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1.
Nat Chem Biol ; 20(7): 924-933, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38942968

ABSTRACT

Keratinicyclins and keratinimicins are recently discovered glycopeptide antibiotics. Keratinimicins show broad-spectrum activity against Gram-positive bacteria, while keratinicyclins form a new chemotype by virtue of an unusual oxazolidinone moiety and exhibit specific antibiosis against Clostridioides difficile. Here we report the mechanism of action of keratinicyclin B (KCB). We find that steric constraints preclude KCB from binding peptidoglycan termini. Instead, KCB inhibits C. difficile growth by binding wall teichoic acids (WTAs) and interfering with cell wall remodeling. A computational model, guided by biochemical studies, provides an image of the interaction of KCB with C. difficile WTAs and shows that the same H-bonding framework used by glycopeptide antibiotics to bind peptidoglycan termini is used by KCB for interacting with WTAs. Analysis of KCB in combination with vancomycin (VAN) shows highly synergistic and specific antimicrobial activity, and that nanomolar combinations of the two drugs are sufficient for complete growth inhibition of C. difficile, while leaving common commensal strains unaffected.


Subject(s)
Anti-Bacterial Agents , Clostridioides difficile , Microbial Sensitivity Tests , Clostridioides difficile/drug effects , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Vancomycin/pharmacology , Vancomycin/chemistry , Cell Wall/drug effects , Cell Wall/metabolism , Teichoic Acids/metabolism , Peptidoglycan/metabolism , Peptidoglycan/chemistry , Drug Therapy, Combination , Peptides, Cyclic , Lipopeptides
2.
Environ Sci Technol ; 58(16): 7056-7065, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38608141

ABSTRACT

The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production. Depth-resolved metagenomes showed that consumption of nitrous oxide near the surface was correlated with an enrichment of Clade II nitrous oxide reducers, consistent with a growing appreciation of their importance in controlling release of nitrous oxide to the atmosphere. Our work also provides evidence for the reduction of nitrous oxide at a pH of 4, well below the generally accepted limit of pH 5.


Subject(s)
Nitrous Oxide , Nitrous Oxide/metabolism , Bacteria/metabolism , Oxidoreductases/metabolism , Denitrification
3.
Biochemistry ; 62(23): 3337-3342, 2023 12 05.
Article in English | MEDLINE | ID: mdl-37966244

ABSTRACT

Selenium (Se) is an essential micronutrient that is found naturally in proteins, nucleic acids, and natural products. Unlike selenoproteins and selenonucleic acids, little is known about the structures of biosynthetic enzymes that incorporate Se into small molecules. Here, we report the X-ray crystal structure of SenB, the first known Se-glycosyltransferase that was recently found to be involved in the biosynthesis of the Se-containing metabolite selenoneine. SenB catalyzes C-Se bond formation using selenophosphate and an activated uridine diphosphate sugar as a Se and glycosyl donor, respectively, making it the first known selenosugar synthase and one of only four bona fide C-Se bond-forming enzymes discovered to date. Our crystal structure, determined to 2.25 Å resolution, reveals that SenB is a type B glycosyltransferase, displaying the prototypical fold with two globular Rossmann-like domains and a catalytic interdomain cleft. By employing complementary structural biology techniques, we find that SenB undergoes both local and global substrate-induced conformational changes, demonstrating a significant increase in α-helicity and a transition to a more compact conformation. Our results provide the first structure of SenB and set the stage for further biochemical characterization in the future.


Subject(s)
Selenium , Selenium/metabolism , Glycosyltransferases , Ligands , Selenoproteins , Crystallography, X-Ray
4.
BMC Infect Dis ; 23(1): 262, 2023 Apr 26.
Article in English | MEDLINE | ID: mdl-37101147

ABSTRACT

BACKGROUND: Index-linked HIV testing for children, whereby HIV testing is offered to children of individuals living with HIV, has the potential to identify children living with undiagnosed HIV. The "Bridging the Gap in HIV Testing and Care for Children in Zimbabwe" (B-GAP) study implemented and evaluated the provision of index-linked HIV testing for children aged 2-18 years in Zimbabwe. We conducted a process evaluation to understand the considerations for programmatic delivery and scale-up of this strategy. METHODS: We used implementation documentation to explore experiences of the field teams and project manager who delivered the index-linked testing program, and to describe barriers and facilitators to index-linked testing from their perspectives. Qualitative data were drawn from weekly logs maintained by the field teams, monthly project meeting minutes, the project coordinator's incident reports and WhatsApp group chats between the study team and the coordinator. Data from each of the sources was analysed thematically and synthesised to inform the scale-up of this intervention. RESULTS: Five main themes were identified related to the implementation of the intervention: (1) there was reduced clinic attendance of potentially eligible indexes due to community-based differentiated HIV care delivery and collection of HIV treatment by proxy individuals; (2) some indexes reported that they did not live in the same household as their children, reflecting the high levels of community mobility; (3) there were also thought to be some instances of 'soft refusal'; (4) further, delivery of HIV testing was limited by difficulties faced by indexes in attending health facilities with their children for clinic-based testing, stigma around community-based testing, and the lack of familiarity of indexes with caregiver provided oral HIV testing; (5) and finally, test kit stockouts and inadequate staffing also constrained delivery of index-linked HIV testing. CONCLUSIONS: There was attrition along the index-linked HIV testing cascade of children. While challenges remain at all levels of implementation, programmatic adaptations of index-linked HIV testing approaches to suit patterns of clinic attendance and household structures may strengthen implementation of this strategy. Our findings highlight the need to tailor index-linked HIV testing to subpopulations and contexts to maximise its effectiveness.


Subject(s)
HIV Infections , HIV Testing , Child , Humans , HIV Infections/diagnosis , HIV Testing/methods , HIV Testing/standards , Social Stigma , Zimbabwe , National Health Programs/organization & administration , National Health Programs/statistics & numerical data , Demography , Male , Female , Infant , Child, Preschool , Adolescent , Adult
5.
J Phycol ; 59(3): 538-551, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37005360

ABSTRACT

Kelp are important primary producers that are colonized by diverse microbes that can have both positive and negative effects on their hosts. The kelp microbiome could support the burgeoning kelp cultivation sector by improving host growth, stress tolerance, and resistance to disease. Fundamental questions about the cultivated kelp microbiome still need to be addressed before microbiome-based approaches can be developed. A critical knowledge gap is how cultivated kelp microbiomes change as hosts grow, particularly following outplanting to sites that vary in abiotic conditions and microbial source pools. In this study we assessed if microbes that colonize kelp in the nursery stage persist after outplanting. We characterized microbiome succession over time on two species of kelp, Alaria marginata and Saccharina latissima, outplanted to open ocean cultivation sites in multiple geographic locations. We tested for host-species specificity of the microbiome and the effect of different abiotic conditions and microbial source pools on kelp microbiome stability during the cultivation process. We found the microbiome of kelp in the nursery is distinct from that of outplanted kelp. Few bacteria persisted on kelp following outplanting. Instead, we identified significant microbiome differences correlated with host species and microbial source pools at each cultivation site. Microbiome variation related to sampling month also indicates that seasonality in host and/or abiotic factors may influence temporal succession and microbiome turnover in cultivated kelps. This study provides a baseline understanding of microbiome dynamics during kelp cultivation and highlights research needs for applying microbiome manipulation to kelp cultivation.


Subject(s)
Kelp , Microbiota , Phaeophyceae , Bacteria
6.
Psychother Res ; : 1-12, 2023 Jul 03.
Article in English | MEDLINE | ID: mdl-37399573

ABSTRACT

OBJECTIVE: The current study aimed to inform the varied and limited research on clinical variables in the context of teletherapy. Questions remain about the comparative quality of therapeutic alliance and clinical outcome in the context of teletherapy compared to in-person treatment. METHODS: We utilized a cohort design and a noninferiority statistical approach to study a large, matched sample of clients who reported therapeutic alliance as well as psychological distress before every session as part of routine clinical practice at a university counseling center. A cohort of 479 clients undergoing teletherapy after the emergence of the COVID-19 pandemic was compared to a cohort of 479 clients receiving in-person treatment before the onset of the pandemic. Tests of noninferiority were conducted to investigate the absence of meaningful differences between the two modalities of service delivery. Client characteristics were also examined as moderators of the association between modality and alliance or outcome. RESULTS: Clients receiving teletherapy showed noninferior alliance and clinical outcome when compared to clients receiving in-person psychotherapy. A significant main effect on alliance was found with regard to race and ethnicity. A significant main effect on outcome was found with regard to international student status. Significant interactions on alliance were found between cohort and current financial stress. CONCLUSIONS: Study findings support the continued use of teletherapy by demonstrating commensurate clinical process and outcome. Yet, it will be important for providers to be aware of existing mental health disparities that continue to accompany psychotherapy - in person and via teletherapy. Results and findings are discussed in terms of research and clinical implications. Future directions for researching teletherapy as a viable treatment delivery method are also discussed.

7.
Environ Sci Technol ; 56(5): 3225-3233, 2022 03 01.
Article in English | MEDLINE | ID: mdl-35142487

ABSTRACT

Subsurface microbial (biogenic) methane production is an important part of the global carbon cycle that has resulted in natural gas accumulations in many coal beds worldwide. Laboratory studies suggest that complex carbon-containing nutrients (e.g., yeast or algae extract) can stimulate methane production, yet the effectiveness of these nutrients within coal beds is unknown. Here, we use downhole monitoring methods in combination with deuterated water (D2O) and a 200-liter injection of 0.1% yeast extract (YE) to stimulate and isotopically label newly generated methane. A total dissolved gas pressure sensor enabled real-time gas measurements (641 days preinjection and for 478 days postinjection). Downhole samples, collected with subsurface environmental samplers, indicate that methane increased 132% above preinjection levels based on isotopic labeling from D2O, 108% based on pressure readings, and 183% based on methane measurements 266 days postinjection. Demonstrating that YE enhances biogenic coalbed methane production in situ using multiple novel measurement methods has immediate implications for other field-scale biogenic methane investigations, including in situ methods to detect and track microbial activities related to the methanogenic turnover of recalcitrant carbon in the subsurface.


Subject(s)
Coal , Methane , Carbon , Natural Gas
8.
Sensors (Basel) ; 22(6)2022 Mar 09.
Article in English | MEDLINE | ID: mdl-35336271

ABSTRACT

False alerts due to misconfigured or compromised intrusion detection systems (IDS) in industrial control system (ICS) networks can lead to severe economic and operational damage. However, research using deep learning to reduce false alerts often requires the physical and cyber sensor data to be trustworthy. Implicit trust is a major problem for artificial intelligence or machine learning (AI/ML) in cyber-physical system (CPS) security, because when these solutions are most urgently needed is also when they are most at risk (e.g., during an attack). To address this, the Inter-Domain Evidence theoretic Approach for Inference (IDEA-I) is proposed that reframes the detection problem as how to make good decisions given uncertainty. Specifically, an evidence theoretic approach leveraging Dempster-Shafer (DS) combination rules and their variants is proposed for reducing false alerts. A multi-hypothesis mass function model is designed that leverages probability scores obtained from supervised-learning classifiers. Using this model, a location-cum-domain-based fusion framework is proposed to evaluate the detector's performance using disjunctive, conjunctive, and cautious conjunctive rules. The approach is demonstrated in a cyber-physical power system testbed, and the classifiers are trained with datasets from Man-In-The-Middle attack emulation in a large-scale synthetic electric grid. For evaluating the performance, we consider plausibility, belief, pignistic, and general Bayesian theorem-based metrics as decision functions. To improve the performance, a multi-objective-based genetic algorithm is proposed for feature selection considering the decision metrics as the fitness function. Finally, we present a software application to evaluate the DS fusion approaches with different parameters and architectures.


Subject(s)
Artificial Intelligence , Heuristics , Bayes Theorem , Computer Security , Humans , Machine Learning
9.
Psychother Res ; 32(5): 663-677, 2022 06.
Article in English | MEDLINE | ID: mdl-34763613

ABSTRACT

While agreement between clients and their clinicians on therapy goals has frequently been investigated as a process-level variable (i.e., working alliance), dyadic convergence on presenting concerns is also important for initial case formulation. Transdiagnostic presenting problems, like sleep difficulty, pose a particular challenge for client-therapist convergence. The current study describes sleep difficulty in a treatment-seeking college population and investigates the impact of client and therapist baseline sleep problem reports on therapy outcomes.Data were collected through a large practice research network, with the sample comprising 47,023 clients from 99 university counseling centers across the United States.A larger proportion of clients (49.3%) had self-reported high baseline sleep difficulty than those with a clinician-identified sleep concern (16.0%). Clients with baseline sleep difficulty were more likely to end treatment with greater self-reported sleep difficulty and psychological symptom distress, although they may experience larger gross symptom change than clients without baseline sleep difficulty. Clinician-identified sleep concerns were significantly associated with client outcomes, particularly when clients did not report baseline sleep difficulty themselves.Findings from this study suggest that it may be efficacious and efficient with limited time for treatment to address sleep concerns in a college setting.Clinicians' attendance to their clients' transdiagnostic presenting concerns, like sleep difficulty, may increase clients' own awareness of problematic patterns of behavior. When time for therapy is short, as is often the case in college counseling, it may be efficient to prioritize these concerns with the potential to impact a broad range of symptoms.


Subject(s)
Professional-Patient Relations , Sleep Wake Disorders , Counseling , Humans , Self Report , Treatment Outcome
10.
J Am Chem Soc ; 143(5): 2293-2303, 2021 02 10.
Article in English | MEDLINE | ID: mdl-33522811

ABSTRACT

Ethylene-forming enzyme (EFE) is an ambifunctional iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase. In its major (EF) reaction, it converts carbons 1, 2, and 5 of 2OG to CO2 and carbons 3 and 4 to ethylene, a four-electron oxidation drastically different from the simpler decarboxylation of 2OG to succinate mediated by all other Fe/2OG enzymes. EFE also catalyzes a minor reaction, in which the normal decarboxylation is coupled to oxidation of l-arginine (a required activator for the EF pathway), resulting in its conversion to l-glutamate semialdehyde and guanidine. Here we show that, consistent with precedent, the l-Arg-oxidation (RO) pathway proceeds via an iron(IV)-oxo (ferryl) intermediate. Use of 5,5-[2H2]-l-Arg slows decay of the ferryl complex by >16-fold, implying that RO is initiated by hydrogen-atom transfer (HAT) from C5. That this large substrate deuterium kinetic isotope effect has no impact on the EF:RO partition ratio implies that the same ferryl intermediate cannot be on the EF pathway; the pathways must diverge earlier. Consistent with this conclusion, the variant enzyme bearing the Asp191Glu ligand substitution accumulates ∼4 times as much of the ferryl complex as the wild-type enzyme and exhibits a ∼40-fold diminished EF:RO partition ratio. The selective detriment of this nearly conservative substitution to the EF pathway implies that it has unusually stringent stereoelectronic requirements. An active-site, like-charge guanidinium pair, which involves the l-Arg substrate/activator and is unique to EFE among four crystallographically characterized l-Arg-modifying Fe/2OG oxygenases, may serve to selectively stabilize the transition state leading to the unique EF branch.


Subject(s)
Arginine/chemistry , Iron/chemistry , Ketoglutaric Acids/metabolism , Oxygenases/metabolism , Models, Molecular , Oxidation-Reduction , Oxygenases/chemistry , Protein Conformation
11.
Environ Microbiol ; 23(5): 2617-2631, 2021 05.
Article in English | MEDLINE | ID: mdl-33817918

ABSTRACT

It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.


Subject(s)
Fucus , Microbiota , Seaweed , Adaptation, Physiological
12.
BMC Med ; 19(1): 105, 2021 05 13.
Article in English | MEDLINE | ID: mdl-33980222

ABSTRACT

BACKGROUND: Improved access to effective antiretroviral therapy has meant that people living with HIV (PLHIV) are surviving to older ages. However, PLHIV may be ageing differently to HIV-negative individuals, with dissimilar burdens of non-communicable diseases, such as hypertension. While some observational studies have reported a higher risk of prevalent hypertension among PLHIV compared to HIV-negative individuals, others have found a reduced burden. To clarify the relationship between HIV and hypertension, we identified observational studies and pooled their results to assess whether there is a difference in hypertension risk by HIV status. METHODS: We performed a global systematic review and meta-analysis of published cross-sectional studies that examined hypertension risk by HIV status among adults aged > 15 (PROSPERO: CRD42019151359). We searched MEDLINE, EMBASE, Global Health and Cochrane CENTRAL to August 23, 2020, and checked reference lists of included articles. Our main outcome was the risk ratio for prevalent hypertension in PLHIV compared to HIV-negative individuals. Summary estimates were pooled with a random effects model and meta-regression explored whether any difference was associated with study-level factors. RESULTS: Of 21,527 identified studies, 59 were eligible (11,101,581 participants). Crude global hypertension risk was lower among PLHIV than HIV-negative individuals (risk ratio 0.90, 95% CI 0.85-0.96), although heterogeneity between studies was high (I2 = 97%, p < 0.0001). The relationship varied by continent, with risk higher among PLHIV in North America (1.12, 1.02-1.23) and lower among PLHIV in Africa (0.75, 0.68-0.83) and Asia (0.77, 0.63-0.95). Meta-regression revealed strong evidence of a difference in risk ratios when comparing North American and European studies to African ones (North America 1.45, 1.21-1.74; Europe 1.20, 1.03-1.40). CONCLUSIONS: Our findings suggest that the relationship between HIV status and prevalent hypertension differs by region. The results highlight the need to tailor hypertension prevention and care to local contexts and underscore the importance of rapidly optimising integration of services for HIV and hypertension in the worst affected regions. The role of different risk factors for hypertension in driving context-specific trends remains unclear, so development of further cohorts of PLHIV and HIV-negative controls focused on this would also be valuable.


Subject(s)
HIV Infections , Hypertension , Adult , Aged , Cross-Sectional Studies , Global Health , HIV Infections/complications , HIV Infections/epidemiology , Humans , Hypertension/epidemiology , Middle Aged , Risk Factors
13.
Nat Chem Biol ; 15(2): 161-168, 2019 02.
Article in English | MEDLINE | ID: mdl-30617293

ABSTRACT

Bacteria contain an immense untapped trove of novel secondary metabolites in the form of 'silent' biosynthetic gene clusters (BGCs). These can be identified bioinformatically but are not expressed under normal laboratory growth conditions. Methods to access their products would dramatically expand the pool of bioactive compounds. We report a universal high-throughput method for activating silent BGCs in diverse microorganisms. Our approach relies on elicitor screening to induce the secondary metabolome of a given strain and imaging mass spectrometry to visualize the resulting metabolomes in response to ~500 conditions. Because it does not require challenging genetic, cloning, or culturing procedures, this method can be used with both sequenced and unsequenced bacteria. We demonstrate the power of the approach by applying it to diverse bacteria and report the discovery of nine cryptic metabolites with potentially therapeutic bioactivities, including a new glycopeptide chemotype with potent inhibitory activity against a pathogenic virus.


Subject(s)
High-Throughput Screening Assays/methods , Mass Spectrometry/methods , Metabolomics/methods , Bacteria , Biological Products , Biosynthetic Pathways/genetics , Metabolome/genetics , Multigene Family/genetics
14.
J Phycol ; 57(4): 1119-1130, 2021 08.
Article in English | MEDLINE | ID: mdl-33749821

ABSTRACT

Seaweed-associated microbiota are essential for the health and resilience of nearshore ecosystems, marine biogeochemical cycling, and host health. Yet much remains unknown about the ecology of seaweed-microbe symbioses. In this study, we quantified fine-scale patterns of microbial community structure across distinct anatomical regions of the kelp Laminaria setchellii. These anatomical regions represent a gradient of tissue ages: perennial holdfasts can be several years old, whereas stipe epicortex and blades are younger annual structures. Within blades, new growth occurs at the base, while the blade tips may be several months old and undergoing senescence. We hypothesized that microbial communities will differ across anatomical regions (holdfast, stipe, blade base, and blade tip), such that younger tissues will harbor fewer microbes that are more consistent across replicate individuals. Our data support this hypothesis, with the composition of bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities showing significant differences across the four anatomical regions, with the surfaces of older tissues (holdfast and blade tips) harboring significantly greater microbial richness compared to the younger tissues of the meristematic region. Additional samples collected from the surfaces of new L. setchellii recruits (<1y old) also showed differences in microbial community structure across anatomical regions, which demonstrates that these microbial differences are established early. We also observed this pattern in two additional algal species, suggesting that microbial community structure across host anatomy may be a common feature of the seaweed microbiome.


Subject(s)
Kelp , Laminaria , Microbiota , Bacteria/genetics , RNA, Ribosomal, 16S/genetics
15.
Am J Respir Crit Care Med ; 201(4): 430-437, 2020 02 15.
Article in English | MEDLINE | ID: mdl-31661302

ABSTRACT

Rationale: Chronic azithromycin is commonly used in cystic fibrosis based on short controlled clinical trials showing reductions in pulmonary exacerbations and improved FEV1. Long-term effects are unknown.Objectives: Examine pulmonary outcomes among chronic azithromycin users compared with matched controls over years of use and consider combined azithromycin use in cohorts using chronic inhaled tobramycin or aztreonam.Methods: This retrospective cohort study used the U.S. cystic fibrosis Foundation Patient Registry. Incident chronic azithromycin users were compared with matched controls by FEV1% predicted rate of decline and rates of intravenous antibiotic use to treat pulmonary exacerbations. Propensity score methods were utilized to address confounding by indication. Predefined sensitivity analyses based on lung function, Pseudomonas aeruginosa (PA) status, and follow-up time intervals were conducted.Measurements and Main Results: Across 3 years, FEV1% predicted per-year decline was nearly 40% less in those with PA using azithromycin compared with matched controls (slopes, -1.53 versus -2.41% predicted per yr; difference: 0.88; 95% confidence interval [CI], 0.30-1.47). This rate of decline did not differ based on azithromycin use in those without PA. Among all cohorts, use of intravenous antibiotics was no different between azithromycin users and controls. Users of inhaled tobramycin and azithromycin had FEV1% predicted per-year decline of -0.16 versus nonusers (95% CI, -0.44 to 0.13), whereas users of inhaled aztreonam lysine and azithromycin experienced a mean 0.49% predicted per year slower decline than matched controls (95% CI, -0.11 to 1.10).Conclusions: Results from this study provide additional rationale for chronic azithromycin use in PA-positive patients to reduce lung function decline.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Azithromycin/therapeutic use , Aztreonam/therapeutic use , Cystic Fibrosis/drug therapy , Tobramycin/therapeutic use , Administration, Inhalation , Adolescent , Adult , Child , Cohort Studies , Female , Humans , Male , Pseudomonas aeruginosa/drug effects , Retrospective Studies , Young Adult
16.
Molecules ; 26(9)2021 Apr 29.
Article in English | MEDLINE | ID: mdl-33946806

ABSTRACT

Enzymes are biological catalysts whose dynamics enable their reactivity. Visualizing conformational changes, in particular, is technically challenging, and little is known about these crucial atomic motions. This is especially problematic for understanding the functional diversity associated with the radical S-adenosyl-L-methionine (SAM) superfamily whose members share a common radical mechanism but ultimately catalyze a broad range of challenging reactions. Computational chemistry approaches provide a readily accessible alternative to exploring the time-resolved behavior of these enzymes that is not limited by experimental logistics. Here, we review the application of molecular docking, molecular dynamics, and density functional theory, as well as hybrid quantum mechanics/molecular mechanics methods to the study of these enzymes, with a focus on understanding the mechanistic dynamics associated with turnover.


Subject(s)
Models, Molecular , S-Adenosylmethionine/chemistry , Acetyltransferases , Density Functional Theory , Molecular Conformation , Molecular Docking Simulation , Molecular Dynamics Simulation , Molecular Structure , Protein Binding , Quantum Theory , Vitamin B 12/chemistry
17.
Nature ; 513(7517): 261-5, 2014 Sep 11.
Article in English | MEDLINE | ID: mdl-25043005

ABSTRACT

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.


Subject(s)
Crystallography, X-Ray , Cyanobacteria/chemistry , Models, Molecular , Photosystem II Protein Complex/chemistry , Protein Structure, Tertiary
18.
Proc Natl Acad Sci U S A ; 114(39): 10420-10425, 2017 09 26.
Article in English | MEDLINE | ID: mdl-28893989

ABSTRACT

Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. Here, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine-tryptophan cross-link, which is installed by the radical S-adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon-carbon cross-link in the streptide family of natural products.


Subject(s)
Phosphotransferases (Alcohol Group Acceptor)/chemistry , S-Adenosylmethionine/chemistry , Streptococcus/metabolism , Computational Biology , Crystallography, X-Ray , Models, Molecular , Protein Binding , Protein Biosynthesis/physiology , Protein Processing, Post-Translational/physiology , Protein Sorting Signals/genetics , Protein Structure, Secondary , Streptococcus/enzymology
19.
J Neurosci ; 38(37): 8044-8059, 2018 09 12.
Article in English | MEDLINE | ID: mdl-30093566

ABSTRACT

Many sex differences in brain and behavior are programmed during development by gonadal hormones, but the cellular mechanisms are incompletely understood. We found that immune-system-derived mast cells are a primary target for the masculinizing hormone estradiol and that mast cells are in turn primary mediators of brain sexual differentiation. Newborn male rats had greater numbers and more activated mast cells in the preoptic area (POA), a brain region essential for male copulatory behavior, than female littermates during the critical period for sexual differentiation. Inhibiting mast cells with a stabilizing agent blunted the masculinization of both POA neuronal and microglial morphology and adult sex behavior, whereas activating mast cells in females, even though fewer in number, induced masculinization. Treatment of newborn females with a masculinizing dose of estradiol increased mast cell number and induced mast cells to release histamine, which then stimulated microglia to release prostaglandins and thereby induced male-typical synaptic patterning. These findings identify a novel non-neuronal origin of brain sex differences and resulting motivated behaviors.SIGNIFICANCE STATEMENT We found that immune-system-derived mast cells are a primary target for the masculinizing hormone estradiol and that mast cells are in turn primary mediators of brain sexual differentiation. These findings identify a novel non-neuronal origin of brain sex differences and resulting motivated behaviors.


Subject(s)
Estradiol/pharmacology , Mast Cells/physiology , Preoptic Area/physiology , Sex Characteristics , Sex Differentiation/physiology , Sexual Behavior, Animal/physiology , Animals , Cell Count , Cell Shape/drug effects , Cell Shape/physiology , Female , Ketotifen/pharmacology , Male , Mast Cells/cytology , Mast Cells/drug effects , Microglia/cytology , Microglia/drug effects , Microglia/physiology , Preoptic Area/cytology , Preoptic Area/drug effects , Rats , Sex Differentiation/drug effects , Sexual Behavior, Animal/drug effects
20.
Biochemistry ; 58(41): 4218-4223, 2019 10 15.
Article in English | MEDLINE | ID: mdl-31503454

ABSTRACT

Iron(II)- and 2-(oxo)-glutarate-dependent (Fe/2OG) oxygenases catalyze a diverse array of oxidation reactions via a common iron(IV)-oxo (ferryl) intermediate. Although the intermediate has been characterized spectroscopically, its short lifetime has precluded crystallograhic characterization. In solution, the ferryl was first observed directly in the archetypal Fe/2OG hydroxylase, taurine:2OG dioxygenase (TauD). Here, we substitute the iron cofactor of TauD with the stable vanadium(IV)-oxo (vanadyl) ion to obtain crystal structures mimicking the key ferryl complex. Intriguingly, whereas the structure of the TauD·(VIV-oxo)·succinate·taurine complex exhibits the expected orientation of the V≡O bond-trans to the His255 ligand and toward the C-H bond to be cleaved, in what has been termed the in-line configuration-the TauD·(VIV-oxo) binary complex is best modeled with its oxo ligand trans to Asp101. This off-line-like configuration is similar to one recently posited as a means to avoid hydroxylation in Fe/2OG enzymes that direct other outcomes, though neither has been visualized in an Fe/2OG structure to date. Whereas an off-line (trans to the proximal His) or off-line-like (trans to the carboxylate ligand) ferryl is unlikely to be important in the hydroxylation reaction of TauD, the observation that the ferryl may deviate from an in-line orientation in the absence of the primary substrate may explain the enzyme's mysterious self-hydroxylation behavior, should the oxo ligand lie trans to His99. This finding reinforces the potential for analogous functional off-line oxo configurations in halogenases, desaturases, and/or cyclases.


Subject(s)
Iron/chemistry , Mixed Function Oxygenases/chemistry , Molecular Mimicry , Vanadates/chemistry , Catalytic Domain , Crystallization , Crystallography, X-Ray , Escherichia coli/chemistry , Hydrogen Bonding , Hydroxylation , Mixed Function Oxygenases/isolation & purification , Protein Structure, Secondary , Succinic Acid/chemistry , Taurine/chemistry , X-Ray Absorption Spectroscopy
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