Free energy for blue copper protein unfolding determined by electrospray ionisation mass spectrometry

Relaxation of structural constraints during Amicyanin unfolding

We study the thermal unfolding of amicyanin by quantifying the resiliency of the native state to structural perturbations. Three signatures characterizing stages of unfolding are identified. The first signature, lateral extension of the polypeptide chain, is calculated directly from the reported crystallographic data. Two other signatures, the radial displacement of each residue from Cu(II) and the angular spread in the chain as the protein unfolds, are calculated using crystallographic data in concert with a geometrical model we introduced previously (J.J. Kozak, H. B. Gray, R. A. Garza-López, J. Inorg. Biochem. 155(2016) 44-55). Particular attention is paid to the resiliency of the two beta sheets in amicyanin. The resiliency of residues in the near neighborhood of the Cu center to destabilization provides information on the persistence of the entatic state. Similarly, examining the resiliency of residues intercalated between structured regions (beta sheets, the alpha helix) provides a basis for identifying a "hydrophobic core." A principal focus of our study is to compare results obtained using our geometrical model with the experimental results (C. La Rosa, D. Milardi, D. M. Grasso, M. P. Verbeet, G. W. Canters, L. Sportelli, R. Guzzi, Eur. Biophy. J.30(8),(2002) 559-570) on the denaturation of amicyanin, and we show that our results support a classical model proposed by these authors.

Stabilization of protein structure through π-π interaction in the second coordination sphere of pseudoazurin

Noncovalent, weak interactions in the second coordination sphere of the copper active site of Pseudoazurin (PAz) from Achromobacter cycloclastes were examined using a series of Met16X variants. In this study, the differences in protein stability due to the changes in the nature of the 16th amino acid (Met, Phe, Val, Ile) were investigated by electrospray ionization mass spectrometry (ESI-MS) and far-UV circular dichroism (CD) as a result of acid denaturation. The percentage of native states (folded holo forms) of Met16Phe variants was estimated to be 75% at pH 2.9 although the wild-type (WT), Met16Val and Met16Ile PAz, became completely unfolded. The high stability under acidic conditions is correlated with the result of the active site being stabilized by the aromatic substitution of the Met16 residue. The π-π interaction in the second coordination sphere makes a significant contribution to the stability of active site and the protein matrix.

Characterization of Arabidopsis thaliana stellacyanin: A comparison with umecyanin

The cupredoxin domain of a putative type 1 blue copper protein (BCB) from Arabidopsis thaliana was overexpressed and purified. A recursive polymerase chain reaction method was used to synthesize an artificial coding region for the cupredoxin domain of horseradish stellacyanin (commonly known as umecyanin), prior to overexpression and purification. The recombinant proteins were refolded from inclusion bodies and reconstituted with copper, and their in vitro characteristics were studied. Recombinant umecyanin, which is nonglycosylated, has identical spectroscopic and redox properties to the native protein. The UV/Vis and EPR spectra of recombinant BCB and umecyanin demonstrate that they have comparable axial type 1 copper binding sites. Paramagnetic (1)H NMR spectroscopy highlights the similarity between the active site architectures of BCB and umecyanin. The reduction potential of recombinant BCB is 252 mV, compared to 293 mV for recombinant umecyanin. Identical pK(a) values of 9.7 are obtained for the alkaline transitions in both proteins. This study demonstrates that BCB is the A. thaliana stellacyanin and the results form the biochemical basis for a discussion of BCB function in the model vascular plant.

Development of new methodologies for the mass spectrometry study of bioorganic macromolecules

In recent years, mass spectrometry has been increasingly used for the analysis of various macromolecules of biological, biomedical, and biochemical interest. This increase has been made possible by two key developments: the advent of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) sources. The two new techniques produce a significant increase in mass range and in sensitivity that led to the development of new applications and of new analyzer designs, software, and robotics. This review, apart from the description of the status of mass spectrometry in the analysis of bioorganic macromolecules, is mainly devoted to the illustration of the more recent promising techniques and on their possible future evolution.

On-chip protein sample desalting and preparation for direct coupling with electrospray ionization mass spectrometry

A membrane-based desalting step integrated in a MS microchip is presented: drugs, peptides and proteins are adsorbed on a hydrophobic poly(vinylidene difluoride) membrane, which allows the washing out of salts. The integration with microfluidics permits a controlled elution of analytes from the membrane and their direct mass spectrometric analysis by electrospray ionisation MS. The desalting process is demonstrated with picomole amounts of propanolol, insulin and cytochrome c. Moreover, this stop-and-go desalting process is tolerant to high concentrations of urea, and to the presence of reductants such as dithiothreitol. This particular feature allowed the chemical tagging of cysteines in beta-lactoglobulin A with iodoacetamide. Finally, the integration of chemical tagging, on-chip desalting and MS microchip paves the way for the development of high-throughput analytical procedure for structural proteomics.

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.

Surface-activated no-discharge atmospheric pressure chemical ionization

A new ionization method named surface-activated chemical ionization (SACI) has been realized. In this invention a commercially available atmospheric pressure chemical ionization (APCI) chamber, employed without any corona discharge (no-discharge APCI), has been modified with the insertion of a gold surface, leading to a significant improvement in the ionization efficiency. The ionization of the sample takes place by both gas-phase and surface-activated processes. This new ionization source is able to generate ions with high molecular mass and low charge states, leading to improved sensitivity and reduced noise. The new device has been tested in the analysis of some peptides. A comparison between the performance with and without the presence of the surface, and the optimization of the operating conditions (nebulizing gas flow, sample solution flow, pH of solution, and surface area), are reported and discussed.

Analysis of peptides using partial (no discharge) atmospheric pressure chemical ionization conditions with ion trap mass spectrometry

A novel approach, based on the use of atmospheric pressure chemical ionization ion trap mass spectrometry (APCI-ITMS) conditions, but without using corona discharge, was used to analyze peptides. The proposed method was applied to three standard peptides (bombesin, trityrosine and tyrosine-glycine-glycine) as well as peptides obtained through enzymatic digestion of two standard proteins (horse cytochrome c and horse myoglobin).

Analysis of protein ions in the range 3000-12000 Th under partial (no discharge) atmospheric pressure chemical ionization conditions using ion trap mass spectrometry

A new approach, based on the use of atmospheric pressure chemical ionization ion trap mass spectrometry (APCI-ITMS), but without a corona discharge, was investigated for application to creating and monitoring protein ions. It must be emphasized that APCI is not usually used in protein analysis. In order to verify the applicability of the proposed method to the analysis of proteins, two standard proteins (horse cytochrome c and horse myoglobin) were analyzed. A mixture of the two proteins was also analyzed showing that this novel approach, based on the use of APCI, can be used in the analysis of protein mixtures.