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1.
Proc Natl Acad Sci U S A ; 118(11)2021 03 16.
Article in English | MEDLINE | ID: mdl-33688047

ABSTRACT

The mosquito protein AEG12 is up-regulated in response to blood meals and flavivirus infection though its function remained elusive. Here, we determine the three-dimensional structure of AEG12 and describe the binding specificity of acyl-chain ligands within its large central hydrophobic cavity. We show that AEG12 displays hemolytic and cytolytic activity by selectively delivering unsaturated fatty acid cargoes into phosphatidylcholine-rich lipid bilayers. This property of AEG12 also enables it to inhibit replication of enveloped viruses such as Dengue and Zika viruses at low micromolar concentrations. Weaker inhibition was observed against more distantly related coronaviruses and lentivirus, while no inhibition was observed against the nonenveloped virus adeno-associated virus. Together, our results uncover the mechanistic understanding of AEG12 function and provide the necessary implications for its use as a broad-spectrum therapeutic against cellular and viral targets.


Subject(s)
Antiviral Agents/metabolism , Hemolytic Agents/metabolism , Insect Proteins/metabolism , Lipids , Animals , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Cell Line , Cell Membrane/metabolism , Culicidae , Erythrocytes/drug effects , Fatty Acids, Unsaturated/metabolism , Hemolytic Agents/chemistry , Hemolytic Agents/pharmacology , Humans , Hydrophobic and Hydrophilic Interactions , Insect Proteins/chemistry , Insect Proteins/pharmacology , Ligands , Lipids/chemistry , Protein Binding , Protein Structure, Tertiary , Viral Envelope/metabolism , Viruses/drug effects , Viruses/metabolism
2.
Biochemistry ; 62(22): 3276-3282, 2023 11 21.
Article in English | MEDLINE | ID: mdl-37936269

ABSTRACT

Chlamydia protein associating with death domains (CADD), the founding member of a recently discovered class of nonheme dimetal enzymes termed hemeoxygenase-like dimetaloxidases (HDOs), plays an indispensable role in pathogen survival. CADD orchestrates the biosynthesis of p-aminobenzoic acid (pABA) for integration into folate via the self-sacrificial excision of a protein-derived tyrosine (Tyr27) and several additional processing steps, the nature and timing of which have yet to be fully clarified. Nuclear magnetic resonance (NMR) and proteomics approaches reveal the source and probable timing of amine installation by a neighboring lysine (Lys152). Turnover studies using limiting O2 have identified a para-aminobenzaldehyde (pABCHO) metabolic intermediate that is formed on the path to pABA formation. The use of pABCHO and other probe substrates shows that the heterobimetallic Fe/Mn form of the enzyme is capable of oxygen insertion to generate the pABA-carboxylate.


Subject(s)
4-Aminobenzoic Acid , para-Aminobenzoates , para-Aminobenzoates/metabolism , 4-Aminobenzoic Acid/metabolism , Folic Acid/metabolism
3.
Ann Clin Psychiatry ; 34(2): e2-e24, 2022 05.
Article in English | MEDLINE | ID: mdl-35550035

ABSTRACT

BACKGROUND: Repetitive transcranial magnetic stimulation (rTMS) is an FDA-approved, noninvasive modality for treating major depressive disorder and obsessive-compulsive disorder. Earlier studies evaluating therapeutic effects of rTMS on symptom scores of patients with generalized anxiety disorder (GAD) and panic disorder (PD) have yielded inconsistent findings. METHODS: We performed a systematic review and meta-analysis of interventional studies assessing the effect of rTMS on symptom scores in patients with GAD or PD with or without psychiatric comorbidities using studies published up to April 2021. We used DerSimonian-Laird random effects models to obtain pooled standardized mean difference (SMD) and 95% CI. RESULTS: A total of 13 studies consisting of 677 participants (404 treated with rTMS and 273 without rTMS) were included in this meta-analysis. In GAD patients with or without any comorbidities, rTMS therapy demonstrated significant improvements in anxiety (SMD = 1.45; P < .001) and depression (SMD = 1.65; P < .001) scores regardless of rTMS parameters. Overall anxiety (SMD = 0.24; P = .48) and panic severity (SMD = 1.19; P = .054) scores did not significantly improve after rTMS therapy in patients with PD. CONCLUSIONS: rTMS is safe and improves anxiety and depression scores only in GAD patients, regardless of underlying comorbidities or rTMS parameters.


Subject(s)
Depressive Disorder, Major , Panic Disorder , Anxiety , Anxiety Disorders/therapy , Depressive Disorder, Major/etiology , Depressive Disorder, Major/therapy , Humans , Panic Disorder/etiology , Panic Disorder/therapy , Transcranial Magnetic Stimulation , Treatment Outcome
4.
J Nerv Ment Dis ; 210(1): 26-31, 2022 01 01.
Article in English | MEDLINE | ID: mdl-34417422

ABSTRACT

ABSTRACT: The present study is aimed to identify the effect of gratitude as an adaptive regulating mechanism from suicidal ideation (SI) for veterans with mental illness (study 1) and student veterans with posttraumatic stress disorder (PTSD) symptoms (study 2) in the United States. Descriptive statistics and regression analyses were used to examine sociodemographic characteristics and relationships between gratitude and SI. Our study 1 consisted of 156 veterans with mental illness. The mean age for study 1 was 37.85. Our study 2 consisted of 232 student veterans with PTSD symptoms. The mean age for study 2 was 28.43. Higher gratitude scores in study 1 and study 2 were significantly associated with lower SI scores after adjusting for demographics and depression. This study partially supports the association between gratitude and SI in veterans with mental illness. Based on the results from this study, gratitude interventions may be effective in reducing SI when working with veterans with mental illness.


Subject(s)
Emotions/physiology , Stress Disorders, Post-Traumatic , Students , Suicidal Ideation , Veterans , Adult , Female , Humans , Interpersonal Relations , Male , Middle Aged , Resilience, Psychological , United States , Young Adult
5.
Nucleic Acids Res ; 47(10): e59, 2019 06 04.
Article in English | MEDLINE | ID: mdl-30869147

ABSTRACT

Deletions in the 16.6 kb mitochondrial genome have been implicated in numerous disorders that often display muscular and/or neurological symptoms due to the high-energy demands of these tissues. We describe a catalogue of 4489 putative mitochondrial DNA (mtDNA) deletions, including their frequency and relative read rate, using a combinatorial approach of mitochondria-targeted PCR, next-generation sequencing, bioinformatics, post-hoc filtering, annotation, and validation steps. Our bioinformatics pipeline uses MapSplice, an RNA-seq splice junction detection algorithm, to detect and quantify mtDNA deletion breakpoints rather than mRNA splices. Analyses of 93 samples from postmortem brain and blood found (i) the 4977 bp 'common deletion' was neither the most frequent deletion nor the most abundant; (ii) brain contained significantly more deletions than blood; (iii) many high frequency deletions were previously reported in MitoBreak, suggesting they are present at low levels in metabolically active tissues and are not exclusive to individuals with diagnosed mitochondrial pathologies; (iv) many individual deletions (and cumulative metrics) had significant and positive correlations with age and (v) the highest deletion burdens were observed in major depressive disorder brain, at levels greater than Kearns-Sayre Syndrome muscle. Collectively, these data suggest the Splice-Break pipeline can detect and quantify mtDNA deletions at a high level of resolution.


Subject(s)
Computational Biology/methods , DNA, Mitochondrial/genetics , Depressive Disorder, Major/genetics , RNA Splice Sites/genetics , Sequence Analysis, RNA/methods , Sequence Deletion , Algorithms , Base Sequence , Brain/metabolism , Brain/pathology , DNA Breaks , DNA, Mitochondrial/chemistry , Depressive Disorder, Major/blood , Female , Humans , Male , Polymerase Chain Reaction
6.
Atmos Environ (1994) ; 2432020 Dec 15.
Article in English | MEDLINE | ID: mdl-32922147

ABSTRACT

The daily pollen forecast provides crucial information for allergic patients to avoid exposure to specific pollen. Pollen counts are typically measured with air samplers and analyzed with microscopy by trained experts. In contrast, this study evaluated the effectiveness of identifying the component pollens using the metabolites extracted from an air-sampled pollen mixture. Ambient air-sampled pollen from Munich in 2016 and 2017 was visually identified from reference pollens and extracts were prepared. The extracts were lyophilized, rehydrated in optimal NMR buffers, and filtered to remove large proteins. NMR spectra were analyzed for pollen associated metabolites. Regression and decision-tree based algorithms using the concentration of metabolites, calculated from the NMR spectra outperformed algorithms using the NMR spectra themselves as input data for pollen identification. Categorical prediction algorithms trained for low, medium, high, and very high pollen count groups had accuracies of 74% for the tree, 82% for the grass, and 93% for the weed pollen count. Deep learning models using convolutional neural networks performed better than regression models using NMR spectral input, and were the overall best method in terms of relative error and classification accuracy (86% for tree, 89% for grass, and 93% for weed pollen count). This study demonstrates that NMR spectra of air-sampled pollen extracts can be used in an automated fashion to provide taxa and type-specific measures of the daily pollen count.

7.
Allergy ; 74(12): 2382-2393, 2019 12.
Article in English | MEDLINE | ID: mdl-31230350

ABSTRACT

BACKGROUND: Over 100 million people worldwide suffer from birch pollen allergy. Bet v 1 has been identified as the major birch pollen allergen. However, the molecular mechanisms of birch allergic sensitization, including the roles of Bet v 1 and other components of the birch pollen extract, remain incompletely understood. Here, we examined how known birch pollen-derived molecules influence the endolysosomal processing of Bet v 1, thereby shaping its allergenicity. METHODS: We analyzed the biochemical and immunological interaction of ligands with Bet v 1. We then investigated the proteolytic processing of Bet v 1 by endosomal extracts in the presence and absence of ligands, followed by a detailed kinetic analysis of Bet v 1 processing by individual endolysosomal proteases as well as the T-cell epitope presentation in BMDCs. RESULTS: We identified E1 phytoprostanes as novel Bet v 1 ligands. Pollen-derived ligands enhanced the proteolytic resistance of Bet v 1, affecting degradation kinetics and preferential cleavage sites of the endolysosomal proteases cathepsin S and legumain. E1 phytoprostanes exhibited a dual role by stabilizing Bet v 1 and inhibiting cathepsin protease activity. CONCLUSION: Bet v 1 can serve as a transporter of pollen-derived, bioactive compounds. When carried to the endolysosome, such compounds can modulate the proteolytic activity, including its processing by cysteine cathepsins. We unveil a paradigm shift from an allergen-centered view to a more systemic view that includes the host endolysosomal enzymes.


Subject(s)
Allergens/immunology , Antigens, Plant/immunology , Endosomes/enzymology , Peptide Hydrolases/metabolism , Basophils/immunology , Basophils/metabolism , Betula/immunology , Cell Degranulation/immunology , Enzyme Activation , Humans , Immunoglobulin E/immunology , Ligands , Pollen/immunology , Protein Binding , Recombinant Proteins
8.
BJU Int ; 118(2): 327-34, 2016 08.
Article in English | MEDLINE | ID: mdl-26917016

ABSTRACT

OBJECTIVES: To conduct an audit of patients presenting with long-term urinary catheter (LTC)-associated problems to our Emergency Department (ED) and to assess the availability of community nursing support for their LTC. We also estimated the cost implication to the health service and the potential solutions to this issue, as although catheter care is provided by community nurses, LTC problems are common presentations to the ED and are often significant burdens to the services. PATIENTS AND METHODS: A study was carried out of all patients presenting to the ED with a urinary catheter problem, specifically studying LTCs and the reason for presentation, district nurses' involvement, and the intervention received. RESULTS: In all, 78 patients with a urinary catheter problem presented to the ED over a 69-day period, of whom 59 (68%) had a LTC. In all, 33 patients (42%) attended during normal working hours between 0900 and 1700 h. The mean (range) age was 74 (42-93) years and the duration the LTC had been in situ was 11 (1-120) months. The most common reasons for attendance were blocked catheter (37 patients, 47%) and catheter-bypass (18, 23%). Only 28 patients (36%) were known to district nursing services, and 14% were referred by a district nurse. Most of the remaining patients self-referred to the ED. No patient had any documented contact with their general practitioner. In addition, 64 patients (82%) had their catheter issues addressed adequately by ED nurses or doctors, without any urology involvement. CONCLUSIONS: The high morbidity of LTCs causes a considerable demand on ED services, and has heavy cost implications to the health system. Most patients had minimal community nurse support, and their catheter problems were easily dealt with by ED nurses and doctors.


Subject(s)
Community Health Services/supply & distribution , Emergency Service, Hospital/statistics & numerical data , Health Services Needs and Demand , Urinary Catheterization/statistics & numerical data , Adult , Aged , Aged, 80 and over , Humans , Middle Aged , Prospective Studies
9.
Alcohol Clin Exp Res ; 40(12): 2557-2562, 2016 12.
Article in English | MEDLINE | ID: mdl-27813125

ABSTRACT

BACKGROUND: Phosphatidylethanol (PEth) is a metabolite of ethanol (EtOH), and its concentration in whole blood samples is a direct biomarker of alcohol consumption. Because PEth is also present in the brain and incorporated in lipid membranes, it can be used to classify deceased individuals on alcohol consumption status at the time of death. The purpose of this study was to detect PEth homologs in postmortem brains of individuals known to have had alcohol use disorder (AUD) and to determine the relationship between serum alcohol at the time of death and PEth in the cerebellum (CE) and orbital frontal cortex (OFC). METHODS: Postmortem brain was collected and stored according to standard protocol. Psychiatric symptoms experienced prior to death were obtained by next of kin psychological autopsy to categorize subjects. Thirty male subjects were chosen for analyses: 10 with AUD with positive serum EtOH levels present at time of autopsy (AUD-W), 10 with AUD without positive serum EtOH levels (AUD-WO), and 10 controls. PEth 16:0/18:1 and 16:0/18:2 were quantified in 50 mg of CE and OFC of human postmortem brain using HPLC and mass spectrometric detection (triple quadrupole). RESULTS: Results of this study were as follows: (i) PEth 16:0/18:1 and 16:0/18:2 were detected in the CE and OFC of all subjects diagnosed with AUD, (ii) PEth 16:0/18:1 levels were about 10-fold higher than PEth 16:0/18:2 in all subjects and both areas of brain, (iii) AUD-W subjects had higher PEth homolog levels in CE and OFC than controls and AUD-WO subjects, (iv) PEth 16:0/18:1, but not PEth 16:0/18:2, levels in CE and OFC of AUD-W subjects correlated significantly with serum EtOH levels at the time of death. CONCLUSIONS: Quantification of combined PEth homolog levels in postmortem human brain is a good candidate as a diagnostic factor to classify drinking status, especially for those with AUD at the time of death. For alcohol research studies with postmortem brain, verification of drinking status is essential.


Subject(s)
Alcohol-Related Disorders/metabolism , Cerebellum/metabolism , Death , Ethanol/blood , Frontal Lobe/metabolism , Glycerophospholipids/metabolism , Adult , Aged , Biomarkers/blood , Biomarkers/metabolism , Case-Control Studies , Humans , Male , Middle Aged , Postmortem Changes , Sequence Homology, Amino Acid , Young Adult
10.
Neuropathol Appl Neurobiol ; 41(7): 941-51, 2015 Dec.
Article in English | MEDLINE | ID: mdl-25640985

ABSTRACT

AIMS: The enzyme catechol-O-methyltransferase (COMT) plays a primary role in the metabolism of catecholamine neurotransmitters and is implicated in the modulation of cognitive and emotional responses. The best characterized single nucleotide polymorphism (SNP) of the COMT gene consists of a valine (Val)-to-methionine (Met) substitution at codon 108/158. The Met-containing variant confers a marked reduction in COMT catalytic activity. We recently showed that the activity of recombinant COMT is positively regulated by the enzyme Met sulphoxide reductase (MSR), which counters the oxidation of Met residues of proteins. The current study was designed to assess whether brain COMT activity may be correlated to MSR in an allele-dependent fashion. METHODS: COMT and MSR activities were measured from post-mortem samples of prefrontal cortices, striata and cerebella of 32 subjects by using catechol and dabsyl-Met sulphoxide as substrates, respectively. Allelic discrimination of COMT Val(108/185) Met SNP was performed using the Taqman 5'nuclease assay. RESULTS: Our studies revealed that, in homozygous carriers of Met, but not Val alleles, the activity of COMT and MSR was significantly correlated throughout all tested brain regions. CONCLUSION: These results suggest that the reduced enzymatic activity of Met-containing COMT may be secondary to Met sulphoxidation and point to MSR as a key molecular determinant for the modulation of COMT activity.


Subject(s)
Brain/enzymology , Catechol O-Methyltransferase/metabolism , Genotype , Methionine Sulfoxide Reductases/metabolism , Polymorphism, Single Nucleotide , Adult , Alleles , Bipolar Disorder/enzymology , Bipolar Disorder/genetics , Catechol O-Methyltransferase/genetics , Female , Humans , Male , Methionine Sulfoxide Reductases/genetics , Middle Aged , Schizophrenia/enzymology , Schizophrenia/genetics
11.
BMC Bioinformatics ; 15: 334, 2014 Oct 30.
Article in English | MEDLINE | ID: mdl-25359079

ABSTRACT

BACKGROUND: Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations. RESULTS: SketchBio is presented, a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular structures and animations. It includes three novel features: crystal-by-example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their consequences are presented, including cases where iterative design was required to produce effective approaches. CONCLUSIONS: The design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.


Subject(s)
Computer Simulation , Models, Molecular , Software , Humans , Molecular Conformation
12.
Biochemistry ; 53(34): 5526-36, 2014 Sep 02.
Article in English | MEDLINE | ID: mdl-25115937

ABSTRACT

Vinculin is an essential structural adaptor protein that localizes to sites of adhesion and is involved in a number of cell processes including adhesion, spreading, motility, force transduction, and cell survival. The C-terminal vinculin tail domain (Vt) contains the necessary structural components to bind and cross-link actin filaments. Actin binding to Vt induces a conformational change that promotes dimerization through the C-terminal hairpin of Vt and enables actin filament cross-linking. Here we show that Src phosphorylation of Y1065 within the C-terminal hairpin regulates Vt-mediated actin bundling and provide a detailed characterization of Y1065 mutations. Furthermore, we show that phosphorylation at Y1065 plays a role in cell spreading and the response to the application of mechanical force.


Subject(s)
Actins/chemistry , Vinculin/physiology , Animals , Cells, Cultured , Circular Dichroism , Magnetic Resonance Spectroscopy , Mice , Microscopy, Fluorescence , Mutation , Phosphorylation , Protein Binding , Vinculin/chemistry , Vinculin/genetics
13.
Int J Neuropsychopharmacol ; 17(10): 1707-13, 2014 Oct.
Article in English | MEDLINE | ID: mdl-24735585

ABSTRACT

Catechol-O-methyl transferase (COMT) plays a key role in the degradation of brain dopamine (DA). Specifically, low COMT activity results in higher DA levels in the prefrontal cortex (PFC), thereby reducing the vulnerability for attentional and cognitive deficits in both psychotic and healthy individuals. COMT activity is markedly reduced by a non-synonymous single-nucleotide polymorphism (SNP) that generates a valine-to-methionine substitution on the residue 108/158, by means of as-yet incompletely understood post-translational mechanisms. One post-translational modification is methionine sulfoxide, which can be reduced by the methionine sulfoxide reductase (Msr) A and B enzymes. We used recombinant COMT proteins (Val/Met108) and mice (wild-type (WT) and MsrA knockout) to determine the effect of methionine oxidation on COMT activity and COMT interaction with Msr, through a combination of enzymatic activity and Western blot assays. Recombinant COMT activity is positively regulated by MsrA, especially under oxidative conditions, whereas brains of MsrA knockout mice exhibited lower COMT activity (as compared with their WT counterparts). These results suggest that COMT activity may be reduced by methionine oxidation, and point to Msr as a key molecular determinant for the modulation of COMT activity in the brain. The role of Msr in modulating cognitive functions in healthy individuals and schizophrenia patients is yet to be determined.


Subject(s)
Brain/enzymology , Catechol O-Methyltransferase/metabolism , Gene Expression Regulation/genetics , Methionine Sulfoxide Reductases/metabolism , Animals , Dithiothreitol/pharmacology , Dose-Response Relationship, Drug , Humans , Methionine Sulfoxide Reductases/genetics , Mice , Mice, Knockout , Mutation/genetics , RNA, Messenger/metabolism , Statistics, Nonparametric
14.
J Phys Chem B ; 128(14): 3383-3397, 2024 Apr 11.
Article in English | MEDLINE | ID: mdl-38563384

ABSTRACT

Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.


Subject(s)
Histidine , Polychaeta , Animals , Histidine/chemistry , Isoenzymes/metabolism , Hydrogen Peroxide/metabolism , Hemoglobins/chemistry , Peroxidases/chemistry , Peroxidase/chemistry , Polychaeta/chemistry , Polychaeta/metabolism , Crystallography, X-Ray
15.
ACS Biomater Sci Eng ; 10(2): 905-920, 2024 02 12.
Article in English | MEDLINE | ID: mdl-38240491

ABSTRACT

Localized delivery of immunotherapeutics within a tumor has the potential to reduce systemic toxicities and improve treatment outcomes in cancer patients. Unfortunately, local retention of therapeutics following intratumoral injection is problematic and is insufficiently considered. Dense tumor architectures and high interstitial pressures rapidly exclude injections of saline and other low-viscosity solutions. Hydrogel-based delivery systems, on the other hand, can resist shear forces that cause tumor leakage and thus stand to improve the local retention of coformulated therapeutics. The goal of the present work was to construct a novel, injectable hydrogel that could be tuned for localized immunotherapy delivery. A chitosan-based hydrogel, called XCSgel, was developed and subsequently characterized. Nuclear magnetic resonance studies were performed to describe the chemical properties of the new entity, while cryo-scanning electron microscopy allowed for visualization of the hydrogel's cross-linked network. Rheology experiments demonstrated that XCSgel was shear-thinning and self-healing. Biocompatibility studies, both in vitro and in vivo, showed that XCSgel was nontoxic and induced transient mild-to-moderate inflammation. Release studies revealed that coformulated immunotherapeutics were released over days to weeks in a charge-dependent manner. Overall, XCSgel displayed several clinically important features, including injectability, biocompatibility, and imageability. Furthermore, the properties of XCSgel could also be controlled to tune the release of coformulated immunotherapeutics.


Subject(s)
Chitosan , Neoplasms , Humans , Hydrogels/chemistry , Injections
16.
Proteins ; 81(7): 1245-55, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23504819

ABSTRACT

We computationally designed a de novo protein-protein interaction between wild-type ubiquitin and a redesigned scaffold. Our strategy was to incorporate zinc at the designed interface to promote affinity and orientation specificity. A large set of monomeric scaffold surfaces were computationally engineered with three-residue zinc coordination sites, and the ubiquitin residue H68 was docked to the open coordination site to complete a tetrahedral zinc site. This single coordination bond was intended as a hotspot and polar interaction for ubiquitin binding, and surrounding residues on the scaffold were optimized primarily as hydrophobic residues using a rotamer-based sequence design protocol in Rosetta. From thousands of independent design simulations, four sequences were selected for experimental characterization. The best performing design, called Spelter, binds tightly to zinc (Kd < 10 nM) and binds ubiquitin with a Kd of 20 µM in the presence of zinc and 68 µM in the absence of zinc. Mutagenesis studies and nuclear magnetic resonance chemical shift perturbation experiments indicate that Spelter interacts with H68 and the target surface on ubiquitin; however, H68 does not form a hotspot as intended. Instead, mutation of H68 to alanine results in tighter binding. Although a 3/1 zinc coordination arrangement at an interface cannot be ruled out as a means to improve affinity, our study led us to conclude that 2/2 coordination arrangements or multiple-zinc designs are more likely to promote high-affinity protein interactions.


Subject(s)
Protein Binding , Ubiquitin/chemistry , Zinc/chemistry , Alanine/chemistry , Binding Sites , Magnetic Resonance Spectroscopy , Mutagenesis , Protein Interaction Maps
17.
Front Psychiatry ; 14: 1104563, 2023.
Article in English | MEDLINE | ID: mdl-36846236

ABSTRACT

Introduction: Chronic nicotine exposure induces changes in the expression of key regulatory genes associated with metabolic function and neuronal alterations in the brain. Many bioregulatory genes have been associated with exposure to nicotine, but the modulating effects of sex and diet on gene expression in nicotine-exposed brains have been largely unexplored. Both humans and rodents display motivation for nicotine use and the emergence of withdrawal symptoms during abstinence. Research comparing pre-clinical models with human subjects provides an important opportunity to understand common biomarkers of the harmful effects of nicotine as well as information that may help guide the development of more effective interventions for nicotine cessation. Methods: Human postmortem dorsolateral prefrontal cortex (dLPFC) tissue BA9 was collected from female and male subjects, smokers and non-smokers (N = 12 per group). Rat frontal lobes were collected from female and male rats that received a regular diet (RD) or a high-fat diet (HFD) (N = 12 per group) for 14 days following implantation of a osmotic mini-pump (Alzet) that delivered nicotine continuously. Controls (control-s) received a sham surgical procedure. RNA was extracted from tissue from human and rat samples and reversed-transcribed to cDNA. Gene expression of CHRNA10 (Cholinergic receptor nicotinic alpha 10), CERKL (Ceramide Kinase-Like), SMYD1 (SET and MYD Domin Containing 1), and FA2H (Fatty Acid 2-Hydrolase) in humans was compared to rats in each subset of groups and quantified by qPCR methods. Additionally, protein expression of FA2H was analyzed by immunohistochemistry (IHC) in human dLPFC. Results: Humans with a history of smoking displayed decreased CHRNA10 (p = 0.0005), CERKL (p ≤ 0.0001), and SMYD1 (p = 0.0005) expression and increased FA2H (p = 0.0097) expression compared to non-smokers (p < 0.05). Similar patterns of results were observed in nicotine exposed vs. control rats. Interestingly, sex-related differences in gene expression for CERKL and FA2H were observed. In addition, ANCOVA analysis showed a significant effect of nicotine in a sex-different manner, including an increase in CERKL in male and female rats with RD or HFD. In rats exposed to an HFD, FA2H gene expression was lower in nicotine-treated rats compared to RD rats treated with nicotine. Protein expression of FA2H (p = 0.001) by IHC was significantly higher in smokers compared to non-smokers. Conclusion: These results suggest that a history of long-term nicotine exposure in humans alters the expression of sphingolipid metabolism-related (CERKL, SMYD1, and FA2H) and neuronal (CHRNA10) marker genes similarly as compared to rats. Sex- and diet-dependent differences appear in nicotine-exposed rats, critical in regulating sphingolipid metabolism and nicotinic acetylcholine receptors. This research enhances the construct validity of rat models of nicotine usage by showing a similar pattern of changes in gene expression in human subjects with a smoking history.

18.
J Vis Exp ; (168)2021 02 24.
Article in English | MEDLINE | ID: mdl-33720118

ABSTRACT

Many major allergens bind to hydrophobic lipid-like molecules, including Mus m 1, Bet v 1, Der p 2, and Fel d 1. These ligands are strongly retained and have the potential to influence the sensitization process either through directly stimulating the immune system or altering the biophysical properties of the allergenic protein. In order to control for these variables, techniques are required for the removal of endogenously bound ligands and, if necessary, replacement with lipids of known composition. The cockroach allergen Bla g 1 encloses a large hydrophobic cavity which binds a heterogeneous mixture of endogenous lipids when purified using traditional techniques. Here, we describe a method through which these lipids are removed using reverse-phase HPLC followed by thermal annealing to yield Bla g 1 in either its Apo-form or reloaded with a user-defined mixture of fatty acid or phospholipid cargoes. Coupling this protocol with biochemical assays reveal that fatty acid cargoes significantly alter the thermostability and proteolytic resistance of Bla g 1, with downstream implications for the rate of T-cell epitope generation and allergenicity. These results highlight the importance of lipid removal/reloading protocols such as the one described herein when studying allergens from both recombinant and natural sources. The protocol is generalizable to other allergen families including lipocalins (Mus m 1), PR-10 (Bet v 1), MD-2 (Der p 2) and Uteroglobin (Fel d 1), providing a valuable tool to study the role of lipids in the allergic response.


Subject(s)
Allergens/metabolism , Lipids/chemistry , Proteins/metabolism , Allergens/isolation & purification , Animals , Chromatography, High Pressure Liquid , Cockroaches , Hypersensitivity/immunology , Ligands , Magnetic Resonance Spectroscopy , Phospholipids/chemistry , Protein Binding , Protein Folding , Reproducibility of Results
19.
Transl Psychiatry ; 11(1): 341, 2021 06 02.
Article in English | MEDLINE | ID: mdl-34078872

ABSTRACT

Interleukins and neurotrophins levels are altered in the periphery of patients with major depression and suicidal behavior, however it is not clear if similar abnormalities occur in the central nervous system. Our objective was to examine the association of IL-6, IL-1ß, BDNF, and GDNF levels between postmortem plasma, cerebrospinal fluid (CSF), and brain tissue in a heterogeneous diagnostic subject groups including normal controls, mood disorders only, mood disorders with AUD/SUD (alcohol abuse disorder, substance abuse disorder), and AUD/SUD without mood disorders. To address these questions we collected postmortem plasma (n = 29), CSF (n = 28), and brain (BA10) (n = 57) samples from individuals with mood disorder, mood disorder with AUD/SUD, AUD/SUD and normal controls. These samples were analyzed using a multiplex based luminex assay with a customized 4-plex cytokine/interleukins- IL-6, IL-1ß, BDNF, and GDNF human acute phase based on xMAP technology platform. Protein levels were determined using a Luminex 200 instrument equipped with Xponent-analyzing software. We observed IL-6 (p = 2.1e-07), and GDNF (p = 0.046) were significantly correlated between brain and CSF. In addition, IL-6 (p = 0.031), were significantly correlated between brain and plasma. Overall diagnostic group analysis showed a significant difference with brain GDNF, p = 0.0106. Pairwise comparisons showed that GDNF level is-39.9 ± 12 pg/ml, p = 0.0106, was significantly higher than in the brains derived from mood disorders compared to normal controls, -23.8 ± 5.5 pg/ml, p = 0.034. Brain BDNF was higher in suicide (p = 0.0023), males compared to females (p = 0.017), and psychiatric medication treated vs. non-treated (p = 0.005) individuals. Overall, we demonstrate that blood IL-6, GDNF and BDNF could be informative peripheral biomarkers of brain biology associated with mood disorders, substance disorders, and suicide.


Subject(s)
Depressive Disorder, Major , Suicide , Brain-Derived Neurotrophic Factor , Central Nervous System , Female , Glial Cell Line-Derived Neurotrophic Factor , Humans , Male , Mood Disorders
20.
Psychiatry Res ; 175(3): 221-6, 2010 Feb 28.
Article in English | MEDLINE | ID: mdl-20022384

ABSTRACT

Current symptom rating scales and diagnostic categories for bipolar disorder (BD) do not provide dimensional profiles of the types of behavior disturbed in this complex disorder. To overcome these limitations we identified the principal domains of behavioral symptomatology in bipolar individuals, including all mood states, and used a more comprehensive rating scale for BD: the Bipolar Inventory of Signs and Symptoms Scale (BISS). A total of 246 patients with BD (196 with BD type I, and 50 with BD type II) were interviewed using the BISS. Exploratory factor analysis was performed on the BISS results using the maximum likelihood factor extraction method, followed by oblique rotation of the extracted factor loadings. We determined the strength of relationships between factor scores using the Pearson correlation coefficient. The following five factors were extracted: mania, depression, irritability, anxiety and psychosis. Anxiety was significantly correlated with depression and irritability. The mania factor score was only weakly associated with the other four factors. The domains of the BISS capture both the historical categories of depression and mania, plus irritability, psychosis, and an additional principal domain, anxiety. Despite the common occurrence of anxiety in BD, it has not been identified in most prior factor analyses, in part due to limited coverage of anxiety symptoms in the source scales.


Subject(s)
Bipolar Disorder/complications , Bipolar Disorder/diagnosis , Psychopathology/methods , Adolescent , Adult , Aged , Aged, 80 and over , Bipolar Disorder/classification , Factor Analysis, Statistical , Female , Humans , Male , Middle Aged , Psychiatric Status Rating Scales , Psychometrics , Statistics as Topic , Young Adult
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