Judit Fidy

Photochemical holes under pressure: Compressibility and volume fluctuations of a protein

From the pressure induced frequency shift of photochemical holes burnt into mesomorphyrin substituted horseradish peroxidase, we determined the compressibility of the protein and the vacuum frequency of the chromophore. From the compressibility, an estimation of the volume fluctuations of the biomolecule is possible.

Proteins in electric fields and pressure fields: basic aspects

This paper emphasizes the basic aspects of the interactions of chromoproteins at low temperatures with external pressure fields and electric fields. We discuss how the respective spectral properties can be modified and what we can learn from the spectral changes about the thermodynamic, electrostatic, functional and structural properties of proteins. A few examples are discussed in more detail.

Active site closure facilitates juxtaposition of reactant atoms for initiation of catalysis by human dUTPase

Human dUTPase, essential for DNA integrity, is an important survival factor for cancer cells. We determined the crystal structure of the enzyme:α,β‐imino‐dUTP:Mg complex and performed equilibrium binding experiments in solution. Ordering of the C‐terminus upon the active site induces close juxtaposition of the incoming nucleophile attacker water oxygen and the α‐phosphorus of the substrate, decreasing their distance below the van der Waals limit. Complex interactions of the C‐terminus with both substrate and product were observed via a specifically designed tryptophan sensor, suitable for further detailed kinetic and ligand binding studies. Results explain the key functional role of the C‐terminus.

The Endogenous Calcium Ions of Horseradish Peroxidase C Are Required to Maintain the Functional Nonplanarity of the Heme

Horseradish peroxidase C (HRPC) binds 2 mol calcium per mol of enzyme with binding sites located distal and proximal to the heme group. The effect of calcium depletion on the conformation of the heme was investigated by combining polarized resonance Raman dispersion spectroscopy with normal coordinate structural decomposition analysis of the hemes extracted from models of Ca(2+)-bound and Ca(2+)-depleted HRPC generated and equilibrated using molecular dynamics simulations. Results show that calcium removal causes reorientation of heme pocket residues. We propose that these rearrangements significantly affect both the in-plane and out-of-plane deformations of the heme. Analysis of the experimental depolarization ratios are clearly consistent with increased B(1g)- and B(2g)-type distortions in the Ca(2+)-depleted species while the normal coordinate structural decomposition results are indicative of increased planarity for the heme of Ca(2+)-depleted HRPC and of significant changes in the relative contributions of three of the six lowest frequency deformations. Most noteworthy is the decrease of the strong saddling deformation that is typical of all peroxidases, and an increase in ruffling. Our results confirm previous work proposing that calcium is required to maintain the structural integrity of the heme in that we show that the preferred geometry for catalysis is lost upon calcium depletion.

The two spectroscopically different short wavelength protochlorophyllide forms in pea epicotyls are both monomeric

The spectral properties of the protochlorophyllide forms in the epicotyls of dark-grown pea seedlings have been studied in a temperature range, from 10 to 293 K with conventional fluorescence emission and excitation spectroscopy as well as by fluorescence line narrowing (FLN) at cryogenic temperatures. The conventional fluorescence techniques at lower temperatures revealed separate bands at 628, 634-636, 644 and 655 nm. At room temperature (293 K) the 628 and 634-636 nm emission bands strongly overlapped and the band shape was almost independent of the excitation wavelength. Under FLN conditions, vibronically resolved fluorescence spectra could be measured for the 628 and 634-636 nm bands. The high resolution of this technique excluded the excitonic nature of respective excited states and made it possible to determine the pure electronic (0,0) range of the spectra of the two components. Thus it was concluded that the 628 and 634-636 nm (0,0) emission bands originate from two monomeric forms of protochlorophyllide and the spectral difference is interpreted as a consequence of environmental effects of the surrounding matrix. On the basis of earlier results and the data presented here, a model is discussed in which the 636 nm form is considered as an enzyme-bound protochlorophyllide and the 628 nm form as a protochlorophyllide pool from which the substrate is replaced when the epicotyl is illuminated with continuous light.

Methylene substitution at the α-β bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site

dUTP pyrophosphatase, a preventive DNA repair enzyme, contributes to maintain the appropriate cellular dUTP/dTTP ratio by catalyzing dUTP hydrolysis. dUTPase is essential for viability in bacteria and eukaryotes alike. Identification of species‐specific antagonists of bacterial dUTPases is expected to contribute to the development of novel antimicrobial agents. As a first general step, design of dUTPase inhibitors should be based on modifications of the substrate dUTP phosphate chain, as modifications in either base or sugar moieties strongly impair ligand binding. Based on structural differences between bacterial and human dUTPases, derivatization of dUTP‐analogous compounds will be required as a second step to invoke species‐specific character. Studies performed with dUTP analogues also offer insights into substrate binding characteristics of this important and structurally peculiar enzyme. In this study, α,β‐methylene‐dUDP was synthesized and its complex with dUTPase was characterized. Enzymatic phosphorylation of this substrate analogue by pyruvate kinase was not possible in contrast to the successful enzymatic phosphorylation of α,β‐imino‐dUDP. One explanation for this finding is that the different bond angles and the presence of the methylene group may preclude formation of a catalytically competent complex with the kinase. Crystal structure of E. coli dUTPase:α,β‐methylene‐dUDP and E. coli dUTPase:dUDP:Mn complexes were determined and analyzed in comparison with previous data. Results show that the “trans” α‐phosphate conformation of α,β‐methylene‐dUDP differs from the catalytically competent “gauche” α‐phosphate conformation of the imino analogue and the oxo substrate, manifested in the shifted position of the α‐phosphorus by more than 3 Å. The three‐dimensional structures determined in this work show that the binding of the methylene analogue with the α‐phosphorus in the “gauche” conformation would result in steric clash of the methylene group with the protein atoms. In addition, the metal ion cofactor was not bound in the crystal of the complex with the methylene analogue while it was clearly visible as coordinated to dUDP, arguing that the altered phosphate chain conformation also perturbs metal ion complexation. Isothermal calorimetry titrations indicate that the binding affinity of α,β‐methylene‐dUDP toward dUTPase is drastically decreased when compared with that of dUDP. In conclusion, the present data suggest that while α,β‐methylene‐dUDP seems to be practically nonhydrolyzable, it is not a strong binding inhibitor of dUTPase probably due to the altered binding mode of the phosphate chain. Results indicate that in some cases methylene analogues may not faithfully reflect the competent substrate ligand properties, especially if the methylene hydrogens are in steric conflict with the protein. Proteins 2008.

Trehalose Effect on Low Temperature Protein Dynamics: Fluctuation and Relaxation Phenomena

We performed spectral diffusion experiments in trehalose-enriched glycerol/buffer-glass on horseradish peroxidase where the heme was replaced by metal-free mesoporphyrin IX, and compared them with the respective behavior in a pure glycerol/buffer-glass (Schlichter et al., J. Chem. Phys. 2000, 112:3045-3050). Trehalose has a significant influence: spectral diffusion broadening speeds up compared to the trehalose-free glass. This speeding up is attributed to a shortening of the correlation time of the frequency fluctuations most probably by preventing water molecules from leaving the protein interior. Superimposed to the frequency fluctuation dynamics is a relaxation dynamics that manifests itself as an aging process in the spectral diffusion broadening. Although the trehalose environment speeds up the fluctuations, it does not have any influence on the relaxation. Both relaxation and fluctuations are governed by power laws in time. The respective exponents do not seem to change with the protein environment. From the spectral dynamics, the mean square displacement in conformation space can be determined. It is governed by anomalous diffusion. The associated frequency correlation time is incredibly long, demonstrating that proteins at low temperatures are truly nonergodic systems.

δ-aminolaevulinic acid-induced porphyrin synthesis and photodynamic inactivation of Escherichia coli B.

The possibility and conditions for the induction of porphyrin synthesis by exogenous delta-aminolaevulinic acid (ALA) and its applicability for the inactivation of Gram-negative bacteria Escherichia coli B. by photodynamic therapy (PDT) have been studied. The bacteria are supplemented with ALA in the log phase of growth, and are grown in a synthetic medium at 37 degrees C in the dark. The efficiency of porphyrin synthesis is detected by fluorescence spectroscopy performed on the isolated bacterial cells and the medium, respectively, and compared with results of high-performance liquid chromatography (HPLC) analysis. ALA stimulates the synthesis of protoporphyrin in the bacteria by a factor of five to six, and an increased amount of the more hydrophilic derivatives with a significant contribution of mesoporphyrin by a factor of two to three is observed in the culturing medium. The optimal conditions of ALA treatment with respect to PDT are 10-15 min of incubation of a bacterial culture of 2 x 10(7) cells ml-1 with (5-9) x 10(-3) mol l-1 ALA. The ALA-treated cells are irradiated by white light of 80 mW cm-2 under growth conditions and a decrease to 0.6% of the number of colony-forming units (CFUs ml-1) is observed after 90 min of irradiation.

R-state hemoglobin bound to heterotropic effectors: models of the DPG, IHP and RSR13 binding sites

We performed a docking study followed by a 500‐ps molecular dynamics simulation of R‐state human adult hemoglobin (HbA) complexed to different heterotropic effectors [2,3‐diphosphoglycerate (DPG), inositol hexaphosphate (IHP), and 2‐[4‐[(3,5‐dichlorophenylcarbamoyl)‐]methyl]‐phenoxy]‐2‐methylpropionic acid (RSR13)) to propose a molecular basis for recently reported interactions of effectors with oxygenated hemoglobin. The simulations were carried out with counterions and explicit solvation. As reported for T‐state HbA, the effector binding sites are also located in the central cavity of the R‐state and differ depending on effector anionic character. DPG and IHP bind between the α‐subunits and the RSR13 site spans the α1‐, α2‐ and β2‐subunits. The generated models provide the first report of the molecular details of R‐state HbA bound to heterotropic effectors.

Mechanism of lysophosphatidic acid-induced amyloid fibril formation of β2-microglobulin in vitro under physiological conditions

Beta(2)-microglobulin- (beta2m-) based fibril deposition is the key symptom in dialysis-related amyloidosis. beta2m readily forms amyloid fibrils in vitro at pH 2.5. However, it is not well understood which factors promote this process in vivo, because beta2m cannot polymerize at neutral pH without additives even at elevated concentration. Here we show that lysophosphatidic acid (LPA), an in vivo occurring lysophospholipid mediator, promotes amyloid formation under physiological conditions through a complex mechanism. In the presence of LPA, at and above its critical micelle concentration, native beta2m became sensitive to limited proteolytic digestion, indicating increased conformational flexibility. Isothermal titration calorimetry indicates that beta2m exhibits high affinity for LPA. Fluorescence and CD spectroscopy, as well as calorimetry, showed that LPA destabilizes the structure of monomeric beta2m inducing a partially unfolded form. This intermediate is capable of fibril extension in a nucleation-dependent manner. Our findings also indicate that the molecular organization of fibrils formed under physiological conditions differs from that of fibrils formed at pH 2.5. Fibrils grown in the presence of LPA depolymerize very slowly in the absence of LPA; moreover, LPA stabilizes the fibrils even below its critical micelle concentration. Neither the amyloidogenic nor the fibril-stabilizing effects of LPA were mimicked by its structural and functional lysophospholipid analogues, showing its selectivity. On the basis of our findings and the observed increase in blood LPA levels in dialysis patients, we suggest that the interaction of LPA with beta2m might contribute to the pathomechanism of dialysis-related amyloidosis.