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Trimigno A, Holderman NR, Dong C, Boardman KD, Zhao J, O’Day EM. NMR Precision Metabolomics: Dynamic Peak Sum Thresholding and Navigators for Highly Standardized and Reproducible Metabolite Profiling of Clinical Urine Samples. Metabolites 2024; 14:275. [PMID: 38786752 PMCID: PMC11122845 DOI: 10.3390/metabo14050275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Metabolomics, especially urine-based studies, offers incredible promise for the discovery and development of clinically impactful biomarkers. However, due to the unique challenges of urine, a highly precise and reproducible workflow for NMR-based urine metabolomics is lacking. Using 1D and 2D non-uniform sampled (NUS) 1H-13C NMR spectroscopy, we systematically explored how changes in hydration or specific gravity (SG) and pH can impact biomarker discovery. Further, we examined additional sources of error in metabolomics studies and identified Navigator molecules that could monitor for those biases. Adjustment of SG to 1.002-1.02 coupled with a dynamic sum-based peak thresholding eliminates false positives associated with urine hydration and reduces variation in chemical shift. We identified Navigator molecules that can effectively monitor for inconsistencies in sample processing, SG, protein contamination, and pH. The workflow described provides quality assurance and quality control tools to generate high-quality urine metabolomics data, which is the first step in biomarker discovery.
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Nazeer N, Simmons JR, Rainey JK, Rodriguez-Lecompte JC, Ahmed M. Antibacterial activities of physiologically stable, self-assembled peptide nanoparticles. J Mater Chem B 2021; 9:9041-9054. [PMID: 34664611 DOI: 10.1039/d1tb01864g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we report that host defense protein-derived ten amino acid long disulfide-linked peptides self-assemble in the form of β-sheets and β-turns, and exhibit concentration-dependent self-assembly in the form of nanospheres, termed as disulfide linked nanospheres (DSNs). As expected, bare DSNs are prone to aggregation in ionic solutions and in the presence of serum proteins. To yield physiologically stable self-assembled peptide-based materials, DSNs are stabilized in the form of supramolecular assemblies using β-cyclodextrins (β-CD) and fucoidan, as delivery carriers. The inclusion complexes of DSNs with β-CD (β-CD-DSN) and electrostatic complexation of fucoidan with DSNs (FC-DSN) stabilizes the secondary structure of DSNs. Comparison of β-CD-DSNs with FC-DSNs reveals that inclusion complexes of DSNs formed in the presence of β-CD are highly stable under physiological conditions, show high cellular uptake, exhibit bacterial flocculation, and enhance antibacterial efficacies of DSNs in a range of Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Nauman Nazeer
- Department of Chemistry, University of Prince Edward Island, Charlottetown, Prince Edward Island, C1A 4P3, Canada.
| | - Jeffrey R Simmons
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.,School of Biomedical Engineering, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Juan Carlos Rodriguez-Lecompte
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, C1A 4P3, Canada
| | - Marya Ahmed
- Department of Chemistry, University of Prince Edward Island, Charlottetown, Prince Edward Island, C1A 4P3, Canada. .,Faculty of Sustainable Design Engineering, University of Prince Edward Island, Charlottetown, Prince Edward Island, C1A 4P3, Canada
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Abstract
Interactions of intrinsically disordered proteins are central to their cellular functions, and solution-state NMR spectroscopy provides a powerful tool for characterizing both structural and mechanistic aspects of such interactions. Here we focus on the analysis of IDP interactions using NMR titration measurements. Changes in resonance lineshapes in two-dimensional NMR spectra upon titration with a ligand contain rich information on structural changes in the protein and the thermodynamics and kinetics of the interaction, as well as on the microscopic association mechanism. Here we present protocols for the optimal design of titration experiments, data acquisition, and data analysis by two-dimensional lineshape fitting using the TITAN software package.
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Sarker M, Speckert M, Rainey JK. Bicelle composition-dependent modulation of phospholipid dynamics by apelin peptides 1. Biochem Cell Biol 2018; 97:325-332. [PMID: 30092142 DOI: 10.1139/bcb-2018-0172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Apelin peptides are cognate ligands for the apelin receptor, a G-protein-coupled receptor (GPCR). The apelinergic system plays critical roles in wide-ranging physiological activities including function and development of the central nervous and cardiovascular systems. Apelin is found in 13-55 residue isoforms in vivo, all of which share the C-terminal portion of the preproapelin precursor. Characterization of high-resolution structures and detergent micelle interactions of apelin-17 led to a two-step membrane-catalyzed binding and GPCR activation mechanism hypothesis recapitulated in longer isoforms. Here, we examine interactions of the apelin-13 and -17 isoforms with isotropic zwitterionic and mixed zwitterionic-anionic lipid bicelles to test for hallmarks of membrane catalysis in a more physiological membrane-mimetic environment than a micelle. Specifically, 1H and 31P relaxation and diffusion solution-state NMR techniques demonstrate that both apelin isoforms interact with both types of isotropic bicelles. Bicelle hydrodynamics were observed to be differentially modulated by apelin peptides, although these effects were minimal. Phospholipid headgroup 31P spin relaxation behaviour was, conversely, clearly perturbed. Perturbation of this nature was also observed in magnetically aligned bicelles by 31P solid-state NMR spectroscopy and spin relaxation experiments. This behaviour is consistent with an apelin-bicelle binding process allowing significant peptide mobility, facilitating membrane-catalyzed GPCR encounter.
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Affiliation(s)
- Muzaddid Sarker
- a Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Matt Speckert
- a Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jan K Rainey
- a Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.,b Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada
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