Structural changes of ultrasonicated bovine serum albumin revealed by hydrogen–deuterium exchange and mass spectrometry

The structural changes of bovine serum albumin (BSA) under high-intensity ultrasonication were investigated by fluorescence spectroscopy and mass spectrometry. Evidence for the ultrasonication-induced conformational changes of BSA was provided by the intensity changes and maximum-wavelength shift in fluorescence spectrometry. Matrix-assisted laser desorption–ionization time-of-flight mass spectroscopy (MALDI-TOF MS) revealed the increased intensity of the peak at the charge state +5 and a newly emerged peak at charge state +6, indicating that the protein became unfolded after ultrasonication. Prevalent unfolding of BSA after ultrasonication was revealed by hydrogen–deuterium exchange coupled with mass spectrometry (HDX-MS). Increased intensity and duration of ultrasonication further promoted the unfolding of the protein. The unfolding induced by ultrasonication goes through an intermediate state similar to that induced by a low concentration of denaturant.     

Three-pulse photon echo peak shift spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding

We investigate the equilibrium unfolding of Zn-cytochrome c in guanidine hydrochloride by three-pulse photon echo peak shift (3PEPS) spectroscopy. Unexpectedly, the measurements reveal that inhomogeneous broadening of the sample at the midpoint of the denaturation is larger than that of either native or unfolded states. To interpret this finding, we present simulations of the peak shift for both two-state and three-state unfolding models. Both the denaturant concentration dependence of the asymptotic peak shift (APS) and the wavelength dependence of the APS at the midpoint of the denaturation are different for the two models. Our data are consistent with two-state unfolding.     

Identification of non-covalent structure in apocytochrome c by hydrogen exchange and mass spectrometry

Apocytochrome c, the in vivo precursor to active cytochrome c, was analyzed by amide hydrogen exchange and mass spectrometry to search for fixed, non-covalent structure. The protein was incubated in H(2)O at pH 3.3 or 6.7 for various times, then exposed to D(2)O to initiate isotope labeling of unfolded regions. Following acid quenching of hydrogen exchange, the labeled apocytochrome c was digested with pepsin into fragments that were analyzed by directly coupled high-performance liquid chromatography/electrospray ionization mass spectrometry. The intermolecular distribution of deuterium and the deuterium levels in structurally distinctive populations were determined from the mass spectra of the peptic fragments. Spectra of peptic fragments derived from apocytochrome c incubated at pH 3.3 had single envelopes of isotope peaks with masses indicating that all of the amide hydrogens had been replaced with deuterium. These results showed that apocytochrome c at pH 3.3 offered little resistance to hydrogen exchange, indicating that it was unfolded with little fixed structure. However, mass spectra of peptic fragments including residues 81-94 of apocytochrome c incubated at pH 6.7 had two envelopes of isotope peaks, indicating that one population was unfolded and the other population was highly structured in this region. Mass spectra of peptic fragments including residues N-terminal to residue 81 indicated that this region of the protein remained unfolded with little fixed structure at pH 6.7.     

Distribution and Transition of Native and Completely Unfolded Conformations in the Unfolding of Bovine Heart Cytochrome c Induced by Urea and Guanidine Hydrochloride

The unfolding of bovine heart cytochrome c induced by urea and guanidine hydrochloride was first studied through intrinsic fluorescence emission spectra and fluorescence phase diagram and the results showed that both of them separately followed a two‐state model. As the simplest sample of the unfolding of protein molecules induced by denaturants, an equation was presented to show the effect of the denaturant concentrations in denaturation solution on the residual activity ratios of bovine heart cytochrome c in their two‐state unfolding. There are two characteristic unfolding parameters K and m in this equation. The former is the thermodynamic equilibrium constant of the unfolding of bovine heart cytochrome c induced by denaturants, the latter is the number of denaturant molecules associated with a bovine heart cytochrome c molecule during the unfolding procedure, and through them the distribution and transition of native and completely unfolded bovine heart cytochrome c conformations under different concentrations of urea or guanidine hydrochloride in denaturation solution can be accurately described.     

A laccase study by electrospray ionization Fourier transform ion cyclotron resonance MS: copper depletion, glycoforms and stability

The molecular properties and stability of a laccase from the white-rot fungus Trametes hirsuta (ThL) were studied to exploit the unique capability of electrospray ionization mass spectrometry (ESI-MS) to monitor conformational and molecular-based heterogeneities and metal ion binding simultaneously. Acid and organic solvents were applied as denaturing agents. In aqueous acidic solution, ThL existed in two major forms, distinguished by their mass difference; in addition to these, two other forms were detected. This molecular heterogeneity was due to the variable glycan content of ThL. Additionally, copper-depleted forms of laccase were observed in mass spectra measured from aqueous acidic solution. A small amount of organic solvent (acetonitrile, CH(3)CN) increased the loss of one Cu atom from folded states and led to unfolding. In the unfolded state, ThL was depleted of all four copper atoms, and the charge state distribution was shifted to lower mass-to-charge region. Thus, denaturation took place in two stages: first, the loss of one Cu resulting in an inactive form; second, complete denaturation with the loss of the three remaining Cu atoms. After all coppers were lost, ThL was unfolded, as was clearly seen in the increased number of charge states in the mass spectra. Different stabilities of the glycoforms were observed in the denaturation triggered in acid and organic solvents.     

Using mass spectrometry to probe the subtle differences in conformations of several cytochromes c in aqueous and methanol solutions

We have detected, using electrospray mass spectrometry, minor changes in the H/D exchange rates in various solvents for cytochromes c obtained from five different species. We compared the exchange rates exhibited by these proteins by mixing horse cytochrome c with each of the other four species and monitoring their exchanges simultaneously by mass spectrometry. The use of horse cytochrome c as a reference allowed us to make very accurate comparisons of the small differences in hydrogen exchange rates among the various species. The exchange experiments were performed in water and methanol at several concentrations in an effort to determine whether the cytochromes c of these five species have different conformations in specific solvents, which would cause their exchange rates to differ. Therefore, monitoring the level of exchange as a function of time in both water and water-methanol mixtures is a method for detecting subtle structural changes of proteins in their native or unfolded intermediate states.     

Local Transient Unfolding of Native State PAI‐1 Associated with Serpin Metastability

The metastability of the native fold makes serpin (serine protease inhibitor) proteins prone to pathological conformational change, often by insertion of an extra β‐strand into the central β‐sheet A. How this insertion is made possible is a hitherto unresolved question. By the use of advanced hydrogen/deuterium‐exchange mass spectrometry (HDX‐MS) it is shown that the serpin plasminogen activator inhibitor 1 (PAI‐1) transiently unfolds under native condition, on a second‐to‐minute time scale. The unfolding regions comprise β‐strand 5A as well as the underlying hydrophobic core, including β‐strand 6B and parts of helices A, B, and C. Based thereon, a mechanism is proposed by which PAI‐1 makes transitions through progressively more unfolded states along the reaction coordinate to the inactive, so‐called latent form. Our results highlight the profound utility of HDX‐MS in detecting sparsely populated, transiently unfolded protein states.     

牛血清IgG热化学变性和热变性的研究

使用差示扫描量热仪(DSC)和荧光光谱法研究了在pH 7.4时牛血清IgG (bIgG)热变性, 热化学变性和等温化学变性过程(变性剂为尿素和盐酸胍), 首次报道了bIgG在热化学变性和等温化学变性过程中的相关热力学参数. DSC和荧光光谱实验结果表明, bIgG的热变性和热化学变性过程都是较复杂的不可逆过程, 这个过程可被看作一个三态变构过程. DSC实验表明在热化学变性过程中bIgG的变性温度和焓变值会随着环境中的变性剂浓度的升高而降低. 使用荧光光谱法对bIgG在尿素或盐酸胍存在下的等温化学变性过程进行了研究, 结果显示bIgG的化学变性过程也是一个较复杂的非二态过程. 实验数据分析表明, 变性剂尿素和盐酸胍与bIgG之间主要是依靠氢键相互作用的, 而热变性过程中bIgG的凝集是由于bIgG热变性时结构改变后暴露出的疏水结构互相作用造成的. 实验结果还表明单纯的热变性只能导致bIgG的不完全变性, 而即使是在高浓度变性剂存在时的bIgG热化学变性, 尿素和盐酸胍分别导致的bIgG热化学变性的去折叠态也是不同的.     

荧光相图法研究脲诱导牛血清白蛋白的去折叠过程

作为从分子水平上阐明生命奥秘的中心课题之一,蛋白质的折叠问题一直受到生物化学、生物物理学和结构生物学等领域研究工作者的高度关注。在蛋白质的变性过程中,它们往往达不到完全去折叠,而是会形成不同的部分折叠中间态[1-3],这些部分折叠中间态在蛋白质折叠过程中起着重要作     

Improving hydrogen/deuterium exchange mass spectrometry by reduction of the back-exchange effect

The measurement of deuterium incorporation kinetics using hydrogen/deuterium (H/D) exchange experiments is a valuable tool for the investigation of the conformational dynamics of biomolecules in solution. Experiments consist of two parts when using H/D exchange mass spectrometry to analyse the deuterium incorporation. After deuterium incorporation at high D(2)O concentration, it is necessary to decrease the D(2)O concentration before the mass analysis to avoid deuterium incorporation under artificial conditions of mass spectrometric preparation and measurement. A low D(2)O concentration, however, leads to back-exchange of incorporated deuterons during mass analysis. This back-exchange is one of the major problems in H/D exchange mass spectrometry and must be reduced as much as possible. In the past, techniques using electrospray ionization (ESI) had the lowest back-exchange values possible in H/D exchange mass spectrometry. Methods for the measurement of H/D exchange by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) that have been developed since 1998 have some significant advantages, but they could not achieve the back-exchange minima of ESI methods. Here, we present a protocol for H/D exchange MALDI-MS which allows for greater minimization of back-exchange compared with H/D exchange ESI-MS under similar conditions.     

The methanol-induced conformational transitions of β-lactoglobulin, cytochrome c, and ubiquitin at low pH: A study by electrospray ionization mass spectrometry

The methanol-induced conformational transitions under acidic conditions for beta-lactoglobulin, cytochrome c, and ubiquitin, representing three different classes of proteins with beta-sheets, alpha-helices, and both alpha-helices and beta-sheets, respectively, are studied under equilibrium conditions by electrospray ionization mass spectrometry (ESI-MS). The folding states of proteins in solution are monitored by the charge state distributions that they produce during ESI and by hydrogen/deuterium (H/D) exchange followed by ESI-MS. The changes in charge state distributions are correlated with earlier studies by optical and other methods which have shown that, in methanol, these proteins form partially unfolded intermediates with induced alpha-helix structure. Intermediate states formed at about 35% methanol concentration are found to give bimodal charge state distributions. The same rate of H/D exchange is shown by the two contributions to the bimodal distributions. This suggests the intermediates are highly flexible and may consist of a mixture of two or more rapidly interconverting conformers. H/D exchange of proteins followed by ESI-MS shows that helical denatured states, populated at around 50% methanol concentration, transform into more protected structures with further increases in methanol concentration, consistent with previous circular dicroism studies. These more protected structures still produce high charge states in ESI, similar to those of the fully denatured proteins.     

Acetonitrile-induced unfolding of the photosystem II manganese-stabilizing protein studied by electrospray mass spectrometry

In this paper an acetonitrile-induced unfolding of the manganese-stabilizing protein (MSP) of photosystem II was discovered. More distinct unfolding states of MSP were identified than previously by using mainly electrospray ionization mass spectrometry (ESI-MS), together with fluorescence spectra and far-UV circular dichroism (CD) at pH 2.0, 6.2 or 11.6, and with acetonitrile concentrations from 0 to 50%. At pH 6.2 with acetonitrile concentration changing from 0 to 10%, relatively broad charge-state distributions and poor intensity were observed in ESI-MS, indicating the presence of coexisting conformers. It was concluded that the structure of the MSP protein is unlikely to be a tightly folded form. When the concentration of acetonitrile was 20-40%, simulating the state in the biological membrane, changes in the state of unfolding of MSP were observed to a certain extent using ESI-MS, fluorescence and CD spectroscopy. The charge-state distribution in ESI-MS was found to move toward high states (from 13+ to 27+ to 15+ to 31+) with increasing acetonitrile concentration. At pH 2.0, the MSP structure is rearranged into an unfolded state, and at pH 11.6 the MSP structure is induced to assume another unordered state by deprotonation of appropriate residues. An interesting observation was that a second peak envelope emerged with 20-50% acetonitrile in the medium at pH 11.6.     

Irreversible thermal denaturation of cytochrome c studied by electrospray mass spectrometry

This work uses electrospray ionization mass spectrometry (ESI-MS) in conjunction with hydrogen/deuterium exchange (HDX) and optical spectroscopy for characterizing the solution-phase properties of cytochrome c (cyt c) after heat exposure. Previous work demonstrated that heating results in irreversible denaturation for a subpopulation of proteins in the sample. However, that study did not investigate the physical reasons underlying this interesting effect. Here we report that the formation of oxidative modifications at elevated temperature plays a key role for the observed behavior. Tryptic digestion followed by tandem mass spectrometry is used to identify individual oxidation sites. Trp59 and Met80 are among the modified amino acids. In native cyt c both of these residues are buried deep within the protein structure, such that covalent modifications would be expected to be particularly disruptive. ESI-MS analysis after heat exposure results in a bimodal charge-state distribution. Oxidized protein appears predominantly in charge states around 11+, whereas a considerably lower degree of oxidation is observed for the 7+ and 8+ peaks. This finding confirms that different oxidation levels are associated with different solution-phase conformations. HDX measurements for different charge states are complicated by peak distortions arising from oxygen adduction. Nonetheless, comparison with simulated peak shapes clearly shows that the HDX properties are different for high- and low-charge states, confirming that interconversion between unfolded and folded conformers is blocked in solution. In addition to oxidation, partial aggregation upon heat exposure likely contributes to the formation of irreversibly denatured protein.     

Fourier transform mass spectrometry to monitor hyaluronan-protein interactions: use of hydrogen/deuterium amide exchange

The use of Fourier transform mass spectrometry (FTMS) to monitor noncovalent complex formation in the gas phase under native conditions between the Link module from human tumor necrosis factor stimulated gene-6 (Link_TSG6) and hyaluronan (HA) oligosaccharides is reported. In particular, a titration experiment with increasing concentrations of octasaccharide (HA(8)) to protein produced a noncovalent complex with 1:1 stoichiometry when the oligosaccharide was in molar excess. However, in the presence of a molar excess of tetrasaccharide (HA(4)) nearly all proteins and oligosaccharides were observed in their unbound charge states. These results are consistent with solution-phase properties for this interaction in which HA(8), but not HA(4), supports high affinity Link_TSG6 binding. Hydrogen/deuterium amide exchange mass spectrometry (H/D-EX MS) was also utilized to investigate the level of global deuterium incorporation, over time, for Link_TSG6 in both the absence and presence of HA(8). After dilution into quenching conditions, deuterium incorporation reached limiting asymptotic values of 37 and 26 deuterons for the free and bound protein at 240 and 480 min, respectively, indicating that the oligosaccharide interferes with amide exchange on binding. To detect sequence-specific deuterium incorporation, pepsin digestion of Link_TSG6 in both the absence and presence of HA(8) was performed. A level of deuterium incorporation of 10-30% was observed for peptides analyzed in free Link_TSG6. Interestingly, HA(8) blocked some sites of proteolysis in Link_TSG6 compared to the free protein. Molecular modeling indicated that amino acids proximal to the ligand correlated with regions of the protein that were resistant to enzymatic digestion. Of the peptides that could be analyzed by H/D-EX MS in the presence of the ligand, a 30-60% reduction in deuterium incorporation, relative to the free protein, was observed, even for those sequences not directly involved in HA binding. These results support the utility of FTMS as a method for the characterization of protein-carbohydrate interactions.     

Probing protein unfolding through monitoring cysteine alkylation by matrix-assisted laser desorption/ionisation mass spectrometry

Matrix-assisted laser desorption/ionisation mass spectrometry was used to monitor interaction between three proteins and two basic Immobiline chemicals (pK 10.3 and pK >12) commonly used in immobilised pH gradients (IPG). For two of the investigated proteins, the observed alkylation channels of the cysteine residues exhibited unmistakable response to their gradual denaturation following treatment with different concentrations (0-8 M) of two commonly used denaturants, urea and guanidine hydrochloride. Our assessment for protein unfolding is based on the number and relative intensity of the alkylation channels, yet the present mass spectrometry data are in good agreement with data based on optical rotatory dispersion, in which another approach was used to assess protein unfolding. Whether the present simple, fast and specific mass spectrometry method can be developed as a probe for monitoring folding/unfolding of cysteine-containing proteins can only be demonstrated by generating similar data for a larger number of proteins.     

Comparison of continuous and pulsed labeling amide hydrogen exchange/mass spectrometry for studies of protein dynamics

In contrast to the rigid structures portrayed by X-ray diffraction, proteins in solution display constant motion which leads to populations that are momentarily unfolded. To begin to understand protein dynamics, we must have experimental methods for determining rates of folding and unfolding, as well as for identifying structures of folding and unfolding intermediates. Amide hydrogen exchange has become an important tool for such measurements. When urea is used to stabilize unfolded forms of proteins, the refolding rates may become slower than the rates of isotope exchange. In such cases, the intermolecular distribution of deuterium among the entire population of molecules may become bimodal, giving rise to a bimodal distribution of isotope peaks in mass spectra of the protein or its peptic fragments. When the protein is exposed continuously to D2O, the relative intensities of the two envelopes of isotope peaks give an integrated account of populations participating in the folding/unfolding process. However, when the protein is exposed only briefly to D2O, the relative intensities of the two envelopes of isotope peaks give an instantaneous measure of the folded/unfolded populations. Application of these two labeling methods to a large protein, aldolase, is described along with a discussion of specific parameters required to optimize these experiments.     

The Mass Spectrometry of Helical Unfolding in Peptides

Two model peptides, melittin and a growth hormone releasing factor (GRF) analog, have been studied by mass spectrometry and tandem mass spectrometry during the course of their deuterium exchange. Both peptides are known from previous work to form α-helices in solution. When the peptides are exposed to deuterated solvents, their masses increase as deuterium atoms replace protons in the exchangeable sites of the peptides. The mass spectrometry results clearly indicate multiple populations of exchangeable protons: Some exchange very fast, and are presumably on the surface and not involved in hydrogen bonding; others exchange much more slowly, indicating that they are probably participating in hydrogen bonding. Tandem mass spectrometric experiments were conducted, and the masses of the product (fragment) ions were used to determine where in the peptide the deuterium atoms were incorporated. The results agree very well with NMR studies of the same peptides. Melittin appears as two helical segments with a kink around Pro-14. The GRF analog contains a single long helix, spanning almost the entire length of the peptide. The dynamics of the unfolding of the helices can also be explored by observing how the exchange progresses with time.     

High-resolution H/D exchange studies on the HET-s218-295 prion protein

In a search for improved resolution of hydrogen/deuterium (H/D) exchange experiments analyzed by mass spectrometry (HXMS), we evaluated two methodologies for a detailed structural study of solvent accessibility in the case of the HET-s(218-295) prion protein. For the first approach, after incubation in the deuterated solvent, aggregated HET-s(218-295) was digested with pepsin and the generated peptides were analyzed by nanospray mass spectrometry in an ion trap, with and without collision-induced dissociation (CID). We compared deuterium incorporation in peptides as determined on peptide pseudomolecular ions and on b and y fragments produced by longer peptides under CID conditions. For both b and y fragment ions, an extensive H/D scrambling phenomenon was observed, in contrast with previous studies comparing CID-MS experiments and (1)H NMR data. Thus, the spatial resolution of HXMS experiments could not be improved by means of MS/MS data generated by an ion trap mass spectrometer. In a second approach, the incorporation of deuterium was analyzed by MS for 76 peptides of the HET-s(218-289) peptide mass fingerprint, and the use of shared boundaries among peptic peptides allowed us to determine deuteration levels of small regions ranging from one to four amino acids. This methodology led to evidence of highly protected regions along the HET-s(218-295) sequence.     

Protein Unfolding of metMyoglobin Monitored by Spectroscopic Techniques

In this experiment the unfolding of the protein, myoglobin, will be monitored using both fluorescence and UV-vis absorption spectroscopy. Changes in the absorbance at 409.5 nm, the absorption maximum of the native state, will be monitored in order to probe changes in the protein conformation after initiation of unfolding by addition of a chemical denaturant. Protein unfolding will also be monitored after exciting the sample at 280 nm and following protein fluorescence emission at 345 nm, the fluorescence maximum for the unfolded state. The absorption run follows the time-dependent decrease in the concentration of the native-state species, whereas the fluorescence experiment monitors the increase in the concentration of the unfolded state. Kinetic rate constants obtained using the two techniques will be compared.     

Understanding cold denaturation: the case study of Yfh1

All globular proteins undergo transitions from their native to unfolded states if exposed either to cold or to heat perturbation. While the heat-induced transition is well described for a large number of proteins, in media compatible with natural environments, the limited number of examples of cold denatured states concern proteins artificially destabilized, for instance, by the presence of denaturants, ad hoc point mutations, or both. Here, we provide a characterization of the low temperature unfolded state of Yfh1, a natural protein that undergoes cold denaturation around water freezing temperature, in the absence of any denaturant. By achieving nearly full assignment of the NMR spectrum, we show that at -1 °C, Yfh1 has all the features of an unfolded protein, although retaining some local, residual secondary structure. The effect is not uniform along the sequence and does not merely reflect the secondary structural features of the folded species. The N-terminus seems to be dynamically more flexible, although retaining some nascent helix character. Interestingly, this region is the one containing functionally important hot-spots. The β-sheet region and the C-terminal helix are completely unfolded, although experiencing some conformational exchange, partly due to the presence of several prolines. Ours is the first step toward a full characterization of the low temperature unfolded state of a natural protein, reached without the aid of any destabilizing agent. We discuss the implications of our findings for understanding cold denatured states.