Generalized polarization and time-resolved fluorescence provide evidence for different populations of Laurdan in lipid vesicles

The solvatochromic dye Laurdan is widely used in sensing the lipid packing of both model and biological membranes. The fluorescence emission maximum shifts from about 440 nm (blue channel) in condensed membranes (So) to about 490 nm (green channel) in the liquid-crystalline phase (Lα). Although the fluorescence intensity based generalized polarization (GP) is widely used to characterize lipid membranes, the fluorescence lifetime of Laurdan, in the blue and the green channel, is less used for that purpose. Here we explore the correlation between GP and fluorescence lifetimes by spectroscopic measurements on the So and Lα phases of large unilamellar vesicles of DMPC and DPPC. A positive correlation between GP and the lifetimes is observed in each of the optical channels for the two lipid phases. Microfluorimetric determinations on giant unilamellar vesicles of DPPC and DOPC at room temperature are performed under linearly polarized two-photon excitation to disentangle possible subpopulations of Laurdan at a scale below the optical resolution. Fluorescence intensities, GP and fluorescence lifetimes depend on the angle between the orientation of the linear polarization of the excitation light and the local normal to the membrane of the optical cross-section. This angular variation depends on the lipid phase and the emission channel. GP and fluorescence intensities in the blue and green channel in So and in the blue channel in Lα exhibit a minimum near 90o. Surprisingly, the intensity in the green channel in Lα reaches a maximum near 90o. The fluorescence lifetimes in the two optical channels also reach a pronounced minimum near 90o in So and Lα, apart from the lifetime in the blue channel in Lα where the lifetime is short with minimal angular variation. To our knowledge, these experimental observations are the first to demonstrate the existence of a bent conformation of Laurdan in lipid membranes, as previously suggested by molecular dynamics calculations.

Perturbed post-translational modification (PTM) network atlas of collagen I during stent-induced neointima formation

Myocardial infarction (MI) leading to heart failure contributes to almost 85% of deaths associated with CVDs. MI results from plaque formation in the coronary artery which leads to a lack of oxygen and nutrients in the myocardium. To date, stenting is a widely used gold-standard technique to maintain the proper blood flow through coronary circulation in the myocardium. Bare metal stents (BMS) and drug-eluting stents (DES) are majorly used in implantation. However, BMS and DES both can induce neointima formation by depositing excessive collagens in the coronary arteries leading to restenosis. Identification and quantitative analysis of site-specific post-translational modifications (PTMs) of deposited COL1A1 from neointima ECM are not known. Applying our in-house workflow, we re-analyzed a previously published mass-spectrometry data set to comprehensively map site-specific prolyl-hydroxylation, lysyl hydroxylation, and O-glycosylation sites in COL1A1 from neointima ECM. Furthermore, we quantitated the occupancy level of 9 3-hydroxyproline (3-HyP) sites, 2 hydroxylysine sites, and glycosylation microheterogeneity on 6 lysine sites of COL1A1. Although the total level of COL1A1 was decreased in DES-induced neointima, the occupancy levels of 2 3-HyP sites (P⁸⁷², and P⁸⁸¹) and 2 HyK (K⁴³⁵ and K⁷⁶⁸) sites of COL1A1 were significantly (p < 0.05) elevated in DES-induced neointima compared to BMS-induced neointima. We also found O-glycosylation to be significantly elevated on 3 lysine sites (K⁵⁷³, K³³⁹, and K and K⁸⁴⁹) of COL1A1 in DES-induced neointima compared to BMS-induced neointima. Taken together, our first comprehensive PTM analysis of COL1A1 reflected significant site-specific alterations that may play a very important role in the ECM remodeling during stent-induced neointima formation in MI patients. SIGNIFICANCE: The knowledge about site-specific post-translational modifications (PTMs) of collagen 1 deposited in the neointima ECM during the post-stenting restenosis process is absent. Here for the first time, we report the altered levels of COL1A1 PTMs during metal stent and drug-eluting stent-induced neointima formation. Our study showcases a novel ECM remodeling through site-specific collagen PTMs during stent-induced restenosis.

Sequential in vitro enzymatic N-glycoprotein modification reveals site-specific rates of glycoenzyme processing

N-glycosylation is an essential eukaryotic posttranslational modification that affects various glycoprotein properties, including folding, solubility, protein–protein interactions, and half-life. N-glycans are processed in the secretory pathway to form varied ensembles of structures, and diversity at a single site on a glycoprotein is termed ‘microheterogeneity’. To understand the factors that influence glycan microheterogeneity, we hypothesized that local steric and electrostatic factors surrounding each site influence glycan availability for enzymatic modification. We tested this hypothesis via expression of reporter N-linked glycoproteins in N-acetylglucosaminyltransferase MGAT1-null HEK293 cells to produce immature Man₅GlcNAc₂ glycoforms (38 glycan sites total). These glycoproteins were then sequentially modified in vitro from high mannose to hybrid and on to biantennary, core-fucosylated, complex structures by a panel of N-glycosylation enzymes, and each reaction time course was quantified by LC-MS/MS. Substantial differences in rates of in vitro enzymatic modification were observed between glycan sites on the same protein, and differences in modification rates varied depending on the glycoenzyme being evaluated. In comparison, proteolytic digestion of the reporters prior to N-glycan processing eliminated differences in in vitro enzymatic modification. Furthermore, comparison of in vitro rates of enzymatic modification with the glycan structures found on the mature reporters expressed in WT cells correlated well with the enzymatic bottlenecks observed in vivo. These data suggest higher order local structures surrounding each glycosylation site contribute to the efficiency of modification both in vitro and in vivo to establish the spectrum of microheterogeneity in N-linked glycoproteins.

Assessment of Macro- and Microheterogeneity of Monoclonal Antibodies Using Capillary Zone Electrophoresis Hyphenated with Mass Spectrometry

This chapter focuses on the application of capillary zone electrophoresis hyphenated with mass spectrometry (CZE-MS) for the characterization of monoclonal antibodies (mAbs). mAbs are complex molecules comprising different glycoforms and many other posttranslational modifications. In addition to this inherent microheterogeneity, misassembling of antibodies can take place during production contributing to their macroheterogeneity. CZE-MS is a versatile and powerful technique which has demonstrated high potential for the assessment of both micro- and macroheterogeneity of mAbs. In this chapter, technical and practical considerations for the characterization of mAbs by CZE-MS are described. CE-MS interfacing, capillary coatings for the prevention of mAb adsorption, and sample preparation considerations are covered in detail. The assessment of the macro- and microheterogeneity is discussed and exemplified through three different approaches involving analysis of intact, enzymatically digested, and reduced antibodies. The examples also illustrate the use of two commercially available interfacing techniques (i.e., sheath liquid and sheathless) as well as different types of capillary coatings (positively charged and neutral coatings).

Site-Specific N-glycosylation Analysis of Recombinant Proteins by LC/MSE

The glycosylation process is extremely heterogeneous, dynamic, and complex compared with any other post-translational modification of protein. In the context of recombinant glycoproteins, glycosylation is a critical attribute as glycans could dramatically alter protein functions and properties including activity, half-life, in vivo localization, stability, and, last but not least, immunogenicity. Liquid chromatography combined to mass spectrometry constitutes the most powerful analytical approach to achieve the comprehensive glycan profile description or comparison of glycoproteins. This chapter details a versatile yet straightforward LC-MS approach for sample preparation, analysis, and data interpretation, enabling the evaluation of site-specific N-glycosylation of recombinant glycoproteins.

Assessing the microscale heterogeneity in Standard Reference Material 4600 Surrogate Post-detonation Urban Debris

Nondestructive microbeam X-ray fluorescence (μXRF) spectrometry has been used to investigate the elemental microheterogeneity in a nuclear forensics reference material (RM), NIST SRM 4600 Surrogate Post-detonation Urban Debris. Using a principal component analysis (PCA) model, results indicate the majority of elements appear homogeneous; however, zinc (Zn) exhibits microscale heterogeneity for this SRM. To minimize contributions to the measurement uncertainty from elemental microheterogeneity, a minimum sample mass of 24 mg is recommended for analysis.

Microheterogeneity and preanalytical stability of protein biomarkers of inflammation and renal function

Protein biomarker microheterogeneity has attracted increasing attention in epidemiological and clinical research studies. Knowledge concerning the preanalytical stability of proteins is paramount to assess the biological significance of their proteoforms. We investigated the stability of the inflammatory markers C-reactive protein (CRP), serum amyloid A (SAA), and calprotectin (S100A8/9), and the renal function marker, cystatin C (CnC). In total 16 proteoforms were quantified by immuno-MALDI-TOF MS in EDTA plasma and serum samples from 15 healthy volunteers. Prior to analysis blood samples were stored at either room temperature from 1 h up to 8 days, or underwent up to 9 consecutive freeze/thaw cycles. Pearson's correlation coefficient and t-test, intra-class correlation coefficient (ICC), and Autoregressive Integrated Moving-Average (ARIMA) models were used to investigate the stability of proteoform concentrations and distributions in blood. Plasma and serum concentrations of CRP and SAA proteoforms were highly stable during room temperature exposure and repeated freeze/thaw cycles, demonstrating excellent reproducibility (ICC > 0.75), no serial dependency in ARIMA models, and stable distribution of proteoforms. Stability analyses for proteoforms of S100A8/9 and CnC identified only minor preanalytical changes in concentrations and distributions, and none of the proteoforms were produced during prolonged exposure to room temperature or repeated freezing/thawing. The four proteins and their proteoforms are stable during sub-optimal sample handling, and represent robust biomarker candidates for future biobank studies aimed at investigating the microheterogeneity of SAA, S100A8/9, and CnC in relation to inflammation, renal dysfunction and various clinical outcomes.

Data-Independent Acquisition for Yeast Glycoproteomics

Glycosylation is a complex posttranslational modification that is critical for regulating the functions of diverse proteins. Analysis of protein glycosylation is made challenging by the high degree of heterogeneity in both glycan occupancy and structure. Here, we describe methods for data-independent acquisition (SWATH) mass spectrometry analysis of structure and occupancy of N-glycans from yeast cell wall glycoproteins.

A statistical geometry analysis of simulated water-DMSO and water-MeCN binary mixtures for biomolecular studies

Water-Dimethylsulfoxide (DMSO) and water-Acetonitrile (MeCN) binary mixtures at various molar ratios ranging from 0 to 1 are studied using Molecular Dynamics (MD) simulations. Hydration properties of water in different regions of MeCN/DMSO are investigated by using the statistical geometry approach. The obtained results reveal that in water-DMSO simulations both water and solvent molecules prefer to be in mixed cluster forms, depending upon the concentration of DMSO. While in case of water-MeCN mixtures, self-association of water and acetonitrile molecules, take place, showing microheterogeneity associated with the water- MeCN binary mixtures. The results highlight the utility of statistical geometric analysis of MD simulation data of binary liquid mixtures for rapid screening of polar organic solvents in non-aqueous enzymology.

Microheterogeneity in binary mixtures of water with CH3OH and CD3OH: ATR-IR spectroscopic, chemometric and DFT studies

Here we report ATR-IR spectroscopic study on the separation at a molecular level (microheterogeneity) and the degree of deviation of H₂O/CH₃OH and H₂O/CD₃OH mixtures from the ideal mixture. Of particular interest is the effect of isotopic substitution in methyl group on molecular structure and interactions in both mixtures. To obtain comprehensive information from the multivariate data we applied the excess molar absorptivity spectra together with two-dimensional correlation analysis (2DCOS) and chemometric methods. In addition, the experimental results were compared and discussed with the structures of various model clusters obtained from theoretical (DFT) calculations. Our results evidence the presence of separation at a molecular level and deviation from the ideal mixture for both mixtures. The experimental and theoretical results show that the maximum of these deviations appears at equimolar mixture. Both mixtures consist of three kinds of species: homoclusters of water and methanol and mixed clusters (heteroclusters). The heteroclusters exist in the whole range of mole fractions with the maximum close to the equimolar mixture. At this mixture composition near 55-60% of molecules are involved in heteroclusters. In contrast, the homoclusters of water occur in a limited range of mole fractions (X_ME < 0.85-0.9). Upon mixing the molecules of methanol form weaker hydrogen bonding as compared with the pure alcohol. In contrast, the molecules of water in the mixture are involved in stronger hydrogen bonding than those in bulk water. All these results indicate that both mixtures have similar degree of deviation from the ideal mixture.

Microheterogeneity in CH3OH/CD3OH mixture

Recently, we demonstrated the presence of microheterogeneity in binary mixtures of unlike alcohols. [RSC Adv. 2016, 6, 37195-37202] The aim of this work was examination if this phenomenon occurs also in the mixture of very similar alcohols like CH₃OH and CD₃OH. Theoretical calculations suggest that the isotopic substitution in methyl group influences properties of the OH group. Hence, one can expect that this effect may lead to partial separation of CH₃OH and CD₃OH at a molecular level and it contributes to deviation from the ideal mixture. This work evidences that CH₃OH/CD₃OH mixture also deviates from the ideal one, but the extent of this deviation is much smaller as compared with the mixtures of other alcohols. It is of particular note that this deviation results mainly from the difference between the CH₃ and CD₃ groups, while the contribution from the OH groups is small. The structure of CH₃OH/CD₃OH mixture at a molecular level is similar to the structure of binary mixtures of other alcohols. The mixture is composed of the homoclusters of both alcohols and the mixed clusters. The homoclusters existing in the mixture are similar to those present in bulk alcohols. The highest population of the heteroclusters and the largest deviation from the ideal mixture were observed at equimolar mixture. Both the experimental and theoretical results reveal that in CH₃OH/CD₃OH mixture dominate the cyclic tetramers and larger clusters, while the population of the linear clusters is negligible. Though the extent and strength of hydrogen bonding in both alcohols are the same, the position and intensity of the 2ν(OH) band for CH₃OH and CD₃OH are different. We propose possible explanation of this observation.

Charge heterogeneity: Basic antibody charge variants with increased binding to Fc receptors

We identified active isoforms of the chimeric anti-GD2 antibody, ch14.18, a recombinant antibody produced in Chinese hamster ovary cells, which is already used in clinical trials.^1,2,3 We separated the antibody by high resolution ion-exchange chromatography with linear pH gradient elution into acidic, main and basic charge variants on a preparative scale yielding enough material for an in-depth study of the sources and the effects of microheterogeneity. The binding affinity of the charge variants toward the antigen and various cell surface receptors was studied by Biacore. Effector functions were evaluated using cellular assays for antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. Basic charge variants showed increased binding to cell surface receptor FcγRIIIa, which plays a major role in regulating effector functions. Furthermore, increased binding of the basic fractions to the neonatal receptor was observed. As this receptor mediates the prolonged half-life of IgG in human serum, this data may well hint at an increased serum half-life of these basic variants compared to their more acidic counterparts. Different glycoform patterns, C-terminal lysine clipping and N-terminal pyroglutamate formation were identified as the main structural sources for the observed isoform pattern. Potential differences in structural stability between individual charge variant fractions by nano differential scanning calorimetry could not been detected. Our in-vitro data suggests that the connection between microheterogeneity and the biological activity of recombinant antibody therapeutics deserves more attention than commonly accepted.

A case for protein-level and site-level specificity in glycoproteomic studies of disease

Abnormal glycosylation of proteins is known to be either resultant or causative of a variety of diseases. This makes glycoproteins appealing targets as potential biomarkers and focal points of molecular studies on the development and progression of human ailment. To date, a majority of efforts in disease glycoproteomics have tended to center on either determining the concentration of a given glycoprotein, or on profiling the total population of glycans released from a mixture of glycoproteins. While these approaches have demonstrated some diagnostic potential, they are inherently insensitive to the fine molecular detail which distinguishes unique and possibly disease relevant glycoforms of specific proteins. As a consequence, such analyses can be of limited sensitivity, specificity, and accuracy because they do not comprehensively consider the glycosylation status of any particular glycoprotein, or of any particular glycosylation site. Therefore, significant opportunities exist to improve glycoproteomic inquiry into disease by engaging in these studies at the level of individual glycoproteins and their exact loci of glycosylation. In this concise review, the rationale for glycoprotein and glycosylation site specificity is developed in the context of human disease glycoproteomics with an emphasis on N-glycosylation. Recent examples highlighting disease-related perturbations in glycosylation will be presented, including those involving alterations in the overall glycosylation of a specific protein, alterations in the occupancy of a given glycosylation site, and alterations in the compositional heterogeneity of glycans occurring at a given glycosylation site. Each will be discussed with particular emphasis on how protein-specific and site-specific approaches can contribute to improved discrimination between glycoproteomes and glycoproteins associated with healthy and unhealthy states.

Membrane glycoproteomics of fetal lung fibroblasts using LC/MS

Some aberrant N-glycosylations are being used as tumor markers, and glycoproteomics is expected to provide novel diagnosis markers and targets of drug developments. However, one has trouble in mass spectrometric glycoproteomics of membrane fraction because of lower intensity of glycopeptides in the existence of surfactants. Previously, we developed a glycopeptide enrichment method by acetone precipitation, and it was successfully applied to human serum glycoproteomics. In this study, we confirmed that this method is useful to remove the surfactants and applicable to membrane glycoproteomics. The glycoproteomic approach to the human fetal lung fibroblasts membrane fraction resulted in the identification of over 272 glycoforms on 63 sites of the 44 glycoproteins. According to the existing databases, the structural features on 41 sites are previously unreported. The most frequently occurring forms at N-glycosylation site were high-mannose type containing nine mannose residues (M9) and monosialo-fucosylated biantennary oligosaccharides. Several unexpected N-glycans, such as fucosylated complex-type and fucosylated high-mannose and/or fucosylated pauci-mannose types were found in ER and lysosome proteins. Our method provides new insights into transport, biosynthesis, and degradation of glycoproteins.

Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene)

Diversity analysis of Clostridium botulinum strains is complicated by high microheterogeneity caused by the presence of 9-22 copies of rrs (16S rRNA gene). The need is to mine genetic markers to identify very closely related strains. Multiple alignments of the nucleotide sequences of the 212 rrs of 13 C. botulinum strains revealed intra- and inter-genomic heterogeneity. Low intragenomic heterogeneity in rrs was evident in strains 230613, Alaska E43, Okra, Eklund 17B, Langeland, 657, Kyoto, BKT015925, and Loch Maree. The most heterogenous rrs sequences were those of C. botulinum strains ATCC 19397, Hall, H04402065, and ATCC 3502. In silico restriction mapping of these rrs sequences was observable with 137 type II Restriction endonucleases (REs). Nucleotide changes (NC) at these RE sites resulted in appearance of distinct and additional sites, and loss in certain others. De novo appearances of RE sites due to NC were recorded at different positions in rrs gene. A nucleotide transition A>G in rrs of C. botulinum Loch Maree and 657 resulted in the generation of 4 and 10 distinct RE sites, respectively. Transitions A>G, G>A, and T>C led to the loss of RE sites. A perusal of the entire NC and in silico RE mapping of rrs of C. botulinum strains provided insights into their evolution. Segregation of strains on the basis of RE digestion patterns of rrs was validated by the cladistic analysis involving six house keeping genes: dnaN, gyrB, metG, prfA, pyrG, and Rho.

Isotope dilution assay in peptide quantification: the challenge of microheterogeneity of internal standard

Isotope dilution analysis allows quantitation of elements and different compounds in complex mixtures. The quantitation is based on a known amount of reference material (internal standard, IS) added to a sample that makes the result critically dependent on the value assigned to the standard. In the case of peptides, IS concentration is determined by nitrogen and amino acid analysis while purity is normally assessed by methods such as chromatography or electrophoresis that might not be able to detect many possible amino acid modifications, either naturally occurring or chemically induced. Microheterogeneity of the IS, if it is not accounted for when assigning a reference value to the standard, results in highly overestimated values in target analyte quantitation. In this viewpoint article, we illustrate the problem of internal standard microheterogeneity by analyzing synthetic human C-peptide labeled analogs.