Molecular mechanics and molecular dynamics simulations of porphyrins, metalloporphyrins, heme proteins and cobalt corrinoids

Comparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy

Molecular dynamics (MD) simulations are a powerful approach to studying the structure and dynamics of proteins related to health and disease. Advances in the MD field allow modeling proteins with high accuracy. However, modeling metal ions and their interactions with proteins is still challenging. NPL4 is a zinc-binding protein and works as a cofactor for p97 to regulate protein homeostasis. NPL4 is of biomedical importance and has been proposed as the target of disulfiram, a drug recently repurposed for cancer treatment. Experimental studies proposed that the disulfiram metabolites, bis-(diethyldithiocarbamate)‑copper and cupric ions, induce NPL4 misfolding and aggregation. However, the molecular details of their interactions with NPL4 and consequent structural effects are still elusive. Here, biomolecular simulations can help to shed light on the related structural details. To apply MD simulations to NPL4 and its interaction with copper the first important step is identifying a suitable force field to describe the protein in its zinc-bound states. We examined different sets of non-bonded parameters because we want to study the misfolding mechanism and cannot rule out that the zinc may detach from the protein during the process and copper replaces it. We investigated the force-field ability to model the coordination geometry of the metal ions by comparing the results from MD simulations with optimized geometries from quantum mechanics (QM) calculations using model systems of NPL4. Furthermore, we investigated the performance of a force field including bonded parameters to treat copper ions in NPL4 that we obtained based on QM calculations.

The inorganic chemistry of the cobalt corrinoids - an update

The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B₁₂, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B₁₂-dependent enzymes is also given for the reader's convenience.

Multi-component redox system for selective and potent antineoplastic activity towards ovarian cancer cells

Ovarian cancer is the deadliest gynecological cancer which rarely causes symptoms, and goes undetected until reaching the advanced stage of drug-resistant metastases. The cationic porphyrin meso-tetra(4-N-methylpyridyl)porphine (TMPyP) is a well-known photosensitizer (PS) used in photodyamic therapy (PDT) for curing cancer due to its strong affinity for DNA and high yield of reactive oxygen species (ROS) upon light activation. The practicality to irradiate tumor cells alone in the physiological system being slim (due to the close proximity of healthy cells and tumors), we looked for a variation in the PDT using a mixture of TMPyP with 1,5-dihydroxynapthalene (DHN) and Fe(III) ions at a mole ratio of 1:20:17 (drug combo) respectively in aqueous solution. The drug combo needs no photoactivation in H₂O₂ rich environment (mimicking the microenvironment of cancer/tumor), where it generates ȮH and juglone, the latter being a known potent anticancer agent. In vitro studies of the drug combo in drug resistant and sensitive ovarian cancer cell lines showed drastic growth inhibition and cell death compared to normal epithelial cells. The drug combo provides an effective and non-invasive alternative to conventional PDT, exploiting the cytosolic carcinogenic H₂O₂ to produce an efficient anticancer treatment. The unique action of cancer-specific cytotoxicity arises from the redox chemistry involving activation of Fe(III) as the oxidizing agent to generate juglone, which utilizes the cytosolic ROS in cancer cells against itself.

Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model

Heme is an active center in many proteins. Here we explore computationally the role of heme in protein folding and protein structure. We model heme proteins using a hybrid model employing the AWSEM Hamiltonian, a coarse-grained forcefield for the protein chain along with AMBER, an all-atom forcefield for the heme. We carefully designed transferable force fields that model the interactions between the protein and the heme. The types of protein-ligand interactions in the hybrid model include thioester covalent bonds, coordinated covalent bonds, hydrogen bonds, and electrostatics. We explore the influence of different types of hemes (heme b and heme c) on folding and structure prediction. Including both types of heme improves the quality of protein structure predictions. The free energy landscape shows that both types of heme can act as nucleation sites for protein folding and stabilize the protein folded state. In binding the heme, coordinated covalent bonds and thioester covalent bonds for heme c drive the heme toward the native pocket. The electrostatics also facilitates the search for the binding site.

Activity adaptability of a DhHP-6 peroxidase-mimic in wide pH and temperature ranges and solvent media

Deuterohemin-β-Ala-His-Thr-Val-Glu-Lys (DhHp-6): peroxidase with high activity.

Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum

Chlorosome antennae form an interesting class of materials for studying the role of structural motifs and dynamics in nonadiabatic energy transfer. They perform robust and highly quantum-efficient transfer of excitonic energy while allowing for compositional variation and completely lacking the usual regulatory proteins. Here, we first cast the geometrical analysis for ideal tubular scaffolding models into a formal framework, to relate effective helical properties of the assembly structures to established characterization data for various types of chlorosomes. This analysis shows that helicity is uniquely defined for chlorosomes composed of bacteriochlorophyll (BChl) d and that three chiral angles are consistent with the nuclear magnetic resonance (NMR) and electron microscope data for BChl c, including two novel ones that are at variance with current interpretations of optical data based on perfect cylindrical symmetry. We use this information as a starting point for investigating dynamic and static heterogeneity at the molecular level by unconstrained molecular dynamics. We first identify a rotational degree of freedom, along the Mg-OH coordination bond, that alternates along the syn-anti stacks and underlies the (flexible) curvature on a larger scale. Because rotation directly relates to the formation or breaking of interstack hydrogen bonds of the O-H···O=C structural motif along the syn-anti stacks, we analyzed the relative fractions of hydrogen-bonded and the nonbonded regions, forming stripe domains in otherwise spectroscopically homogeneous curved slabs. The ratios 7:3 for BChl c and 9:1 for BChl d for the two distinct structural components agree well with the signal intensities determined by NMR. In addition, rotation with curvature-independent formation of stripe domains offers a viable explanation for the localization and dispersion of exciton states over two fractions, as observed in single chlorosome fluorescence decay studies.

Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations

Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co³⁺, Co²⁺, and Co¹⁺, and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.

Ultrafast dynamics of ligand and substrate interaction in endothelial nitric oxide synthase under Soret excitation

Ultrafast transient absorption spectroscopy of endothelial NOS oxygenase domain (eNOS-oxy) was performed to study dynamics of ligand or substrate interaction under Soret band excitation. Photo-excitation dissociates imidazole ligand in <300fs, then followed by vibrational cooling and recombination within 2ps. Such impulsive bond breaking and late rebinding generate proteinquakes, which relaxes in several tens of picoseconds. The photo excited dynamics of eNOS-oxy with L-arginine substrate mainly occurs at the local site of heme, including ultrafast internal conversion within 400fs, vibrational cooling, charge transfer, and complete ground-state recovery within 1.4ps. The eNOS-oxy without additive is partially bound with water molecule, thus its photoexcited dynamics also shows ligand dissociation in <800fs. Then it followed by vibrational cooling coupled with charge transfer in 4.8ps, and recombination of ligand to distal side of heme in 12ps.

Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA

Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Co(NH3)6 (3+) (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive. However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become 'internal binding' into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit 'external binding' to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.

Synthesis, coordination chemistry, and physico-chemical properties of the 2-chloroethoxy-iron(III)(ethylthio) porphyrazine

Reaction of octakis(ethylthio)porphyrazine ( H 2 OESPz ) with FeBr 2 in ClCH 2 CH 2 OH at 135 °C affords the 2-chloroethoxy-iron(III)-(ethylthio)porphyrazine, ( ClCH 2 CH 2 O ) Fe III OESPz , ( LFe III OESPz ) in good yield. The spectroscopic, redox, and coordination properties of the complex and its μ-oxo dimer derivative, [ Fe III OESPz ]2 O , are investigated and compared to those of the iron(III)porphyrin analogs.

Combined spectroscopic/computational studies of vitamin B12 precursors: geometric and electronic structures of cobinamides

Vitamin B(12) (cyanocobalamin) and its biologically active derivatives, methylcobalamin and adenosylcobalamin, are members of the family of corrinoids, which also includes cobinamides. As biological precursors to cobalamins, cobinamides possess the same structural core, consisting of a low-spin Co(3+) ion that is ligated equatorially by the four nitrogens of a highly substituted tetrapyrrole macrocycle (the corrin ring), but differ with respect to the lower axial ligation. Specifically, cobinamides possess a water molecule instead of the nucleotide loop that coordinates axially to Co(3+)cobalamins via its dimethylbenzimidazole (DMB) base. Compared to the cobalamin species, cobinamides have proven much more difficult to study experimentally, thus far eluding characterization by X-ray crystallography. In this study, we have utilized combined quantum mechanics/molecular mechanics (QM/MM) computations to generate complete structural models of a representative set of cobinamide species with varying upper axial ligands. To validate the use of this approach, analogous QM/MM geometry optimizations were carried out on entire models of the cobalamin counterparts for which high-resolution X-ray structural data are available. The accuracy of the cobinamide structures was assessed further by comparing electronic absorption spectra computed using time-dependent density functional theory to those obtained experimentally. Collectively, the results obtained in this study indicate that the DMB → H(2)O lower axial ligand switch primarily affects the energies of the Co 3d(z(2))-based molecular orbital (MO) and, to a lesser extent, the other Co 3d-based MOs as well as the corrin π-based highest energy MO. Thus, while the energy of the lowest-energy electronic transition of cobalamins changes considerably as a function of the upper axial ligand, it is nearly invariant for the cobinamides.

Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF)

Currently the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262-8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement.

Axial bonding in alkylcobalamins: DFT analysis of the inverse versus normal trans influence

Density functional theory has been applied to study the origin of the inverse and normal trans influence in alkylcobalamins. In order to cover the X-ray structural data available for alkylcobalamins with a variety of axial substituents, geometries of 28 related corrin-containing models have been optimized and analyzed. The BP86/6-31G(d) level of theory was applied which showed good reliability in reproducing the axial bond lengths. Comparison of experimental and calculated data allowed to conclude that the inverse trans influence is not a general feature of cobalamins, as it appeared from the experimental data analysis alone. Inverse trans influence is observed for the series of R groups with increasing bulk and electron donating ability. For the series of R groups having similar medium bulk, but differing significantly in the electron donating ability, normal trans influence was found. Finally, it was determined, that the axial bond lengths correlate well but differently in the two series of R groups with the orbital energies of the six molecular orbitals essential in axial interligand bonding.

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.

Mg-Al layered double hydroxide intercalated with porphyrin anions: molecular simulations and experiments

Molecular modeling in combination with powder X-ray diffraction (XRD) provided new information on the organization of the interlayer space of Mg-Al layered double hydroxide (LDH) containing intercalated porphyrin anions [5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS)]. Anion-exchange and rehydration procedures were used for the preparation of TPPS-containing LDH with an Mg/Al molar ratio of 2. Molecular modeling was carried out in the Cerius(2) and Materials Studio modeling environment. Three types of models were created in order to simulate the experimental XRD patterns of LDH intercalates with a TPPS loading of 70-80% with respect to the theoretical anion exchange capacity (AEC). The models represent single-phase systems with a 100% TPPS loading in the interlayer space (Type 1) and models represent the coexistence of two phases corresponding to the total exchange from 75 to 92% (Type 2). To cover other possible arrangements, models with the coexistence of both TPPS and NO(3)(-) anions in the same interlayer space were calculated (Type 3). The models are described and compared with experimental data. In all cases, guest TPPS anions are tilted with respect to the hydroxide layers, and are horizontally shifted to each other by up to one-half of the TPPS diameter. According to the energy characteristics and simulated XRD, the most probable arrangement is of Type 2, where some layers are saturated with TPPS anions and others are filled with original NO(3)(-) anions.

Adsorption, manipulation and self-assembling of TBrPP-Co molecules on a Ag/Si(111) surface by scanning tunnelling microscopy

Individual adsorption and two-dimensional assembling of 5,10,15,20-tetrakis-(4-bromophenyl)-porphyrin-Co (TBrPP-Co) molecules on a Si(111)-[Formula: see text] Ag reconstructed surface have been studied using low-temperature scanning tunnelling microscopy (STM). All the isolated molecules are observed in a planar shape with slight distortion. The isolated molecules can be controllably rotated with an STM tip to the orientation along the trigonal lattice ([Formula: see text] direction) of the substrate. With an increased coverage (0.07 ML) and appropriate annealing, the molecules assemble to form three types of ordered phase. The long-range ordered structures, however, disappear at higher coverage (0.75 ML).

Conformational Adaptation and Selective Adatom Capturing of Tetrapyridyl-porphyrin Molecules on a Copper (111) Surface

We present a combined low-temperature scanning tunneling microscopy and near-edge X-ray adsorption fine structure study on the interaction of tetrapyridyl-porphyrin (TPyP) molecules with a Cu(111) surface. A novel approach using data from complementary experimental techniques and charge density calculations allows us to determine the adsorption geometry of TPyP on Cu(111). The molecules are centered on "bridge" sites of the substrate lattice and exhibit a strong deformation involving a saddle-shaped macrocycle distortion as well as considerable rotation and tilting of the meso-substituents. We propose a bonding mechanism based on the pyridyl-surface interaction, which mediates the molecular deformation upon adsorption. Accordingly, a functionalization by pyridyl groups opens up pathways to control the anchoring of large organic molecules on metal surfaces and tune their conformational state. Furthermore, we demonstrate that the affinity of the terminal groups for metal centers permits the selective capture of individual iron atoms at low temperature.

Influence of electronic and steric effects on stability constants and electrochemical reversibility of divalent ion complexes with glycine and sarcosine. A glass electrode potentiometric, sampled direct current polarographic, virtual potentiometric, and molecular modelling study

Cd(II) complexes with glycine (gly) and sarcosine (sar) were studied by glass electrode potentiometry, direct current polarography, virtual potentiometry, and molecular modelling. The electrochemically reversible Cd(II)-glycine-OH labile system was best described by a model consisting of M(HL), ML, ML2, ML3, ML(OH) and ML2(OH) (M = Cd(II), L = gly) with the overall stability constants, as log beta, determined to be 10.30+/-0.05, 4.21+/-0.03, 7.30+/-0.05, 9.84+/-0.04, 8.9+/-0.1, and 10.75+/-0.10, respectively. In case of the electrochemically quasi-reversible Cd(II)-sarcosine-OH labile system, only ML, ML2 and ML3 (M = Cd(II), L = sar) were found and their stability constants, as log beta, were determined to be 3.80+/-0.03, 6.91+/-0.07, and 8.9+/-0.4, respectively. Stability constants for the ML complexes, the prime focus of this work, were thus established with an uncertainty smaller than 0.05 log units. The observed departure from electrochemical reversibility for the Cd-sarcosine-OH system was attributed mainly to the decrease in the transfer coefficient alpha. The MM2 force field, supplemented by additional parameters, reproduced the reported crystal structures of diaqua-bis(glycinato-O,N)nickel(II) and fac-tri(glycinato)-nickelate(II) very well. These parameters were used to predict structures of all possible isomers of (i) [Ni(H2O)4(gly)]+ and [Ni(H2O)4(sar)]+; and (ii) [Ni(H2O)3(IDA)] and [Ni(H2O)3(MIDA)] (IDA = iminodiacetic acid, MIDA = N-methyl iminodiacetic acid) by molecular mechanics/simulated annealing methods. The change in strain energy, deltaU(str), that accompanies the substitution of one ligand by another (ML + L' --> ML' + L), was computed and a strain energy deltaU(str) = +0.28 kcal mol(-1) for the reaction [Ni(H2O)4(gly)]+ + sar --> [Ni(H2O)4(sar)]+ + gly was found. This predicts the monoglycine complex to be marginally more stable. By contrast, for the reaction [Ni(H2O)3IDA] + MIDA --> [Ni(H2O)3MIDA] + IDA, deltaU(str) = -0.64 kcal mol(-1), and the monoMIDA complex is predicted to be more stable. This correlates well with (i) stability constants for Cd-gly and Cd-sar reported here; and (ii) known stability constants of ML complex for glycine, sarcosine, IDA, and MIDA.

Controlled metalation of self-assembled porphyrin nanoarrays in two dimensions

We report a bottom-up approach for the fabrication of metallo-porphyrin compounds and nanoarchitectures in two dimensions. Scanning tunneling microscopy and tunneling spectroscopy observations elucidate the interaction of highly regular porphyrin layers self-assembled on a Ag(111) surface with iron monomers supplied by an atomic beam. The Fe is shown to be incorporated selectively in the porphyrin macrocycle whereby the template structure is strictly preserved. The immobilization of the molecular reactants allows the identification of single metalation events in a novel reaction scheme. Because the template layers provide extended arrays of reaction sites, superlattices of coordinatively unsaturated and magnetically active metal centers are obtained. This approach offers novel pathways to realize metallo-porphyrin compounds, low-dimensional metal-organic architectures and patterned surfaces which cannot be achieved by conventional means.

Pentacoordinate and hexacoordinate ferric hemes in acid medium: EPR, UV–Vis and CD studies of the giant extracellular hemoglobin of Glossoscolex paulistus

The equilibrium complexity involving different axially coordinated hemes is peculiar to hemoglobins. The pH dependence of the spontaneous exchange of ligands in the extracellular hemoglobin from Glossoscolex paulistus was studied using UV-Vis, EPR, and CD spectroscopies. This protein has a complex oligomeric assembly with molecular weight of 3.1 MDa that presents an important cooperative effect. A complex coexistence of different species was observed in almost all pH values, except pH 7.0, where just aquomet species is present. Four new species were formed and coexist with the aquomethemoglobin upon acidification: (i) a "pure" low-spin hemichrome (Type II), also called hemichrome B, with an usual spin state (d(xy))(2)(d(xz),d(yz))(3); (ii) a strong g(max) hemichrome (Type I), also showing an usual spin state (d(xy))(2)(d(xz),d(yz))(3); (iii) a hemichrome with unusual spin state (d(xz),d(yz))(4)(d(xy))(1) (Type III); (iv) and a high-spin pentacoordinate species. CD measurements suggest that the mechanism of species formation could be related with an initial process of acid denaturation. However, it is worth mentioning that based on EPR the aquomet species remains even at acidic pH, indicating that the transitions are not complete. The "pure" low-spin hemichrome presents a parallel orientation of the imidazole ring planes but the strong g(max) hemichrome is a HALS (highly anisotropic low-spin) species indicating a reciprocally perpendicular orientation of the imidazole ring planes. The hemichromes and pentacoordinate formation mechanisms are discussed in detail.

Heme-peptide/protein ions and phosphorous ligands: search for site-specific addition reactions

High-resolution Fourier transform ion cyclotron resonance mass spectrometry is employed to gain thorough kinetics and thermodynamics information on the reaction of free and ligated heme-type ions with selected ligands, with the aim of obtaining an insight into the coordination environment of the prosthetic group in a variety of biomolecular ions. Adopting a stepwise approach towards systems of increasing complexity, we examined the reactivity of free gaseous iron(III) protoporphyrin IX ions, Fe(III)-heme(+), of the charged species from microperoxidase-11 (MP11) (covalently peptide bound heme), and of the multiply charged ions from heme proteins, namely, cytochrome c (cyt c) and myoglobin (examples of noncovalently protein bound hemes). Among an array of test compounds allowed to react with Fe(III)-heme(+), OP(OMe)(3) and P(OMe)(3) proved to be similarly efficient ligands in the first addition step, yet displayed markedly distinct reactivity towards heme iron already engaged in axial coordination. The ease with which P(OMe)(3) acts as a second axial ligand is exploited to probe structural and conformational features of biomolecular ions. In this way, circumstantial evidence is gained of a folded conformation of +2 charge state ions from MP11 and an elongated one for the +3 charge state ions. Similarly, both the general reaction pattern and detailed kinetics and thermodynamics data point to a regiospecific addition reaction of P(OMe)(3) directed at the heme iron within multiply charged ions from cyt c. This unprecedented example of ion-molecule reaction which specifically involves a prosthetic group belonging to protein ions stands in contrast to the multiple, nonspecific interactions established by OP(OMe)(3) molecules with the protonated sites of multiply charged cyt c and apomyoglobin ions. This finding may develop and provide sensitive probes of the structure and bonding features of protein ions in the gas phase.