Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions

For decades, formaldehyde has been routinely used to cross-link proteins in cells, tissue, and in some instances, even entire organisms. Due to its small size, formaldehyde can readily permeate cell walls and membranes, resulting in efficient cross-linking, i.e. the formation of covalent bonds between proteins, DNA, and other reactive molecules. Indeed, formaldehyde cross-linking is an instrumental component of many mainstream analytical/cell biology techniques including chromatin immunoprecipitation (ChIP) of protein-DNA complexes found in nuclei; immunohistological analysis of protein expression and localization within cells, tissues, and organs; and mass spectrometry (MS)-compatible silver-staining methodologies used to visualize low abundance proteins in polyacrylamide gels. However, despite its exquisite suitability for use in the analysis of protein environments within cells, formaldehyde has yet to be commonly employed in the directed analysis of protein-protein interactions and cellular networks. The general purpose of this article is to discuss recent advancements in the use of formaldehyde cross-linking in combination with MS-based methodologies. Key advantages and limitations to the use of formaldehyde over other cross-linkers and technologies currently used to study protein-protein interactions are highlighted, and formaldehyde-based experimental approaches that are proving very promising in their ability to accurately and efficiently identify novel protein-protein and multiprotein interaction complexes are presented.     

A FlAsH-based cross-linker to study protein interactions in living cells

As you like it: xCrAsH, a dimeric derivative of the arsenical compound FlAsH, enables the highly specific, covalent cross-linking of two proteins containing a 12?amino acid peptide tag. This inducible and (by addition of dithiols) reversible system can be used to detect and manipulate protein-protein interactions both in?vitro and in living cells (see picture).     

Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes

Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.     

Affinity‐Labeling‐Based Introduction of a Reactive Handle for Natural Protein Modification

A new chemical method to site‐specifically modify natural proteins without the need for genetic manipulation is described. Our strategy involves the affinity‐labeling‐based attachment of a unique reactive handle at the surface of the target protein, and the subsequent selective transformation of the reactive handle by a bioorthogonal reaction to introduce a variety of functional probes into the protein. To demonstrate this approach, we synthesized labeling reagents that contain: 1) a benzenesulfonamide ligand that directs specifically to bovine carbonic anhydrase II (bCA), 2) an electrophilic epoxide group for protein labeling, 3) an exchangeable hydrazone bond linking the ligand and the epoxide group, and 4) an iodophenyl or acetylene handle. By incubating the labeling reagent with bCA, the reactive handle was covalently attached at the surface of bCA through epoxide ring opening. Either after or before removing the ligand by a hydrazone/oxime‐exhange reaction, which restores the enzymatic activity, the reactive handle incorporated could be derivatized by Suzuki coupling or Huisgen cycloaddition reactions. This method is also applicable to the target‐specific multiple modification in a protein mixture. The availability of various (photo)affinity‐labeling reagents and bioorthogonal reactions should extend the flexibility of this strategy for the site‐selective incorporation of many functional molecules into proteins.     

Modulation of protein-protein interactions with small organic molecules

Many proteins exert their biological roles as components of complexes, and the functions of proteins are often determined by their specific interactions with other proteins. Because of the central importance of protein-protein interactions for cellular processes, the ability to interfere with specific protein-protein interactions provides a powerful means of influencing the function of selected proteins within the cell. Cell-permeable small organic modulators of protein-protein interactions are thus highly desirable tools both for the study of physiological cellular processes and for the treatment of numerous diseased states. Herein a number of protein-protein interactions that are considered to be pharmaceutical targets are presented, which will familiarize the reader with the strategies that have been employed for the successful identification of small molecule modulators of these protein-protein interactions. These encouraging examples suggest that combined research efforts in the areas of functional proteomics, assay development, and organic synthesis will open up novel possibilities for the treatment of human diseases in the future.     

MALDI‐MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single‐stranded DNA‐binding protein

The Escherichia coli single‐stranded DNA binding protein (SSB) selectively binds single‐stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB?ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross‐linking, combined with high‐mass matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB?ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19 100) can be detected with standard MALDI‐MS. With chemical cross‐linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79 500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB?ssDNA complex at m/z 94 200 even in the absence of chemical cross‐linking. The stability of the SSB?ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB?ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB?ssDNA complex is how ssDNA binds to SSB, rather than the protein‐to‐DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non‐specific aggregation in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

In‐Membrane Chemical Modification (IMCM) for Site‐Specific Chromophore Labeling of GPCRs

We present in‐membrane chemical modification (IMCM) for obtaining selective chromophore labeling of intracellular surface cysteines in G‐protein‐coupled receptors (GPCRs) with minimal mutagenesis. This method takes advantage of the natural protection of most cysteines by the membrane environment. Practical use of IMCM is illustrated with the site‐specific introduction of chromophores for NMR and fluorescence spectroscopy in the human κ‐opioid receptor (KOR) and the human A_2A adenosine receptor (A_2AAR). IMCM is applicable to a wide range of in vitro studies of GPCRs, including single‐molecule spectroscopy, and is a promising platform for in‐cell spectroscopy experiments.     

Fragmentation behavior of a thiourea‐based reagent for protein structure analysis by collision‐induced dissociative chemical cross‐linking

The fragmentation behavior of a novel thiourea‐based cross‐linker molecule specifically designed for collision‐induced dissociation (CID) MS/MS experiments is described. The development of this cross‐linker is part of our ongoing efforts to synthesize novel reagents, which create either characteristic fragment ions or indicative constant neutral losses (CNLs) during tandem mass spectrometry allowing a selective and sensitive analysis of cross‐linked products. The new derivatizing reagent for chemical cross‐linking solely contains a thiourea moiety that is flanked by two amine‐reactive N‐hydroxy succinimide (NHS) ester moieties for reaction with lysines or free N‐termini in proteins. The new reagent offers simple synthetic access and easy structural variation of either length or functionalities at both ends. The thiourea moiety exhibits specifically tailored CID fragmentation capabilities—a characteristic CNL of 85 u—ensuring a reliable detection of derivatized peptides by both electrospray ionization (ESI) and matrix‐assisted laser desorption/ionization (MALDI) tandem mass spectrometry and as such possesses a versatile applicability for chemical cross‐linking studies. A detailed examination of the CID behavior of the presented thiourea‐based reagent reveals that slight structural variations of the reagent will be necessary to ensure its comprehensive and efficient application for chemical cross‐linking of proteins. Copyright © 2010 John Wiley & Sons, Ltd.     

Fabrication and Application of Photocrosslinked,Nanometer‐Scale,Physically Adsorbed Films for Tissue Culture Regeneration

This study describes the development and cell culture application of nanometer thick photocrosslinkable thermoresponsive polymer films prepared by physical adsorption. Two thermoresponsive polymers, poly(N‐isopropylacrylamide (NIPAm)‐co‐acrylamidebenzophenone (AcBzPh)) and poly(NIPAm‐co‐AcBzPh‐co‐N‐tertbutylacrylamide) are investigated. Films are prepared both above and below the polymers' lower critical solution temperatures (LCSTs) and cross‐linked, to determine the effect, adsorption preparation temperature has on the resultant film. The films prepared at temperatures below the LCST are smoother, thinner, and more hydrophilic than those prepared above. Human pulmonary microvascular endothelial cell (HPMEC) adhesion and proliferation are superior on the films produced below the polymers LCST compared to those produced above. Cells sheets are detached by simply lowering the ambient temperature to below the LCST. Transmission electron, scanning electron, and light microscopies indicate that the detached HPMEC sheets maintain their integrity.

     

Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins

The electrostatic potential plays a key role in many biological processes like determining the affinity of a ligand to a given protein target, and they are responsible for the catalytic activity of many enzymes. Understanding the effect that amino acid mutations will have on the electrostatic potential of a protein, will allow a thorough understanding of which residues are the most important in a protein. MutantElec, is a friendly web application for in silico generation of site‐directed mutagenesis of proteins and the comparison of electrostatic potential between the wild type protein and the mutant(s), based on the three‐dimensional structure of the protein. The effect of the mutation is evaluated using different approach to the traditional surface map. MutantElec provides a graphical display of the results that allows the visualization of changes occurring at close distance from the mutation and thus uncovers the local and global impact of a specific change. © 2017 Wiley Periodicals, Inc.     

Fragmentation features of intermolecular cross‐linked peptides using N‐hydroxy‐ succinimide esters by MALDI‐ and ESI‐MS/MS for use in structural proteomics

The use of mass spectrometry coupled with chemical cross‐linking of proteins has become one of the most useful tools for proteins structure and interactions studies. One of the challenges in these studies is the identification of the cross‐linked peptides. The interpretation of the MS/MS data generated in cross‐linking experiments using N‐hydroxy succinimide esters is not trivial once a new amide bond is formed allowing new fragmentation pathways, unlike linear peptides. Intermolecular cross‐linked peptides occur when two different peptides are connected by the cross‐linker and they yield information on the spatial proximity of different domains (within a protein) or proteins (within a complex). In this article, we report a detailed fragmentation study of intermolecular cross‐linked peptides, generated from a set of synthetic peptides, using both ESI and MALDI to generate the precursor ions. The fragmentation features observed here can be helpful in the interpretation and identification of cross‐linked peptides present in cross‐linking experiments and be further implemented in search engine's algorithms. Copyright © 2011 John Wiley & Sons, Ltd.     

Prediction of the interaction of metallic moieties with proteins: An update for protein‐ligand docking techniques

In this article, we present a new approach to expand the range of application of protein‐ligand docking methods in the prediction of the interaction of coordination complexes (i.e., metallodrugs, natural and artificial cofactors, etc.) with proteins. To do so, we assume that, from a pure computational point of view, hydrogen bond functions could be an adequate model for the coordination bonds as both share directionality and polarity aspects. In this model, docking of metalloligands can be performed without using any geometrical constraints or energy restraints. The hard work consists in generating the convenient atom types and scoring functions. To test this approach, we applied our model to 39 high‐quality X‐ray structures with transition and main group metal complexes bound via a unique coordination bond to a protein. This concept was implemented in the protein‐ligand docking program GOLD. The results are in very good agreement with the experimental structures: the percentage for which the RMSD of the simulated pose is smaller than the X‐ray spectra resolution is 92.3% and the mean value of RMSD is < 1.0 Å. Such results also show the viability of the method to predict metal complexes–proteins interactions when the X‐ray structure is not available. This work could be the first step for novel applicability of docking techniques in medicinal and bioinorganic chemistry and appears generalizable enough to be implemented in most protein‐ligand docking programs nowadays available. © 2017 Wiley Periodicals, Inc.     

A Bayesian statistical approach of improving knowledge‐based scoring functions for protein–ligand interactions

Knowledge‐based scoring functions are widely used for assessing putative complexes in protein–ligand and protein–protein docking and for structure prediction. Even with large training sets, knowledge‐based scoring functions face the inevitable problem of sparse data. Here, we have developed a novel approach for handling the sparse data problem that is based on estimating the inaccuracies in knowledge‐based scoring functions. This inaccuracy estimation is used to automatically weight the knowledge‐based scoring function with an alternative, force‐field‐based potential (FFP) that does not rely on training data and can, therefore, provide an improved approximation of the interactions between rare chemical groups. The current version of STScore, a protein–ligand scoring function using our method, achieves a binding mode prediction success rate of 91% on the set of 100 complexes by Wang et al., and a binding affinity correlation of 0.514 with the experimentally determined affinities in PDBbind. The method presented here may be used with other FFPs and other knowledge‐based scoring functions and can also be applied to protein–protein docking and protein structure prediction. © 2014 Wiley Periodicals, Inc.     

Synthesis of Site‐Specific Dye‐Labeled Polymer via Atom Transfer Radical Polymerization (ATRP) for Quantitative Characterization of the Well‐Defined Interchain Distance

Novel difunctional initiators that incorporate Förster/fluorescence resonance energy transfer (FRET) pairs are generated to carry out atom transfer radical polymerization of styrene, methyl methacrylate, and n‐butyl methacrylate monomers by an efficient manner. Based on the chemical structures of the initiators, the locations of the fluorophore moiety are dictated to be in the center of the chain with accurately quantified chain functionality (>90% labeling ratio). The site‐specific integration of FRET dyes into separate polymer chain centers allows for characterization of the well‐defined interchain distance quantitatively based on the response between these fluorescent probes. The reliability of this technique is verified in bulk state, which is in well agreement with the theoretical ones. This well‐defined FRET system is expected to be a promising candidate to provide a distinct physical image at a microscopic level regarding scaling chain dimension, chain interpenetration, and polymer compatibility.