ILDN force field and applied to the simulation of Histatin 5, our IDP model, we obtain results which are in excellent agreement with the best performing IDP-suitable force field from the earlier study and with experiment. We then assess the representativeness of the IDP models used in these and similar studies, finding that most are too short in comparison to the average IDP and contain a bias toward hydrophilic amino acid residues. Moreover, several key order- and disorder-promoting residues are also found to be misrepresented. It seems appropriate for future studies to address these issues.

Detaljer

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Forskningsområden

Ämnesklassifikation (UKÄ) – OBLIGATORISK

  • Teoretisk kemi
Originalspråkengelska
Sidor (från-till)3407–3415
Antal sidor9
TidskriftJournal of Chemical Theory and Computation
Volym12
Utgivningsnummer7
StatusPublished - 2016 maj 31
PublikationskategoriForskning
Peer review utfördJa

Relaterad forskningsoutput

Henriques, J., 2016 nov, Lund: Lund University, Faculty of Science, Department of Chemistry, Theoretical Chemistry. 90 s.

Forskningsoutput: AvhandlingDoktorsavhandling (sammanläggning)

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