Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

Crittenden, Christopher M.; Parker, William R.; Jenner, Zachary B.; Bruns, Kerry A.; Akin, Lucas D.; McGee, William M.; Ciccimaro, Eugene; Brodbelt, Jennifer S.

doi:10.1007/s13361-016-1355-7

Cited by 11 publications

(9 citation statements)

References 53 publications

(59 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Applications of UVPD for bottom-up proteomics began to surface over a decade ago, primarily using 193 nm photons. − The high sequence coverage offered by UVPD and its lack of dependence on charge state were recognized as advantageous attributes of 193 nm UVPD for analysis of peptides using both positive and negative ionization modes. − UVPD (193 nm) has also been used to characterize cyclic peptides, including ones representative of stapled peptides, developed as a new type of biostable therapeutic; antimicrobial cyclotides, disulfide-rich peptides derived from plants; and microcystins, nonribosomal peptides generated as metabolites in cyanobacteria. For characterization of nonconventional peptides like the aforementioned cyclic ones, CID and 193 nm UVPD have typically been used in a comparative manner, resulting in the general outcome that the two methods often yielded orthogonal information that could be used in a complementary fashion to enhance characterization of the most intractable structures.…”

Section: Uvpd For Peptidesmentioning

confidence: 99%

Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules

2019

Self Cite

View full text Add to dashboard Cite

The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review. CONTENTS 1. Introduction 3328 1.1. Scope of Review 3328 1.2. Instrumentation 3330 2. UVPD for Peptides 3330 2.1. Mechanistic Studies of Peptides 3330 2.2. UVPD for Peptide Sequencing and Bottom-Up Proteomics 3332 2.3. UVPD for Identification of Post-Translational Modifications 3333 2.4. PTM Analysis Using Other Wavelengths 3336 2.5. Improving S/N of UVPD 3336 2.6. UVPD and Derivatization Strategies 3337 2.6.1. Radical-Directed Dissociation 3337 2.6.2. Photoelectron-Transfer Dissociation 3340 2.6.3. UVPD (266 nm) for Selective Bond Cleavages 3340 2.6.4. UVPD Using 351/355 nm Photons 3340 2.6.5. UVPD with Online Reactions and Hydrogen/Deuterium Exchange 3342 2.6.6. Derivatization and Photodissociation Using Visible Wavelengths 3343 2.7. UVPD for Middle-Down Proteomics 3343 3. UVPD for Intact Proteins 3345 3.1. Fundamental Aspects 3347 3.2. Hybrid Methods and New Concepts for Top-Down Analysis 3347 3.3. Other Wavelengths for Top-Down Analysis 3351 4. UVPD for Native Mass Spectrometry and Structural Biology Applications 3352 4.1. Chemical-Probe Methods 3352 4.2. Native MS 3354 4.2.1. Protein−Ligand Complexes 3355 4.2.2. UVPD for Multimeric Protein Complexes 3357 4.3. UVPD and Ion Mobility 3359 5. UVPD for Lipids 3360 5.1. Radical-Directed Dissociation 3360 5.2. UVPD (193 nm) 3361 5.3. UVPD (213 nm) 3362 5.4. UVPD and DESI 3364 5.5. Lipid A and Lipopolysaccharides 3364 6.

show abstract

Section: Uvpd For Peptidesmentioning

confidence: 99%

Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules

2019

Self Cite

View full text Add to dashboard Cite

show abstract

“…Derivative “ 2 – H 2 O” has not been fully characterized, but it must come about via a process that is faster than the attack of the resin-bound peptide on HBTU-activated 2 . We, therefore, favor a structure in which N ε of the side-chain has undergone intramolecular cyclization with the backbone CO group, yielding a six-membered ring reminiscent of an ornithine lactam. , In efforts to minimize the nucleophilicity of the side-chain of 2 , subsequent peptide coupling reactions were run using organic-soluble sources of HCO 3 – or H 2 PO 4 – in place of N , N -diisopropylethylamine. The anions were envisioned to hydrogen bond to the guanidine moiety, shielding it from further reactions, while being sufficiently basic to deprotonate the COOH of 2 .…”

Section: Resultsmentioning

confidence: 99%

Side-Chain Protonation States of a Fluorescent Arginine

et al. 2019

View full text Add to dashboard Cite

An arginine derivative with a fluorescent side-chain, Boc-Arg(Nap)-OH, was prepared by palladium(0)-catalyzed coupling of Boc-Arg-OH with a 4-bromonaphthalimide. The presence of the fluorophore lowers the pK a of the side-chain guanidinium group by several orders of magnitude, to 9.0 (±0.1), allowing the derivative to access an electrically neutral protonation state that is not generally available to arginine itself. Computational modeling (DFT) predicts that protonation takes place at the side-chain CN atom that bears the fluorophore. Calculated electronic absorptions for the protonated (356 nm) and neutral species (440 nm) are in good agreement with experiment. When irradiated with light, excited-state proton transfer (ESPT) occurs from cationic side-chains to suitably basic solvents, resulting in fluorescence emission from the neutral species. Arg(Nap) can be incorporated into peptides with sterically accessible N-termini using specially adapted conditions of solid-phase peptide synthesis.

show abstract

“…a, b, c, x, y , and z ) (Supplemental Figure 1) (Shaw et al, 2013). UVPD has been used to fragment circular (stapled) peptides (Crittenden et al, 2016), but no cyclotides have been sequenced with UVPD previously.…”

Section: Introductionmentioning

confidence: 99%

PepSAVI-MS reveals anticancer and antifungal cycloviolacins in Viola odorata

et al. 2018

Self Cite

View full text Add to dashboard Cite

Widespread resistance to antimicrobial and cancer therapeutics is evolving in every country worldwide and has a direct impact on global health, agriculture and the economy. The specificity and selectivity of bioactive peptide natural products present a possible stopgap measure to address the ongoing deficit of new therapeutic compounds. PepSAVI-MS (Statistically-guided bioActive Peptides prioritized VIa Mass Spectrometry) is an adaptable method for the analysis of natural product libraries to rapidly identify bioactive peptides. This pipeline was validated via screening of the cyclotide-rich botanical species Viola odorata and identification of the known antimicrobial and anticancer cyclotide cycloviolacin O2. Herein we present and validate novel bioactivities of the anthelmintic V. odorata cyclotide, cycloviolacin O8 (cyO8), including micromolar anticancer activity against PC-3 prostate, MDA-MB-231 breast, and OVCAR-3 ovarian cancer cell lines and antifungal activity against the agricultural pathogen Fusarium graminearum. A reduction/alkylation strategy in tandem with PepSAVI-MS analysis also revealed several previously uncharacterized putatively bioactive cyclotides. Downstream implementation of ultraviolet photodissociation (UVPD) tandem mass spectrometry is demonstrated for cyO8 as a method to address traditionally difficult-to-sequence cyclotide species. This work emphasizes the therapeutic and agricultural potential of natural product bioactive peptides and the necessity of developing robust analytical tools to deconvolute nature's complexity.

show abstract

Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

Cited by 11 publications

References 53 publications

Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules

Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules

Side-Chain Protonation States of a Fluorescent Arginine

PepSAVI-MS reveals anticancer and antifungal cycloviolacins in Viola odorata

Contact Info

Product

Resources

About