Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS.

Mutations in the gene encoding Cu-Zn superoxide dismutase 1 (SOD1) cause a subset of familial amyotrophic lateral sclerosis (fALS) cases. A shared effect of these mutations is that SOD1, which is normally a stable dimer, dissociates into toxic monomers that seed toxic aggregates. Considerable research effort has been devoted to developing compounds that stabilize the dimer of fALS SOD1 variants, but unfortunately, this has not yet resulted in a treatment. We hypothesized that cyclic thiosulfinate cross-linkers, which selectively target a rare, 2 cysteine-containing motif, can stabilize fALS-causing SOD1 variants in vivo. We created a library of chemically diverse cyclic thiosulfinates and determined structure-cross-linking-activity relationships. A pre-lead compound, "S-XL6," was selected based upon its cross-linking rate and drug-like properties. Co-crystallographic structure clearly establishes the binding of S-XL6 at Cys 111 bridging the monomers and stabilizing the SOD1 dimer. Biophysical studies reveal that the degree of stabilization afforded by S-XL6 (up to 24°C) is unprecedented for fALS, and to our knowledge, for any protein target of any kinetic stabilizer. Gene silencing and protein degrading therapeutic approaches require careful dose titration to balance the benefit of diminished fALS SOD1 expression with the toxic loss-of-enzymatic function. We show that S-XL6 does not share this liability because it rescues the activity of fALS SOD1 variants. No pharmacological agent has been proven to bind to SOD1 in vivo. Here, using a fALS mouse model, we demonstrate oral bioavailability; rapid engagement of SOD1G93A by S-XL6 that increases SOD1G93A's in vivo half-life; and that S-XL6 crosses the blood-brain barrier. S-XL6 demonstrated a degree of selectivity by avoiding off-target binding to plasma proteins. Taken together, our results indicate that cyclic thiosulfinate-mediated SOD1 stabilization should receive further attention as a potential therapeutic approach for fALS.

Loss of angiogenin function is related to earlier ALS onset and a paradoxical increase in ALS duration.

0.5-1% of ALS (Amyotrophic Lateral Sclerosis) and Parkinson's disease (PD) are associated with mutations in the angiogenin (ANG). These mutations are thought to cause disease through a loss of ANG function, but this hypothesis has not been evaluated statistically. In addition, the potential for ANG to promote disease has not been considered. With the goal of better defining the etiology of ANG-ALS, we assembled all clinical onset and disease duration data and determined if these were correlated with biochemical properties of ANG variants. Loss of ANG stability and ribonuclease activity were found to correlate with early ALS onset, confirming an aspect of the prevailing model of ANG-ALS. Conversely, loss of ANG stability and ribonuclease activity correlated with longer survival following diagnosis, which is inconsistent with the prevailing model. These results indicate that functional ANG appears to decrease the risk of developing ALS but exacerbate ALS once in progress. These findings are rationalized in terms of studies demonstrating that distinct mechanisms contribute to ALS onset and progression and propose that ANG replacement or stabilization would benefit pre-symptomatic ANG-ALS patients. However, this study challenges the prevailing hypothesis that augmenting ANG will benefit symptomatic ANG-ALS patients. Instead, our results suggest that silencing of ANG activity may be beneficial for symptomatic ALS patients. This study will serve as a call-to-arms for neurologists to consistently publish ALS and PD patient's clinical data-if all ANG-ALS patients' data were available our findings could be tested with considerable statistical power.

Safety and Lack of Negative Effects of Wearable Augmented-Reality Social Communication Aid for Children and Adults with Autism.

There is a growing interest in the use of augmented reality (AR) to assist children and adults with autism spectrum disorders (ASD); however, little investigation has been conducted into the safety of AR devices, such as smartglasses. The objective of this report was to assess the safety and potential negative effects of the Empowered Brain system, a novel AR smartglasses-based social communication aid for people with ASD. The version of the Empowered Brain in this report utilized Google Glass (Google, Mountain View, CA, USA) as its hardware platform. A sequential series of 18 children and adults, aged 4.4 to 21.5 years (mean 12.2 years), with clinically diagnosed ASD of varying severity used the system. Users and caregivers were interviewed about the perceived negative effects and design concerns. Most users were able to wear and use the Empowered Brain (n = 16/18, 89%), with most of them reporting no negative effects (n = 14/16, 87.5%). Caregivers observed no negative effects in users (n = 16/16, 100%). Most users (77.8%) and caregivers (88.9%) had no design concerns. This report found no major negative effects in using an AR smartglasses-based social communication aid across a wide age and severity range of people with ASD. Further research is needed to explore longer-term effects of using AR smartglasses in this population.

Cyclic Thiosulfinates and Cyclic Disulfides Selectively Cross-Link Thiols While Avoiding Modification of Lone Thiols.

This work addresses the need for chemical tools that can selectively form cross-links. Contemporary thiol-selective cross-linkers, for example, modify all accessible thiols, but only form cross-links between a subset. The resulting terminal "dead-end" modifications of lone thiols are toxic, confound cross-linking-based studies of macromolecular structure, and are an undesired, and currently unavoidable, byproduct in polymer synthesis. Using the thiol pair of Cu/Zn-superoxide dismutase (SOD1), we demonstrated that cyclic disulfides, including the drug/nutritional supplement lipoic acid, efficiently cross-linked thiol pairs but avoided dead-end modifications. Thiolate-directed nucleophilic attack upon the cyclic disulfide resulted in thiol-disulfide exchange and ring cleavage. The resulting disulfide-tethered terminal thiolate moiety either directed the reverse reaction, releasing the cyclic disulfide, or participated in oxidative disulfide (cross-link) formation. We hypothesized, and confirmed with density functional theory (DFT) calculations, that mono- S-oxo derivatives of cyclic disulfides formed a terminal sulfenic acid upon ring cleavage that obviated the previously rate-limiting step, thiol oxidation, and accelerated the new rate-determining step, ring cleavage. Our calculations suggest that the origin of accelerated ring cleavage is improved frontier molecular orbital overlap in the thiolate-disulfide interchange transition. Five- to seven-membered cyclic thiosulfinates were synthesized and efficiently cross-linked up to 104-fold faster than their cyclic disulfide precursors; functioned in the presence of biological concentrations of glutathione; and acted as cell-permeable, potent, tolerable, intracellular cross-linkers. This new class of thiol cross-linkers exhibited click-like attributes including, high yields driven by the enthalpies of disulfide and water formation, orthogonality with common functional groups, water-compatibility, and ring strain-dependence.

Improvement of Attention-Deficit/Hyperactivity Disorder Symptoms in School-Aged Children, Adolescents, and Young Adults With Autism via a Digital Smartglasses-Based Socioemotional Coaching Aid: Short-Term, Uncontrolled Pilot Study.

BACKGROUND: People with autism spectrum disorder (ASD) commonly experience symptoms related to attention-deficit/hyperactivity disorder (ADHD), including hyperactivity, inattention, and impulsivity. One-third of ASD cases may be complicated by the presence of ADHD. Individuals with dual diagnoses face greater barriers to accessing treatment for ADHD and respond less positively to primary pharmacologic interventions. Nonpharmacologic technology-aided tools for hyperactivity and inattention in people with ASD are being developed, although research into their efficacy and safety remains limited. OBJECTIVE: The objective of this preliminary study was to describe the changes in ADHD-related symptoms in children, adolescents, and young adults with ASD immediately after use of the Empowered Brain system, a behavioral and social communication aid for ASD running on augmented reality smartglasses. METHODS: We recruited 8 children, adolescents, and young adults with ASD (male to female ratio of 7:1, mean age 15 years, range 11.7-20.5 years) through a Web-based research signup form. The baseline score on the hyperactivity subscale of the Aberrant Behavioral Checklist (ABC-H), a measure of hyperactivity, inattention, and impulsivity, determined their classification into a high ADHD-related symptom group (n=4, ABC-H≥13) and a low ADHD-related symptom group (n=4, ABC-H<13). All participants received an intervention with Empowered Brain, where they used smartglasses-based social communication and behavioral modules while interacting with their caregiver. We then calculated caregiver-reported ABC-H scores at 24 and 48 hours after the session. RESULTS: All 8 participants were able to complete the intervention session. Postintervention ABC-H scores were lower for most participants at 24 hours (n=6, 75%) and for all participants at 48 hours (n=8, 100%). At 24 hours after the session, average participant ABC-H scores decreased by 54.9% in the high ADHD symptom group and by 20% in the low ADHD symptom group. At 48 hours after the session, ABC-H scores compared with baseline decreased by 56.4% in the high ADHD symptom group and by 66.3% in the low ADHD symptom group. CONCLUSIONS: This study provides initial evidence for the possible potential of the Empowered Brain system to reduce ADHD-related symptoms, such as hyperactivity, inattention, and impulsivity, in school-aged children, adolescents, and young adults with ASD. This digital smartglasses intervention can potentially be targeted at a broader array of mental health conditions that exhibit transdiagnostic attentional and social communication deficits, including schizophrenia and bipolar disorder. Further research is required to understand the clinical importance of these observed changes and to conduct longitudinal studies on this intervention with control groups and larger sample sizes.

Concussion Assessment With Smartglasses: Validation Study of Balance Measurement Toward a Lightweight, Multimodal, Field-Ready Platform.

BACKGROUND: Lightweight and portable devices that objectively measure concussion-related impairments could improve injury detection and critical decision-making in contact sports and the military, where brain injuries commonly occur but remain underreported. Current standard assessments often rely heavily on subjective methods such as symptom self-reporting. Head-mounted wearables, such as smartglasses, provide an emerging platform for consideration that could deliver the range of assessments necessary to develop a rapid and objective screen for brain injury. Standing balance assessment, one parameter that may inform a concussion diagnosis, could theoretically be performed quantitatively using current off-the-shelf smartglasses with an internal accelerometer. However, the validity of balance measurement using smartglasses has not been investigated. OBJECTIVE: This study aimed to perform preliminary validation of a smartglasses-based balance accelerometer measure (BAM) compared with the well-described and characterized waist-based BAM. METHODS: Forty-two healthy individuals (26 male, 16 female; mean age 23.8 [SD 5.2] years) participated in the study. Following the BAM protocol, each subject performed 2 trials of 6 balance stances while accelerometer and gyroscope data were recorded from smartglasses (Glass Explorer Edition). Test-retest reliability and correlation were determined relative to waist-based BAM as used in the National Institutes of Health's Standing Balance Toolbox. RESULTS: Balance measurements obtained using a head-mounted wearable were highly correlated with those obtained through a waist-mounted accelerometer (Spearman rho, ρ=.85). Test-retest reliability was high (intraclass correlation coefficient, ICC2,1=0.85, 95% CI 0.81-0.88) and in good agreement with waist balance measurements (ICC2,1=0.84, 95% CI 0.80-0.88). Considering the normalized path length magnitude across all 3 axes improved interdevice correlation (ρ=.90) while maintaining test-retest reliability (ICC2,1=0.87, 95% CI 0.83-0.90). All subjects successfully completed the study, demonstrating the feasibility of using a head-mounted wearable to assess balance in a healthy population. CONCLUSIONS: Balance measurements derived from the smartglasses-based accelerometer were consistent with those obtained using a waist-mounted accelerometer. Additional research is necessary to determine to what extent smartglasses-based accelerometry measures can detect balance dysfunction associated with concussion. However, given the potential for smartglasses to perform additional concussion-related assessments in an integrated, wearable platform, continued development and validation of a smartglasses-based balance assessment is warranted. This approach could lead to a wearable platform for real-time assessment of concussion-related impairments that could be further augmented with telemedicine capabilities to integrate professional clinical guidance. Smartglasses may be superior to fully immersive virtual reality headsets for this application, given their lighter weight and reduced likelihood of potential safety concerns.

Second Version of Google Glass as a Wearable Socio-Affective Aid: Positive School Desirability, High Usability, and Theoretical Framework in a Sample of Children with Autism.

BACKGROUND: Computerized smartglasses are being developed as an assistive technology for daily activities in children and adults with autism spectrum disorder (ASD). While smartglasses may be able to help with educational and behavioral needs, their usability and acceptability in children with ASD is largely unknown. There have been reports of negative social perceptions surrounding smartglasses use in mainstream populations, a concern given that assistive technologies may already carry their own stigma. Children with ASD may also have a range of additional behavioral, developmental, and social challenges when asked to use this emerging technology in school and home settings. OBJECTIVE: The usability and acceptability of Glass Enterprise Edition (Glass), the successor to Google Glass smartglasses, were explored in children with ASD and their caregivers. METHODS: Eight children with ASD and their caregivers were recruited to attend a demonstration session with Glass smartglasses the week they were publicly released. The children had a wide range of ability, including limited speech to speaking, and represented a full range of school ages (6 to 17 years). Children and caregivers were interviewed about their experience of using the smartglasses and whether they would use them at school and home. RESULTS: All 8 children succeeded in using Glass and did not feel stressed (8/8, 100%) or experience any overwhelming sensory or emotional issues during the session (8/8, 100%). All 8 children (8/8, 100%) endorsed that they would be willing to wear and use the device in both home and school settings. Caregivers felt the experience was fun for the children (8/8, 100%), and most caregivers felt the experience was better than they had expected (6/8, 75%). CONCLUSIONS: A wide age and ability range of children with ASD used Glass immediately after it was released and found it to be usable and acceptable. Despite concerns about potential stigma or social acceptability, all of the children were prepared to use the technology in both home and school settings. Encouragingly, most caregivers noted a very positive response. There were no behavioral, developmental, or social- or stigma-related concerns during or after the session. Smartglasses may be a useful future technology for children with ASD and are readily accepted for use by children with ASD and their caregivers.

Integrated Bottom-Up and Top-Down Liquid Chromatography-Mass Spectrometry for Characterization of Recombinant Human Growth Hormone Degradation Products.

With the advent of biosimilars to the U.S. market, it is important to have better analytical tools to ensure product quality from batch to batch. In addition, the recent popularity of using a continuous process for production of biopharmaceuticals, the traditional bottom-up method, alone for product characterization and quality analysis is no longer sufficient. Bottom-up method requires large amounts of material for analysis and is labor-intensive and time-consuming. Additionally, in this analysis, digestion of the protein with enzymes such as trypsin could induce artifacts and modifications which would increase the complexity of the analysis. On the other hand, a top-down method requires a minimum amount of sample and allows for analysis of the intact protein mass and sequence generated from fragmentation within the instrument. However, fragmentation usually occurs at the N-terminal and C-terminal ends of the protein with less internal fragmentation. Herein, we combine the use of the complementary techniques, a top-down and bottom-up method, for the characterization of human growth hormone degradation products. Notably, our approach required small amounts of sample, which is a requirement due to the sample constraints of small scale manufacturing. Using this approach, we were able to characterize various protein variants, including post-translational modifications such as oxidation and deamidation, residual leader sequence, and proteolytic cleavage. Thus, we were able to highlight the complementarity of top-down and bottom-up approaches, which achieved the characterization of a wide range of product variants in samples of human growth hormone secreted from Pichia pastoris.

Social Communication Coaching Smartglasses: Well Tolerated in a Diverse Sample of Children and Adults With Autism.

BACKGROUND: Augmented reality (AR) smartglasses are an emerging technology that is under investigation as a social communication aid for children and adults with autism spectrum disorder (ASD) and as a research tool to aid with digital phenotyping. Tolerability of this wearable technology in people with ASD is an important area for research, especially as these individuals may experience sensory, cognitive, and attentional challenges. OBJECTIVE: The aim of this study was to assess the tolerability and usability of a novel smartglasses system that has been designed as a social communication aid for children and adults with autism (the Brain Power Autism System [BPAS]). BPAS runs on Google Glass Explorer Edition and other smartglasses, uses both AR and affective artificial intelligence, and helps users learn key social and emotional skills. METHODS: A total of 21 children and adults with ASD across a spectrum of severity used BPAS for a coaching session. The user's tolerability to the smartglasses, user being able to wear the smartglasses for 1 minute (initial tolerability threshold), and user being able to wear the smartglasses for the entire duration of the coaching session (whole session tolerability threshold) were determined through caregiver report. RESULTS: Of 21 users, 19 (91%) demonstrated tolerability on all 3 measures. Caregivers reported 21 out of 21 users (100%) as tolerating the experience, while study staff found only 19 out of 21 users managed to demonstrate initial tolerability (91%). Of the 19 users who demonstrated initial tolerability, all 19 (100%) were able to use the smartglasses for the entire session (whole session tolerability threshold). Caregivers reported that 19 out of 21 users (91%) successfully used BPAS, and users surpassed caregiver expectations in 15 of 21 cases (71%). Users who could communicate reported BPAS as being comfortable (94%). CONCLUSIONS: This preliminary report suggests that BPAS is well tolerated and usable to a diverse age- and severity-range of people with ASD. This is encouraging as these devices are being developed as assistive technologies for people with ASD. Further research should focus on improving smartglasses design and exploring their efficacy in helping with social communication in children and adults with ASD.

Feasibility of an Autism-Focused Augmented Reality Smartglasses System for Social Communication and Behavioral Coaching.

BACKGROUND: Autism spectrum disorder (ASD) is a childhood-onset neurodevelopmental disorder with a rapidly rising prevalence, currently affecting 1 in 68 children, and over 3.5 million people in the United States. Current ASD interventions are primarily based on in-person behavioral therapies that are both costly and difficult to access. These interventions aim to address some of the fundamental deficits that clinically characterize ASD, including deficits in social communication, and the presence of stereotypies, and other autism-related behaviors. Current diagnostic and therapeutic approaches seldom rely on quantitative data measures of symptomatology, severity, or condition trajectory. METHODS: Given the current situation, we report on the Brain Power System (BPS), a digital behavioral aid with quantitative data gathering and reporting features. The BPS includes customized smartglasses, providing targeted personalized coaching experiences through a family of gamified augmented-reality applications utilizing artificial intelligence. These applications provide children and adults with coaching for emotion recognition, face directed gaze, eye contact, and behavioral self-regulation. This preliminary case report, part of a larger set of upcoming research reports, explores the feasibility of the BPS to provide coaching in two boys with clinically diagnosed ASD, aged 8 and 9 years. RESULTS: The coaching intervention was found to be well tolerated and rated as being both engaging and fun. Both males could easily use the system, and no technical problems were noted. During the intervention, caregivers reported improved non-verbal communication, eye contact, and social engagement during the intervention. Both boys demonstrated decreased symptoms of ASD, as measured by the aberrant behavior checklist at 24-h post-intervention. Specifically, both cases demonstrated improvements in irritability, lethargy, stereotypy, hyperactivity/non-compliance, and inappropriate speech. CONCLUSION: Smartglasses using augmented reality may have an important future role in helping address the therapeutic needs of children with ASD. Quantitative data gathering from such sensor-rich systems may allow for digital phenotyping and the refinement of social communication constructs of the research domain criteria. This report provides evidence for the feasibility, usability, and tolerability of one such specialized smartglasses system.

Heavy Sugar and Heavy Water Create Tunable Intact Protein Mass Increases for Quantitative Mass Spectrometry in Any Feed and Organism.

Stable isotope labeling techniques for quantitative top-down proteomics face unique challenges. These include unpredictable mass shifts following isotope labeling, which impedes analysis of unknown proteins and complex mixtures and exponentially greater susceptibility to incomplete isotope incorporation, manifesting as broadening of labeled intact protein peaks. Like popular bottom-up isotope labeling techniques, most top-down labeling methods are restricted to defined media/feed as well as amino acid auxotrophic organisms. We present a labeling method optimized for top-down proteomics that overcomes these challenges. We demonstrated this method through the spiking of 13C-sugar or 2H-water into standard laboratory feedstocks, resulting in tunable intact protein mass increases (TIPMI). After mixing of labeled and unlabeled samples, direct comparison of light and heavy peaks allowed for the relative quantitation of intact proteins in three popular model organisms, including prokaryotic and eukaryotic microorganisms and an animal. This internal standard method proved to be more accurate than label-free quantitation in our hands. Advantages over top-down SILAC include working equally well in nutrient-rich media, conceivably expanding applicability to any organism and all classes of biomolecules, not requiring high-resolving power MS for quantitation and being relatively inexpensive.

Imaging and Mapping of Tissue Constituents at the Single-Cell Level Using MALDI MSI and Quantitative Laser Scanning Cytometry.

For nearly a century, histopathology involved the laborious morphological analyses of tissues stained with broad-spectrum dyes (i.e., eosin to label proteins). With the advent of antibody-labeling, immunostaining (fluorescein and rhodamine for fluorescent labeling) and immunohistochemistry (DAB and hematoxylin), it became possible to identify specific immunological targets in cells and tissue preparations. Technical advances, including the development of monoclonal antibody technology, led to an ever-increasing palate of dyes, both fluorescent and chromatic. This provides an incredibly rich menu of molecular entities that can be visualized and quantified in cells-giving rise to the new discipline of Molecular Pathology. We describe the evolution of two analytical techniques, cytometry and mass spectrometry, which complement histopathological visual analysis by providing automated, cellular-resolution constituent maps. For the first time, laser scanning cytometry (LSC) and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) are combined for the analysis of tissue sections. The utility of the marriage of these techniques is demonstrated by analyzing mouse brains with neuron-specific, genetically encoded, fluorescent proteins. We present a workflow that: (1) can be used with or without expensive matrix deposition methods, (2) uses LSC images to reveal the diverse landscape of neural tissue as well as the matrix, and (3) uses a tissue fixation method compatible with a DNA stain. The proposed workflow can be adapted for a variety of sample preparation and matrix deposition methods.

The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation.

BACKGROUND: The brown ghost knifefish (Apteronotus leptorhynchus) is a weakly electric teleost fish of particular interest as a versatile model system for a variety of research areas in neuroscience and biology. The comprehensive information available on the neurophysiology and neuroanatomy of this organism has enabled significant advances in such areas as the study of the neural basis of behavior, the development of adult-born neurons in the central nervous system and their involvement in the regeneration of nervous tissue, as well as brain aging and senescence. Despite substantial scientific interest in this species, no genomic resources are currently available. RESULTS: Here, we report the de novo assembly and annotation of the A. leptorhynchus transcriptome. After evaluating several trimming and transcript reconstruction strategies, de novo assembly using Trinity uncovered 42,459 unique contigs containing at least a partial protein-coding sequence based on alignment to a reference set of known Actinopterygii sequences. As many as 11,847 of these contigs contained full or near-full length protein sequences, providing broad coverage of the proteome. A variety of non-coding RNA sequences were also identified and annotated, including conserved long intergenic non-coding RNA and other long non-coding RNA observed previously to be expressed in adult zebrafish (Danio rerio) brain, as well as a variety of miRNA, snRNA, and snoRNA. Shotgun proteomics confirmed translation of open reading frames from over 2,000 transcripts, including alternative splice variants. Assignment of tandem mass spectra was greatly improved by use of the assembly compared to databases of sequences from closely related organisms. The assembly and raw reads have been deposited at DDBJ/EMBL/GenBank under the accession number GBKR00000000. Tandem mass spectrometry data is available via ProteomeXchange with identifier PXD001285. CONCLUSIONS: Presented here is the first release of an annotated de novo transcriptome assembly from Apteronotus leptorhynchus, providing a broad overview of RNA expressed in central nervous system tissue. The assembly, which includes substantial coverage of a wide variety of both protein coding and non-coding transcripts, will allow the development of better tools to understand the mechanisms underlying unique characteristics of the knifefish model system, such as their tremendous regenerative capacity and negligible brain senescence.

QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure.

BACKGROUND: Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13. Recent studies demonstrated that high-performance mass spectrometers could resolve isotopic fine structure and eliminate this peak overlap, allowing direct detection and quantification of deuterium incorporation. RESULTS: Here, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure. Given a peptide sequence (or elemental formula) and charge state, the mass-to-charge ratios of deuterium-associated peaks of the specified ion is determined. Intensities of peaks in an experimental mass spectrum within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated based on the estimated distribution of deuterium exchange to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter. A tool is also incorporated into QUDeX-MS to help in assigning ion signals from peptides arising from enzymatic digestion of proteins. MATLAB-deployable and standalone versions are available for academic use at qudex-ms.sourceforge.net and agarlabs.com . CONCLUSION: Isotopic fine structure HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mass accuracy and deconvolution of overlapping ion signals. As previously demonstrated, however, the data analysis workflow for HDX-MS data with resolved isotopic fine structure is distinct. QUDeX-MS we hope will aid in the adoption of isotopic fine structure HDX-MS by providing an intuitive workflow and interface for data analysis.

The first pilot project of the consortium for top-down proteomics: a status report.

Pilot Project #1--the identification and characterization of human histone H4 proteoforms by top-down MS--is the first project launched by the Consortium for Top-Down Proteomics (CTDP) to refine and validate top-down MS. Within the initial results from seven participating laboratories, all reported the probability-based identification of human histone H4 (UniProt accession P62805) with expectation values ranging from 10(-13) to 10(-105). Regarding characterization, a total of 74 proteoforms were reported, with 21 done so unambiguously; one new PTM, K79ac, was identified. Inter-laboratory comparison reveals aspects of the results that are consistent, such as the localization of individual PTMs and binary combinations, while other aspects are more variable, such as the accurate characterization of low-abundance proteoforms harboring >2 PTMs. An open-access tool and discussion of proteoform scoring are included, along with a description of general challenges that lie ahead including improved proteoform separations prior to mass spectrometric analysis, better instrumentation performance, and software development.

Artifacts to avoid while taking advantage of top-down mass spectrometry based detection of protein S-thiolation.

Bottom-up MS studies typically employ a reduction and alkylation step that eliminates a class of PTM, S-thiolation. Given that molecular oxygen can mediate S-thiolation from reduced thiols, which are abundant in the reducing intracellular milieu, we investigated the possibility that some S-thiolation modifications are artifacts of protein preparation. Cu/Zn-superoxide dismutase (SOD1) was chosen for this case study as it has a reactive surface cysteine residue, which is readily cysteinylated in vitro. The ability of oxygen to generate S-thiolation artifacts was tested by comparing purification of SOD1 from postmortem human cerebral cortex under aerobic and anaerobic conditions. S-thiolation was ∼50% higher in aerobically processed preparations, consistent with oxygen-dependent artifactual S-thiolation. The ability of endogenous small molecule disulfides (e.g. cystine) to participate in artifactual S-thiolation was tested by blocking reactive protein cysteine residues during anaerobic homogenization. A 50-fold reduction in S-thiolation occurred indicating that the majority of S-thiolation observed aerobically was artifact. Tissue-specific artifacts were explored by comparing brain- and blood-derived protein, with remarkably more artifacts observed in brain-derived SOD1. Given the potential for such artifacts, rules of thumb for sample preparation are provided. This study demonstrates that without taking extraordinary precaution, artifactual S-thiolation of highly reactive, surface-exposed, cysteine residues can result.

A rapid MALDI-TOF mass spectrometry workflow for Drosophila melanogaster differential neuropeptidomics.

BACKGROUND: Neuropeptides are a diverse category of signaling molecules in the nervous system regulating a variety of processes including food intake, social behavior, circadian rhythms, learning, and memory. Both the identification and functional characterization of specific neuropeptides are ongoing fields of research. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis of nervous tissues from a variety of organisms allows direct detection and identification of neuropeptides. Here, we demonstrate an analysis workflow that allows for the detection of differences in specific neuropeptides amongst a variety of neuropeptides being simultaneously measured. For sample preparation, we describe a straight-forward and rapid (minutes) method where individual adult Drosophila melanogaster brains are analyzed. Using a MATLAB-based data analysis workflow, also compatible with MALDI-TOF mass spectra obtained from other sample preparations and instrumentation, we demonstrate how changes in neuropeptides levels can be detected with this method. RESULTS: Over fifty isotopically resolved ion signals in the peptide mass range are reproducibly observed across experiments. MALDI-TOF MS profile spectra were used to statistically identify distinct relative differences in organ-wide endogenous levels of detected neuropeptides between biological conditions. In particular, three distinct levels of a particular neuropeptide, pigment dispersing factor, were detected by comparing groups of preprocessed spectra obtained from individual brains across three different D. melanogaster strains, each of which express different amounts of this neuropeptide. Using the same sample preparation, MALDI-TOF/TOF tandem mass spectrometry confirmed that at least 14 ion signals observed across experiments are indeed neuropeptides. Among the identified neuropeptides were three products of the neuropeptide-like precursor 1 gene previously not identified in the literature. CONCLUSIONS: Using MALDI-TOF MS and preprocessing/statistical analysis, changes in relative levels of a particular neuropeptide in D. melanogaster tissue can be statistically detected amongst a variety of neuropeptides. While the data analysis methods should be compatible with other sample preparations, the presented sample preparation method was sufficient to identify previously unconfirmed D. melanogaster neuropeptides.

Post-translational modification by cysteine protects Cu/Zn-superoxide dismutase from oxidative damage.

Reactive oxygen species (ROS) are cytotoxic. To remove ROS, cells have developed ROS-specific defense mechanisms, including the enzyme Cu/Zn superoxide dismutase (SOD1), which catalyzes the disproportionation of superoxide anions into molecular oxygen and hydrogen peroxide. Although hydrogen peroxide is less reactive than superoxide, it is still capable of oxidizing, unfolding, and inactivating SOD1, at least in vitro. To explore the relevance of post-translational modification (PTM) of SOD1, including peroxide-related modifications, SOD1 was purified from postmortem human nervous tissue. As much as half of all purified SOD1 protein contained non-native post-translational modifications (PTMs), the most prevalent modifications being cysteinylation and peroxide-related oxidations. Many PTMs targeted a single reactive SOD1 cysteine, Cys111. An intriguing observation was that unlike native SOD1, cysteinylated SOD1 was not oxidized. To further characterize how cysteinylation may protect SOD1 from oxidation, cysteine-modified SOD1 was prepared in vitro and exposed to peroxide. Cysteinylation conferred nearly complete protection from peroxide-induced oxidation of SOD1. Moreover, SOD1 that has been cysteinylated and peroxide oxidized in vitro comprised a set of PTMs that bear a striking resemblance to the myriad of PTMs observed in SOD1 purified from human tissue.

Docking study of triphenylphosphonium cations as estrogen receptor alpha modulators.

Virtual high throughput screening (VHTS) was performed to assess possible interactions which might occur between commercially available triphenylphosphonium (TPP) cations and estrogen receptor alpha (ERalpha) that could be exploited to design novel ERalpha modulators. One application of TPP cations is for delivering bioactive molecules to targets in mitochondria as the large membrane potential of mitochondria leads cations to accumulate inside them. The estrogen receptors (ERs) alpha and beta, normally activated by the endogenous hormone 17beta-estradiol, are responsible for controlling transcription of nuclear DNA necessary for human development and reproduction. ERs are also associated with the plasma membrane and have been found in the mitochondria of a variety of cell types. Selective estrogen receptor modulators (SERMs) are synthetic compounds which are used to modulate ER activity. Different SERMs display varying combinations of agonistic, antagonistic and neutral effects upon estrogen receptors depending upon the tissue type and cellular location of the receptor. Thus, they are being employed to treat a range of ER-related disorders. A common feature shared by many SERMs is the close arrangement of three aromatic rings similar to TPP cations. Given this structural similarity, the estrogenic activity of triphenyl phosphonium salts was investigated using the automated docking program eHiTS. Compounds were docked into ten different crystal structures of ERalpha. Structures were chosen based upon eHiTS ability to accurately identify the majority of estrogenically active compounds given a set of active and decoy molecules. The results of the VHTS suggest hybrids of TPP cations and known SERMs could serve as potent mitochondrial SERMs.