Academic literature on the topic 'Truncated hemoglobin'

The diversity of functional roles played by heme proteins in all kingdoms of life is to a large extent regulated by the thermodynamic and kinetic properties of their interaction with small gaseous molecules. The aim of this PhD thesis is to examine the structural and dynamical properties of two hemeproteins, the truncated hemoglobin N from M. Tuberculosis and nitrophorin 7 from R. Proxilus, and to examine their relationships with the biological role of these proteins. Particular attention has been paid to the diffusion of small ligands between the internal cavities in the two hemeproteins, and the entry/release pathways from the protein matrix to the solvent. Qualitative and semi-quantitative agreements between experiment and simulations are obtained for the identities of the cavities that physically trap the ligand and for the connections between them. The truncated hemoglobin N (trHbN) is believed to constitute a defense mechanism of M. Tuberculosis against NO produced by the macrophages during the initial growth infection stage, which is converted to the harmless nitrate anion, through the chemical reaction NO+ FE(II)-O2 ->FE(III)+ [NO3]-. The dual path ligand-dependent mechanism proposed in previous studies of the group ensures the access of NO to the heme cavity in the oxygenated form of the protein, which should warrant survival of the microorganism under stress conditions and allowing the bacillus to stay in latency. As a consequence, the processes mediated by trHbN are worth for searching a therapeutical intervention, since the inactivation of the NO scavenging should reduce significantly the bacteria resistance. In this work we have validated the importance of the PheE15 residue in the previous proposed dual path mechanism, as PheE15 was proposed to act as a gate that regulates the access of NO to the heme cavity in the oxygenated form of the protein. Thus, we have studied the impact of three residue mutations of the gate residue, PheE15Ala, PheE15Ile and PheE15Tyr, in the ligand migration mechanism and in the NO detoxification activity. The results support the gating role played by PheE15, because all the mutations are predicted to either block the long branch of the tunnel (PheE15Ile, PheE15Tyr) or to induce structural alterations that affect the passage of NO at the entrance of the tunnel (PheE15Ala). After release of the NO3- anion, the protein, which rests in its ferric form, is assumed to be recycled by a putative reductase, rendering trHbN in the ferrous form suitable to bind a new O2 molecule, thus ensuring an efficient detoxification mechanism. In order to gain insight into the reduction process, we have examined the interaction between trHbN and a flavodocin reductase (FdR) from E. Coli, which has shown to be very efficient in restoring the ferrous form of the protein. Thus, our studies have yielded a 3D model of the complex between trHbN and FdR, which allows to identify the residues implicated in the binding of the two proteins. Moreover, the model predicts that the heme and flavin cofactors are close (between 6 and 9 Å) in the complex, which facilitates an efficient electron transfer, as reinforced by the calculated electron couplings. Nitrophorin 7 is a hemeprotein implicated in the NO transport, which can be found in the saliva of blood feeding insects. One of the bugs, Rhodnius prolixus, is the causative agent of Chagas disease, and is responsible for a high number of deaths (approximately 15000 each year). Among the nitrophorin family, we have examined nitrophorin 7, which presents three extra residues in N-terminal sequence and the unique ability to bind membranes negatively charged. The results point out the existence of up to three inner cavities, which may define an internal pathway for migration of a gaseous ligand (NO) from the heme to the back of the protein. This topological feature is not present in other nitrphorins, such as NP4, and justifies a more complex kinetic rebinding scheme in NP7. In conjunction with the ability to interact with membranes, these findings might support a specific role in NO-controlled release. Both projects are carried out in closed collaboration with experimental groups, and we believe that in the future such collaborations will allow the development of new strategies with therapeutically implications in these diseases.
El proyecto a desarrollar se centrará en los aspectos dinámicos del transporte de ligandos en hemoproteínas, centrándose en dos tipos principales. Por un lado la hemoglobina truncada N de Mycobacterium tuberculosis, y por otro nitroforina. La hemoglobina truncada N desempeña un papel muy importante como mecanismo de defensa del microorganismo, pues transforma el óxido nítrico (NO) generado por los macrófagos durante las etapas iniciales de respuesta a la infección en anión nitrato. Ello, pues, permite la subsistencia del microorganismo, que permanece en estado de latencia, dificultando la recuperación del paciente de tuberculosis. En consecuencia, dicha proteína aparece como una diana de potencial valor terapéutico, puesto que su inactivación debería reducir significativamente la resistencia del microorganismo. Los estudios del Prof. Luque han perseguido dilucidar los aspectos moleculares que subyacen en la capacidad de la proteína de captar O2 y NO, y de llevar a cabo la reacción química de conversión a nitrato. En particular, se ha propuesto un mecanismo de transporte de ligandos, y el objetivo que se plantea es su validación mediante el examen de diversos mutantes obtenidos al modificar el residuo que controla la migración a través del canal. En cuanto a nitroforina, es una hemoproteína transportadora de NO que se halla en la saliva de insectos cuya alimentación se basa en sangre. Uno de ellos, Rhodnius prolixus, está implicado en la enfermedad de Chagas, que causa un número elevado de muertes (aproximadamente 15000 por año). De entre los diversos tipos de nitroforinas, nuestro interés se centra en nitroforina 7 (NP7), que difiere en el extremo N-terminal respecto a otras nitroforinas. El objetivo del trabajo se centra en determinar el efecto de dichas diferencias sobre la capacidad de captación y transporte de NO. En ambos casos, los proyectos se llevan a cabo en colaboración con grupos experimentales, y confiamos que dicha colaboración permita abrir estrategias de intervención terapéutica.

Abstract In plants, there are at least three types of haemoglobins (Hbs): symbiotic, non-symbiotic and truncated. Symbiotic Hbs are known to participate in nitrogen fixation, but the roles of the latter two groups are more obscure. Previous reports have connected both plant non-symbiotic and truncated Hbs to the scavenging of an important signal molecule, nitric oxide (NO). The aim of the present thesis was to study the effects of a bacterial Hb of Vitreoscilla sp. (VHb) on a woody model organism, hybrid aspen (Populus tremula x tremuloides), and the role of endogenous hybrid aspen Hbs. To store the produced hybrid aspen lines, the suitability of different cryopreservation methods was also tested. VHb-expressing hybrid aspens were generated by Agrobacterium-mediated gene transfer. The effects of VHb expression were examined in standard greenhouse conditions, under elevated UV-B light as well as during culture with ectomycorrhizal fungi. Both slow cooling and vitrification methods were applied in cryostoring samples of the different genetic backgrounds. Hybrid aspen non-symbiotic and truncated Hb genes PttHb1 and PttTrHb, respectively, were also isolated. The function of the genes and corresponding proteins PttHb1 and PttTrHb were studied using non-transgenic and VHb hybrid aspen lines as well as a mutant yeast (Saccharomyces cerevisiae) defective in NO resistance. VHb expression did not improve the general growth of hybrid aspen but resulted in enhanced starch accumulation in chloroplasts, pointing to changes in energy metabolism. Of the studied cryopreservation protocols, the slow cooling of dormant in vivo buds proved to be the most feasible way of cryostoring hybrid aspen lines. The culture with the ectomycorrhizal fungus was shown to increase the expression of both PttHb1 and PttTrHb in the roots of non-transgenic lines. However, the fungi did not up-regulate the hybrid aspen Hb genes in the VHb lines. Therefore, it is hypothesized that endogenous Hbs may contribute to the growth of roots and that VHb may compensate this function. When expressed alone in the mutant yeast, the recombinant PttHb1 and PttTrHb did not protect cells against the toxicity of NO. Subsequently, a novel mRNA transcript of the heterotrophic ferredoxin NADP+ oxidoreductase gene PtthFNR was found. The absence of a plastid presequence in the transcript suggests targeting of the encoded protein into cytosol. The coexpression of PttHb1 and cytosolic PtthFNR partially rescued the mutant yeast during NO treatment, demonstrating for the first time that plant Hb1 with an applicable reductase scavenges NO in vivo at a physiologically relevant rate. This thesis extends current knowledge about plant Hbs and the effects of VHb on a phenotype of a tree. It also provides new information about plant ferredoxin reductase genes
Tiivistelmä Kasvihemoglobiinit jaetaan symbioottisiin, ei-symbioottisiin sekä ns. katkaistuihin eli truncated-hemoglobiineihin. Symbioottisten hemoglobiinien tiedetään osallistuvan typen sitomiseen, kun taas kahden muun ryhmän toiminta tunnetaan heikosti. Aiemmissa tutkimuksissa ei-symbioottiset ja truncated-hemoglobiinit on yhdistetty tärkeän signaalimolekyylin, typpimonoksidin (NO), haitallisuuden vähentämiseen. Tämän työn tarkoituksena oli tutkia Vitreoscilla sp. -bakteerin VHb-hemoglobiinin vaikutuksia puuvartiseen mallikasviin, hybridihaapaan (Populus tremula x tremuloides), sekä hybridihaavan omien hemoglobiinien merkitystä. Lisäksi työssä kokeiltiin eri nestetyppisäilytysmenetelmiä hybridihaapalinjojen varastoimiseksi. VHb:tä ilmentävät hybridihaavat tuotettiin Agrobacterium-välitteisellä geeninsiirrolla. VHb:n vaikutuksia tutkittiin kasvihuoneolosuhteissa, kohotetussa UV-B-säteilyssä sekä sienijuurikasvatuksen aikana. Eri linjojen nestetyppisäilytykseen sovellettiin sekä hidasta että nopeaa jäähdytystä. Tutkimuksissa myös eristettiin hybridihaavan PttHb1- ja PttTrHb-hemoglobiinigeenit. Näiden geenien sekä niiden koodaamien PttHb1- ja PttTrHb-proteiinien toimintaa tutkittiin siirtogeenittömien ja VHb-hybridihaapalinjojen sekä NO-herkän hiivamutantin (Saccharomyces cerevisiae) avulla. VHb-ilmennys ei parantanut hybridihaavan kasvua, mutta lisäsi tärkkelyksen kertymistä viherhiukkasiin, mikä viittaa muutoksiin energia-aineenvaihdunnassa. Tutkituista menetelmistä parhaiten hybridihaapalinjojen nestetyppisäilytykseen soveltui lepovaiheessa olevien in vivo -silmujen hidas jäähdytys. Toisin kuin VHb-kasveissa, sienijuurikasvatus voimisti sekä PttHb1:n että PttTrHb:n ilmenemistä siirtogeenittömien hybridihaapojen juurissa. Tästä johtuen esitettiin, että hybridihaavan hemoglobiinit voivat vaikuttaa juurien kasvuun ja VHb pystyy korvaamaan tämän toiminnon. Kun PttHb1 ja PttTrHb ilmennettiin yksin mutanttihiivassa, proteiinit eivät suojanneet soluja NO:n myrkyllisyydeltä. Tämän jälkeen työssä kuvattiin heterotrofisen ferredoksiini-NADP+-oksidoreduktaasi-geenin PtthFNR:n uusi mRNA-muoto. Plastidiin ohjaavan sekvenssin puuttuminen geenituotteesta viittaa siihen, että mRNA:n koodaama proteiini sijoittuu solulimaan. PttHb1:n ja PtthFNR:n yhtäaikainen ilmentäminen mutanttihiivassa paransi solujen elossa säilymistä NO-käsittelyn aikana, mikä osoittaa ensimmäistä kertaa, että kasvin Hb1 pystyy sopivan reduktaasin kanssa vähentämään NO-pitoisuutta elävässä eliössä. Tämä työ laajentaa tietämystä kasvihemoglobiineista sekä VHb:n vaikutuksesta puiden ilmiasuun. Työ myös lisää tietoa kasvien ferredoksiinireduktaasi-geeneistä

The possibility to follow CO recombination dynamics, in the middle infrared spectral region, after photolysis induced by a short laser pulse provides unique information about the influence of structural and electrostatic properties of the distal heme pocket on the ligand dissociation and rebinding processes occurring in globin proteins. Time-Resolved Infrared Spectroscopy can probe the dynamics of the vibrational bands of the ligand before and after photolysis, thus providing a direct snapshot of the transient state of the photolyzed CO in truncated hemoglobins.

Resonance Raman (RR) spectroscopy complemented by UV-Vis absorption spectroscopy is a very powerful technique to investigate the structure-function relationships of heme proteins, a widely distributed and biological relevant class of proteins which can play different biological functions. Since the protein activity is tightly linked to the structure of the heme active site, my study has been devoted to the investigation of several heme proteins involved in important biological processes, to obtain a comprehensive spectroscopic signature, with the aim to highlight the relationship between the heme pocket architecture and the protein function. The studies were carried out on native proteins and selected site-directed mutants, at both room (298 K) and low (80 K) temperature, at various pH, and in presence of various exogenous ligands, spanning the excitation wavelengths from UV to the visible region.