Horse Heart Metmyoglobin Research Articles

Ribose sugars generate internal glycation cross-links in horse heart myoglobin

Glycation of horse heart metmyoglobin with d-ribose 5-phosphate (R5P), d-2-deoxyribose 5-phosphate (dR5P), and d-ribose with inorganic phosphate at 37 °C generates an altered protein (Myo-X) with increased SDS–PAGE mobility. The novel protein product has been observed only for reactions with the protein myoglobin and it is not evident with other common sugars reacted over a 1 week period. Myo-X is first observed at 1–2 days at 37 °C along with a second form that is consistent in mass with that of myoglobin attached to several sugars. MALDI mass spectrometry and other techniques show no evidence of the cleavage of a peptide from the myoglobin chain. Apomyoglobin in reaction with R5P also exhibited this protein form suggesting its occurrence was not heme-related. While significant amounts of O 2 − and H 2O 2 are generated during the R5P glycation reaction, they do not appear to play roles in the formation of the new form. The modification is likely due to an internal cross-link formed during a glycation reaction involving the N-terminus and an internal amine group; most likely the neighboring Lys133. The study shows the unique nature of these common pentose sugars in spontaneous glycation reactions with proteins.

Heme Proteins: The Role of Solvent on the Dynamics of Gates and Portals Revealed by MD Simulations

In the family of respiratory proteins, hemoglobins and myoglobins have been the first to be crystallized in ‘50. Despite the availability of 3D structures, issues regarding the microscopic functioning remain open, such as, for instance, the R to T switching mechanism in hemoglobin or the ligand escape process in myoglobin. Due to the relatively small number of residues, myoglobin is the suitable candidate to investigate the more general structure-function paradigm, being defined as the hydrogen atom of biology. In this work, to complement our recent study on the dynamics of internal cavities of myoglobin[1], the effect of solvation on these intrinsic pathways has been explored. In particular, 60ns-long molecular dynamics simulation of horse heart met-myoglobin was further analyzed and the dynamics of waters residing around/inside the protein with average residence times of up to tens of nanoseconds was monitored. Together with the knowledge obtained previously[1], the analysis of solvent revealed that myoglobin has in fact only few stable hydration sites in which a water molecule can stay for time longer than 2 ns. Strikingly, all of these sites are close to protein/solvent portals observed in previous studies focused on the entry/escape and migration of various ligands in myoglobin[2-4].1. Scorciapino, M. A.; Robertazzi, A.; Casu, M.; Ruggerone, P.; Ceccarelli, M. J. Am. Chem. Soc. 2009, 131, 11825-11832.2. Cohen, J.; Arkhipov, A.; Braun, R.; Schulten, K. Biophys. J. 2006, 91, 1844-1857.3. Ruscio, J. Z.; Kumar, D.; Shukla, M.; Prisant, M. G.; Murali, T. M.; Onufriev, A. V. Proc. Natl. Acad. Sci. USA 2008, 105, 9204-9209.4. Ceccarelli, M.; Anedda, R.; Casu, M.; Ruggerone, P. Proteins 2008, 71, 1231-1236.

Breathing Motions of a Respiratory Protein Revealed by Molecular Dynamics Simulations

Internal cavities, which are central to the biological functions of myoglobin, are exploited by gaseous ligands (e.g., O(2), NO, CO, etc.) to migrate inside the protein matrix. At present, it is not clear whether the ligand makes its own way inside the protein or instead the internal cavities are an intrinsic feature of myoglobin. To address this issue, standard molecular dynamics simulations were performed on horse-heart met-myoglobin with no ligand migrating inside the protein matrix. To reveal intrinsic internal pathways, the use of a statistical approach was applied to the cavity calculation, with special emphasis on the major pathway from the distal pocket to Xe1. Our study points out the remarkable dynamical behavior of Xe4, whose "breathing motions" may facilitate migration of ligands through the distal region. Additionally, our results highlight a two-way path for a ligand to diffuse through the proximal region, possibly allowing an alternative route in case Xe1 is occupied. Finally, our approach has led us to the identification of key residues, such as leucines, that may work as switches between cavities.

Intramolecular Electron-Transfer Pathway for Deoxy and Zinc Myoglobins Modified with N,N,N′,N″,N″-Diethylenetriaminepentaacetatocobaltate(III)

Abstract Horse heart metmyoglobin (metMb), whose N-terminal Gly1 is linked by an N,N,N′,N″,N″-diethylenetriaminepentaacetatocobaltate(III) ion ([CoIII(dtpa)]) with an amide bond, was prepared and characterized. A one-electron reduced protein, [deoxyMb{CoIII(dtpa)}], was prepared by reduction with a methylviologen-radical cation, which was produced in situ by a photoreduction using a tris(2,2′-bipyridine)ruthenium(II) ion in the presence of disodium dihydrogen ethylenediaminetetraacetate at 25 °C, pH 7.5 (a 0.010 mol dm−3 tris(hydroxymethyl)aminomethane–HCl buffer), and an ionic strength of 0.50 mol dm−3 (NaCl). The reaction of [deoxyMb{CoIII(dtpa)}] to form [metMb{CoII(dtpa)}] obeyed a first-order rate law on the protein concentration. The first-order rate constant was dependent on the concentration of the protein, indicating that both intra- and intermolecular electron-transfer (ET) processes simultaneously occur. The latter is the reaction with excess [metMb{CoIII(dtpa)}] remaining. Both intra- and intermolecular ET rates could be explained by the Marcus theory, including the distance dependence of the rate of the reaction, and might arise mainly from the very large reorganization energy for the Co(III)/Co(II) couple. Zinc-substituted myoglobin, [ZnMb{CoIII(dtpa)}], was also prepared and the photoinduced ET reaction from the excited triplet state of zinc myoglobin to the Co(III) moiety was examined. The observed ET quenching rate constant is reasonably explained by the Marcus theory through the same ET pathway as that for [deoxyMb{CoIII(dtpa)}]. It is suggested that the ET occurs with through-bond and van der Waals interactions from the heme edge to the Co(III) edge via Phe138 and Leu137 over 18.8 Å (1 Å = 1 × 10−10 m) both in deoxy and zinc myoglobins.

Radical Formation and Migration in Myoglobins

Three EPR signals from individual free radical species have been identified in the EPR spectra of horse heart metmyoglobin (HH metMb) mixed with hydrogen peroxide (H2O2). The peroxyl radical EPR signal was assigned to the Trp14-OO• radical, the seven component signal – to the Tyr103• radical and the singlet EPR signal was assigned to the Tyr146• radical. Apo-Mb (haem free HH Mb) added in various concentrations to the native metMb prior to H2O2 addition affected the yields of the three types of radicals. As the concentrations of metMb and H2O2 were kept constant, the yield of the primary radical formed is the same in all experiments, H2O2 being unable to produce any radical in the reaction with a haem free protein. Nevertheless, the addition of apo-Mb resulted in an increase of the Tyr146• radical concentration and in a quantitatively similar decrease of the Tyr103• radical concentration. These changes were dependent on the concentration of the added apo-Mb. Thus we show that a radical transfer Tyr103• → Tyr146• occurs and that this reaction is protein concentration dependent. The question whether this radical transfer is inter- or intra-molecular is discussed. A similarity is drawn between the system studied and the sperm whale metMb/H2O2 system, for which the radical transfer Tyr103• → Tyr151• has been previously suggested.

Changes in protein dynamics induced under Gdn-HCl denaturation

We have performed a study of protein dynamics in native and partially denatured horse-heart met-myoglobin (Mb-met) diluted in D2O. Protein dynamics is shown to be strongly solvent-dependent; in particular, higher degrees of macromolecular motions have been observed in the denatured states of Mb-met.

Comparative Study of Tyrosine Radicals in Hemoglobin and Myoglobins Treated with Hydrogen Peroxide

The reactions of hydrogen peroxide with human methemoglobin, sperm whale metmyoglobin, and horse heart metmyoglobin were studied by electron paramagnetic resonance (EPR) spectroscopy at 10 K and room temperature. The singlet EPR signal, one of the three signals seen in these systems at 10 K, is characterized by a poorly resolved, but still detectable, hyperfine structure that can be used to assign it to a tyrosyl radical. The singlet is detectable as a quintet at room temperature in methemoglobin with identical spectral features to those of the well characterized tyrosyl radical in photosystem II. Hyperfine splitting constants found for Tyr radicals were used to find the rotation angle of the phenoxyl group. Analysis of these angles in the crystal structures suggests that the radical resides on Tyr151 in sperm whale myoglobin, Tyr133 in soybean leghemoglobin, and either αTyr42, βTyr35, or βTyr130 in hemoglobin. In the sperm whale metmyoglobin Tyr103Phe mutant, there is no detectable tyrosyl radical present. Yet the rotation angle of Tyr103 (134 o) is too large to account for the observed EPR spectrum in the wild type. Tyr103 is the closest to the heme. We suggest that Tyr103 is the initial site of the radical, which then rapidly migrates to Tyr151.

High-pressure effects on horse heart metmyoglobin studied by small-angle neutron scattering.

Small-angle neutron scattering experiments were performed on horse azidometmyoglobin (MbN3) at pressures up to 300 MPa. Other spectroscopic techniques have shown that a reorganization of the secondary structure and of the active site occur in this pressure range. The present measurements, performed using various concentrations of MbN3, show that the compactness of the protein is not altered as the value of its radius of gyration remains constant up to 300 MPa. The value of the second virial coefficient of the protein solution indicates that the interactions between the molecules are always strongly repulsive even if their magnitude decreases with increasing pressure. Taking advantage of the pressure-induced contrast variation, these experiments allow the partial specific volume of MbN3 to be determined as a function of pressure. Its value decreases by 5.4% between atmospheric pressure and 300 MPa. In this pressure range the isothermal compressibility of hydrated MbN3 is found to be almost constant. Its value is (1.6 +/- 0.1) 10-4 MPa-1.

Water penetration and binding to ferric myoglobin.

Flash photolysis investigations of horse heart metmyoglobin bound with NO (Mb(3+)NO) reveal the kinetics of water entry and binding to the heme iron. Photodissociation of NO leaves the sample in the dehydrated Mb(3+) (5-coordinate) state. After NO photolysis and escape, a water molecule enters the heme pocket and binds to the heme iron, forming the 6-coordinate aquometMb state (Mb(3+)H2O). At longer times, NO displaces the H2O ligand to reestablish equilibrium. At 293 K, we determine a value k(w) approximately 5.7 x 10(6) s(-1) for the rate of H2O binding and estimate the H2O dissociation constant as 60 mM. The Arrhenius barrier height H(w) = 42 +/- 3 kJ/mol determined for H2O binding is identical to the barrier for CO escape after photolysis of Mb(2+)CO, within experimental uncertainty, consistent with a common mechanism for entry and exit of small molecules from the heme pocket. We propose that both processes are gated by displacement of His-64 from the heme pocket. We also observe that the bimolecular NO rebinding rate is enhanced by 3 orders of magnitude both for the H64L mutant, which does not bind water, and for the H64G mutant, where the bound water is no longer stabilized by hydrogen bonding with His-64. These results emphasize the importance of the hydrogen bond in stabilizing H2O binding and thus preventing NO scavenging by ferric heme proteins at physiological NO concentrations.

An EPR study of the peroxyl radicals induced by hydrogen peroxide in the haem proteins

The reaction of hydrogen peroxide H 2O 2 with horse heart metmyoglobin (HH metMb), sperm whale metmyoglobin (SW metMb) and human metHb (metHbA) was studied at pH 6–8 by low temperature (10 K) EPR spectroscopy with the emphasis on the peroxyl radicals formed during the reaction. The same type of peroxyl radical was found in both myoglobin systems, as was concluded from close similarities in the spectroscopic properties of the radicals and in their kinetic dependences. This is consistent with previous reports of the peroxyl radical being localised on the Trp14 of SW and HH myoglobins. There are two types of peroxyl radical found in the metHbA/H 2O 2 system, one (ROO-I) having spectral parameters, kinetic and pH dependences similar to those of the peroxyl radical found in both myoglobin systems. The other peroxyl radical (ROO-II) found in metHbA treated with H 2O 2 has slightly different, though distinguishable, spectral parameters and a significantly different kinetic dependence as compared to those of the peroxyl radical common for all three proteins studied (ROO-I). The concentration of ROO-I radical formed in the three proteins on addition of H 2O 2 correlates with the effectiveness of incorporating molecular oxygen into styrene oxide reported before for these three proteins. It is shown that a different distance from Trp14 to haem iron in the three proteins might be the structural basis for the different yield of the peroxyl radical and the different efficiency of incorporation of molecular oxygen into styrene. The site of the peroxyl radical found only in metHbA (ROO-II) is speculated to be the Trp37 residue of the β-subunit of HbA.

Pressure effect on the temperature-induced unfolding and tendency to aggregate of myoglobin.

This work demonstrates that pressure-induced partially unfolded states play a very important role in the aggregation of proteins. The high-pressure unfolding of horse heart metmyoglobin results in an intermediate form that shows a strong tendency to aggregate after pressure release. These aggregates are similar to those that are usually observed upon temperature denaturation. Infrared spectra in the amide I region indicate the formation of an intermolecular antiparallel beta-sheet stabilized by hydrogen bonding. The formation of the aggregates is temperature-dependent. Below 30 degrees C, no aggregation is taking place as seen from the infrared spectra. At 45 and 60 degrees C, two types of aggregates are formed: one that can be dissociated by moderate pressures and one that is pressure-insensitive. When precompressed at 5 degrees C, temperature-induced aggregation takes place at lower temperature (38 degrees C) than without pressure pretreatment (74 degrees C).

An Introduction to Research in Protein Folding for Undergraduates

The objective of this article is to introduce students to current research activity on folding via experimentation and a literature survey. Major effort in the field of biophysical chemistry today is focused on elucidating those factors controlling the transformation of a from a nascent polypeptide chain to a unique, functionally active three-dimensional structure. The possible involvement of misfolded or aggregated proteins in diseases such as Altzheimer's, cystic fibrosis, and cataracts as well as various neurodegenerative diseases has increased the incentive to solve the protein folding problem. In this experiment the guanidine-hydrochloride induced unfolding of horse heart metmyoglobin is monitored spectrophotometrically via the fluorescence emission. The data are analyzed using a simple thermodynamic model which assumes a two-state system and fitted using nonlinear curve fitting. Background information on structure, fluorescence, simple models for fol...

Conversion of metmyoglobin to NO myoglobin in the presence of nitrite and reductants

Formation of NO myoglobin through the reaction of horse heart metmyoglobin with NADH in the presence of nitrite was observed optically at pH 5.5. Superoxide generation during the reaction was demonstrated using the ESR spin trap, 5,5-dimethyl-1-pyrroline-1-oxide. A weak optical spectrum corresponding to oxymyoglobin appeared transiently and the spectrum of NO myoglobin then developed. The conversion to NO myoglobin was eliminated in the presence of catalase, SOD or 5,5-dimethyl-1-pyrroline-1-oxide. The kinetics of NADH oxidation and oxygen cod consumption catalyzed by myoglobin showed an initial lag phase, indicating a chain reaction. When the oxygen was exhausted, the NO form emerged. The duration of the lag phase was prolonged by an increase in the concentration of catalase, SOD or 5,5-dimethyl-1-pyrolline-1-oxide, whereas it disappeared in the presence of H 2O 2. The spectral change from metmyoglobin to NO myoglobin was also observed under anaerobic conditions through the rate was slower than that obtained under aerobic conditions, while the spectral change was accelerated in the presence of H 2O 2. Nitric oxide (NO) was derived through the reaction of nitrite with NADH. The formation of NO myoglobin from metmyoglobin is explained in terms of the NADH-oxidase reaction catalyzed by myoglobin. Ascorbate and GSH also serve as reductants though NO myoglobin was formed slowly.

Trapping and LC−MS Identification of Protein Radicals Formed in the Horse Heart Metmyoglobin−H2O2 Reaction

Trapping and LC−MS Identification of Protein Radicals Formed in the Horse Heart Metmyoglobin−H₂O₂ Reaction

Kinetics and Mechanisms of Photoinduced Electron-Transfer Reaction of Magnesium Myoglobin

Horse heart metmyoglobin was reconstituted with magnesium(II) porphyrin, [Mg(dp)] (3,7,12,17-tetramethyl-2,18-bis(2-carboxyethyl)porphyrinatomagnesium(II)). Photoinduced electron-transfer (ET) between magnesium myoglobin (MgDPMb) and cationic and anionic quenchers, such as viologens and anthraquinone-2-sulfonate (AQS−), has been studied in an aqueous degassed solution. None of the quenchers examined in this work formed a detectable associated complex with MgDPMb. The thermal backward ET reaction was observed for these quenchers. Not only photoinduced ET but also thermal backward ET reactions were insensitive to the driving force of the reactions. Moreover, there was little effect of metal-ion substitution; the rate of reaction was similar to that for zinc myoglobin. Thus, the reactions are controlled by conformational changes in the myoglobins.

High-resolution study of the three-dimensional structure of horse heart metmyoglobin

The three-dimensional structure of horse heart metmyoglobin has been refined to a final R-factor of 15.5% for all observed data in the 6.0 to 1.9 A resolution range. The final model consists of 1242 non-hydrogen protein atoms, 154 water molecules and one sulfate ion. This structure has nearly ideal bonding and bond angle geometry. A Luzzati plot of the variation in R-factor with resolution yields an estimated mean co-ordinate error of 0.18 A. An extensive analysis of the pattern of hydrogen bonds formed in horse heart metmyoglobin has been completed. Over 80% of the polypeptide chain is involved in eight helical segments, of which seven are composed mainly of alpha-helical (3.6(13))-type hydrogen bonds; the remaining helix is composed entirely of 3(10) hydrogen bonds. Altogether, of 102 hydrogen bonds between main-chain atoms only six are not involved in helical structures, and four of these six occur within beta-turns. The majority of water molecules in horse heart metmyoglobin are found in solvent networks that range in size from two to 35 members. The size of water molecule networks can be rationalized on the basis of three factors: the number of hydrogen bonds to the protein surface, the presence of charged side-chain atoms, and the ability to bridge to neighboring molecules in the crystal lattice. Bridging water networks form the dominant intermolecular interactions. The backbone conformation of horse heart metmyoglobin is very similar to sperm whale metmyoglobin, with significant differences in secondary structure occurring only near residues 119 and 120, where residues 120 to 123 in sperm whale form a distorted type I reverse turn and the horse heart protein has a type II turn at residues 119 to 122. Nearly all of the hydrogen bonds between main-chain atoms (occurring mainly in helical regions) are common to both proteins, and more than half of the hydrogen bonds involving side-chain atoms observed in horse heart are also found in sperm whale metmyoglobin. Unlike sperm whale metmyoglobin, the heme iron atom in horse heart metmyoglobin is not significantly displaced from the plane of the heme group.

Electron spin resonance spectrum of Tyr-151 free radical formed in reactions of sperm whale metmyoglobin with ethyl hydroperoxide and potassium irridate

A five-line ESR spectrum was observed at room temperature in reactions of sperm whale metmyoglobin with ethyl hydroperoxide (EtOOH) at pH 9.5 and with potassium irridate at pH's 7.0 and 9.5. A spectrum with the same g value and hyperfine splitting constant appeared in a reaction of sperm whale apomyoglobin with potassium irridate and was assigned to a tyrosyl radical on the basis of optical spectrum data obtained under the same reaction conditions. It was concluded that this radical arose from Tyr-151 for the following reasons, (i) This ESR spectrum could not be observed in the reaction of horse heart metmyoglobin, which lacks Tyr-151. (ii) Sperm whale metmyoglobin no longer gave this spectrum when treated with tetranitromethane (TNM) under conditions in which approximately one tyrosine is lost in sperm whale metmyoglobin but none is lost in horse heart metmyoglobin. (iii) A complex ESR spectrum observed in the reaction of sperm whale metmyoglobin with EtOOH at neutral pH was found to be a mixture of this five-line spectrum and one arising from an unidentified free radical formed in the reaction of horse heart metmyoglobin with EtOOH. The TNM-treated sperm whale metmyoglobin gave the same ESR spectrum as that observed in the reaction of horse heart metmyoglobin With EtOOH.

Structural Characterization of Nitrimyoglobin

Nitrimyoglobin was formed in greater than 94% yield by a simple reaction between excess nitrite and horse heart metmyoglobin at pH 5.5. This dark green pigment was shown by 1H NMR spectroscopy to be a single, pure product with a well defined tertiary structure that is highly similar to the starting myoglobin. Electronic spin states parallel those of myoglobin, although the relaxation times differ. Ligand binding reactions of nitrimyoglobin parallel those of normal myoglobin, but lead to a unique series of UV-visible spectra. In the ferrous state, nitrimyoglobin reversibly binds O2 with half-saturation of sites at an O2 partial pressure of 10.4 +/- 1.4 mm Hg. 1H NMR data indicate that the altered heme of nitrimyoglobin has not undergone reaction at any meso proton position, nor has it been partially saturated to the level of a chlorin. 15N NMR spectra indicate that only a single nitrogen was added to the protein as a nitro group. Extraction of the modified heme from nitrimyoglobin and spectroscopic characterization of the nitriheme by infrared spectroscopy and of the free base porphyrin methyl ester derived from nitriheme by 1H NMR indicate that the modification is regiospecific. The heme in nitrimyoglobin is 3-(trans-2-nitrovinyl)-2,7,12,18-tetramethyl-8-vinylporphyrin-13,1 7-dipropionic acid. In the Fisher nomenclature scheme, the 2-vinyl substituent is the site of modification and has been converted to a nitrovinyl group by substitution of a proton by -NO2.

Horse heart metmyoglobin. A 2.8-A resolution three-dimensional structure determination.

The structure of horse heart metmyoglobin has been determined with a molecular replacement approach and subsequently refined using rigid body and restrained-parameter least squares methods to a conventional crystallographic R-factor of 0.16 for all observed reflections in the 6.0-2.8-A resolution range. The polypeptide chain of this protein is found to be organized into eight helical regions (labeled A-H) which collectively form a hydrophobic pocket in which the heme prosthetic group is bound. Our results show that the overall thermal motions of individual residues of horse heart metmyoglobin are correlated with their mean distances from the heme group. In comparisons with the structure of sperm whale metmyoglobin it has been found that horse heart metmyoglobin has unique polypeptide chain conformations in four regions. These include residues in the immediate vicinity of the amino and carboxyl termini, residues about Lys-16, and residues 117-124 which are in the interhelical region between helices G and H. Many of these conformational changes appear to occur as a consequence of a different pattern of salt-bridging interactions between charged residues on the surface of horse heart metmyoglobin. The overall average positional deviation observed between corresponding alpha-carbons in the polypeptide chains of horse heart and sperm whale metmyoglobin is 0.50 A. This value for atoms of the porphyrin core of the central heme group is 0.39 A. A total of 12 well defined water molecules and 1 sulfate ion are included in the current structural model of horse heart metmyoglobin. One of these water molecules is found to be coordinated to the heme iron atom and hydrogen bonded to the side chain of His-64. The sulfate ion is hydrogen bonded to amide groups at the amino-terminal end of the E-helix and, as well, forms similar interactions with the amino-terminal end of the D-helix of an adjacent protein molecule in the crystalline lattice.

Crystallization and preliminary diffraction data for horse heart metmyoglobin

Reddish-brown crystals of metmyoglobin from horse heart have been obtained by both the hanging drop and batch crystallization methods in the space group P2 1, having a = 64.3 A ̊ , b = 28.9 A ̊ and c = 35.9 A ̊ , with β = 107.1 ° . Morphologically similar crystal forms have been obtained for three derivatives of horse heart myoglobin having modified heme prosthetic groups.