Informatics and Artificial Intelligence-Guided Assessment of the Regulatory and Translational Research Landscape of First-in-Class Oncology Drugs in the United States, 2018-2022.

PURPOSE: Cancer drug development remains a critical but challenging process that affects millions of patients and their families. Using biomedical informatics and artificial intelligence (AI) approaches, we assessed the regulatory and translational research landscape defining successful first-in-class drugs for patients with cancer. METHODS: This is a retrospective observational study of all novel first-in-class drugs approved by the US Food and Drug Administration (FDA) from 2018 to 2022, stratified by cancer versus noncancer drugs. A biomedical informatics pipeline leveraging interoperability standards and ChatGPT performed integration and analysis of public databases provided by the FDA, National Institutes of Health, and WHO. RESULTS: Between 2018 and 2022, the FDA approved a total of 247 novel drugs, of which 107 (43.3%) were first-in-class drugs involving a new biologic target. Of these first-in-class drugs, 30 (28%) treatments were indicated for patients with cancer, including 19 (63.3%) for solid tumors and the remaining 11 (36.7%) for hematologic cancers. A median of 68 publications of basic, clinical, and other relevant translational science preceded successful FDA approval of first-in-class cancer drugs, with oncology-related treatments involving fewer median years of target-based research than therapies not related to cancer (33 v 43 years; P < .05). Overall, 94.4% of first-in-class drugs had at least 25 years of target-related research papers, while 85.5% of first-in-class drugs had at least 10 years of translational research publications. CONCLUSION: Novel first-in-class cancer treatments are defined by diverse clinical indications, personalized molecular targets, dependence on expedited regulatory pathways, and translational research metrics reflecting this complex landscape. Biomedical informatics and AI provide scalable, data-driven ways to assess and even address important challenges in the drug development pipeline.

Practical Aspects of Using Large Language Models to Screen Abstracts for Cardiovascular Drug Development: Cross-Sectional Study.

Unlabelled: Cardiovascular drug development requires synthesizing relevant literature about indications, mechanisms, biomarkers, and outcomes. This short study investigates the performance, cost, and prompt engineering trade-offs of 3 large language models accelerating the literature screening process for cardiovascular drug development applications.

Patient Acceptability and Preferences for Solid Oral Dosage Form Drug Product Attributes: A Scoping Review.

Background: There is no consistent framework for patient-centric drug product design, despite the common understanding that drug product acceptability and preferences influence adherence and, therefore, drug product effectiveness. The aim of this review was to assess current understanding of patient acceptability and preferences for solid oral dosage form (SODF) drug product attributes, and the potential impact of these attributes on patient behaviors and outcomes. Patients and Methods: A scoping review was conducted. Embase, Ovid MEDLINE®, and PubMed® were searched for full-text articles published between January 2013 and May 2023. Following screening and assessment against predefined inclusion criteria, data were analyzed thematically. Results: Nineteen studies were included. Four overarching domains of drug product attributes were identified and summarized in a framework: appearance, swallowability, palatability, and handling. Each domain was informed by specific drug product attributes: texture, form, size, shape, color, marking, taste, mouthfeel, and smell. The most frequently studied domains were swallowability and appearance, while the most studied attributes were size, shape, and texture. Smell, marking, and mouthfeel were the least studied attributes. Texture intersected all domains, while form, shape, and size intersected appearance, swallowability, and handling. Swallowability and size appeared to be the key domain and attribute, respectively, to consider when designing drug products. Few studies explored the impact of drug product attributes on behaviors and outcomes. Conclusion: While existing studies of drug product attributes have focused on appearance and swallowability, this review highlighted the importance of two less well-understood domains-palatability and handling-in understanding patients' acceptability and preferences for SODF drug products. The framework provides a tool to facilitate patient-centric design of drug products, organizing and categorizing physical drug product attributes into four overarching domains (appearance, swallowability, palatability, and handling), encouraging researchers to comprehensively assess the impact of drug product attributes on patient acceptability, preferences, and outcomes.

Medicines come in a variety of types and forms. These include tablets and capsules. Factors, such as the size and shape of tablets, can affect how people take medicines. However, patients are rarely involved in designing the medicines that they take. In this study, researchers summarized 19 studies published between 2013 and 2023. They wanted to understand how different factors, like size and shape, affect patients' preferences, ability, and willingness to take medicines. Researchers focused on the "physical" aspects of medicines and found 4 common themes: 1) what they look like (appearance), 2) how easy they are to swallow (swallowability), 3) how they taste and feel in the mouth (palatability), and 4) how easy they are to handle (handling). Eight factors were also found: color, markings, shape, size, smell, taste, texture, and how a medicine feels in the mouth (mouthfeel). Most studies focused on what medicines look like and how easy they are to swallow. The factors that researchers mostly looked at were the size, shape, and texture of medicines. The design of medicines can impact patients of different ages, though there may be specific needs for certain groups of patients, including children, older adults, and people with certain diseases. Patient input should become a part of future medicines design to ensure their acceptability.

Cognitive symptoms and welding fume exposure.

BACKGROUND: Prevalence of moderate to severe cognitive symptoms is markedly higher in UK professional divers who have also worked as a welder (28%) than in either divers who have not welded (18%) or offshore workers who have worked neither as a diver nor as a welder (6%). OBJECTIVES: To determine whether cognitive symptoms are related to welding fume exposure or diving. METHODS: Three age-matched groups of male workers were studied using postal questionnaire: professional divers who had worked as a welder (PDW, n = 361), professional welders who had not dived (NDW, n = 352), and offshore oil field workers who had neither dived nor welded (NDNW, n =503). Health-related quality of life was assessed by the Short Form 12 questionnaire (SF12). Cognitive symptomatology was assessed using the Cognitive Failures Questionnaire (CFQ). A single variable for welding fume exposure (mg m(-3) days) was calculated, incorporating welding experience in different environments and using different welding techniques and respiratory protective equipment. The level of fume exposure during hyperbaric welding operations was measured during such work as ambient PM(10) (particles of 10 µm or less). Diving exposure was assessed as the number of dives performed plus the number of days spent working during saturation diving. RESULTS: Questionnaires were returned by 153 PDW, 108 NDW, and 252 NDNW. SF12 scores were the same in all groups and fell within normative values. Mean (95% CI) CFQ scores were higher in PDW [40.3 (37.7-42.9)] than in both NDW [34.6 (31.6-37.7)] and NDNW [32.1 (30.4-33.9)], but the scores in no groups fell outside the normative range. The mean PM(10) exposure during hyperbaric welding operations was 2.58 mg m(-3). The geometric mean mg m(-3) days (95% CI) for welding fume exposure in NDW [33 128 (24 625-44 567) n = 85] was higher than for that in PDW [10 904 (8103-14 673) n = 112]. For PDW the geometric mean (95% CI) diving exposure was 1491 [(1192-1866) n = 94] dives and days in saturation. In the general linear model regression analyses adjusted for age, alcohol consumption, and somatization, there was no signification association of CFQ score with either welding fume exposure (F = 0.072, P = 0.79, n = 152) or diving exposure (F = 0.042, P = 0.84, n = 74). CONCLUSIONS: In conclusion, cognitive sympomatology was not related to retrospectively assessed measures of welding fume exposure or diving experience. In addition, the levels of cognitive symptomatology, even in PDW, did not exceed normative values.

Priority Outcomes in Sickle Cell Disease Treatment: Co-Creation and Implementation of a Preference Exercise With Patients and Caregivers to Inform Drug Development.

Involving patients as co-leaders and co-creators in research is key to reflecting the patient's voice in decision-making. However, co-creation of patient-centered data to inform decisions is rare, especially in early drug development where patient input is critical to prioritizing patient-relevant outcomes and endpoints for use in clinical trials. Despite the industry's growing commitment to patient centricity, most patients are excluded from sharing their expertise in research; more inclusive methods of engaging patients as research partners are needed. We describe a collaboration between a pharmaceutical company and a patient organization in co-leading and co-creating a program to understand priorities of patients and caregivers for treatment features and outcomes in sickle cell disease to inform endpoint selection in clinical development. The results of this program will be used as a basis for continued interaction between patients and the sponsor and to inform ongoing clinical development and evidence-generation activities. This case study demonstrates an approach to meaningful collaborations between patient organizations and pharmaceutical companies aimed at including the patient's voice early in the medical product lifecycle.

Hearing symptoms and audiometry in professional divers and offshore workers.

AIMS: The aims are to compare hearing loss between professional divers and offshore workers and to study whether hearing loss symptoms reflected physical disorder. A secondary objective was to study total threshold shift assessment as a method of detecting noise-induced hearing loss (NIHL). METHODS: Participants (151 divers and 120 offshore workers) completed a questionnaire for symptoms and screening audiometry. Audiograms were assessed for total threshold shift at 1, 2, 3, 4 and 6 kHz and the prevalence of referral (within population 5th centile) or warning levels (within population 20th centile) of hearing loss. Audiograms were assessed for an NIHL pattern at four levels by two occupational physicians. RESULTS: Hearing loss symptoms were commoner in divers at all levels of hearing loss regardless of differences between groups on audiometry. Hearing loss in offshore workers was within the population age-adjusted norm. Thirteen per cent of divers were within the 5th percentile for threshold shift for the population norm in contrast to 4% of offshore workers and this was predominantly left sided (OR 3.16, 95% CI 1.13-8.93). This difference was lost after adjustment for history of regular exposure to explosion or gunfire. Divers were more likely to have a pattern of severe NIHL on the left (OR 4.61, 95% CI 1.39-15.39, P < 0.05). Approximately 50% of participants with severe NIHL did not have a referral level of hearing loss. CONCLUSIONS: Divers suffer more NIHL than a control population. Current guidance on the assessment of total threshold shift for the detection of significant NIHL was inadequate in the sample studied.

The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes.

The structure of the glycerophosphodiesterase (GDPD) from Enterobacter aerogenes, GpdQ, has been solved by SAD phasing from the active site metal ions. Structural analysis indicates that GpdQ belongs to the alpha/beta sandwich metallo-phosphoesterase family, rather than the (alpha/beta)(8) barrel GDPD family, suggesting that GpdQ is a structurally novel GDPD. Hexameric GpdQ is generated by interactions between three dimers. The dimers are formed through domain swapping, stabilised by an inter-chain disulfide bond, and beta-sheet extension. The active site contains a binuclear metal centre, with a fully occupied alpha-metal ion site, and partially occupied beta-metal ion site, as revealed by anomalous scattering analysis. Using a combination of TLS refinement and normal mode analysis, the dynamic movement of GpdQ was investigated. This analysis suggests that the hexameric quaternary structure stabilises the base of the dimer, which promotes "breathing" of the active site cleft. Comparison with other metallo-phosphodiesterases shows that although the central, catalytic, domain is highly conserved, many of these enzymes possess structurally unrelated secondary domains located at the entrance of the active site. We suggest that this could be a common structural feature of metallo-phosphodiesterases that constrains substrate specificity, preventing non-specific phosphodiester hydrolysis.

Effect of protein stabilization on charge state distribution in positive- and negative-ion electrospray ionization mass spectra.

Changes in protein conformation are thought to alter charge state distributions observed in electrospray ionization mass spectra (ESI-MS) of proteins. In most cases, this has been demonstrated by unfolding proteins through acidification of the solution. This methodology changes the properties of the solvent so that changes in the ESI-MS charge envelopes from conformational changes are difficult to separate from the effects of changing solvent on the ionization process. A novel strategy is presented enabling comparison of ESI mass spectra of a folded and partially unfolded protein of the same amino acid sequence subjected to the same experimental protocols and conditions. The N-terminal domain of the Escherichia coli DnaB protein was cyclized by in vivo formation of an amide bond between its N- and C-termini. The properties of this stabilized protein were compared with its linear counterpart. When the linear form was unfolded by decreasing pH, a charge envelope at lower m/z appeared consistent with the presence of a population of unfolded protein. This was observed in both positive-ion and negative-ion ESI mass spectra. Under the same conditions, this low m/z envelope was not present in the ESI mass spectrum of the stable cyclized form. The effects of changing the desolvation temperature in the ionization source of the Q-TOF mass spectrometer were also investigated. Increasing the desolvation temperature had little effect on positive-ion ESI mass spectra, but in negative-ion spectra, a charge envelope at lower m/z appeared, consistent with an increase in the abundance of unfolded protein molecules.

The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria.

F420 is a low-potential redox cofactor that mediates the transformations of a wide range of complex organic compounds. Considered one of the rarest cofactors in biology, F420 is best known for its role in methanogenesis and has only been chemically identified in two phyla to date, the Euryarchaeota and Actinobacteria. In this work, we show that this cofactor is more widely distributed than previously reported. We detected the genes encoding all five known F420 biosynthesis enzymes (cofC, cofD, cofE, cofG and cofH) in at least 653 bacterial and 173 archaeal species, including members of the dominant soil phyla Proteobacteria, Chloroflexi and Firmicutes. Metagenome datamining validated that these genes were disproportionately abundant in aerated soils compared with other ecosystems. We confirmed through high-performance liquid chromatography analysis that aerobically grown stationary-phase cultures of three bacterial species, Paracoccus denitrificans, Oligotropha carboxidovorans and Thermomicrobium roseum, synthesized F420, with oligoglutamate sidechains of different lengths. To understand the evolution of F420 biosynthesis, we also analyzed the distribution, phylogeny and genetic organization of the cof genes. Our data suggest that although the Fo precursor to F420 originated in methanogens, F420 itself was first synthesized in an ancestral actinobacterium. F420 biosynthesis genes were then disseminated horizontally to archaea and other bacteria. Together, our findings suggest that the cofactor is more significant in aerobic bacterial metabolism and soil ecosystem composition than previously thought. The cofactor may confer several competitive advantages for aerobic soil bacteria by mediating their central metabolic processes and broadening the range of organic compounds they can synthesize, detoxify and mineralize.

Stabilization of native protein fold by intein-mediated covalent cyclization.

A mutant version of the N-terminal domain of Escherichia coli DnaB helicase was used as a model system to assess the stabilization against unfolding gained by covalent cyclization. Cyclization was achieved in vivo by formation of an amide bond between the N and C termini with the help of a split mini-intein. Linear and circular proteins were constructed to be identical in amino acid sequence. Mutagenesis of Phe102 to Glu rendered the protein monomeric even at high concentration. A difference in free energy of unfolding, DeltaDeltaG, between circular and linear protein of 2.3(+/-0.5) kcal mol(-1) was measured at 10 degrees C by circular dichroism. A theoretical estimate of the difference in conformational entropy of linear and circular random chains in a three-dimensional cubic lattice model predicted DeltaDeltaG=2.3 kcal mol(-1), suggesting that stabilization by protein cyclization is driven by the reduced conformational entropy of the unfolded state. Amide-proton exchange rates measured by NMR spectroscopy and mass spectrometry showed a uniform, approximately tenfold decrease of the exchange rates of the most slowly exchanging amide protons, demonstrating that cyclization globally decreases the unfolding rate of the protein. The amide proton exchange was found to follow EX1 kinetics at near-neutral pH, in agreement with an unusually slow refolding rate of less than 4 min(-1) measured by stopped-flow circular dichroism. The linear and circular proteins differed more in their unfolding than in their folding rates. Global unfolding of the N-terminal domain of E.coli DnaB is thus promoted strongly by spatial separation of the N and C termini, whereas their proximity is much less important for folding.

Proteomic dissection of DNA polymerization.

DNA polymerases replicate the genome by associating with a range of other proteins that enable rapid, high-fidelity copying of DNA. This complex of proteins and nucleic acids is termed the replisome. Proteins of the replisome must interact with other networks of proteins, such as those involved in DNA repair. Many of the proteins involved in DNA polymerization and the accessory proteins are known, but the array of proteins they interact with, and the spatial and temporal arrangement of these interactions, are current research topics. Mass spectrometry is a technique that can be used to identify the sites of these interactions and to determine the precise stoichiometries of binding partners in a functional complex. A complete understanding of the macromolecular interactions involved in DNA replication and repair may lead to discovery of new targets for antibiotics against bacteria and biomarkers for diagnosis of diseases, such as cancer, in humans.

Objective neuropsychological test performance of professional divers reporting a subjective complaint of "forgetfulness or loss of concentration".

OBJECTIVE: This study attempted to determine whether the higher prevalence of reported "forgetfulness or loss of concentration" among professional divers can be confirmed using objective neuropsychological tests. Secondary aims were to qualify the functional nature of the complaints and to ascertain whether reduced performance was linked to diving history. METHODS: In a case-control study, the neuropsychological test performance of divers complaining of moderate or severe "forgetfulness or loss of concentration" was compared with two age-matched control groups reporting no or slight "forgetfulness or loss of concentration" ("nonforgetful" divers and "nonforgetful" nondivers). The group differences were analyzed using a multivariate analysis of co-variance, followed by canonical discriminant function analysis. Altogether 102 divers with a complaint, 100 nonforgetful divers, and 100 nonforgetful nondivers completed the study. RESULTS: The overall neuropsychological performance differed significantly between the groups [Pillai's trace: F(24,484)=2.04, P=0.003]. Verbal memory (Logical Memory and the California Verbal Learning Test), current intelligence (Wechsler Abbreviated Scale of Intelligence), and sustained attention (rapid visual processing) were poorer among the divers with a complaint than among the nonforgetful divers or the nonforgetful nondivers. The tests of memory, but not those of executive function, differentiated the divers with complaints from the two control groups. Mixed gas bounce diving and surface oxygen decompression diving, but not other techniques, were negatively associated with memory performance. CONCLUSIONS: A cognitive complaint of divers was confirmed using objective tests of neuropsychological performance. Memory, rather than executive function, was affected at the group level, but only to a mild degree. The relationships between diving experience and neuropsychological test performance were small and only seen with diving techniques used in the offshore oil and gas industry.

Effect of hypobaric hypoxia, simulating conditions during long-haul air travel, on coagulation, fibrinolysis, platelet function, and endothelial activation.

CONTEXT: The link between long-haul air travel and venous thromboembolism is the subject of continuing debate. It remains unclear whether the reduced cabin pressure and oxygen tension in the airplane cabin create an increased risk compared with seated immobility at ground level. OBJECTIVE: To determine whether hypobaric hypoxia, which may be encountered during air travel, activates hemostasis. DESIGN, SETTING, AND PARTICIPANTS: A single-blind, crossover study, performed in a hypobaric chamber, to assess the effect of an 8-hour seated exposure to hypobaric hypoxia on hemostasis in 73 healthy volunteers, which was conducted in the United Kingdom from September 2003 to November 2005. Participants were screened for factor V Leiden G1691A and prothrombin G20210A mutation and were excluded if they tested positive. Blood was drawn before and after exposure to assess activation of hemostasis. INTERVENTIONS: Individuals were exposed alternately (> or =1 week apart) to hypobaric hypoxia, similar to the conditions of reduced cabin pressure during commercial air travel (equivalent to atmospheric pressure at an altitude of 2438 m), and normobaric normoxia (control condition; equivalent to atmospheric conditions at ground level, circa 70 m above sea level). MAIN OUTCOME MEASURES: Comparative changes in markers of coagulation activation, fibrinolysis, platelet activation, and endothelial cell activation. RESULTS: Changes were observed in some hemostatic markers during the normobaric exposure, attributed to prolonged sitting and circadian variation. However, there were no significant differences between the changes in the hypobaric and the normobaric exposures. For example, the median difference in change between the hypobaric and normobaric exposure was 0 ng/mL for thrombin-antithrombin complex (95% CI, -0.30 to 0.30 ng/mL); -0.02 [corrected] nmol/L for prothrombin fragment 1 + 2 (95% CI, -0.03 to 0.01 nmol/L); 1.38 ng/mL for D-dimer (95% CI, -3.63 to 9.72 ng/mL); and -2.00% for endogenous thrombin potential (95% CI, -4.00% to 1.00%). CONCLUSION: Our findings do not support the hypothesis that hypobaric hypoxia, of the degree that might be encountered during long-haul air travel, is associated with prothrombotic alterations in the hemostatic system in healthy individuals at low risk of venous thromboembolism.

Translational incorporation of L-3,4-dihydroxyphenylalanine into proteins.

An Escherichia coli cell-free transcription/translation system was used to explore the high-level incorporation of L-3,4-dihydroxyphenylalanine (DOPA) into proteins by replacing tyrosine with DOPA in the reaction mixtures. ESI-MS showed specific incorporation of DOPA in place of tyrosine. More than 90% DOPA incorporation at each tyrosine site was achieved, allowing the recording of clean 15N-HSQC NMR spectra. A redox-staining method specific for DOPA was shown to provide a sensitive and generally applicable method for assessing the cell-free production of proteins. Of four proteins produced in soluble form in the presence of tyrosine, two resulted in insoluble aggregates in the presence of high levels of DOPA. DOPA has been found in human proteins, often in association with various disease states that implicate protein aggregation and/or misfolding. Our results suggest that misfolded and aggregated proteins may result, in principle, from ribosome-mediated misincorporation of intracellular DOPA accumulated due to oxidative stress. High-yield cell-free protein expression systems are uniquely suited to obtain rapid information on solubility and aggregation of nascent polypeptide chains.

DNA-binding properties of cosmomycin D, an anthracycline with two trisaccharide chains.

Cosmomycin D (CosD) is the major constituent fraction isolated from a culture of Streptomyces olindensis ICB20. The ability of this compound to intercalate with double-stranded DNA was studied by gel mobility shift assays and electrospray ionization mass spectrometry (ESI-MS). ESI-MS experiments showed that the complex of CosD with 16-mer double-stranded DNA was at least as stable as a complex of daunorubicin with the same DNA sequence. This is the first study showing DNA binding properties of an anthracycline containing a beta-rhodomycinone aglycone chromophore O-linked to two trisaccharide chains.

Psychological and physical correlates of musculoskeletal symptoms in male professional divers and offshore workers.

BACKGROUND: Underwater divers are more likely to complain of musculoskeletal symptoms than a control population. Accordingly, we conducted a study to determine whether musculoskeletal symptoms reflected observable physical disorder, to ascertain the relationship between symptoms and measures of mood, memory and executive function and to assess any need for future screening. METHODS: A 10% random sample of responders to a prior postal health questionnaire was examined (151 divers, 120 non-diving offshore workers). Participants underwent physical examination and a neuropsychological test battery for memory and executive function. Participants also completed the Hospital Anxiety and Depression Scale for anxiety (HADSa) and depression (HADSd), and questionnaires for physical health-related quality of life (SF36 PCS), mental health-related quality of life (SF36 MCS), memory (Cognitive Failures Questionnaire (CFQ), Prospective and Retrospective Memory Questionnaire (PRMQ)), executive function (dysexecutive syndrome questionnaire (DEX)), musculoskeletal symptoms (MSS) and general unrelated symptom reporting. RESULTS: Of participants with moderate/severe musculoskeletal symptoms, 52% had physical signs, and of participants with no symptoms, 73% had no physical signs. There was no difference in the prevalence of signs or symptoms between groups. Musculoskeletal symptoms were associated with lower SF36 PCS for both groups. In divers, musculoskeletal symptoms were associated with higher general unrelated symptom reporting and poorer scoring for HADSa, PRMQ, CFQ and DEX with scores remaining within the normative range. A positive physical examination was associated with general unrelated symptom reporting in divers. There were no differences in neuropsychological test scores attributable to either group or musculoskeletal symptoms. CONCLUSIONS: Musculoskeletal symptoms were associated with physical signs, but this was not a strong effect. Reporting of musculoskeletal symptoms by the divers studied was also associated with a tendency to report symptoms generally or somatisation, and caution should be exercised regarding their interpretation as an indication of physical disease or their use for health screening.

Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination.

Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(epsilon) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins.

Binding studies of nNOS-active amphibian peptides and Ca2+ calmodulin, using negative ion electrospray ionisation mass spectrometry.

Amphibian peptides which inhibit the formation of nitric oxide by neuronal nitric oxide synthase (nNOS) do so by binding to the protein cofactor, Ca2+calmodulin (Ca2+CaM). Complex formation between active peptides and Ca2+CaM has been demonstrated by negative ion electrospray ionisation mass spectrometry using an aqueous ammonium acetate buffer system. In all cases studied, the assemblies are formed with a 1:1:4 calmodulin/peptide/Ca2+ stoichiometry. In contrast, the complex involving the 20-residue binding domain of the plasma Ca2+ pump C20W (LRRGQILWFRGLNRIQTQIK-OH) with CaM has been shown by previous two-dimensional nuclear magnetic resonance (2D NMR) studies to involve complexation of the C-terminal end of CaM. Under identical conditions to those used for the amphibian peptide study, the ESI complex between C20W and CaM shows specific 1:1:2 stoichiometry. Since complex formation with the studied amphibian peptides requires Ca2+CaM to contain its full complement of four Ca2+ ions, this indicates that the amphibian peptides require both ends of the CaM to effect complex formation. Charge-state analysis and an H/D exchange experiment (with caerin 1.8) suggest that complexation involves Ca2+CaM undergoing a conformational change to a more compact structure.

The N-terminal domain of alphaB-crystallin is protected from proteolysis by bound substrate.

Alpha-crystallin, a major structural protein of the lens can also function as a molecular chaperone by binding to unfolding substrate proteins. We have used a combination of limited proteolysis at low temperature, and mass spectrometry to identify the regions of alpha-crystallin directly involved in binding to the structurally compromised substrate, reduced alpha-lactalbumin. In the presence of trypsin, alpha-crystallin which had been pre-incubated with substrate showed markedly reduced proteolysis at the C-terminus compared with a control, indicating that the bound substrate restricted access of trypsin to R157, the main cleavage site. Chymotrypsin was able to cleave at residues in both the N- and C-terminal domains. In the presence of substrate, alpha-crystallin showed markedly reduced proteolysis at four sites in the N-terminal domain when compared with the control. Minor differences in cleavage were observed within the C-terminal domain suggesting that the N-terminal region of alpha-crystallin contains the major substrate interaction sites.

A chronic pneumothorax and fitness to fly.

According to Boyle's law, as the pressure falls, the volume of gas rises in an inversely proportional manner. This means that during an aircraft flight, the volume of trapped air in gas filled body chambers will increase. As a consequence, it is fairly well established that individuals with an untreated pneumothorax should not participate in commercial flying due to the risk of it enlarging and the possible development of tension. However, whether this also applies to individuals who have a long-standing, clinically stable pneumothorax is uncertain. The following article describes two adult patients each with a chronic pneumothorax who asked whether they would be fit to fly in an aircraft. We outline their histories and subsequent evaluation which consisted of clinical assessment, computed tomographic imaging, a hypoxic challenge test and exposure to a hypoxic hypobaric environment in a decompression chamber.