The Enzyme Horseradish Peroxidase Is Less Compressible at Higher Pressures

AbstractFluorescence line-narrowing (FLN) spectroscopy at 10K was used to study the effect of high pressure through the prosthetic group in horseradish peroxidase (HRP), which was Mg-mesoporphyrin (MgMP) replacing the heme of the enzyme. The same measurement was performed on MgMP in a solid-state amorphous organic matrix, dimethyl sulfoxide (DMSO). Series of FLN spectra were registered to determine the (0, 0) band shape through the inhomogeneous distribution function (IDF). In the range of 0–2GPa a red-shift of the IDF was determined, and yielded the isothermal compressibility of MgMP-HRP as 0.066GPa−1, which is significantly smaller than that found earlier as 0.106 GPa−1 by fine-tuning the pressure in the range up to 1.1MPa. The vibrational frequencies also shifted with pressure increase, as expected. The compressibility in the DMSO matrix was smaller, 0.042GPa−1, both when the pressure was applied at room temperature before cooling to 10K, or at 10K. At 200K or above, the bimodal (0, 0) band shape in DMSO showed a population conversion under pressure that was not observed at or below 150K. A significant atomic rearrangement was estimated from the volume change, 3.3±0.7cm3/mol upon conversion. The compressibility in proteins and in amorphous solids seems not to significantly depend on the temperature and in the protein it decreases toward higher pressures

Role of Domain Interactions in the Collective Motion of Phosphoglycerate Kinase

ABSTRACT Protein function is governed by the underlying conformational dynamics of the molecule. The experimental and theoretical work leading to contemporary understanding of enzyme dynamics was mostly restricted to the large-scale movements of single-domain proteins. Collective movements resulting from a regulatory interplay between protein domains is often crucial for enzymatic activity. It is not clear, however, how our knowledge could be extended to describe collective near-equilibrium motions of multidomain enzymes. We examined the effect of domain interactions on the low temperature near equilibrium dynamics of the native state, using phosphoglycerate kinase as model protein. We measured thermal activation of tryptophan phosphorescence quenching to explore millisecond-range protein motions. The two protein domains of phosphoglycerate kinase correspond to two dynamic units, but interdomain interactions link the motion of the two domains. The effect of the interdomain interactions on the activation of motions in the individual domains is asymmetric. As the temperature of the frozen protein is increased from the cryogenic, motions of the N domain are activated first. This is a partial activation, however, and the full dynamics of the domain becomes activated only after the activation of the C domai

Influence of static and dynamic disorder on the visible and infrared absorption spectra of carbonmonoxy horseradish peroxidase

Spectroscopy of horseradish peroxidase with and without the substrate analog, benzohydroxamic acid, was monitored in a glycerol/water solvent as a function of temperature. It was determined from the water infrared (IR) absorption that the solvent has a glass transition at 170-180 K. In the absence of substrate, both the heme optical Q(0,0) absorption band and the IR absorption band of CO bound to heme broaden markedly upon heating from 10-300 K. The Q(0,0) band broadens smoothly in the whole temperature interval, whereas the IR bandwidth is constant in the glassy matrix and increases from 7 to 16 cm(-1) upon heating above the glass transition. Binding of substrate strongly diminishes temperature broadening of both the bands. The results are consistent with the view that the substrate strongly reduces the amplitude of motions of amino acids forming the heme pocket. The main contribution to the Q(0,0) bandwidth arises from the heme vibrations that are not affected by the phase transition. The CO band thermal broadening stems from the anharmonic coupling with motions of the heme environment, which, in the glassy state, are frozen in. Unusually strong temperature broadening of the CO band is interpreted to be caused by thermal population of a very flexible excited conformational substrate. Analysis of literature data on the thermal broadening of the A, band of Mb(CO) (Ansari et al., 1987. Biophys. Chem. 26:337-355) shows that such a state presents itself also in myoglobin

Fémek szerepe a fehérjeszerkezetben és - működésben = The role of metals in protein structure and function

Fehérjekrisztallográfia, mágneses magrezonancia-spektroszkópia és molekulamodellezés segítségével vizsgáltuk az összefüggéseket néhány metalloprotein, valamint egy új típusú, rendezetlen fehérje szerkezete és működése között. Hatékony módszert fejlesztettünk ki a reakcióút kvantummechanikai számítására enzimekben. Tisztáztuk a DNS javításában fontos szerepet játszó dUTPáz által katalizált reakció legtöbb részletét. Meggyőző bizonyítékokat szolgáltattunk arra, hogy az enzimatikus foszfáthidrolízis során a dUTPázban nagy energiájú, trigonális bipiramisos elrendeződésű intermedier keletkezik. Kimutattuk, hogy a KAR-2 nevű molekula más, biszindol típusú ligandumoktól eltérő módon kötődik a kalmodulinhoz, ez magyarázza különleges fiziológiai hatását. Elvégeztük a hemoglobin hem-csoportjainak normál koordináták szerinti analízisét, amiből következtetéseket vontunk le a szerkezetre vonatkozóan. A deformációk azt mutatják, hogy a hem csoport szerkezete érzékeny a molekula távoli részében kötődő effektor jelenlétére, ami az allosztérikus szabályozás hatásmechanizmusának a tercier szerkezettel való kapcsolatát támasztja alá. A közelmúltban egy új agy-specifikus fehérjét izoláltunk, melynek átlagos rendezetlensége 46-47%, tehát szerkezet nélkülinek tekinthető. Részletes vizsgálatokat végeztünk e fehérje, illetve különböző fehérjékkel képezett komplexe szerkezetére vonatkozóan. | We investigated the relationship between the structure and activity of some metalloproteins and a new unfolded protein. We developed an efficient method for the quantum mechanical calculation of the reaction path in enzymes. Most details of the reaction catalysed by dUTPase, playing an important role in DNA repair, have been clarified. We provided convincing evidence that during enzymatic phosphate hydrolysis a high-energy, trigonal bipyramidal intermediate is formed. We have shown that the molecule KAR-2, in contrast to other bisindole-type ligands, has a different binding mode to calmodulin, which explains its special physiological effect. We performed the normal co-ordinate analysis of the hem groups of haemoglobin and derived conclusions on their structure. The deformations indicate that the structure of the hem group is sensitive to the presence of an effector bound in a distant region of the molecule. This finding supports the relation between the allosteric mechanism of action and the tertiary structure. Recently we isolated a new brain-specific protein, which is 46 to 47 per cent disordered, i.e. it can be considered as unfolded. We made detailed studies on the structure of this protein and its complex with others

Role of Domain Interactions in the Collective Motion of Phosphoglycerate Kinase

Protein function is governed by the underlying conformational dynamics of the molecule. The experimental and theoretical work leading to contemporary understanding of enzyme dynamics was mostly restricted to the large-scale movements of single-domain proteins. Collective movements resulting from a regulatory interplay between protein domains is often crucial for enzymatic activity. It is not clear, however, how our knowledge could be extended to describe collective near-equilibrium motions of multidomain enzymes. We examined the effect of domain interactions on the low temperature near equilibrium dynamics of the native state, using phosphoglycerate kinase as model protein. We measured thermal activation of tryptophan phosphorescence quenching to explore millisecond-range protein motions. The two protein domains of phosphoglycerate kinase correspond to two dynamic units, but interdomain interactions link the motion of the two domains. The effect of the interdomain interactions on the activation of motions in the individual domains is asymmetric. As the temperature of the frozen protein is increased from the cryogenic, motions of the N domain are activated first. This is a partial activation, however, and the full dynamics of the domain becomes activated only after the activation of the C domain

Processus d'association des protéines membranaires dans un système modèle bactérien et dans les récepteurs du facteur de croissance épidermique humain (HER/ErbB)

PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF