Accessibility governs the relative reactivity of basic residues in formaldehyde-induced protein modifications

Toews, Judy; Rogalski, Jason C.; Kast, Juergen

doi:10.1016/j.aca.2010.07.040

Cited by 26 publications

(25 citation statements)

References 39 publications

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“…vent-accessible lysine residues have been found to provide the most reactive functional groups in native proteins, and moreover, modification of native proteins by formaldehyde does not appear to perturb tertiary structure very much (20). This is consistent with early work in the chromatin field that established that lysine residues are the predominant sites of formation of methylene bridges in histone complexes; such studies led to the suggestion as well that formaldehyde crosslinking does not in general perturb protein structure (21).…”

Section: Formaldehyde Reactivity With Proteinssupporting

confidence: 70%

Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes

Hoffman

Frey

Smith

et al. 2015

Journal of Biological Chemistry

345

261

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Formaldehyde has been used for decades to probe macromolecular structure and function and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is routinely employed for detection and quantification of protein-DNA interactions, interactions between chromatin proteins, and interactions between distal segments of the chromatin fiber. Despite widespread use and a rich biochemical literature, important aspects of formaldehyde behavior in cells have not been well described. Here, we highlight features of formaldehyde chemistry relevant to its use in analyses of chromatin complexes, focusing on how its properties may influence studies of chromatin structure and function.Prior to its use in the chromatin field, formaldehyde use had a long history in a number of fields, including vaccine production (1, 2) and histology (3). In this review, we focus on its use in chromatin immunoprecipitation approaches and protein-protein interaction studies applied to understand the location and abundance of transcription factor binding along DNA. A recent complementary perspective highlights gaps in knowledge with a particular focus on how formaldehyde crosslinking data have been used to interpret aspects of chromatin three-dimensional organization (4). Here, we briefly review prior work describing formaldehyde reactivity toward proteins, DNA, and their constituent monomers. This information provides a basis for understanding how formaldehyde functions in widely used assays in the chromatin field, and conversely, highlights less well understood aspects of formaldehyde behavior in cells. These issues are of significance for designing crosslinkingbased studies as well as for properly interpreting the resulting data. The analysis of formaldehyde-fixed chromatin has provided fundamental insights into where and when regulatory factors associate with the DNA template in vivo, but it in general does not provide unambiguous information about chromatin binding kinetics. A major goal of ongoing work is to understand kinetic and thermodynamic aspects of chromatin complex assembly at single copy loci in vivo. Development of experimental strategies to achieve these goals will require a deeper and more comprehensive understanding of the effects mediated by formaldehyde in cells.The following discussion provides a framework for understanding aspects of formaldehyde function when used to trap macromolecular complexes in cells, with the main features shown in Fig. 1. Beginning with basic chemical reactivity, this review will explore the ability of formaldehyde to crosslink with proteins and DNA to form protein-protein or protein-DNA complexes, common molecular quenchers, and the potential for crosslink reversal. Progress in capturing crosslinked complexes will also be discussed with an emphasis on the impact of a better understanding of formaldehyde chemistry in vivo. Basic ChemistryFormaldehyde is the smallest aldehyde, an electrophilic molecule susceptible to chemical attack by a wide range of nucleophilic species of ...

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Section: Formaldehyde Reactivity With Proteinssupporting

confidence: 70%

Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes

Hoffman

Frey

Smith

et al. 2015

Journal of Biological Chemistry

345

261

View full text Add to dashboard Cite

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“…4a, when formaldehyde treated and untreated myoglobin samples were unfolded by decreasing the pH, both samples experienced similar increases in charge states, i.e. unfolding, irrespective of formaldehyde treatment [54]. This agrees with the previously mentioned dimethyl labeling experiments reporting that formaldehyde modification maintained the charge state of proteins and peptides [17].…”

Section: Formaldehyde Modification: Model Protein and Peptide Ms Studsupporting

confidence: 76%

“…In contrast, under reaction conditions derived for specific in vivo cross-linking in protein interaction studies (physiological pH buffer, 1% formaldehyde concentration and 5-20 min incubation time), only the N-terminus and cysteine, lysine, and to a lesser extent, arginine side chains, were primary reactive sites in the formaldehyde modification reaction [51,54].…”

Section: Formaldehyde Modification: Model Protein and Peptide Ms Studmentioning

confidence: 79%

Formaldehyde cross-linking and structural proteomics: Bridging the gap

Srinivasa

Ding

Kast

2015

Methods

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“…However, studies using varying incubation times with formaldehyde have shown that in addition to the N-termini, lysine, tryptophan, and cysteine become modified first in model peptides [13]. Furthermore, it has been found for model proteins that, mainly, lysines were readily modified and therefore are assumed to be involved in the cross-linking reaction [14]. This assumption can be supported by observations from experiments using dimethylation labelling, which also involves reaction with formaldehyde in a first step and in which the modification is almost exclusively detected on lysines [15].…”

Section: Chemistry Of Formaldehyde Cross-linkingmentioning

confidence: 97%

“…It is assumed that formaldehyde "fixes" and preserves protein structures, but it is possible formaldehyde treatment alters protein structures in some way. Two studies have addressed the effect of formaldehyde on the secondary and tertiary structure of model proteins, but neither was able to detect any effect of the modifications on the protein structure [14,17]. Thus, until further information is available, the effect of formaldehyde on protein structure can be assumed to be negligible.…”

Section: Chemistry Of Formaldehyde Cross-linkingmentioning

confidence: 98%

Advancing formaldehyde cross-linking towards quantitative proteomic applications

2012

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Formaldehyde is a key fixation reagent. This review explores its application in combination with qualitative and quantitative mass spectrometry (MS). Formalin-fixed and paraffin-embedded (FFPE) tissues form a large reservoir of biologically valuable samples and their investigation by MS has only recently started. Furthermore, formaldehyde can be used to stabilise protein-protein interactions in living cells. Because formaldehyde is able to modify proteins, performing MS analysis on these samples can pose a challenge. Here we discuss the chemistry of formaldehyde cross-linking, describe the problems of and progress in these two applications and their common aspects, and evaluate the potential of these methods for the future.

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Accessibility governs the relative reactivity of basic residues in formaldehyde-induced protein modifications

Cited by 26 publications

References 39 publications

Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes

Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes

Formaldehyde cross-linking and structural proteomics: Bridging the gap

Advancing formaldehyde cross-linking towards quantitative proteomic applications

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