Study of noncovalent enzyme-inhibitor complexes and metal binding stoichiometry of matrilysin by electrospray ionization mass spectrometry

THE USE OF MASS SPECTROMETRY TO STUDY ZN-METALLOPROTEASE-SUBSTRATE INTERACTIONS

Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the development of several different diseases. For this reason, in recent years, many analytical approaches have been applied for studying the interaction between ZnMPs and their substrates and how environmental factors can affect enzyme activities. In this scenario, mass spectrometric methods occupy a very important role in elucidating different aspects of ZnMPs-substrates interaction. These range from identification of cleavage sites to quantitation of kinetic parameters. In this work, an overview of all the main achievements regarding the application of mass spectrometric methods to investigating ZnMPs-substrates interactions is presented. A general experimental protocol is also described which may prove useful to the study of similar interactions. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Application of immobilized metal affinity chromatography in proteomics

It has been proved that the progress of proteomics is mostly determined by the development of advanced and sensitive protein separation technologies. Immobilized metal affinity chromatography (IMAC) is a powerful protein fractionation method used to enrich metal-associated proteins and peptides. In proteomics, IMAC has been widely employed as a prefractionation method to increase the resolution in protein separation. The combination of IMAC with other protein analytical technologies has been successfully utilized to characterize metalloproteome and post-translational modifications. In the near future, newly developed IMAC integrated with other proteomic methods will greatly contribute to the revolution of expression, cell-mapping and structural proteomics.

Electrospray ionization mass spectrometry in the study of biomolecular non-covalent interactions

In the past mass spectrometry has been limited to the study of small, stable molecules, however, with the emergence of electrospray ionization mass spectrometry (ESI-MS) large biomolecules as well as non-covalent biomolecular complexes can be studied. ESI-MS has been used to study non-covalent interactions involving proteins with metals, ligands, peptides, oligonucleotides, as well as other proteins. Although complementary to other well-established techniques such as circular dichroism and fluorescence spectroscopy, ESI-MS offers some advantages in speed, sensitivity, and directness particularly in the determination of the stoichiometry of the complex. One major advantage is the ability of ESI-MS to provide multiple signals each arising from a distinct population within the sample. In this review I will discuss some of the different types of non-covalent biomolecular interactions that have been studied using ESI-MS, highlighting examples which show the efficacy of using ESI-MS to probe the structure of biomolecular complexes.

Nonspecific protein-carbohydrate complexes produced by nanoelectrospray ionization. Factors influencing their formation and stability

Factors influencing the formation of nonspecific protein-carbohydrate complexes during the nanoelectrospray (nanoES) process have been investigated. Protonated and deprotonated nonspecific complexes of ubiquitin (Ubq) and protonated complexes of carbonic anhydrase (CA) with carbohydrates, ranging in size from mono- to tetrasaccharide, were produced by nanoES and detected with a Fourier transform ion cyclotron resonance mass spectrometer. Both the fraction of protein engaged in nonspecific binding with the carbohydrates and the number of carbohydrates bound to the protein increase with increasing carbohydrate concentration. At a given concentration of protein and carbohydrate, nonspecific binding is favored for small (mono- and disaccharide) or hydrophilic carbohydrates over larger or more hydrophobic molecules, which tend to form gaseous monomer or cluster ions by nanoES. However, the extent of nonspecific binding is insensitive to the structure of the protein, with similar distributions of nonspecific complexes observed for both CA and Ubq. Nonspecific association is also insensitive to the charge state of the complex. A comparable degree of binding is observed for complexes in their protonated and deprotonated forms. Furthermore, the number of bound ligands can exceed significantly the charge state of the complex. Thermal dissociation experiments performed on the gaseous nonspecific complexes reveal that their kinetic stability is sensitive to both the structure of the carbohydrate (i.e., mono- < di- < tri- < tetrasaccharide) and the protein (Ubq < CA) and to the charge state, although no simple relationship between stability and charge state was identified. Taken together, the results of this study suggest that neutral protein-carbohydrate interactions (e.g., hydrogen bonds) contribute significantly and, perhaps, predominantly to the formation and stabilization of the nonspecific complexes. A strategy to minimize the formation of the nonspecific complexes, which is based on the enhancement of gaseous carbohydrate ion formation through the addition of metal salts (e.g., CaCl2) to the nanoES solution, is demonstrated.

In situ AP/MALDI-MS characterization of anchored matrix metalloproteinases

Several different procedures are available for the immobilization of proteins on solid supports, as many advantages derive from this approach, such as the possibility to develop new protein solid-state assays. Enzymes that are anchored on gold surfaces can interact with several different molecules in a tag-free environment, opening the way to surface plasmon resonance (SPR) investigations. Nevertheless, it is often important to know the identity of the affinity-retained analyte, and mass spectrometric analysis, via its unique molecular mass identification, represents a very valuable complementary method. There are many pieces of evidence to suggest that matrix metalloproteinases (MMPs) are involved in normal and pathological processes, including embryogenesis, wound healing, inflammation, arthritis and cancer, but presumably also exhibiting other functions. The search for new inhibitors of MMPs has prompted research towards the development of new solid-state assays for the rapid evaluation of MMP activity. We have already reported the possibility of measuring the activity of MMP-1 anchored on solid support by coupling SPR with ESI-MS analysis. In this work, we show the in situ atmospheric pressure (AP) MALDI-MS characterization of MMPs anchored on a gold chip with known surface coverage. The study extends the MS analysis to different proteins, and sequence coverage is reported for different digestion and MS procedures.

Studies on ternary metallo-beta lactamase-inhibitor complexes using electrospray ionization mass spectrometry

Metallo-beta-lactamases (MBLs) are targets for medicinal chemistry as they mediate bacterial resistance to beta-lactam antibiotics. Electrospray-ionization mass spectrometry (ESI-MS) was used to study the inhibition by a set of mercaptocarboxylates of two representative MBLs with different optimal metal stoichiometries for catalysis. BcII is a dizinc MBL (Class B1), whilst the CphA MBL (Class B2) exhibits highest activity with a single zinc ion in the active site. Experimental parameters for the detection of the metallo-enzyme and the metallo-enzyme-inhibitor complexes were evaluated and optimized. Following investigations on the stoichiometry of metal binding, the affinity of the inhibitors was investigated by measuring the relative abundance of the complex compared to the metalloprotein. The results for the BcII enzyme were in general agreement with solution assays and demonstrated that the inhibitors bind to the dizinc form of the BcII enzyme. The results for the CphA(ZnII) complex unexpectedly revealed an increased affinity for the binding of a second metal ion in the presence of thiomandelic acid. The results demonstrate that direct ESI-MS analysis of enzyme:inhibitor complexes is a viable method for screening inhibitors and for the rapid assay of the enzyme:metal:inhibitor ratios.

Proteomics of Metal Transport and Metal-Associated Diseases

Proteomics technology has the potential to identify groups of proteins that have similar biological function. However, few attempts have been made to identify and characterize metal-binding proteins by using proteomics strategies. Many transition metals are essential to sustain life. Copper, iron, and zinc are the most abundant transition metals relevant to biological systems. In addition to their important biological functions, metals can also catalyze the formation of damaging free radical species. Hence, their intracellular transport is tightly regulated. Despite recent insights into the intracellular transport of copper and other metals, our overall understanding of intracellular metal metabolism remains incomplete and it is likely that many metal-binding proteins remain undiscovered. Furthermore, the protein targets for metals during metal-associated disease states or during exposure to toxic levels of environmental metals are yet to be unravelled. A proteomics strategy for the analysis of metal-transporting or metal-binding proteins has the potential to uncover how a large number of proteins function in normal or metal-associated diseased states. Here we discuss the principal aspects of metal metabolism, and the recent developments in the area of the proteomics of metal transport.

Molecular recognition by mass spectrometry

A recent major advance in the field of mass spectrometry in the biomolecular sciences is represented by the study of the supramolecular interactions among two or more partners in the gas phase. A great deal of chemistry and most of biochemistry concerns molecular interactions taking place in solution. The electrospray technique, which allows direct sampling from solution, and soft ionization of the solute without deposition into the analyte of large amounts of energy, guarantees in many cases the survival of noncovalent bondings and, hence, the direct analysis of the supramolecular complexes present in the condensed phase. The proper preparation of the solution to be studied and also the expert and accurate setting and use of the instrumental parameters are the prerequisites for gaining results as to the specific interactions between, for instance, a protein conformationally modified by its specific metal ion, eventually, and a ligand molecule. The analysis of the charge state of the protein itself and of the modifications of the complex integrity by activating collisions are also methods for studying the biomolecule-molecule interactions. Accordingly, this new mass spectrometric approach to the supramolecular chemistry, which could be also defined as 'supramolecular mass spectrometry', allows the study of ion-protein, protein-protein, protein-ligand and DNA-drug interactions. Chiral recognition can also be performed in the gas phase, studying by electrospray mass spectrometry the fragmentation of diastereomeric complex ions. Not the least, a deep insight can also be obtained into the formation and nature of inclusion complexes like those formed with crown ethers, cyclodextrins and calixarenes as host molecules. All these topics are treated to a certain extent in this special feature article.

Identification of Metal-binding Proteins in Human Hepatoma Lines by Immobilized Metal Affinity Chromatography and Mass Spectrometry

The metalloproteome is defined as the set of proteins that have metal-binding capacity by being metalloproteins or having metal-binding sites. A different metalloproteome may exist for each metal. Mass spectrometric characterization of metalloproteomes provides valuable information relating to cellular disposition of metals physiologically and in metal-associated diseases. We examined the Cu and Zn metalloproteomes in three human hepatoma lines: Hep G2 and Mz-Hep-1, which retain many functional characteristics of normal human hepatocytes, and SK-Hep-1, which is poorly differentiated. Additionally we studied a single specimen of normal human liver and Hep G2 cells depleted in vitro of cellular copper. We used matrix-assisted laser desorption ionization and electrospray ionization quadrupole time-of-flight mass spectrometry to analyze peptide sequences of tryptic digests obtained by either in-gel digestion of metal-binding proteins or peptides on an immobilized metal affinity chromatography column loaded with either Cu or Zn. Mainly high abundance proteins were identified. Cu-binding proteins identified included enolase, albumin, transferrin, and alcohol dehydrogenase as well as certain intracellular chaperone proteins. The Cu metalloproteome was not identical to the Zn metalloproteome. Peptide binding experiments demonstrated that Cu coordination prefers the order of residues histidine > methionine > cysteine. Although the Cu metalloproteome was similar from line to line, subtle differences were apparent. Gel profiling showed more extensive variation in expression of annexin II in SK-Hep-1 and Mz-Hep-1 than in Hep G2 and normal liver tissue. Glycerylphosphorylethanolamine was identified as a post-translational modification at residue Glu-301 of elongation factor 1-alpha in Hep G2. Intracellular copper depletion was associated with loss of the glycerylphosphoryl side group. These findings suggest that post-translational modification could be affected by intracellular actions of copper. Comparison of the Cu and Zn metalloproteomes in Hep G2 with a published general proteome of Hep G2 disclosed little overlap (Seow, T. K., et al. (2001) Proteomics 1, 1249-1263). Proteins in the metalloproteomes of human hepatocytes can be identified by these methods. Variations in these metalloproteomes may have important physiological relevance.

Tandem mass spectrometry of metal nitrate negative ions produced by electrospray ionization

M(NO(3))(x)(-) ions are generated by electrospray ionization (ESI) of metal solutions in nitric acid in negative ion mode. Collision-induced reactions of these ions are monitored in a tandem mass spectrometer (MS) of quadrupole-octopole-quadrupole (QoQ) geometry. For Group 1 and 2 elements, the M(NO(3))(x)(-) ions dissociate into NO(3)(-) and neutral metal nitrate molecules. These elements also form some M(x)(NO(3))x+1- clusters, especially Li(+). Metal nitrate ions from transition elements and Group 13 elements fragment into oxo products and also undergo internal electron transfer to leave the M atom in a lower oxidation state. To calibrate the collision energy, the dissociation energy of O-NO(2)(-) is found to be 5.55 eV, about 0.76 eV lower than a value derived from thermochemistry. The product ions from Fe(NO(3))(4)(-) ions have low formation thresholds of only 0.5 to 2 eV.

Monitoring of unfolding of metallo-proteins by electrospray ionization mass spectrometry

An electrospray ionisation (ESI) mass spectrometric method for the determination of the equilibrium constant and free energy (DeltaG) of protein unfolding was used to monitor the denaturation process at different pH of three metallo-proteins, i.e. wild-type copper azurin, zinc azurin and wild-type amicyanin. The time course of the unfolding process was followed by dissolving the proteins under denaturing conditions (methanol-water (1 : 1, v/v)) at different pH (2.5, 3.0, 3.5) and recording ESI spectra at time intervals. The spectra showed two series of peaks, corresponding to the native holo-protein and the unfolded apo-protein. From the intensity ratio of these two series of peaks at increasing time and at equilibrium, the equilibrium constants for the unfolding process for the three proteins could be determined. From these equilibrium constants a DeltaG degrees derivation was attempted. The DeltaG degrees values obtained decrease with decrease in pH, in agreement with the expected reduction of conformational stability of proteins at lower pH. The results obtained confirm that ESI-MS can be used for monitoring of unfolding process and to derive quantitative thermodynamic data.

Using solution phase hydrogen/deuterium (H/D) exchange to determine the origin of non-covalent complexes observed by electrospray ionization mass spectrometry: in solution or in vacuo?

Electrospray ionization (ESI) is a soft ionization technique that is able to transfer intact ions, as well as solution phase non-covalent complexes into the gas phase. With small molecules that have a high tendency to form hydrogen bonds, the observation of non-covalent complexes by ESI-MS can be the result of a non-specific interaction, due to the nature of the electrospray process. Special precautions and additional steps should be performed to identify the origin of the complexes observed with ESI-MS, and we have utilized solution phase hydrogen/deuterium (H/D) exchange as a method to determine the specificity of the complexes. By comparing the average number of exchanges for the monomer subunits to the average number of exchanges for the complex, one can distinguish if a specific complex is formed in solution. In this paper we have investigated non-covalent complexes of some common chemotherapy agents: paclitaxel, doxorubicin, and etoposide by ESI-MS. By using the solution phase H/D exchange, we were able to identify several specific drug-drug complexes. Thus, solution phase H/D exchange combined with ESI-MS provides for a convenient method in ascertaining the specificity of non-covalent complexes as being formed in solution or in vacuo.

Electrospray ionization of alkali and alkaline earth metal species. Electrochemical oxidation and pH effects

The utility of electrospray ionization mass spectrometry (ESI-MS) for characterizing dissolved metal species has generated considerable interest in the use of this technique for metal speciation. However, the development of accurate speciation methods based on ESI-MS requires a detailed understanding of the mechanisms by which dissolved metal species are ionized during electrospray. We report how the analysis of alkali and alkaline earth metal species provides new information about some of the processes that affect electrospray ion yield. Selected metal ions and organic ligands were combined in 50 : 50 water-acetonitrile buffered with acetic acid or ammonium acetate and analyzed by flow injection ESI-MS using mild electrospray conditions. Species formed by alkali metal ions with thiol and oxygen-donating ligands were detected in acidic and neutral pH solutions. Electrochemical oxidation of N, N-diethyldithiocarbamate and glutathione during electrospray was indicated by detection of the corresponding disulfides as protonated or alkali metal species. The extent of ligand oxidation depended on solution pH and the dissociation constant of the thiol group. Tandem mass spectrometric experiments suggested that radical cations such as [NaL](+.) (where L=N,N-diethyldithiocarbamate) can be generated by in-source fragmentation of disulfide species. Greater complexation of alkali metals at neutral pH was indicated by a corresponding decrease in the relative abundance of the free metal ion. The number of alkali metal ions bound by glutathione and phthalic acid also increased with increasing pH, in accordance with thermodynamic equilibrium theory. Alkaline earth metal species were detected only in acidic solutions, the absence of 8-hydroxyquinoline complexes being attributed to their relative instability and subsequent dissociation during electrospray. Hence, accurate speciation by ESI-MS depends on experimental conditions and the intrinsic properties of each analyte. Copyright 2000 John Wiley & Sons, Ltd.

Noncovalent associations of glutathione S-transferase and ligands: a study using electrospray quadrupole/time-of-flight mass spectrometry

Human glutathione S-transferase A1-1 was observed predominantly as dimeric ions (51 kDa) during electrospray mass spectrometric analysis from aqueous solution at pH 7.4, in keeping with the known dimeric structure in solution. When analyses were performed on solutions of the enzyme containing glutathione (GSH), noncovalent adducts of protein dimer and one or two ligand molecules were observed; each mass increment, which exceeded the mass of GSH alone, was provisionally interpreted to indicate concomitant association of two water molecules per bound GSH. Noncovalent adducts of ligand and protein dimer were similarly observed for oxidized glutathione and for two glutathione inhibitors, both incorporating substituted thiol structures. In these instances, the mass increments exactly matched the ligand masses, suggesting that the apparent concomitant binding of water was associated with the presence in the ligand of a free thiol group. Collisionally activated decomposition during tandem mass spectrometry analyses of noncovalent adducts incorporating protein dimer and ligands yielded initially the denuded dimer; at higher collision energies the monomer and a protein fragment were formed.

Metal-ion binding and limited proteolysis of betabellin 15D, a designed beta-sandwich protein

Betabellin 15D is a 64-residue, disulfide-bridged homodimer. When folded into a beta structure, the protein is predicted to have two clusters of three histidine residues, each cluster able to bind a divalent metal ion. When the protein was incubated with Cu2+, Zn2+, Co2+, or Mn2+, metal complexes of betabellin 15D were observed by electrospray-ionization mass spectrometry. The relative abundances of the ionic complexes suggested an order of affinities of Cu2+ > Zn2+ > Co2+ > Mn2+, consistent with solution-phase affinities for nitrogen- or sulfur-containing ligands. Limited proteolysis of betabellin 15D by immobilized pepsin, as measured by nanoelectrospray-ionization mass spectrometry, showed that the Phe12-Ser13 peptide bond of betabellin 15D was cleaved more slowly in the presence of Cu2+ than in its absence. Because Cu2+ has little or no effect on the catalytic rate of pepsin, the slower cleavage of the Phe12-Ser13 peptide bond may be due to its decreased accessibility caused by Cu(2+)-induced folding of betabellin 15D.

Binding of aldose reductase inhibitors: correlation of crystallographic and mass spectrometric studies

Aldose reductase is a NADP(H)-dependent enzyme, believed to be strongly implicated in the development of degenerative complications of Diabetes Mellitus. The search for specific inhibitors of this enzyme has thus become a major pharmaceutic challenge. In this study, we applied both X-ray crystallography and mass spectrometry to characterize the interactions between aldose reductase and four representative inhibitors: AminoSNM, Imirestat, LCB3071, and IDD384. If crystallography remains obviously the only way to get an extensive description of the contacts between an inhibitor and the enzymatic site, the duration of the crystallographic analysis makes this technique incompatible with high throughput screenings of inhibitors. On the other hand, dissociation experiments monitored by mass spectrometry permitted us to evaluate rapidly the relative gas-phase stabilities of the aldose reductase-inhibitor noncovalent complexes. In our experiments, dissociation in the gas-phase was provoked by increasing the accelerating voltage of the ions (Vc) in the source-analyzer interface region: the Vc value needed to dissociate 50% of the noncovalent complex initially present (Vc50) was taken as a gas-phase stability parameter of the enzyme-inhibitor complex. Interestingly, the Vc50 were found to correlate with the energy of the electrostatic and H-bond interactions involved in the contact aldose reductase/inhibitor (Eel-H), computed from the crystallographic model. This finding may be specially interesting in a context of drug development. Actually, during a drug design optimization phase, the binding of the drug to the target enzyme is often optimized by modifying its interatomic electrostatic and H-bond contacts; because they usually depend on a single atom change on the drug, and are easier to introduce than the hydrophobic interactions. Therefore, the Vc50 may help to monitor the chemical modifications introduced in new inhibitors. X-ray crystallography is clearly needed to get the details of the contacts and to rationalize the design. Nevertheless, once the cycle of chemical modification is engaged, mass spectrometry can be used to select a priori the drug candidates which are worthy of further crystallographic investigation. We thus propose to use the two techniques in a complementary way, to improve the screening of large collections of inhibitors.

Study of FK-binding protein: FK506-metabolite complexes by electrospray mass spectrometry: correlation to immunosuppressive activity

Electrospray ionization mass spectrometry was used to study several non-covalent FK-binding protein (FKBP) immunosuppressant complexes in the gas phase. Relative FKBP binding affinities were determined from the signal ratio for the 7+ charge states of bound and unbound complexes as a function of capillary exit voltage. All complexes displayed a 1:1 binding stoichiometry. The relative gas-phase binding affinities were found to be well correlated with in vitro FKBP binding and in vitro immunosuppression (rapamycin > FK506 > or = 31-demethyl FK506 > 13-demethyl FK506 >> Cyclosporin A; CsA). The method demonstrates potential as a simple, rapid, and automatable technique for prediction of the immunosuppressive activity of FKBP:drug complexes.

Electrospray ionization mass spectrometry: analysis of the Ca2+-binding properties of human recombinant alpha-parvalbumin and nine mutant proteins

A set of 10 different recombinant human parvalbumins was used to establish a method for the investigation of the Ca2+-binding properties of proteins by electrospray ionization mass spectrometry (ESI-MS). Human PVWT was found to bind 2 mol Ca2+ ions/mol of protein, whereas its mutants (PVE101V, PVD90A, PVE62V, PVD51A, PVD90A,E101V, PVE62V,E101V, PVD51A,D90A, PVD51A,E62V, PVD51A,E62V, D90A,E101V) containing inactivating substitutions in the Ca2+-binding loops bind 0 or 1 Ca2+ ion per protein molecule, depending on the degree of inactivation. These findings fully agree with previously reported results obtained by flow dialysis experiments. The RP-HPLC desalted metal-free proteins were analyzed in 10 mM ammonium acetate at pH 7.0. The experimental conditions were optimized with the recombinant parvalbumin test system before analyzing the Ca2+-binding properties of rat and murine parvalbumins in muscle tissue extracts. ESI-MS revealed that (i) rat and murine alpha-parvalbumins each bind specifically two Ca2+ ions per protein molecule and (ii) both extracted parvalbumins were found to be posttranslationally modified; each protein is acetylated at the N-terminus. Finally, during our investigations of the murine parvalbumin a sequencing error was detected at the C-terminus where the amino acid at position 109 is Ser and not Thr as mentioned in the SwissProt data base (Accession No. P32848). This work demonstrates the great potential of the ESI-MS technique as a sensitive, specific, and rapid method for direct identification and determination of the stoichiometry of Ca2+-binding proteins and other metalloproteins.

High-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase determined by multidimensional NMR

The high-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase (MMP-1), a protein of 18.7 kDa, which is a member of the matrix metalloproteinase family, has been determined using three-dimensional heteronuclear NMR spectroscopy. A total of 30 structures were calculated by means of hybrid distance geometry-simulated annealing using a total of 3333 experimental NMR restraints, consisting of 2409 approximate interproton distance restraints, 84 distance restraints for 42 backbone hydrogen bonds, 426 torsion angle restraints, 125 3JNH alpha restraints, 153 C alpha restraints, and 136 C beta restraints. The atomic rms distribution about the mean coordinate positions for the 30 structures for residues 7-137 and 145-163 is 0.42 +/- 0.04 A for the backbone atoms, 0.80 +/- 0.04 A for all atoms, and 0.50 +/- 0.03 A for all atoms excluding disordered side chains. The overall structure of MMP-1 is composed of a beta-sheet consisting of five beta-strands in a mixed parallel and anti-parallel arrangement and three alpha-helices. A best-fit superposition of the NMR structure of inhibitor-free MMP-1 with the 1.56 A resolution X-ray structure by Spurlino et al. [Spurlino, J. C., Smallwood, A. M., Carlton, D. D., Banks, T. M., Vavra, K. J., Johnson, J. S., Cook, E. R., Falvo, J., and Wahl, R. C., et al. (1994) Proteins: Struct., Funct., Genet. 19, 98-109] complexed with a hydroxamate inhibitor yields a backbone atomic rms difference of 1.22 A. The majority of differences between the NMR and X-ray structure occur in the vicinity of the active site for MMP-1. This includes an increase in mobility for residues 138-144 and a displacement for the Ca(2+)-loop (residues 74-80). Distinct differences were observed for side-chain torsion angles, in particular, the chi 1 for N80 is -60 degrees in the NMR structure compared to 180 degrees in the X-ray. This results in the side chain of N80 occupying and partially blocking access to the active site of MMP-1.

Dissociation of heme-globin complexes by blackbody infrared radiative dissociation: molecular specificity in the gas phase?

The temperature dependence of the unimolecular kinetics for dissociation of the heme group from holo-myoglobin (Mb) and holo-hemoglobin alpha-chain (Hb-alpha) was investigated with blackbody infrared radiative dissociation (BIRD). The rate constant for dissociation of the 9 + charge state of Mb formed by electrospray ionization from a "pseudo-native" solution is 60% lower than that of Hb-alpha at each of the temperatures investigated. In solutions of pH 5.5-8.0, the thermal dissociation rate for Mb is also lower than that of HB-alpha (Hargrove, M. S. et al. J. Biol. Chem.1994, 269, 4207-4214). Thus, Mb is thermally more stable with respect to heme loss than Hb-alpha both in the gas phase and in solution. The Arrhenius activation parameters for both dissociation processes are indistinguishable within the current experimental error (activation energy 0.9 eV and pre-exponential factor of 10(8-10) s(-1)). The 9+ to 12+ charge states of Mb have similar Arrhenius parameters when these ions are formed from pseudo-native solutions. In contrast, the activation energies and pre-exponential factors decrease from 0.8 to 0.3 eV and 10(7) to 10(2) s(-1), respectively, for the 9 + to 12 + charge states formed from acidified solutions in which at least 50% of the secondary structure is lost. These results demonstrate that gas-phase Mb ions retain clear memory of the composition of the solution from which they are formed and that these differences can be probed by BIRD.

Study of non-covalent enzyme-inhibitor complexes of aldose reductase by electrospray mass spectrometry

Specific non-covalent interactions between aldose reductase (AR), its NADP+ cofactor and five inhibitors have been characterized by electrospray mass spectrometry (ES-MS). These results indicated that the protein could be desorbed and maintained in the gas phase in a form very close to its native conformation. Collisionally induced dissociation (CID)-MS and CID-MS-MS showed that the adenosine diphosphate part of the cofactor interacts strongly with AR. The relative stability of the ternary AR x NADP+ x inhibitor complexes was established and successfully correlated with the IC50 values. All inhibitors were shown to only bind to AR holoenzyme. These results are important for the field of drug development insofar as ES-MS might provide a rapid and very sensitive method for the screening of potential drugs or for the identification of compounds displaying high binding affinity to a target biomolecule.

Studying noncovalent protein complexes by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry has been used to study protein interactions driven by noncovalent forces. The gentleness of the electrospray ionization process allows intact protein complexes to be directly detected by mass spectrometry. Evidence from the growing body of literature suggests that the ESI-MS observations for these weakly bound systems reflect, to some extent, the nature of the interaction found in the condensed phase. Stoichiometry of the complex can be easily obtained from the resulting mass spectrum because the molecular weight of the complex is directly measured. For the study of protein interactions, ESI-MS is complementary to other biophysical methods, such as NMR and analytical ultracentrifugation. However, mass spectrometry offers advantages in speed and sensitivity. The experimental variables that play a role in the outcome of ESI-MS studies of noncovalently bound complexes are reviewed. Several applications of ESI-MS are discussed, including protein interactions with metal ions and nucleic acids and subunit protein structures (quaternary structure).

Metal and pH dependence of heptapeptide catalysis by human matrilysin

Human matrilysin devoid of its propeptide is expressed in Escherichia coli and purified to homogeneity by heparin chromatography after refolding of the guanidine hydrochloride solubilized protein. Matrilysin autolytically removes its N-terminal tripeptide Met-Tyr-Ser during the refolding process. The enzyme contains 1.91 +/- 0.08 zinc atoms/mol of protein and retains full activity when stored several months at 4 degrees C. It hydrolyzes the fluorescent substrate Dns-PLALWAR at the Ala-Leu bond with a kcat of 3.1 s-1 and K(m) of 1.8 x 10(-5) M at pH 7.5, 37 degrees C, values closely similar to those for the matrilysin produced by activation of the Chinese hamster ovary and E. coli-expressed promatrilysin. The properties of this form of matrilysin demonstrate that the propeptide is not essential for proper folding or stability of the enzyme but likely determines the N-terminal amino acid of the mature enzyme. The pH dependence of kcat/K(m) for Dns-PLALWAR shows that matrilysin has a broad pH optimum (5.0-9.0) and the pKa values obtained are 4.3 and 9.6 at 25 degrees C. The activity is inhibited by several metal binding agents including 1, 10-phenanthroline, OP, but not by the nonchelating isomer, 1,7-phenanthroline. OP inhibits instantaneously by likely forming a transient ternary enzyme.metal.chelator complex. The zinc atom is then removed from the protein in a time-dependent manner. In agreement with the kinetic studies, dialysis in the presence of OP and CaCl2 removes only the catalytic zinc atom. The monozinc enzyme can be reactivated to 90%, 56%, 27%, and 17% of the native activity by addition of zinc, manganese, nickel, and cobalt, respectively. Cadmium, on the other hand, forms an inactive Cd/Zn hybrid. The differences in the chelator accessibility properties of the two zinc sites can thus be exploited to yield metallohybrids of matrilysin.