Cryogenic IR spectroscopy combined with ion mobility spectrometry for the analysis of human milk oligosaccharides.

We report here our combination of cryogenic, messenger-tagging, infrared (IR) spectroscopy with ion mobility spectrometry (IMS) and mass spectrometry (MS) as a way to identify and analyze a set of human milk oligosaccharides (HMOs) ranging from trisaccharides to hexasaccharides. The added dimension of IR spectroscopy provides a diagnostic fingerprint in the OH and NH stretching region, which is crucial to identify these oligosaccharides, which are difficult to distinguish by IMS alone. These results extend our previous work in demonstrating the generality of this combined approach for distinguishing subtly different structural and regioisomers of glycans of biologically relevant size.

Multiple solution structures of the disordered peptide indolicidin from IMS-MS analysis.

The solution-favored conformations of the 13-residue disordered peptide, indolicidin (Ile1-Leu2-Pro3-Trp4-Lys5-Trp6-Pro7-Trp8-Trp9-Pro10-Trp11-Arg12-Arg13), are evaluated using electrospray ionization (ESI) coupled to ion mobility spectrometry-mass spectrometry (IMS-MS). The ESI-IMS-MS distributions for the dominant [M+4H]4+ ions indicate that three populations of structures coexist in a range of aqueous to non-aqueous solutions (water:dioxane, water:trifluoroethanol, and water:hexafluoroisopropanol). Conformer types and their relative abundances change in response to different solution environments suggesting that the gas phase conformers reflect on the solution populations present in different solvent environments. Collisional activation of isolated gas phase conformations with IMS-IMS-MS experiments provides additional insight about the relative stabilities of different structural types in the absence of solvent. Simulated annealing studies suggest that proline configuration may be important for the presence of multiple conformations.

Glycosaminoglycan Analysis by Cryogenic Messenger-Tagging IR Spectroscopy Combined with IMS-MS.

We combine ion mobility spectrometry with cryogenic, messenger-tagging, infrared spectroscopy and mass spectrometry to identify different isomeric disaccharides of chondroitin sulfate (CS) and heparan sulfate (HS), which are representatives of two major subclasses of glycosaminoglycans. Our analysis shows that while CS and HS disaccharide isomers have similar drift times, they can be uniquely distinguished by their vibrational spectrum between ∼3200 and 3700 cm-1 due to their different OH hydrogen-bonding patterns. We suggest that this combination of techniques is well suited to identify and characterize glycan isomers directly, which presents tremendous challenges for existing methods.

Configurationally-Coupled Protonation of Polyproline-7.

Structure and dynamics regulate protein function, but much less is known about how biomolecule-solvent interactions affect the structure-function relationship. Even less is known about the thermodynamics of biomolecule-solvent interactions and how such interactions influence conformational entropy. When transferred from propanol into 40:60 propanol:water under acidic conditions, a remarkably slow protonation reaction coupled with the conversion of the polyproline-I helix (PPI, having all cis-configured peptide bonds) into polyproline-II (PPII, all trans) helix is observed in this work. Kinetics and equilibrium measurements as a function of temperature allow determination of the thermochemistry and insight into how proton transfer is regulated in this system. For the proton-transfer process, PPI(+)(PrOH) + H3O(+) → PPII(2+)(PrOH/aq) + H2O, we determine ΔG = -20 ± 19 kJ·mol(-1), ΔH = -75 ± 14 kJ·mol(-1), and ΔS= -188 ± 48 J·mol(-1)·K(-1) for the overall reaction, and values of ΔG(⧧) = 91 ± 3 kJ·mol(-1), ΔH(⧧) = 84 ± 9 kJ·mol(-1), and ΔS(⧧) = -23 ± 31 J·mol(-1)·K(-1) for the transition state. For a minor process, PPI(+)(PrOH) → PPII(+)(PrOH/aq) without protonation, we determine ΔG = -9 ± 20 kJ·mol(-1), ΔH = 64 ± 14 kJ·mol(-1), and ΔS= 247 ± 50 J·mol(-1)·K(-1). This thermochemistry yields ΔG = -10 ± 29 kJ·mol(-1), ΔH = -139 ± 20 kJ·mol(-1), and ΔS= -435 ± 70 J·mol(-1)·K(-1) for PPII(+)(PrOH/aq) + H3O(+) → PPII(2+)(PrOH/aq) +H2O. The extraordinarily slow proton transfer appears to be an outcome of configurational coupling through a PPI-like transition state.

Stop-Codon Readthrough in Therapeutic Protein Candidates Expressed from Mammalian Cells.

Stop codon readthroughs were examined in 48 recombinant therapeutic protein candidates produced from multiple clones of Chinese hamster ovary cells, using peptide mapping with LC-MS/MS detection. We found that stop codon readthrough is a common phenomenon occurring in most of these candidates, with levels varying from below the detection limit of ∼0.001 % to ∼1 %. The readthrough propensity depends on the stop codon being used, as well as the nucleotides surrounding it. The amino acids misincorporated into the stop position can be well-predicted by a third-base wobble mismatch and a first-base U/G mismatch during codon recognition, i.e., tyrosine or glutamine insertion for the UAA and UAG stop codons, and tryptophan, cysteine or arginine insertion for the UGA stop codon. Data shown in this report demonstrate the importance of optimizing the DNA sequence near the stop codon, and the importance of detecting stop codon readthroughs during the development of a therapeutic product.

Development of in silico models to predict viscosity and mouse clearance using a comprehensive analytical data set collected on 83 scaffold-consistent monoclonal antibodies.

Biologic drug discovery pipelines are designed to deliver protein therapeutics that have exquisite functional potency and selectivity while also manifesting biophysical characteristics suitable for manufacturing, storage, and convenient administration to patients. The ability to use computational methods to predict biophysical properties from protein sequence, potentially in combination with high throughput assays, could decrease timelines and increase the success rates for therapeutic developability engineering by eliminating lengthy and expensive cycles of recombinant protein production and testing. To support development of high-quality predictive models for antibody developability, we designed a sequence-diverse panel of 83 effector functionless IgG1 antibodies displaying a range of biophysical properties, produced and formulated each protein under standard platform conditions, and collected a comprehensive package of analytical data, including in vitro assays and in vivo mouse pharmacokinetics. We used this robust training data set to build machine learning classifier models that can predict complex protein behavior from these data and features derived from predicted and/or experimental structures. Our models predict with 87% accuracy whether viscosity at 150 mg/mL is above or below a threshold of 15 centipoise (cP) and with 75% accuracy whether the area under the plasma drug concentration-time curve (AUC0-672 h) in normal mouse is above or below a threshold of 3.9 × 106 h x ng/mL.

Systematic optimization of targeted and multiplexed MS-based screening workflows for protein biomarkers.

Background: The capability of targeted MS-based methods to simultaneously measure multiple analytes with high selectivity and sensitivity greatly facilitates the discovery and quantitation of novel biomarkers. However, the complexity of biological samples is a major bottleneck that requires extensive sample preparation. Results: This paper reports a generic workflow to optimize surrogate peptide-based protein biomarker screening for seven human proteins in a multiplexed manner without the need for any specific affinity reagents. Each step of the sample processing and LC-MS methods is systematically assessed and optimized for better analytical performance. Conclusion: The established method is used for the screening of multiple myeloma patient samples to determine which proteins could be robustly measured and serve as potential biomarkers of the disease.

Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification.

The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. Graphical Abstract ᅟ.

Position of Proline Mediates the Reactivity of S-Palmitoylation.

Palmitoylation, a post-translational modification in which a saturated 16-carbon chain is added predominantly to a cysteine residue, participates in various biological functions. The position of proline relative to other residues being post-translationally modified has been previously reported as being important. We determined that proline is statistically enriched around cysteines known to be S-palmitoylated. The goal of this work was to determine how the position of proline influences the palmitoylation of the cysteine residue. We established a mass spectrometry-based approach to investigate time- and temperature-dependent kinetics of autopalmitoylation in vitro and to derive the thermodynamic parameters of the transition state associated with palmitoylation; to the best of our knowledge, our work is the first to study the kinetics and activation properties of the palmitoylation process. We then used these thermochemical parameters to determine if the position of proline relative to the modified cysteine is important for palmitoylation. Our results show that peptides with proline at the -1 position of cysteine in their sequence (PC) have lower enthalpic barriers and higher entropic barriers in comparison to the same peptides with proline at the +1 position of cysteine (CP); interestingly, the free-energy barriers for both pairs are almost identical. Molecular dynamics studies demonstrate that the flexibility of the cysteine backbone in the PC-containing peptide when compared to the CP-containing peptide explains the increased entropic barrier and decreased enthalpic barrier observed experimentally.