Ultrafast solvation dynamics of flavin mononucleotide in the reductase component of p-hydroxyphenylacetate hydroxylase

Conformational difference between two subunits in flavin mononucleotide binding protein dimers from Desulfovibrio vulgaris (MF): molecular dynamics simulation

The structural and dynamical properties of five FMN binding protein (FBP) dimers, WT (wild type), E13K (Glu13 replaced by Lys), E13R (Glu13 replaced by Arg), E13T (Glu13 replaced by Thr) and E13Q (Glu13 replaced by Gln), were investigated using a method of molecular dynamics simulation (MDS). In crystal structures, subunit A (Sub A) and subunit B (Sub B) were almost completely equivalent in all of the five FBP dimers. However, the predicted MDS structures of the two subunits were not equivalent in solution, revealed by the distances and inter-planar angles between isoalloxazine (Iso) and aromatic amino acids (Trp32, Tyr35 and Trp106) as well as the hydrogen bonding pairs between Iso and nearby amino acids. Residue root of mean square fluctuations (RMSF) also displayed considerable differences between Sub A and Sub B and in the five FBP dimers. The dynamics of the whole protein structures were examined with the distance (RNN) between the peptide N atom of the N terminal (Met1) and the peptide N atom of the C terminal (Leu122). Water molecules were rarely accessible to Iso in all FBP dimers which are in contrast with other flavoenzymes.

Validation of response function construction and probing heterogeneous protein hydration by intrinsic tryptophan

Protein solvation dynamics usually occur on multiple time scales with site specificity, and the characterization of such heterogeneous dynamics requires a convenient optical probe. We proposed a tryptophan methodology, and with site-directed mutagenesis we can use a tryptophan scan to probe any desirable position around protein surfaces. Here, we report our extended solvation model for construction of response functions for probes such as tryptophan with multiple emission peaks and lifetimes. We show our systematic construction procedure and careful analyses of the possible missing percentage of an initial ultrafast component with the established zero-time emission spectrum and limited temporal resolution through two methods of the direct mapping of femtosecond-resolved fluorescence spectra (3D FRES) and the constructed FRES (2D) from the fluorescence transients. We unambiguously validate our extended model with reexamination of solvation dynamics (methanol, water, and proteins) using conventional dye coumarin, intrinsic tryptophan, and cofactor flavin. Using mutant proteins of GB1, we show again the generality of the powerful probe tryptophan for protein hydration (solvation) and the slowdown of the hydration layer dynamics especially at the water-protein interface. These results justify the necessity of our extended solvation model, clarify the confusion of protein hydration in the recent literature, and establish the universal optical probe of tryptophan for heterogeneous protein dynamics.

The C-terminal domain of 4-hydroxyphenylacetate 3-hydroxylase from Acinetobacter baumannii is an autoinhibitory domain

p-Hydroxyphenylacetate (HPA) 3-hydroxylase from Acinetobacter baumannii consists of a reductase component (C(1)) and an oxygenase component (C(2)). C(1) catalyzes the reduction of FMN by NADH to provide FMNH(-) as a substrate for C(2). The rate of reduction of flavin is enhanced ∼20-fold by binding HPA. The N-terminal domain of C(1) is homologous to other flavin reductases, whereas the C-terminal domain (residues 192-315) is similar to MarR, a repressor protein involved in bacterial antibiotic resistance. In this study, three forms of truncated C(1) variants and single site mutation variants of residues Arg-21, Phe-216, Arg-217, Ile-246, and Arg-247 were constructed to investigate the role of the C-terminal domain in regulating C(1). In the absence of HPA, the C(1) variant in which residues 179-315 were removed (t178C(1)) was reduced by NADH and released FMNH(-) at the same rates as wild-type enzyme carries out these functions in the presence of HPA. In contrast, variants with residues 231-315 removed behaved similarly to the wild-type enzyme. Thus, residues 179-230 are involved in repressing the production of FMNH(-) in the absence of HPA. These results are consistent with the C-terminal domain in the wild-type enzyme being an autoinhibitory domain that upon binding the effector HPA undergoes conformational changes to allow faster flavin reduction and release. Most of the single site variants investigated had catalytic properties similar to those of the wild-type enzyme except for the F216A variant, which had a rate of reduction that was not stimulated by HPA. F216A could be involved with HPA binding or in the required conformational change for stimulation of flavin reduction by HPA.

A fluorescence perspective on the differential interaction of riboflavin and flavin adenine dinucleotide with cucurbit[7]uril

The interaction of the macrocyclic host, cucurbit[7]uril (CB7), with riboflavin (RF) and its derivative, flavin adenine dinucleotide (FAD), has been investigated using absorption and steady-state and time-resolved fluorescence measurements. Interestingly, in the presence of CB7, the fluorescence intensity of RF is quenched, whereas the fluorescence intensity of FAD is enhanced. It is proposed that the fluorescence quenching of RF results from the tautomerization of its isoalloxazine moiety from the lactam to the lactim forms, upon binding to CB7. Such a tautomerization can be brought about since the two lactim forms have higher dipole moments than the lactam form of RF, and thus experience much stronger dipole-dipole interactions (and hence greater binding affinities) with CB7 in the former cases than in the latter. This tautomerization in the presence of CB7 leads to a significant reduction in the observed radiative decay rate and hence a reduction in the fluorescence intensity of RF. Binding of CB7 with RF is confirmed by an increase in the rotational correlation time of RF in the presence of CB7. Geometry optimization studies indicate the formation of an exclusion complex between CB7 and RF, possibly stabilized by H-bonding interactions, as also suggested by the characteristic red shift in the absorption spectra of the CB7-RF system. In the case of FAD, both the isoalloxazine ring and the adenine moiety can interact with the CB7 host. In aqueous solutions, a good fraction of FAD molecules exists in a "closed" conformation with the adenine and isoalloxazine rings stacked together, thus leading to very efficient fluorescence quenching due to the ultrafast intramolecular electron transfer from adenine to the isoalloxazine moiety. Binding of the adenine and/or the isoalloxazine moiety of FAD with CB7 inhibits the stacking interaction and changes the "closed" conformation to the "open" conformation, wherein the adenine and isoalloxazine moieties are widely separated, thus prohibiting the electron transfer process. This reduces the inherent fluorescence quenching of FAD molecule and results in the observed fluorescence enhancement. As observed for RF, the interaction of CB7 with the isoalloxazine ring of FAD should cause fluorescence quenching due to the lactam to lactim tautomerization process. However, in the interplay between the above two opposing effects, the fluorescence enhancement due to the modulation in the conformational dynamics of FAD by the CB7 host predominates. The conformational change is in fact supported by the observation of a long lifetime component in the fluorescence decay of FAD in the presence of CB7. Moreover, at acidic pH, when FAD is already present mainly in the "open" form, the conformational dynamics no longer plays any major role and the fluorescence of FAD is quenched by CB7, as expected, due to the tautomerization at the isoalloxazine moiety.

Inhibiting intramolecular electron transfer in flavin adenine dinucleotide by host-guest interaction: a fluorescence study

Modulation in the photophysical properties and intramolecular electron transfer behavior of the flavin adenine dinucleotide (FAD) molecule has been investigated in the presence of the macrocyclic hosts, alpha-, beta- and gamma-cyclodextrins (CDs), using absorption and steady-state and time-resolved fluorescence measurements. The results demonstrate that only the beta-CD host has a suitable cavity dimension to form a weak inclusion complex with FAD by encapsulating the adenine moiety, which is the preferred binding site in the large FAD molecule. Interestingly, in spite of the weak binding interaction, a significant enhancement in the fluorescence intensity of FAD is observed on complexation with beta-CD, and this has been attributed mainly to the modulation in the conformational dynamics of FAD in the presence of beta-CD. In aqueous solutions, a good fraction of FAD molecules exist in a "closed" conformation with the adenine and isoalloxazine rings stacked on each other, thus leading to very efficient fluorescence quenching due to the ultrafast intramolecular electron transfer from adenine to the isoalloxazine moiety. Complex formation with beta-CD inhibits this intramolecular electron transfer by changing the "closed" conformation of FAD to the "open" form, wherein the adenine and isoalloxazine moieties are widely separated, thus prohibiting the fluorescence quenching process. Further evidence for the conformational changes has been obtained by the observation of a long lifetime component in the fluorescence decay of FAD in the presence of beta-CD, which corresponds to the decay of the unquenched "open" form of FAD. Fluorescence up-conversion studies also indicate the absence of any ultrafast component in the fluorescence decay arising from the complexed FAD, thus supporting the formation of the "open" form in the presence of beta-CD, with no intramolecular electron transfer.