Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism

Mycobacterium tuberculosis is the causative agent of human tuberculosis. The nitric oxide reaction with oxy-truncated hemoglobin N (trHbN) has been proposed to be responsible for the resistance mechanism by which this microorganism can evade the toxic effects of NO. In this work, we explore the molecular basis of the NO detoxification mechanism using a combination of classical and hybrid quantum-classical (QM-MM) simulation techniques. We have investigated the structural flexibility of the protein, the ligand affinity properties, and the nitric oxide reaction with coordinated O2. The analysis of the classical MD trajectory allowed us to identify Phe62 as the gate of the main channel for ligand diffusion to the active site. Moreover, the opening of the channel stems from the interplay between collective backbone motions and local rearrangements in the side chains of the residues that form the bottleneck of the tunnel. Even though the protein environment is not found to make a significant contribution to the heme moiety catalyzed reaction, the binding site influences the physiological function of the enzyme at three different levels. First, by isolating the intermediates formed in the reaction, it prevents nondesired reactions from proceeding. Second, it modulates the ligand (O2, NO) affinity of the protein, which can be ascribed to both distal and proximal effects. Finally, the stabilization of the Tyr33-Gln58 pair upon O2 binding might alter the essential dynamics of the protein, leading in turn to a mechanism for ligand-induced regulation.     

Bond or cage effect: how nitrophorins transport and release nitric oxide

Most blood-sucking insects possess salivary proteins which, upon injection into the victim's tissue, help them improve their feeding. One group of these salivary proteins takes advantage of the vasodilator properties of NO to perform this task. These proteins are the so-called nitrophorins (NPs). NPs are heme proteins that store and transport NO, which, when released in the victim's tissue, produces vasodilation and inhibition of blood coagulation. It has been proposed that NO binds tightly to NP at a low pH of around 5.6 and that once NPs are injected in the victims tissue, at a pH of approximately 7.4, a conformational change occurs which lowers NO affinity, allowing it to be released. In this work we have studied the NO release mechanism of NP4 at a molecular level using state of the art computer simulation techniques. We have used molecular dynamics (MD) simulations to study NP4 conformational dynamics at both pH values 5.6 and 7.4 and computed the corresponding free energy profile for NO release using a multiple steering molecular dynamics scheme. We also have used hybrid quantum mechanical/molecular mechanics (QM/MM) techniques to analyze the heme-NO structure and the Fe-NO bond strength in the different NP4 conformations. Our results provide the molecular basis to explain that NO escape from NP4 is determined by differential NO migration rates and not by a difference in the Fe-NO bond strength. In contrast to most heme proteins that control ligand affinity by modulating the bond strength to the iron, NP4 has evolved a cage mechanism that traps the NO at low pH and releases it upon cage opening when the pH rises.     

Genetic engineering of the heme pocket in human serum albumin: modulation of O2 binding of iron protoporphyrin IX by variation of distal amino acids

Complexing an iron protoporphyrin IX into a genetically engineered heme pocket of recombinant human serum albumin (rHSA) generates an artificial hemoprotein, which can bind O2 in much the same way as hemoglobin (Hb). We previously demonstrated a pair of mutations that are required to enable the prosthetic heme group to bind O2 reversibly: (i) Ile-142-->His, which is axially coordinated to the central Fe2+ ion of the heme, and (ii) Tyr-161-->Phe or Leu, which makes the sixth coordinate position available for ligand interactions [I142H/Y161F (HF) or I142H/Y161L (HL)]. Here we describe additional new mutations designed to manipulate the architecture of the heme pocket in rHSA-heme complexes by specifically altering distal amino acids. We show that introduction of a third mutation on the distal side of the heme (at position Leu-185, Leu-182, or Arg-186) can modulate the O2 binding equilibrium. The coordination structures and ligand (O2 and CO) binding properties of nine rHSA(triple mutant)-heme complexes have been physicochemically and kinetically characterized. Several substitutions were severely detrimental to O2 binding: for example, Gln-185, His-185, and His-182 all generated a weak six-coordinate heme, while the rHSA(HF/R186H)-heme complex possessed a typical bis-histidyl hemochrome that was immediately autoxidized by O2. In marked contrast, HSA(HL/L185N)-heme showed very high O2 binding affinity (P1/2O2 1 Torr, 22 degrees C), which is 18-fold greater than that of the original double mutant rHSA(HL)-heme and very close to the affinities exhibited by myoglobin and the high-affinity form of Hb. Introduction of Asn at position 185 enhances O2 binding primarily by reducing the O2 dissociation rate constant. Replacement of polar Arg-186 with Leu or Phe increased the hydrophobicity of the distal environment, yielded a complex with reduced O2 binding affinity (P1/2O2 9-10 Torr, 22 degrees C), which nevertheless is almost the same as that of human red blood cells and therefore better tuned to a role in O2 transport.     

Nonequilibrium dynamics simulations of nitric oxide release: comparative study of nitrophorin and myoglobin

Nitrophorin 4 (NP4) is a heme protein that reversibly binds nitric oxide (NO), with release rates modulated by pH change. High-resolution structures of NP4 revealed that pH changes and NO binding induce a large conformational rearrangement in two loops that serve to protect the heme-bound NO molecule from solvent. We used extended (110 ns) molecular dynamics simulations of NP4 at pH 5 and pH 7, modeled by selective deprotonation of acidic groups. Conformational and dynamic changes were observed, consistent with those found in the crystal. Further, major solvent movement and NO escape were observed at pH 7, while the ligand remained in the heme binding pocket at pH 5. As a control, we also performed molecular dynamics (MD) simulations of sperm whale myoglobin, where NO migration into the interior cavities of the protein was observed, consistent with previous reports. We constructed a kinetic model of ligand escape to quantitatively relate the microscopic rate constants to the observed rates, and tested the predictions against the experimental data. The results suggest that release rates of diatomic molecules from heme proteins can be varied by several orders of magnitude through modest adjustments in geminate rebinding and gating behavior.     

Mechanism of product release in NO detoxification from Mycobacterium tuberculosis truncated hemoglobin N

The capability of Mycobacterium tuberculosis to rest in latency in the infected organism appears to be related to the disposal of detoxification mechanisms, which converts the nitric oxide (NO) produced by macrophages during the initial growth infection stage into a nitrate anion. Such a reaction appears to be associated with the truncated hemoglobin N (trHbN). Even though previous experimental and theoretical studies have examined the pathways used by NO and O2 to access the heme cavity, the eggression pathway of the nitrate anion is still a challenging question. In this work we present results obtained by means of classical and quantum chemistry simulations that show that trHbN is able to release rapidly the nitrate anion using an eggression pathway other than those used for the entry of both O2 and NO and that its release is promoted by hydration of the heme cavity. These results provide a detailed understanding of the molecular basis of the NO detoxification mechanism used by trHbN to guarantee an efficient NO detoxification and thus warrant survival of the microorganism under stress conditions.     

Site‐Specific Investigation of the Steady‐State Kinetics and Dynamics of the Multistep Binding of Bile Acid Molecules to a Lipid Carrier Protein

The investigation of multi‐site ligand–protein binding and multi‐step mechanisms is highly demanding. In this work, advanced NMR methodologies such as 2D ¹H–¹⁵N line‐shape analysis, which allows a reliable investigation of ligand binding occurring on micro‐ to millisecond timescales, have been extended to model a two‐step binding mechanism. The molecular recognition and complex uptake mechanism of two bile salt molecules by lipid carriers is an interesting example that shows that protein dynamics has the potential to modulate the macromolecule–ligand encounter. Kinetic analysis supports a conformational selection model as the initial recognition process in which the dynamics observed in the apo form is essential for ligand uptake, leading to conformations with improved access to the binding cavity. Subsequent multi‐step events could be modelled, for several residues, with a two‐step binding mechanism. The protein in the ligand‐bound state still exhibits a conformational rearrangement that occurs on a very slow timescale, as observed for other proteins of the family. A global mechanism suggesting how bile acids access the macromolecular cavity is thus proposed.     

Nitric oxide interaction with cytochrome c' and its relevance to guanylate cyclase. Why does the iron histidine bond break?

Soluble guanylate cyclase (sGC), the mammalian receptor for nitric oxide (NO), is a heme protein with a histidine as the proximal ligand. Formation of a five-coordinate heme-NO complex with the associated Fe-His bond cleavage is believed to trigger a conformational change that activates the enzyme and transduces the NO signal. Cytochrome c' (cyt c') is a protobacteria heme protein that has several similarities with sGC, including the ability to form a five-coordinate NO adduct and the fact that it does not bind oxygen. Recent crystallographic characterization of cyt c' from Alcaligenes xylosoxidans (AXCP) has yielded the discovery that exogenous ligands are able to bind to the Fe center from either side of the porphyrin plane. In this paper, we explore the molecular basis of the NO interaction with AXCP using hybrid quantum-classical simulation techniques. Our results suggest that Fe-His bond breaking depends not only on the iron-histidine bond strength but also on the existence of a local minimum conformation of the protein with the histidine away from the iron. We also show that AXCP is a useful paradigm for NO interaction with heme proteins, particularly regarding the activation/deactivation mechanism of sGC. The results presented here fully support a recently proposed model of sGC activation in which NO is not only the iron ligand but also catalyzes the activation step.     

ENDOR of NO-ligated cytochrome c'

The five-coordinate NO-bound heme in cytochrome c' from an overexpressing variant of denitrifying R. sphaeroides 2.4.3 was investigated by proton, nitrogen, and deuterium Q-band ENDOR (electron nuclear double resonance). ENDOR was a direct probe of the unpaired electron density on the nitrogen of NO and, as measured across the EPR line shape, showed a hyperfine coupling range from 36 to 44 MHz for 14NO and 51 to 63 MHz for 15NO. The smallest NO coupling occurred at an electronic g-tensor axis perpendicular to the FeNO plane, and the largest hyperfine coupling occurred in the FeNO plane where the highest nitrogen valence spin density is located. The isotropic component of the NO hyperfine coupling indicated that the electron spin on the NO is not simply in a pi orbital having only 2p character but is in an orbital having 2s and 2p character in a 1:2 ratio. ENDOR frequencies from heme meso-protons, assigned with reference to porphyrin models, were determined to result from an anisotropic hyperfine tensor. This tensor indicated the orientation of the heme with respect to the FeNO plane and showed that the FeNO plane bisects the heme N-Fe-N 90 degrees angle. ENDOR provided additional structural information through dipolar couplings, as follows: (1) to the nearest proton of the Phe14 ring, approximately 3.1 A away from the heme iron, where Phe14 is positioned to occlude binding of NO as a 6th (distal) ligand; (2) to exchangeable deuterons assigned to Arg127 which may H-bond with the proximal NO ligand.     

Fluoride as a probe for H-bonding interactions in the active site of heme proteins: the case of Thermobifida fusca hemoglobin

The structural and functional properties of the active site of the bacterial hemoglobin from Thermobifida fusca are largely determined by three polar amino acids: TrpG8, TyrCD1, and TyrB10. We have exploited the availability of a combinatorial set of mutants, in each of which these three amino acids have been singly, doubly, or triply replaced by a Phe residue, to perform a detailed study on H-bonding interactions between the protein and heme-bound fluoride. By appropriate choice of the excitation conditions, ν(Fe-F) stretching bands have been detected in the resonance Raman spectra. In the wild-type protein and one of the mutants, two ν(Fe-F) bands have been observed and assigned to the presence of two protein conformers where fluoride is singly or doubly H-bonded. Furthermore, by plotting the CT1 charge-transfer transition energy vs the ν(Fe-F) wavenumbers, an empirical correlation has been found. The data are well fitted by a straight line with a positive slope. The position along the correlation line can be considered as a novel, general spectroscopic indicator of the extent of H-bonding in the active site of heme proteins. In agreement with the spectroscopic results, we have observed that the rate of ligand dissociation in stopped-flow kinetic measurements progressively increases upon substitution of the H-bonding amino acids. Molecular dynamics simulations have been performed on the fluoride complexes of native and mutated forms, indicating the prevalent interactions at the active site. All the techniques yield evidence that TrpG8 and TyrCD1 can form strong H bonds with fluoride, whereas TyrB10 plays only a minor role in the stabilization of the ligand.     

Characterization of conformational changes and noncovalent complexes of myoglobin by electrospray ionization mass spectrometry,circular dichroism and fluorescence spectroscopy

Electrospray ionization mass spectrometry (ESI‐MS) was employed to monitor the heme release and the conformational changes of myoglobin (Mb) under different solvent conditions, and to observe ligand bindings of Mb. ESI‐MS, complemented by circular dichroism and fluorescence spectroscopy, was used to study the mechanism of acid‐ and organic solvent‐induced denaturation by probing the changes in the secondary and the tertiary structure of Mb. The results obtained show that complete disruption of the heme–protein interactions occurs when Mb is subjected to one of the following solution conditions: pH 3.2–3.6, or solution containing 20–30% acetonitrile or 40–50% methanol. Outside these ranges, Mb is present entirely in its native state (binding with a heme group) or as apomyoglobin (i.e. without the heme). Spectroscopic data demonstrate that the denaturation mechanism of Mb induced by acid may be significantly different from that by the organic solvent. Low pH reduces helices in Mb, whereas certain organic content level in solution results in the loss of the tertiary structure. ESI‐MS conditions were established to observe the H₂O‐ and CO‐bound Mb complexes, respectively. H₂O binding to metmyoglobin (17 585 Da), where the heme iron is in the ferric oxidation state, is observed in ESI‐MS. CO binding to Mb (17 595 Da), on the other hand, can be only observed after the heme iron is reduced to the ferrous form. Therefore, ESI‐MS combined with spectroscopic techniques provides a useful means for probing the formation of ligand‐binding complexes and characterizing protein conformational changes. Copyright © 2010 John Wiley & Sons, Ltd.     

Temperature-dependent studies of NO recombination to heme and heme proteins

The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (approximately 10 ps) recombination phase is found to be zero and a slower geminate phase (approximately 200 ps) reveals a small enthalpic barrier (approximately 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (approximately 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (enthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.     

Heme CD as a probe for monitoring local structural changes in hemeproteins: Alkaline transition in hemeproteins

Structural change due to acid-alkaline transition in hemeproteins were monitored by circular dichroism measurements in the Soret region. It was observed that in cytochrome c and horseradish peroxidase, alkaline transition results in a large change in the heme CD due to significant conformational change in the heme cavity region. In metmyoglobin a simple protolytic mechanism associated with alkaline transition involves very small conformational changes.     

Electronic ground states and vibrational frequency shifts of diatomic ligands in heme adducts

DFT calculations were carried out to study heme complexes with diatomic ligand (CO, NO, or O(2)) and trans-imidazole ligand. The optimized electronic ground states of CO, NO, and O(2) adducts are singlet, doublet, and open-shell singlet, respectively. For O(2) adduct, the open-shell singlet is slightly lower in energy than the close-shell singlet. However, important differences are found in optimized structures and vibrational frequencies. Particularly, the trans-imidazole-induced frequency up-shift of the Fe-O(O) stretching mode can be predicted only with the open-shell singlet as ground state. An analysis of normal modes confirms that the up-shifts in the bent (NO and O(2) ) adducts are mainly due to mixing of Fe-X(O) stretching mode with Fe-X-O bending coordinate. Our study of binding mechanism indicates that a secondary source of the upshifts is the diminished weakening of the Fe-X(O) bonds. The Fe-X(O) bond strengths are modulated by σ competition mechanism, which weakens the Fe-X(O) bond and σ-π cooperation mechanism, which only exists in the bent adducts and enforce the Fe-X(O) bond. -     

Static normal coordinate deformations of the heme group in mutants of ferrocytochrome c from Saccharomyces cerevisiae probed by resonance Raman spectroscopy

The function of heme proteins is, to a significant extent, influenced by the ligand field probed by the heme iron, which itself can be affected by deformations of the heme macrocycle. The exploration of this field is difficult because the heme structure obtained from X-ray crystallography is not resolved enough to unambiguously identify structural changes on the scale of 10(-2) A. However, asymmetric deformations in this order of magnitude affect the depolarization ratio of the resonance Raman lines assignable to normal vibrations of the heme group. We have measured the dispersion of the depolarization ratios of four structure sensitive Raman bands (i.e., nu4, nu11, nu21, and nu28) in yeast iso-1-ferrocytochrome c and its mutants N52V, Y67F, and N52VY67F with B- and Q-band excitation. The DPR dispersion of all bands indicates the presence of asymmetric in-plane and out-of-plane deformations. The replacement of the polar tyrosine residue at position 67 by phenylalanine significantly increases the triclinic B2g deformation, which involves a distortion of the pyrrole symmetry. We relate this deformation to changes of the electronic structure of pyrrole A, which modulates the interaction between its propionate substituents and the protein environment. This specific heme deformation is eliminated in the double mutant N52VY67F. The additional substitution of N52 by valine induces a tetragonal B1g deformation which involves asymmetric changes of the Fe-N distances and increases the rhombicity of the ligand field probed by the heme iron. This heme deformation might be caused by the elimination of the water-protein hydrogen-bonding network in the heme cavity. The single mutation N52V does not significantly perturb the heme symmetry, but a small B1g deformation is consistent with our data and the heme structure obtained from a 1 ns molecular dynamics simulation of the protein.     

A novel kinetic trap for NO release from cytochrome c': a possible mechanism for NO release from activated soluble guanylate cyclase

Flash photolysis studies on the five-coordinate heme nitrosyl of Alcaligenes xylosoxidans cytochrome c' were carried out to investigate the ramifications of its proximal nitrosyl ligand on NO release. Delta absorbance spectra recorded 5 ms after photolysis indicate that approximately 5% of the photolyzed hemes are converted to a five-coordinate high spin ferrous state, revealing that reattachment of the endogenous His ligand is fast enough to trap some of the photolyzed heme. Analysis of NO rebinding suggests that the photolyzed ferrous protein is initially in a strained conformation, which relaxes on a millisecond time scale. The strained ferrous heme appears to contain a significantly labilized Fe-His bond, which allows direct second-order rebinding to the proximal face at high NO-concentrations. In contrast, the NO-binding properties of the relaxed conformation are similar to those previously observed in stopped-flow studies, which showed that a five-coordinate heme-nitrosyl is formed via a six-coordinate intermediate. The discovery of a rapid proximal His ligand reattachment to NO-dissociated heme reveals a novel "kinetic trap" mechanism for lowering the five-coordinate heme nitrosyl population in response to decreased ambient NO concentrations. Thus, NO dissociation from the five-coordinate heme nitrosyl, whether thermal or photochemical, is followed by rapid, and only slowly reversible, His reattachment which acts to kinetically trap the heme in its five-coordinate ferrous state. Because return to the five-coordinate heme nitrosyl requires two NO-dependent steps, the protein uses a kind of kinetic amplification of the thermodynamic dissociation that occurs in response to decreased NO concentrations. The implications of this "kinetic-trap" mechanism for NO release from soluble guanylate cyclase are discussed.     

The heterogeneous chemical kinetics of NO3 on atmospheric mineral dust surrogates

Uptake experiments of NO3 on mineral dust powder were carried out under continuous molecular flow conditions at 298 +/- 2 K using the thermal decomposition of N2O5 as NO3 source. In situ laser detection using resonance enhanced multiphoton ionization (REMPI) to specifically detect NO2 and NO in the presence of N2O5, NO3 and HNO3 was employed in addition to beam-sampling mass spectrometry. At [NO3] = (7.0 +/- 1.0) x 10(11) cm(-3) we found a steady state uptake coefficient gamma(ss) ranging from (3.4 +/- 1.6) x 10(-2) for natural limestone to (0.12 +/- 0.08) for Saharan Dust with gamma(ss) decreasing as [NO3] increased. NO3 adsorbed on mineral dust leads to uptake of NO2 in an Eley-Rideal mechanism that usually is not taken up in the absence of NO3. The disappearance of NO3 was in part accompanied by the formation of N2O5 and HNO3 in the presence of NO2. NO3 uptake performed on small amounts of Kaolinite and CaCO3 leads to formation of some N2O5 according to NO((3ads)) + NO(2(g)) --> N2O(5(ads)) --> N2O(5(g)). Slow formation of gas phase HNO3 on Kaolinite, CaCO3, Arizona Test Dust and natural limestone has also been observed and is clearly related to the presence of adsorbed water involved in the heterogeneous hydrolysis of N2O(5(ads)).     

Oxygen Migration Pathways in NO‐bound Truncated Hemoglobin

Atomistic simulations of dioxygen (O₂) dynamics and migration in nitric oxide‐bound truncated Hemoglobin N (trHbN) of Mycobacterium tuberculosis are reported. From more than 100 ns of simulations the connectivity network involving the metastable states for localization of the O₂ ligand is built and analyzed. It is found that channel I is the primary entrance point for O₂ whereas channel II is predominantly an exit path although access to the protein active site is also possible. For O₂ a new site compared to nitric oxide, from which reaction with the heme group can occur, was found. As this site is close to the heme iron, it could play an important role in the dioxygenation mechanism as O₂ can remain there for hundreds of picoseconds after which it can eventually leave the protein, while NO is localized in Xe2. The present study supports recent experimental work which proposed that O₂ docks in alternative pockets than Xe close to the reactive site. Similar to other proteins, a phenylalanine residue (Phe62) plays the role of a gate along the access route in channel I. The most highly connected site is the Xe3 pocket which is a “hub” and free energy barriers between the different metastable states are ≈1.5 kcal mol^?1 which allows facile O₂ migration within the protein.