2 research outputs found
Comprehensive Analysis of Coupled Proline Cis–Trans States in Bradykinin Using ωBP-REMD Simulations
It is well-known that proline (Pro) cis–trans
isomerization
plays a decisive role in the folding and stabilization of proteins.
The conformational coupling between isomerization states of different
Pro residues in proteins during conformational adaptation processes
is not well understood. In the present work, we investigate the coupled
cis–trans isomerization of three Pro residues using bradykinin
(BK), a partially unstructured nonapeptide hormone, as a model system.
We use a recently developed enhanced-sampling molecular dynamics method
(ω-bias potential replica exchange molecular dynamics; ωBP-REMD)
that allows us to exhaustively sample all combinations of Pro isomer
states and obtain converged probability densities of all eight state
combinations within 885 ns ωBP-REMD simulations. In agreement
with experiment, the all-trans state is seen to be the preferred isomer
of zwitterionic aqueous BK. In about a third of its structures, this
state presents the characteristic C-terminal β-turn conformation;
however, other isomer combinations also contribute significantly to
the structural ensemble. Unbiased probabilities can be projected onto
the peptide bond dihedral angles of the three Pro residues. This unveils
the interdependence of the individual Pro isomerization states, i.e.,
a possible coupling of the different Pro isomers. The cis/trans equilibrium
of a Pro residue can change by up to 2.5 kcal·mol–1, depending on the isomerization state of other Pro residues. For
example, for Pro7, the simulations indicate that its cis state becomes
favored compared to its trans state when Pro2 is switched from the
trans state to the cis state. Our findings demonstrate the efficiency
of the ωBP-REMD methodology and suggest that the coupling of
Pro isomerization states may play an even more decisive role in larger
folded proteins subject to more conformational restraints
Investigation of Ion Binding in Chlorite Dismutases by Means of Molecular Dynamics Simulations
Chlorite
dismutases are prokaryotic heme <i>b</i> oxidoreductases
that convert chlorite to chloride and dioxygen. It has been postulated
that during turnover hypochlorite is formed transiently, which might
be responsible for the observed irreversible inactivation of these
iron proteins. The only charged distal residue in the heme cavity
is a conserved and mobile arginine, but its role in catalysis and
inactivation is not fully understood. In the present study, the pentameric
chlorite dismutase (Cld) from the bacterium <i>Candidatus Nitrospira
defluvii</i> was probed for binding of the low spin ligand cyanide,
the substrate chlorite, and the intermediate hypochlorite. Simulations
were performed with the enzyme in the ferrous, ferric, and compound
I state. Additionally, the variant R173A was studied. We report the
parametrization for the GROMOS force field of the anions ClO<sup>–</sup>, ClO<sub>2</sub><sup>–</sup>, ClO<sub>3</sub><sup>–</sup>, and ClO<sub>4</sub><sup>–</sup> and describe spontaneous
binding, unbinding, and rebinding events of chlorite and hypochlorite,
as well as the dynamics of the conformations of Arg173 during simulations.
The findings suggest that (i) chlorite binding to ferric NdCld occurs
spontaneously and (ii) that Arg173 is important for recognition and
to impair hypochlorite leakage from the reaction sphere. The simulation
data is discussed in comparison with experimental data on catalysis
and inhibition of chlorite dismutase