A targeted approach for the synthesis of multi-phosphorylated peptides: a tool for studying the role of phosphorylation patterns in proteins

Rapid flow-based synthesis of post-translationally modified peptides and proteins: a case study on MYC's transactivation domain

Protein-protein interactions of c-Myc (MYC) are often regulated by post-translational modifications (PTMs), such as phosphorylation, and crosstalk thereof. Studying these interactions requires proteins with unique PTM patterns, which are challenging to obtain by recombinant methods. Standard peptide synthesis and native chemical ligation can produce such modified proteins, but are time-consuming and therefore typically limited to the study of individual PTMs. Herein, we report the development of flow-based methods for the rapid synthesis of phosphorylated MYC sequences (up to 84 AA), and demonstrate the versatility of this approach for the incorporation of other PTMs (N ε-methylation, sulfation, acetylation, glycosylation) and combinations thereof. Peptides containing up to seven PTMs and phosphorylation at up to five sites were successfully prepared and isolated in high yield and purity. We further produced ten PTM-decorated analogues of the MYC Transactivation Domain (TAD) to screen for binding to the tumor suppressor protein, Bin1, using heteronuclear NMR and native mass spectrometry. We determined the effects of phosphorylation and glycosylation on the strength of the MYC:Bin1 interaction, and reveal an influence of MYC sequence length on binding. Our platform for the rapid synthesis of MYC sequences up to 84 AA with distinct PTM patterns thus enables the systematic study of PTM function at a molecular level, and offers a convenient way for expedited screening of constructs.

Multiphosphorylation-Dependent Recognition of Anti-pS2 Antibodies against RNA Polymerase II C-Terminal Domain Revealed by Chemical Synthesis

Phosphorylation is a major constituent of the CTD code, which describes the set of post-translational modifications on 52 repeats of a YSPTSPS consensus heptad that orchestrates the binding of regulatory proteins to the C-terminal domain (CTD) of RNA polymerase II. Phospho-specific antibodies are used to detect CTD phosphorylation patterns. However, their recognition repertoire is underexplored due to limitations in the synthesis of long multiphosphorylated peptides. Herein, we describe the development of a synthesis strategy that provides access to multiphosphorylated CTD peptides in high purity without HPLC purification for immobilization onto microtiter plates. Native chemical ligation was used to assemble 12 heptad repeats in various phosphoforms. The synthesis of >60 CTD peptides, 48-90 amino acids in length and containing up to 6 phosphosites, enabled a detailed and rapid analysis of the binding characteristics of different anti-pSer2 antibodies. The three antibodies tested showed positional selectivity with marked differences in the affinity of the antibodies for pSer2-containing peptides. Furthermore, the length of the phosphopeptides allowed a systematic analysis of the multivalent chelate-type interactions. The absence of multivalency-induced binding enhancements is probably due to the high flexibility of the CTD scaffold. The effect of clustered phosphorylation proved to be more complex. Recognition of pSer2 by anti-pSer2-antibodies can be prevented and, perhaps surprisingly, enhanced by the phosphorylation of "bystander" amino acids in the vicinity. The results have relevance for functional analysis of the CTD in cell biological experiments.

Accelerated Multiphosphorylated Peptide Synthesis

Preparing phosphorylated peptides with multiple adjacent phosphorylations is synthetically difficult, leads to β-elimination, results in low yields, and is extremely slow. We combined synthetic chemical methodologies with computational studies and engineering approaches to develop a strategy that takes advantage of fast stirring, high temperature, and a very low concentration of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) to produce multiphosphorylated peptides at an extremely rapid time and high purity.

Dissecting the role of protein phosphorylation: a chemical biology toolbox

Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most is still unclear. Each phosphoform, the particular combination of phosphorylations, of a protein has distinct and diverse biological consequences. Aberrant phosphorylation is implicated in the development of many diseases. To investigate their function, access to defined protein phosphoforms is essential. Materials obtained from cells often are complex mixtures. Recombinant methods can provide access to defined phosphoforms if site-specifically acting kinases are known, but the methods fail to provide homogenous material when several amino acid side chains compete for phosphorylation. Chemical and chemoenzymatic synthesis has provided an invaluable toolbox to enable access to previously unreachable phosphoforms of proteins. In this review, we selected important tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied. Firstly, we discuss the synthesis of phosphopeptides and proteins through chemical and enzymatic means and their advantages and limitations. Secondly, we showcase illustrative examples that applied these tools to answer biological questions pertaining to proteins involved in signal transduction, control of transcription, neurodegenerative diseases and aggregation, apoptosis and autophagy, and transmembrane proteins. We discuss the opportunities and challenges in the field.

Chemical Synthesis of a Full-Length G-Protein-Coupled Receptor β2-Adrenergic Receptor with Defined Modification Patterns at the C-Terminus

The β₂-adrenergic receptor (β₂AR) is a G-protein-coupled receptor (GPCR) that responds to the hormone adrenaline and is an important drug target in the context of respiratory diseases, including asthma. β₂AR function can be regulated by post-translational modifications such as phosphorylation and ubiquitination at the C-terminus, but access to the full-length β₂AR with well-defined and homogeneous modification patterns critical for biochemical and biophysical studies remains challenging. Here, we report a practical synthesis of differentially modified, full-length β₂AR based on a combined native chemical ligation (NCL) and sortase ligation strategy. An array of homogeneous samples of full-length β₂ARs with distinct modification patterns, including a full-length β₂AR bearing both monoubiquitination and octaphosphorylation modifications, were successfully prepared for the first time. Using these homogeneously modified full-length β₂AR receptors, we found that different phosphorylation patterns mediate different interactions with β-arrestin1 as reflected in different agonist binding affinities. Our experiments also indicated that ubiquitination can further modulate interactions between β₂AR and β-arrestin1. Access to full-length β₂AR with well-defined and homogeneous modification patterns at the C-terminus opens a door to further in-depth mechanistic studies into the structure and dynamics of β₂AR complexes with downstream transducer proteins, including G proteins, arrestins, and GPCR kinases.

Contemporary Enzyme-Based Methods for Recombinant Proteins In Vitro Phosphorylation

Phosphorylation is a reversible, enzyme-controlled posttranslational process affecting approximately one-third of all proteins in eukaryotic cells at any given time. Any deviation in the degree and/or site of phosphorylation leads to an abnormal conformation of proteins, resulting in a decline or loss of their function. Knowledge of phosphorylation-related pathways is essential for understanding the understanding of the disease pathogenesis and for the design of new therapeutic strategies. Recent availability of various kinases at an affordable price differs in activity, specificity, and stability and provides the opportunity of studying and modulating this reaction in vitro. We can exploit this knowledge for other applications. There is an enormous potential to produce fully decorated and active recombinant proteins, either for biomedical or cosmetic applications. Closely related is the possibility to exploit current achievements and develop new safe and efficacious vaccines, drugs, and immunomodulators. In this review, we outlined the current enzyme-based possibilities for in vitro phosphorylation of peptides and recombinant proteins and the added value that immobilized kinases provide.

Optical chemosensors for the detection of proximally phosphorylated peptides and proteins

Proximal multi-site phosphorylation is a critical post-translational modification in protein biology. The additive effects of multiple phosphosite clusters in close spatial proximity triggers integrative and cooperative effects on protein conformation and activity. Proximal phosphorylation has been shown to modulate signal transduction pathways and gene expression, and as a result, is implicated in a broad range of disease states through altered protein function and/or localization including enzyme overactivation or protein aggregation. The role of proximal multi-phosphorylation events is becoming increasingly recognized as mechanistically important, although breakthroughs are limited due to a lack of detection technologies. To date, there is a limited selection of facile and robust sensing tools for proximal phosphorylation. Nonetheless, there have been considerable efforts in developing optical chemosensors for the detection of proximal phosphorylation motifs on peptides and proteins in recent years. This review provides a comprehensive overview of optical chemosensors for proximal phosphorylation, with the majority of work being reported in the past two decades. Optical sensors, in the form of fluorescent and luminescent chemosensors, hybrid biosensors, and inorganic nanoparticles, are described. Emphasis is placed on the rationale behind sensor scaffolds, relevant protein motifs, and applications in protein biology.

Total chemical synthesis of the phosphorylated p62 UBA domain reveals that Ser407Pi but not Ser403Pi enhances ubiquitin binding

As an autophagic adaptor, p62 specifically targets ubiquitinated proteins to an autophagosome for lysosomal degradation through a critical ubiquitin-associated (UBA) domain. Recent research studies reported that the Ser403 and Ser407 sites on the UBA domain were modified by phosphorylation, increasing the binding affinity between p62 and ubiquitin (Ub). However, the exact role of each phosphorylation site in the regulation of the UBA domain and Ub binding remains unclear. In this text, we applied total chemical synthesis to prepare four types of phosphorylated UBAs, among which the bisphosphorylated UBA was successfully synthesized via the pseudo-dipeptide unit and auxiliary-mediated hydrazide-based native chemical ligation (NCL). Isothermal titration calorimetry (ITC) assays showed that the phosphorylation at S407 enhanced the binding affinity between UBA and Ub, while that at S403 did not. It was suggested that phosphorylation at S407 might be important for promoting the interplay between the UBA domain and Ub, whereas phosphorylation at S403 was not directly involved in this interaction.

Multiphosphorylated peptides: importance, synthetic strategies, and applications for studying biological mechanisms

Advances in the synthesis of multiphosphorylated peptides and peptide libraries: tools for studying the effects of phosphorylation patterns on protein function and regulation.