High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid.

In conventional crosslinking mass spectrometry, proteins are crosslinked using a highly selective, bifunctional chemical reagent, which limits crosslinks to residues that are accessible and reactive to the reagent. Genetically incorporating a photoreactive amino acid offers two key advantages: any site can be targeted, including those that are inaccessible to conventional crosslinking reagents, and photoreactive amino acids can potentially react with a broad range of interaction partners. However, broad reactivity imposes additional challenges for crosslink identification. In this study, we incorporate benzoylphenylalanine (BPA), a photoreactive amino acid, at selected sites in an intrinsically disordered region of the human protein HSPB5. We report and characterize a workflow for identifying and visualizing residue-level interactions originating from BPA. We routinely identify 30 to 300 crosslinked peptide spectral matches with this workflow, which is up to ten times more than existing tools for residue-level BPA crosslink identification. Most identified crosslinks are assigned to a precision of one or two residues, which is supported by a high degree of overlap between replicate analyses. Based on these results, we anticipate that this workflow will support the more general use of genetically incorporated, photoreactive amino acids for characterizing the structures of proteins that have resisted high-resolution characterization.

Degronomics: Mapping the Interacting Peptidome of a Ubiquitin Ligase Using an Integrative Mass Spectrometry Strategy.

Human cells make use of hundreds of unique ubiquitin E3 ligases to ensure proteome fidelity and control cellular functions by promoting protein degradation. These processes require exquisite selectivity, but the individual roles of most E3s remain poorly characterized in part due to the challenges associated with identifying, quantifying, and validating substrates for each E3. We report an integrative mass spectrometry (MS) strategy for characterizing protein fragments that interact with KLHDC2, a human E3 that recognizes the extreme C-terminus of substrates. Using a combination of native MS, native top-down MS, MS of destabilized samples, and liquid chromatography MS, we identified and quantified a near complete fraction of the KLHDC2-binding peptidome in E. coli cells. This degronome includes peptides that originate from a variety of proteins. Although all identified protein fragments are terminated by diglycine or glycylalanine, the preceding amino acids are diverse. These results significantly expand our understanding of the sequences that can be recognized by KLHDC2, which provides insight into the potential substrates of this E3 in humans. We anticipate that this integrative MS strategy could be leveraged more broadly to characterize the degronomes of other E3 ligase substrate receptors, including those that adhere to the more common N-end rule for substrate recognition. Therefore, this work advances "degronomics," i.e., identifying, quantifying, and validating functional E3:peptide interactions in order to determine the individual roles of each E3.

Recognition of the Diglycine C-End Degron by CRL2KLHDC2 Ubiquitin Ligase.

Aberrant proteins can be deleterious to cells and are cleared by the ubiquitin-proteasome system. A group of C-end degrons that are recognized by specific cullin-RING ubiquitin E3 ligases (CRLs) has recently been identified in some of these abnormal polypeptides. Here, we report three crystal structures of a CRL2 substrate receptor, KLHDC2, in complex with the diglycine-ending C-end degrons of two early-terminated selenoproteins and the N-terminal proteolytic fragment of USP1. The E3 recognizes the degron peptides in a similarly coiled conformation and cradles their C-terminal diglycine with a deep surface pocket. By hydrogen bonding with multiple backbone carbonyls of the peptides, KLHDC2 further locks in the otherwise degenerate degrons with a compact interface and unexpected high affinities. Our results reveal the structural mechanism by which KLHDC2 recognizes the simplest C-end degron and suggest a functional necessity of the E3 to tightly maintain the low abundance of its select substrates.

Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure.

Ion mobility is emerging as a rapid and sensitive tool for structural characterization. Collision cross-section (Ω) values determined using ion mobility are often compared to values calculated for candidate structures generated through molecular modeling. Several methods exist for calculating Ω values, but the trajectory method explicitly includes contributions from long-range, ion-neutral interactions. Recent implementations of the trajectory method have significantly reduced its expense and have made applications to proteins far more tractable. Here, we use ion mobility experiments and trajectory method calculations to characterize the effects of charge state, charge distribution, and structure on the ion mobility of proteins in nitrogen gas. These results show that ion-induced dipole interactions contribute significantly to the Ω values of these ions with nitrogen gas, even for the modestly charged ions commonly observed in native mass spectrometry experiments. Therefore, these interactions contribute significantly to the values measured in most structural biology and biophysics applications of ion mobility using nitrogen gas. Comparisons between the reciprocal mobilities of protein ions in helium gas and in nitrogen gas show that there are significant, noncorrelated differences between these values. As a consequence, it is challenging to estimate the errors associated with interconverting between helium- and nitrogen-based mobilities without extensive characterization in both gases, even for ions of proteins with similar sequences. Therefore, we recommend reporting Ω and mobility values that are based on the predominant gas present in the separation and applying additional caution when comparing results from mobility experiments performed using different gases.

UHPLC-MS/MS method for the quantitation of penicillin G and metabolites in citrus fruit using internal standards.

Penicillin G has been applied to citrus trees as a potential treatment in the fight against Huanglongbing (HLB). Here, we have developed and validated a method to identify and quantitate penicillin G and two of its metabolites, penillic acid and penilloic acid, in citrus fruit using ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). This method improves upon a previous method by incorporating isotopically labeled internal standards, namely, penillic acid-D5, and penilloic acid-D5. These standards greatly enhanced the accuracy and precision of our measurements by compensating for recovery losses, degradation, and matrix effects. When 2g of citrus fruit sample is extracted, the limits of detection (LOD) were determined to be 0.1ng/g for penicillin G and penilloic acid, and 0.25ng/g for penillic acid. At fortification levels of 0.1, 0.25, 1, and 10ng/g, absolute recoveries for penillic and penilloic acids were generally between 50-70%. Recoveries corrected with the isotopically labeled standards were approximately 90-110%. This method will be useful for the identification and quantitation of drug residues and their degradation products using isotopically labeled standards and UHPLC-MS/MS.

LC-MS/MS Validation of a Residue Analysis Method for Penicillin G and Its Metabolites in Commercial Orange Juice.

Florida citrus depends on a breakthrough in the fight against citrus greening disease. Of the antibiotics used to treat this disease, penicillin G has been one of the most effective. Because orange fruit grown in the state of Florida are mainly used to produce orange juice, we have validated an ultra-HPLC tandem MS method to screen for penicillin G and its metabolites (penillic and penilloic acids) at the chemical residue level after treatment. In this method, three spike levels (0.25, 1, and 20 ng/g) were tested in triplicate. Absolute recoveries for penillic and penilloic acids were 60-75% depending on the matrix used, whereas corrected recoveries of penicillin G using an isotopically labeled internal standard were ~100%. Two product ion transitions per analyte were required for identification, which contributes to a high degree of selectivity.

Identification of Penicillin G Metabolites under Various Environmental Conditions Using UHPLC-MS/MS.

In this work, we investigate the stability of penicillin G in various conditions including acidic, alkaline, natural acidic matrices and after treatment of citrus trees that are infected with citrus greening disease. The identification, confirmation, and quantitation of penicillin G and its various metabolites were evaluated using two UHPLC-MS/MS systems with variable capabilities (i.e., Thermo Q Exactive Orbitrap and Sciex 6500 QTrap). Our data show that under acidic and alkaline conditions, penicillin G at 100 ng/mL degrades quickly, with a determined half-life time of approximately 2 h. Penillic acid, penicilloic acid, and penilloic acid are found to be the most abundant metabolites of penicillin G. These major metabolites, along with isopenillic acid, are found when penicillin G is used for treatment of citrus greening infected trees. The findings of this study will provide insight regarding penicillin G residues in agricultural and biological applications.