Functional characterization of permuted enhanced green fluorescent proteins comprising varying linker peptides

New variants of green fluorescent protein (GFP) can be engineered by circular permutation of their amino acid sequence. We characterized a series of permuted enhanced GFP (PEGFP) with new termini introduced at N144-Y145 and linkers of 1, 3, 5 and 6 residues inserted between G232 and M1, as well as a variant with an extended 7-residues linker between K238 and M1. A minimum linker length of 3 residues was necessary for a functional chromophore to be formed, and linkers exceeding 4 residues yielded almost the same fluorescence quantum yield as enhanced GFP (EGFP). PEGFP exhibited dual-wavelength absorption and fluorescence excitation with peaks at 395 and 490 nm but single-wavelength emission at 512 nm. Fluorescence emission increased with increasing pH for all excitation wavelengths with a pKa of 7.7. Between the pH values of 6 and 8 optical absorption showed an isobestic point at 445 nm. PEGFP rapidly denatured in urea between 50 and 60 degrees C. Renaturation proceeded with a short (approximately 29 s) and a longer (> 150 s) time constant. Transient transfection of HEK293 and HeLa cells revealed the expression dynamics of PEGFP to be similar to that of EGFP. Laser-scanning microscopy of HeLa cells demonstrated that the PEGFP are particularly well suited as fluorescent indicators in two-photon imaging.     

Factors that influence the observed fast fragmentation of peptides in matrix-assisted laser desorption

Fragmentation processes that occur very early during matrix-assisted laser desorption ionization (MALDI) of peptides are examined by utilization of delayed pulsed ion extraction with a linear time-of-flight mass spectrometer. The oxidized B chain of bovine insulin (MW=3495. 95 u), which produces a wide range of fragment ions, is utilized as a probe to examine the effects of several experimental parameters on this process. Experimental evidence suggests that this MALDI process is not prompt fragmentation and involves metastable ion decay that is quite different from that which is observed with postsource decay experiments. This conclusion is based upon the significant differences observed in the fragmentation products produced by the two techniques. This metastable ion decay process also appears to be over within the minimum pulse delay period (320 ns) that is possible with the current pulsed ion extraction hardware. These two observations suggest that either different activation processes are involved in the two techniques or that the much different time frame of the methods influences the observed ion decay pathways. This fast MALDI metastable ion fragmentation also is shown to be influenced by both the MALDI matrix and the laser fluence.     

Energy-dependent kinetic method: application to the multicompetitive fragmentation pathways of protonated peptides

A variation of the kinetic method for the analysis of fragmentation patterns in mass spectra is proposed. The procedure presents three notable features: no evaluation of the effective temperature of the parent ion is required; the ratio of the activation energies for all competitive channels at play are provided; and the measurement is not biased by the mass discrimination of the instrument. The method is based on the analysis of mass spectra recorded as a function of both the excitation energy and the excitation time. Collision-activated dissociation of protonated Leu-enkephalin achieved in a quadrupolar ion trap and analyzed with this method is presented.     

A polyamine coating for enhanced capillary electrophoresis-electrospray ionization-mass spectrometry of proteins and peptides

A procedure for enhanced capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) of proteins is presented. The use of a newly presented capillary coating, PolyE-323, provided fast separations of typically a few minutes with high efficiency, good deactivation, and no bleeding into the mass spectrometer. Capillaries coated with PolyE-323 showed high stability over a range of pH 2-10, and tolerance towards methanol and acetonitrile, two modifiers commonly used in CE-ESI-MS. Due to the speed and simplicity of the coating procedure, the polymeric surface could, if necessary, easily be regenerated. This capability is especially valuable when working with samples of complex matrix, where a capillary surface cleaning step might be desired in order to eliminate possible memory effects. The potential of PolyE-323-coated capillaries in bioanalysis using CE-ESI-MS was demonstrated by analyzing peptides and proteins up to 66 kDa using time of flight (TOF)-MS. Due to the stable, anodal electroosmotic flow generated by the coating, the use of a sheathless ESI interface was enabled, demonstrated in peptide analysis with attomole sensitivity. The fast on-line CE-ESI-TOF system using PolyE-323-coated capillaries provided efficient separation and detection of a large number of peaks in a short time, exemplified by the analysis of a tryptic digest of bovine serum albumin (BSA). The capability of the developed capillary surface coating was demonstrated by the separation of human plasma and cerebrospinal fluid (CSF).     

Analytical methods for the characterization of proteins and peptides in wines

Although proteins and peptides are minor constituents of wine, they make a significant contribution to its quality. Proteins can cause a number of technological problems during vinification and may be responsible for the appearance of turbidity in bottled wine. Peptides exhibit surfactant and sensory properties that can influence the organoleptic characteristics of wine. These reasons make protein and peptide analysis a necessity. In this paper, some of the applications in sample preparation, electrophoretic and chromatographic analysis, and detection of proteins and peptides in wine are examined. Special attention is paid to the methodologies that the authors have used in previously published studies, in some cases developed by them, and in other cases taken from the literature and used routinely in their laboratory.     

Structural characterization of intact antibodies by high‐resolution LTQ Orbitrap mass spectrometry

Recombinant monoclonal antibodies (MAbs) can be heterogeneous due to modifications that can occur during expression, purification or during storage. These large multichain proteins (～150 kDa) are structurally challenging for detailed characterization to identify the sites of modifications. We report the use of LTQ Orbitrap mass spectrometry to accurately measure the average masses of individual glycoforms by direct infusion of an intact antibody. To identify the site‐specific modification of methionines in the antibody caused by forced oxidation, we used a ‘middle‐down’ approach. The antibody was subjected to limited digestion using the endoproteinase Lys‐C and reduced to generate Fab heavy chain, single chain Fc and light chain fragments (～25 kDa each). These species were subjected to on‐line liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS) analysis using an LTQ Orbitrap, where these large precursors were dissociated by higher‐energy collisions in the C‐trap. High resolution and accuracy achieved for resulting fragments allowed us to show in a site‐specific manner that only the methionines in the Fc heavy chain were oxidized under the studied conditions. Copyright © 2009 John Wiley & Sons, Ltd.     

Mass spectrometric characterization of lipid-modified peptides for the analysis of acylated proteins

The analysis of acylated proteins by mass spectrometry (MS) has largely been overshadowed in proteomics by the analysis of glycosylated and phosphorylated proteins; however, lipid modifications on proteins are proving to be of increasing importance in biomedical research. In order to identify the marker ions and/or neutral loss fragments that are produced upon collision-induced dissociation, providing a means to identify the common lipid modifications on proteins, peptides containing an N-terminally myristoylated glycine, a palmitoylated cysteine and a farnesylated cysteine were chemically synthesized. Matrix-assisted laser desorption/ionization time-of-flight time-of-flight (MALDI-TOF-TOF), electrospray ionization quadrupole time-of-flight (ESI Q-TOF), and electrospray ionization hybrid triple-quadrupole/linear ion trap (ESI QqQ(LIT)) mass spectrometers were used for the analysis. The peptide containing the N-terminally myristoylated glycine, upon CID, produced the characteristic fragments a1 (240.4 Th) and b1 (268.4 Th) ions as well as a low-intensity neutral loss of 210 Da (C14H26O). The peptides containing a farnesylated cysteine residue fragmented to produce a marker ion at a m/z of 205 Th (C15H25) as well as other intense farnesyl fragment ions, and a neutral loss of 204 Da (C15H24). The peptides containing a palmitoylated cysteine moiety generated neutral losses of 238 Da (C16H30O) and 272 Da (C16H32OS); however, no marker ions were produced. The neutral losses were more prominent in the MALDI-TOF-TOF spectra, whereas the marker ions were more abundant in the ESI QqQ(LIT) and Q-TOF mass spectra.     

Rapid mass spectral identification of contryphans. Detection of characteristic peptide ions by fragmentation of intact disulfide-bonded peptides in crude venom

The mass spectrometric cleavage of intact disulfide-bonded peptides in conus venom has been investigated. Contryphans containing a single disulfide bond are shown to fragment preferentially at X-Pro bonds, giving rise to linearized, unsymmetrical cystine peptides, which subsequently fragment by multiple pathways at the disulfide bridge. Cleavage at the disulfide bond can be initiated by initial loss of the CalphaH or CbetaH proton, resulting in distinct product ions, with the subsequent loss of elemental sulfur, H2S or H2S2. Contryphans from Conus amadis, Conus loroisii, and Conus striatus are presented as examples, in which detailed assignment of the product ions resulting from tandem mass spectrometric analysis of the intact disulfide is also accomplished. Characteristic fragments arising from conserved contryphan sequences can be used as diagnostic, permitting rapid identification of this class of peptides in crude venom. The observed fragment ions obtained for contryphans in diverse cone snail species are also compared.     

Fast atom bombardment mass spectrometry of Mycobacterial glycopeptidolipid antigens: Structural characterization by charge remote fragmentation

Mycobacteria contain species- and type-specific antigens. Among them, glycopeptidolipids are present in medically relevant organisms belonging to Mycobacterium avium or M. fortuitum complexes. Fast-a tom bombardment mass spectrometry of glycopeptidolipids has proven to be difficult. In this article the cationization method with a metanitrobenzyl alcohol matrix, doped with sodium iodide, is described for analyzing these molecules. The molecular weight of the intact glycopeptidolipids was successfully determined and, using mass-analyzed ion kinetic energy spectrometry, the complete sequences of the peptide and saccharide moieties were elucidated. Moreover, the two structural variants present in these molecules were clearly differentiated. Application of the method showed that the same structural variant occurs in the glycopeptidolipids from two serologically related species of the M. fortuitum complex.     

A new method for rapid characterization of the folding pathways of multidisulfide-containing proteins

Oxidative folding is a composite process that consists of both the conformational folding to the native three-dimensional structure and the regeneration of the native disulfide bonds of a protein, frequently involving over 100 disulfide intermediate species. Understanding the oxidative folding pathways of a multiple-disulfide-containing protein is a very difficult task that often requires years of devoted research due to the high complexity of the process and the very similar features of the large number of intermediates. Here we developed a method for rapidly delineating the major features of the oxidative folding pathways of a protein. The method examines the temperature dependence of the oxidative folding rate of the protein in combination with reduction pulses. Reduction pulses expose the presence of structured intermediates along the pathways. The correlation between the regeneration rate at different temperatures and the stability of the structured intermediates reveals the role that the intermediates play in determining the pathway. The method was first tested with bovine pancreatic ribonuclease A whose folding pathways were defined earlier. Then, it was explored to discern some of the major features of the folding pathways of its homologue, frog Onconase. The results suggest that the stability of the three-dimensional structure of the native protein is a major determinant of the folding rate in oxidative folding.     

Influence of a 4-aminomethylbenzoic acid residue on competitive fragmentation pathways during collision-induced dissociation of metal-cationized peptides

Formation of [bn+17+cat]+ is a prominent collision-induced dissociation (CID) pathway for Li+- and Na+-cationized peptides. Dissociation of protonated and Ag+-cationized peptides instead favors formation of the rival bn+/[bn-1+cat]+ species. In this study the influence of a 4-aminomethylbenzoic acid (4AMBz) residue on the relative intensities of [b(3)-1+cat]+ and [b(3)+17+cat]+ fragment ions was investigated using several model tetrapeptides including those with the general formula A(4AMBz)AX and A(4AMBz)GX (where X=G, A, V). For Li+- and Na+-cationized versions of the peptides there was a significant increase in the intensity of [b(3)-1+cat]+ for the peptides that contain the 4AMBz residue, and in some cases the complete elimination of the [b(3)+17+cat]+ pathway. The influence of the 4AMBz residue may be attributed to the fact that [b(3)-1+cat]+ would be a highly conjugated species containing an aromatic ring substituent. Comparison of CID profiles generated from Na+-cationized AAGV and A(4AMBz)GV suggests an apparent decrease in the critical energy for generation of [b(3)-1+Na]+ relative to that of [b(3)+17+Na]+ when the aromatic amino acid occupies a position such that it leads to the formation of the highly conjugated oxazolinone, thus leading to an increase in formation rate for the former compared to the latter.     

Structural characterization of flexible proteins using small-angle X-ray scattering

Structural analysis of flexible macromolecular systems such as intrinsically disordered or multidomain proteins with flexible linkers is a difficult task as high-resolution techniques are barely applicable. A new approach, ensemble optimization method (EOM), is proposed to quantitatively characterize flexible proteins in solution using small-angle X-ray scattering (SAXS). The flexibility is taken into account by allowing for the coexistence of different conformations of the protein contributing to the experimental scattering pattern. These conformers are selected using a genetic algorithm from a pool containing a large number of randomly generated models covering the protein configurational space. Quantitative criteria are developed to analyze the EOM selected models and to determine the optimum number of conformers in the ensemble. Simultaneous fitting of multiple scattering patterns from deletion mutants, if available, provides yet more detailed local information about the structure. The efficiency of EOM is demonstrated in model and practical examples on completely or partially unfolded proteins and on multidomain proteins interconnected by linkers. In the latter case, EOM is able to distinguish between rigid and flexible proteins and to directly assess the interdomain contacts.     

Structural analysis of biologically active peptides and recombinant proteins and their modified counterparts by mass spectrometry

The structural characterization of the Escherichia coli-expressed human interferon alpha-2b (rh-IFN alpha-2b) was carried out by employing the fast atom bombardment (FAB) and plasma desorption (PD) mapping methods. The mass spectral data of the rh-IFN alpha-2b and the trypsin-generated peptide mixture allowed rapid and facile confirmation of the cDNA-derived sequence and determination of the existing disulfide pattern in the protein molecule. The same PD/FAB mapping approach was successfully employed in the structural determination of the iodination reaction product of rh-IFN alpha-2b and the potent vasoconstrictor peptide endothelin.     

Mass spectrometric evidence for mechanisms of fragmentation of charge-derivatized peptides

Mass spectrometry of charged derivatives of peptides has been a growing area of interest in the past decade. Fragmentation of charged derivatives of peptides is believed to be different from than that of protonated peptides when analyzed by collisionally activated dissociation-tandem mass spectrometry (CAD-MS/MS). The charged derivatives fragment by charge-remote fragmentation mechanisms, which are usually classified as high-energy (HE)-CAD processes. Our objective in the present study is to investigate the mechanism of fragmentation of charged derivatives of peptides when analyzed by matrix-assisted laser desorption/ionization-postsource decay-mass spectrometry (MALDI-PSD-MS) and electrospray ionization (ESI)-CAD-MS/MS (ion trap), which involve low-energy processes. Three major types of hydrogens (alpha, beta, and amide) are available for migration during the formation of the *a(n) ions (the predominant ion series produced from these charged derivatives). To pinpoint which of the three hydrogens is involved in the formation of the *a(n) ions, deuterium-labeled peptide derivatives with labels at specific sites were synthesized and analyzed by MALDI-PSD-MS and ESI-CAD-MS/MS. Our results suggest that the amide hydrogen of the residue at which the cleavage occurs shifts during the formation of *a(n); this observation serves as evidence for the mechanism proposed earlier by Liao et al. for fragmentation of such charged derivatives. The results also help elucidate the structure of the *a(n) ions, *b(n) ions, and others formed during cleavage at the proline residue, as well as the ions formed during loss of the C-terminal residue from these charged derivatives.     

Identification of phosphorylcholine substituted peptides by their characteristic mass spectrometric fragmentation

Phosphorylcholine (PC) substituted biomolecules are wide-spread, highly relevant antigens of parasites, since this small hapten has been found to be a potent immunomodulatory component which allows the establishment of long lasting infections of the host. Structural data, especially of protein bound PC-substituents, are still rare due to the observation that mass spectrometric analyses are mostly hampered by this zwitterionic substituent resulting in low sensitivities and unusual but characteristic fragmentation patterns. Here we investigated the fragmentation behaviour of synthetic PC-substituted peptides by matrix-assisted laser desorption/ionization mass spectrometry and electrospray ionization ion trap mass spectrometry. We could show that the predominant neutral loss of a trimethylamine unit (Hoffmann elimination) leads to cyclic phosphate derivatives which prevent further fragmentation of the peptide backbone by stabilizing the positive charge at this particular side chain. Knowledge of this PC-specific fragmentation might help to identify PC-substituted biomolecules and facilitate their structural analysis.     

Theoretical study of the main fragmentation pathways for protonated glycylglycine

Quantum chemical and RRKM calculations were carried out on protonated glycylglycine in order to determine the atomic details of the main fragmentation pathways leading to formation of a1 and y1 ions. Two possible mechanisms were considered. The first path results in elimination of aziridinone as a neutral counterpart of the y1 ion formed. Our calculations show that this pathway has a relatively high threshold energy (48.6 kcal/mol) and the corresponding unimolecular rate constants are quite small even at large internal energy. An alternative pathway (a1-y1) proposed in the present paper seems, however, to be favored against the above 'aziridinone' one from the points of view of both energetics and kinetics. The 'a1-y1' pathway leads to simultaneous formation of a1 and y1 ions, the ratio of which depends on the energy distribution of the fragmenting species for a particular dipeptide. However, even if y1 ions are formed via the 'a1-y1' pathway, the corresponding neutrals eliminated do not have a strained cyclic aziridinone structure. Instead, in a two-step process, CO and NHCH2 are formed leading to neutral products energetically more favored than aziridinone. The available experimental data reevaluated in the present paper lend support to the 'a1-y1' pathway.     

Improved mass analysis of intact proteins by ion trap instrument on a chromatographic time scale via data-dependant enhanced resolution scan

Analyzing highly charged protein ions by ion trap instruments has been hindered by the low resolving power and the space charge effect. To improve mass resolution, the resonant ejection scan rate was often decreased, causing long cycle time that was not compatible with a chromatographic time scale. We described a new method that allowed the acquisition of high-resolution protein mass spectra on a chromatography time scale. The method was based on the data-dependant enhanced resolution scan (DDER) function of the triple quadrupole linear ion trap (Q Trap). We demonstrated the effectiveness of the method by analyzing liquid chromatography-resolved polypeptide components of a monoclonal antibody. The results showed that DDER-derived spectra significantly improved the resolution and accuracy for deconvoluted mass. Our approach would extend the utilities of ion trap instruments in protein analysis.     

The attempted synthesis of open-chain asymmetric cystine peptides by thio-induced fragmentation of sulfonyl thiocarbonates. Insulin fragments with intact disulfide bridges A20-B19

The thiol-induced fragmentations of sulfenyl thiocarbonates (R? S? S? CO? OCH₃) leading to mixed disulfides was applied to the synthesis of open-chain asymmetrical cystine peptides. Various fragments of insulin containing the disulfide bridge between A²⁰ and B¹⁹ were prepared by this method.     

Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy

The use of a short, three-residue Cu(2+)-binding sequence, the ATCUN motif, is presented as an approach for extracting long-range distance restraints from relaxation enhancement NMR spectroscopy. The ATCUN motif is prepended to the N-termini of proteins and binds Cu(2+) with a very high affinity. Relaxation rates of amide protons in ATCUN-tagged protein in the presence and absence of Cu(2+) can be converted into distance restraints and used for structure refinement by using a new routine, PMAG, that has been written for the structure calculation program CNS. The utility of the approach is demonstrated with an application to ATCUN-tagged ubiquitin. Excellent agreement between measured relaxation rates and those calculated on the basis of the X-ray structure of the protein have been obtained.