Pulsed hydrogen/deuterium exchange mass spectrometry for time‐resolved membrane protein folding studies

Kinetic folding experiments by pulsed hydrogen/deuterium exchange (HDX) mass spectrometry (MS) are a well‐established tool for water‐soluble proteins. To the best of our knowledge, the current study is the first that applies this approach to an integral membrane protein. The native state of bacteriorhodopsin (BR) comprises seven transmembrane helices and a covalently bound retinal cofactor. BR exposure to sodium dodecyl sulfate (SDS) induces partial unfolding and retinal loss. We employ a custom‐built three‐stage mixing device for pulsed‐HDX/MS investigations of BR refolding. The reaction is triggered by mixing SDS‐denatured protein with bicelles. After a variable folding time (10 ms to 24 h), the protein is exposed to excess D₂O buffer under rapid exchange conditions. The HDX pulse is terminated by acid quenching after 24 ms. Subsequent off‐line analysis is performed by size exclusion chromatography and electrospray MS. These measurements yield the number of protected backbone N–H sites as a function of folding time, reflecting the recovery of secondary structure. Our results indicate that much of the BR secondary structure is formed quite late during the reaction, on a time scale of 10 s and beyond. It is hoped that in the future it will be possible to extend the pulsed‐HDX/MS approach employed here to membrane proteins other than BR. Copyright © 2012 John Wiley & Sons, Ltd.     

Protein dynamics revealed by hydrogen/deuterium exchange mass spectrometry: Correlation between experiments and simulation

Hydrogen deuterium exchange mass spectrometry (HDX‐MS) is a powerful technique for studying protein dynamics, which is an important factor governing protein functions. However, the process of hydrogen/deuterium exchange (HDX) of proteins is highly complex and the underlying mechanism has not yet been fully elucidated. Meanwhile, molecular dynamics (MD) simulation is a computational technique that can be used to elucidate HDX behaviour on proteins and facilitate interpretation of HDX‐MS data. This article aims to summarize the current understandings on the mechanism of HDX and its correlation with MD simulation, to discuss the recent developments in the techniques of HDX‐MS and MD simulation and to extend the perspectives of these two techniques in protein dynamics study.     

Conformational analysis of dynorphin A (1-13) using hydrogen-deuterium exchange and tandem mass spectrometry

Trifluoroethanol (TFE)-induced conformational changes in dynorphin A (1-13) were investigated using charge-state distribution (CSD) and hydrogen-deuterium exchange (HDX), combined with electrospray ionization (ESI) mass spectrometry (MS). Individual amino acids involved in secondary structural elements were identified by collision-induced dissociation-tandem mass spectrometry (MS/MS). It was observed that dynorphin A (1-13) largely exists in an unfolded conformation and a folded structure in increasing concentrations of TFE. In 50% TFE, it forms an alpha-helix that encompasses residues 1-9 and remains flexible from residues 10 to 13.     

Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP‐Supported Solid‐State NMR Spectroscopy

Diatom biosilica is an inorganic/organic hybrid with interesting properties. The molecular architecture of the organic material at the atomic and nanometer scale has so far remained unknown, in particular for intact biosilica. A DNP‐supported ssNMR approach assisted by microscopy, MS, and MD simulations was applied to study the structural organization of intact biosilica. For the first time, the secondary structure elements of tightly biosilica‐associated native proteins in diatom biosilica were characterized in situ. Our data suggest that these proteins are rich in a limited set of amino acids and adopt a mixture of random‐coil and β‐strand conformations. Furthermore, biosilica‐associated long‐chain polyamines and carbohydrates were characterized, thereby leading to a model for the supramolecular organization of intact biosilica.     

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.     

Epitope mapping of 7S cashew antigen in complex with antibody by solution‐phase H/D exchange monitored by FT‐ICR mass spectrometry

The potential epitope of a recombinant food allergen protein, cashew Ana o 1, reactive to monoclonal antibody, mAb 2G4, has been mapped by solution‐phase amide backbone H/D exchange (HDX) monitored by Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS). Purified mAb 2G4 was incubated with recombinant Ana o 1 (rAna o 1) to form antigen:monoclonal antibody (Ag:mAb) complexes. Complexed and uncomplexed (free) rAna o 1 were then subjected to HDX‐MS analysis. Five regions protected from H/D exchange upon mAb binding are identified as potential conformational epitope‐contributing segments. Copyright © 2015 John Wiley & Sons, Ltd.     

An Antibody with a Variable‐Region Coiled‐Coil “Knob” Domain

The X‐ray crystal structure of a bovine antibody (BLV1H12) revealed a unique structure in its ultralong heavy chain complementarity determining region 3 (CDR3H) that folds into a solvent‐exposed β‐strand “stalk” fused to a disulfide crosslinked “knob” domain. We have substituted an antiparallel heterodimeric coiled‐coil motif for the β‐strand stalk in this antibody. The resulting antibody (Ab‐coil) expresses in mammalian cells and has a stability similar to that of the parent bovine antibody. MS analysis of H–D exchange supports the coiled‐coil structure of the substituted peptides. Substitution of the knob‐domain of Ab‐coil with bovine granulocyte colony‐stimulating factor (bGCSF) results in a stably expressed chimeric antibody, which proliferates mouse NFS‐60 cells with a potency comparable to that of bGCSF. This work demonstrates the utility of this novel coiled‐coil CDR3 motif as a means for generating stable, potent antibody fusion proteins with useful pharmacological properties.     

The Correlation of Electrochemical Measurements and Molecular Junction Conductance Simulations in β‐Strand Peptides

Understanding the electronic properties of single peptides is not only of fundamental importance, but it is also paramount to the realization of peptide‐based molecular electronic components. Electrochemical and theoretical studies are reported on two β‐strand‐based peptides, one with its backbone constrained with a triazole‐containing tether introduced by Huisgen cycloaddition (peptide 1 ) and the other a direct linear analogue (peptide 2 ). Density functional theory (DFT) and non‐equilibrium Green’s function were used to investigate conductance in molecular junctions containing peptides 3 and 4 (analogues of 1 and 2 ). Although the peptides share a common β‐strand conformation, they display vastly different electronic transport properties due to the presence (or absence) of the side‐bridge constraint and the associated effect on backbone rigidity. These studies reveal that the electron transfer rate constants of 1 and 2 , and the conductance calculated for 3 and 4 , differ by approximately one order of magnitude, thus providing two distinctly different conductance states and what is essentially a molecular switch. A definitive correlation of electrochemical measurements and molecular junction conductance simulations is demonstrated using two different charge transfer techniques. This study furthers our understanding of the electronic properties of peptides at the molecular level, which provides an opportunity to fine‐tune their molecular orbital energies through suitable structural manipulation.     

The unusual hydrogen‐deuterium exchange of α‐carbon protons in N‐substituted glycine‐containing peptides

Hydrogens connected to α‐carbon (α‐C) of amino acid residues are usually resistant to hydrogen‐deuterium exchange (HDX) unless reaction conditions promote racemization. Although N‐methylglycine (sarcosine) residue has been found in biologically active peptide such as cyclosporine, to the best of our knowledge, the HDX of α‐C protons of this residue was not explored yet. Here, we presented a new and efficient methodology of α‐C deuteration in sarcosine residues under basic aqueous conditions. The deuterons, introduced at α‐C atom, do not undergo back‐exchange in acidic aqueous solution. The electrospray ionization‐MS and MS/MS experiments on proposed model peptides confirmed the HDX at α‐C and revealed the unexpected hydrogen scrambling in sarcosine‐containing peptides. Although the observed HDX of α‐C protons is only successful in N‐acylglycine when the amide possesses a certain degree of alkylation, it offers a new approach to the analysis of sarcosine‐containing peptides such as cyclosporine. Copyright © 2014 John Wiley & Sons, Ltd.     

Interrogating Membrane Protein Conformational Dynamics within Native Lipid Compositions

The interplay between membrane proteins and the lipids of the membrane is important for cellular function, however, tools enabling the interrogation of protein dynamics within native lipid environments are scarce and often invasive. We show that the styrene–maleic acid lipid particle (SMALP) technology can be coupled with hydrogen–deuterium exchange mass spectrometry (HDX‐MS) to investigate membrane protein conformational dynamics within native lipid bilayers. We demonstrate changes in accessibility and dynamics of the rhomboid protease GlpG, captured within three different native lipid compositions, and identify protein regions sensitive to changes in the native lipid environment. Our results illuminate the value of this approach for distinguishing the putative role(s) of the native lipid composition in modulating membrane protein conformational dynamics.     

Cutting‐edge mass spectrometry characterization of originator,biosimilar and biobetter antibodies

The approval process for antibody biosimilars relies primarily on comprehensive analytical data to establish comparability and high similarity with the originator. Mass spectrometry (MS) in combination with liquid chromatography (LC) and electrophoretic methods are the corner stone for comparability and biosimilarity evaluation. In this special feature we report head‐to‐head comparison of trastuzumab and cetuximab with corresponding biosimilar and biobetter candidates based on cutting‐edge mass spectrometry techniques such as native MS and ion‐mobility MS at different levels (top, middle and bottom). In addition, we discuss the advantages and the limitations of sample preparation and enzymatic digestion, middle‐up and ‐down strategies and the use of hydrogen/deuterium exchange followed by MS (HDX‐MS). Last but not least, emerging separation methods combined to MS such as capillary zone electrophoresis‐tandem MS (CESI‐MS/MS), electron transfer dissociation (ETD), top down‐sequencing (TDS) and high‐resolution MS (HR‐MS) that complete the panel of state‐of‐the‐art MS‐based options for comparability and biosimilarity evaluation are presented. Copyright © 2015 John Wiley & Sons, Ltd.     

Organization of nucleobase‐functionalized β‐peptides investigated by soft electrospray ionization mass spectrometry

The development and validation of analytical methods is a key to succeed in investigating noncovalent interactions between biomolecules or between small molecules and biomolecules. Electrospray ionization mass spectrometry (ESI‐MS) was applied with a Fourier transform ion cyclotron resonance mass spectrometer (FTICR‐MS) as well as a quadrupole/time‐of‐flight tandem mass spectrometer (QqToF‐MS) for a systematic investigation of noncovalent complexes based on nucleobase pairing in an artificial and noncharged backbone topology. Synthetical β‐peptide helices covalently modified with nucleobases were organized by recognition of a sequence of four nucleobases. Specific duplexes of β‐peptide helices were obtained on the basis of hydrogen bonding base pair complementarity. Oligomer interactions were detected with defined stoichiometry and sensitivity for the respective duplex stability. FTICR‐MS and QqToF‐MS were used equally well to indicate double strand stabilities in agreement with the dissociation data determined by UV spectroscopy. Furthermore, the dissociation energies of gas phase ions of the noncovalent complexes were analyzed with collision induced dissociation (CID)‐MS/MS and infrared multiphoton dissociation (IRMPD)‐MS/MS. The CID conditions turned out to be too harsh for a differentiation of the duplex stabilities, whereas IRMPD might be developed as a technique to detect even small interaction energy differences. Copyright © 2009 John Wiley & Sons, Ltd.     

Structural Transformation of the Peptide Fragments from the Reactive Center Loops of Serpins: Circular Dichroic Studies

Two peptides, derived from the reactive center of ovalbumin (OVARC) and plasminogen activator inhibitor‐1 (PAIRC) respectively were chemically synthesized and investigated by circular dichroic spectroscopy. The secondary structural transformation in solution and in solid state was studied. OVARC shows a nascent helical structure in aqueous solution, and its helical content increases under acidic conditions. There is no obvious structural conversion from solution to solid state. PAIRC, however, undergoes a structural transformation from random coil in aqueous solution to a typical β‐sheet structure in the solid state. Hexafluoroisopropanol (HFIP) prompts helical structures of the two peptides in solution, but it seems to trigger the structural formation of β‐sheets in solid state. The novel structural transformation from random coil or nascent helical structure in aqueous solution to the α‐helix in HFIP and to the β‐sheet structure in solid state may reflect the conformational polymorphism of the serpin reactive centers and is implicated in the structural features of the amyloid aggregates.     

An Off‐Pathway Folding Intermediate of an Acyl Carrier Protein Domain Coexists with the Folded and Unfolded States under Native Conditions

A protein can exist in multiple states under native conditions and those states with low populations are often critical to biological function and self‐assembly. To investigate the role of the minor states of an acyl carrier protein, NMR techniques were applied to determine the number of minor states and characterize their structures and kinetics. The acyl carrier protein from Micromonospora echinospora was found to exist in one major folded state (95.2 %), one unfolded state (4.1 %), and one intermediate state (0.7 %) under native conditions. The three states are in dynamic equilibrium and the intermediate state very likely adopts a native‐like structure and is an off‐pathway folding product. The intermediate state may mediate the formation of oligomers in vitro and play an important role in the recognition of partner enzymes in vivo.     

Steric effects and competitive intra‐ and intermolecular host‐guest complexation between beta‐cyclodextrin and adamantyl substituted poly(acrylate)s in water: A 1H NMR,rheological and preparative study

A ¹H NMR and rheological study of host‐guest complexation interactions between three β‐cyclodextrin and three adamantyl substituted poly(acrylate)s, and also between them and adamantan‐1‐carboxylate and native β‐cyclodextrin, respectively, is reported. A close correllation between molecular level interactions and macroscopic characteristics of polymer networks in aqueous solution exists. It is found that intra‐ and intermolecular host‐guest complexation between the host β‐cyclodextrin and guest adamantyl substituents and the length of the aliphatic tether between them and the poly(acrylate) backbone have important roles. Dominantly, steric effects and competitive intra‐ and intermolecular host‐guest complexation are found to control poly(acrylate) isomeric interstrand linkage in polymer network formation. The preparations of five new 3% randomly substituted poly(acrylate)s are reported. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1818–1825, 2010     

Single‐Molecule Detection Reveals Knot Sliding in TrmD Denaturation

An increasing number of proteins are found to contain a knot in their polypeptide chain. Although some studies have looked into the folding mechanism of knotted proteins, why and how these complex topologies form are still far from being fully answered. Moreover, no experimental information about how the knot moves during the protein‐folding process is available. Herein, by combining single‐molecule fluorescence resonance energy transfer (smFRET) experiments with molecular dynamics (MD) simulations, we performed a detailed study to characterize the knot in the denatured state of TrmD, a knotted tRNA (guanosine‐1) methyltransferase from Escherichia coli, as a model system. We found that the knot still existed in the unfolded state of TrmD, consistent with the results for two other knotted proteins, YibK and YbeA. More interestingly, both smFRET experiments and MD simulations revealed that the knot slid towards the C‐terminal during the unfolding process, which could be explained by the relatively strong interactions between the β‐sheet core at the N terminal of the native knot region. The size of the knot in the unfolded state is not larger than that in the native state. In addition, the knot slid in a “downhill” mode with simultaneous chain collapse in the denatured state.     

Local Unfolding of Fatty Acid Binding Protein to Allow Ligand Entry for Binding

Fatty acid binding proteins are responsible for the transportation of fatty acids in biology. Despite intensive studies, the molecular mechanism of fatty acid entry to and exit from the protein cavity is still unclear. Here a cap‐closed variant of human intestinal fatty acid binding protein was generated by mutagenesis, in which the helical cap is locked to the β‐barrel by a disulfide linkage. Structure determination shows that this variant adopts a closed conformation, but still uptakes fatty acids. Stopped‐flow experiments indicate that a rate‐limiting step exists before the ligand association and this step corresponds to the conversion of the closed form to the open one. NMR relaxation dispersion and H‐D exchange data demonstrate the presence of two excited states: one is native‐like, but the other adopts a locally unfolded structure. Local unfolding of helix 2 generates an opening for ligands to enter the protein cavity, and thus controls the ligand association rate.     

Density functional calculations for Rh(I)‐catalyzed C–C bond activation of siloxyvinylcyclopropanes and diazoesters

Density functional theory was employed to investigate rhodium(I)‐catalyzed C–C bond activation of siloxyvinylcyclopropanes and diazoesters. The B3LYP/6‐31G(d,p) level (LANL2DZ(f) for Rh) was used to optimize completely all intermediates and transition states. The computational results revealed that the most favorable pathway was the channel forming the methyl‐branched acyclic product p1 in path A (cyclooctadiene (cod) as the ligand), and the oxidative addition was the rate‐determining step for this channel. It proceeded mainly through the complexation of diazoester to rhodium, rhodium–carbene formation, coordination of siloxyvinylcyclopropane, oxidative addition (C2–C3 bond cleavage) of siloxyvinylcyclopropane, carbene migratory insertion, β‐hydrogen elimination and reductive elimination. The complexation of diazoester to rhodium occurred prior to the coordination of siloxyvinylcyclopropane. Also, the role of the ligands cod, chlorine and 1,4‐dioxane, the effect of di‐rhodium catalyst and the solvent effect are discussed in detail.     

Absolute free energies of biomolecules from unperturbed ensembles

Computing the absolute free energy of a macromolecule's structural state, F, is a challenging problem of high relevance. This study presents a method that computes F using only information from an unperturbed simulation of the macromolecule in the relevant conformational state, ensemble, and environment. Absolute free energies produced by this method, dubbed V aluation of L ocal C onfiguration I ntegral with D ynamics (VALOCIDY), enable comparison of alternative states. For example, comparing explicitly solvated and vaporous states of amino acid side‐chain analogs produces solvation free energies in good agreement with experiments. Also, comparisons between alternative conformational states of model heptapeptides (including the unfolded state) produce free energy differences in agreement with data from μs molecular‐dynamics simulations and experimental propensities. The potential of using VALOCIDY in computational protein design is explored via a small design problem of stabilizing a β‐turn structure. When VALOCIDY‐based estimation of folding free energy is used as the design metric, the resulting sequence folds into the desired structure within the atomistic force field used in design. The VALOCIDY‐based approach also recognizes the distinct status of the native sequence regardless of minor details of the starting template structure, in stark contrast with a traditional fixed‐backbone approach. © 2013 Wiley Periodicals, Inc.