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Role of a Stem-Loop Structure in Transcript Stability.
Loh JT, Lin AS, Beckett AC, McClain MS, Cover TL
(2019) Infect Immun 87:
MeSH Terms: Antigens, Bacterial, Bacterial Proteins, DNA, Bacterial, Helicobacter Infections, Helicobacter pylori, Humans, Mutagenesis, Site-Directed, RNA Stability, RNA, Messenger
Show Abstract · Added February 7, 2019
CagA is a secreted effector protein that contributes to gastric carcinogenesis. Previous studies showed that there is variation among strains in the steady-state levels of CagA and that a strain-specific motif downstream of the transcriptional start site (the +59 motif) is associated with both high levels of CagA and premalignant gastric histology. The 5' untranslated region contains a predicted stem-loop-forming structure adjacent to the +59 motif. In the current study, we investigated the effect of the +59 motif and the adjacent stem-loop on transcript levels and mRNA stability. Using site-directed mutagenesis, we found that mutations predicted to disrupt the stem-loop structure resulted in decreased steady-state levels of both the transcript and the CagA protein. Additionally, these mutations resulted in a decreased mRNA half-life. Mutagenesis of the +59 motif without altering the stem-loop structure resulted in reduced steady-state transcript and CagA protein levels but did not affect transcript stability. transcript stability was not affected by increased sodium chloride concentrations, an environmental factor known to augment transcript levels and CagA protein levels. These results indicate that both a predicted stem-loop structure and a strain-specific +59 motif in the 5' untranslated region influence the levels of expression.
Copyright © 2019 American Society for Microbiology.
0 Communities
1 Members
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9 MeSH Terms
Broadly Neutralizing Antibody Mediated Clearance of Human Hepatitis C Virus Infection.
Kinchen VJ, Zahid MN, Flyak AI, Soliman MG, Learn GH, Wang S, Davidson E, Doranz BJ, Ray SC, Cox AL, Crowe JE, Bjorkman PJ, Shaw GM, Bailey JR
(2018) Cell Host Microbe 24: 717-730.e5
MeSH Terms: Animals, Antibodies, Monoclonal, Antibodies, Neutralizing, Antibody Specificity, Base Sequence, Binding Sites, Cell Line, Cricetulus, Epitopes, Female, HEK293 Cells, HIV-1, Hepacivirus, Hepatitis C, Hepatitis C Antibodies, Humans, Immunologic Memory, Male, Models, Molecular, Mutagenesis, Site-Directed, Viral Envelope Proteins, Viral Load
Show Abstract · Added March 31, 2019
The role that broadly neutralizing antibodies (bNAbs) play in natural clearance of human hepatitis C virus (HCV) infection and the underlying mechanisms remain unknown. Here, we investigate the mechanism by which bNAbs, isolated from two humans who spontaneously cleared HCV infection, contribute to HCV control. Using viral gene sequences amplified from longitudinal plasma of the two subjects, we found that these bNAbs, which target the front layer of the HCV envelope protein E2, neutralized most autologous HCV strains. Acquisition of resistance to bNAbs by some autologous strains was accompanied by progressive loss of E2 protein function, and temporally associated with HCV clearance. These data demonstrate that bNAbs can mediate clearance of human HCV infection by neutralizing infecting strains and driving escaped viruses to an unfit state. These immunopathologic events distinguish HCV from HIV-1 and suggest that development of an HCV vaccine may be achievable.
Copyright © 2018 Elsevier Inc. All rights reserved.
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22 MeSH Terms
Disrupted structure and aberrant function of CHIP mediates the loss of motor and cognitive function in preclinical models of SCAR16.
Shi CH, Rubel C, Soss SE, Sanchez-Hodge R, Zhang S, Madrigal SC, Ravi S, McDonough H, Page RC, Chazin WJ, Patterson C, Mao CY, Willis MS, Luo HY, Li YS, Stevens DA, Tang MB, Du P, Wang YH, Hu ZW, Xu YM, Schisler JC
(2018) PLoS Genet 14: e1007664
MeSH Terms: Animals, Behavior, Animal, CRISPR-Cas Systems, Cognition, Disease Models, Animal, Female, Humans, Male, Mice, Mice, Inbred C57BL, Models, Molecular, Motor Activity, Mutagenesis, Site-Directed, Phenotype, Point Mutation, Protein Domains, Protein Multimerization, Rats, Rats, Sprague-Dawley, Spinocerebellar Ataxias, Ubiquitin-Protein Ligases
Show Abstract · Added March 26, 2019
CHIP (carboxyl terminus of heat shock 70-interacting protein) has long been recognized as an active member of the cellular protein quality control system given the ability of CHIP to function as both a co-chaperone and ubiquitin ligase. We discovered a genetic disease, now known as spinocerebellar autosomal recessive 16 (SCAR16), resulting from a coding mutation that caused a loss of CHIP ubiquitin ligase function. The initial mutation describing SCAR16 was a missense mutation in the ubiquitin ligase domain of CHIP (p.T246M). Using multiple biophysical and cellular approaches, we demonstrated that T246M mutation results in structural disorganization and misfolding of the CHIP U-box domain, promoting oligomerization, and increased proteasome-dependent turnover. CHIP-T246M has no ligase activity, but maintains interactions with chaperones and chaperone-related functions. To establish preclinical models of SCAR16, we engineered T246M at the endogenous locus in both mice and rats. Animals homozygous for T246M had both cognitive and motor cerebellar dysfunction distinct from those observed in the CHIP null animal model, as well as deficits in learning and memory, reflective of the cognitive deficits reported in SCAR16 patients. We conclude that the T246M mutation is not equivalent to the total loss of CHIP, supporting the concept that disease-causing CHIP mutations have different biophysical and functional repercussions on CHIP function that may directly correlate to the spectrum of clinical phenotypes observed in SCAR16 patients. Our findings both further expand our basic understanding of CHIP biology and provide meaningful mechanistic insight underlying the molecular drivers of SCAR16 disease pathology, which may be used to inform the development of novel therapeutics for this devastating disease.
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MeSH Terms
Discovery, Characterization, and Effects on Renal Fluid and Electrolyte Excretion of the Kir4.1 Potassium Channel Pore Blocker, VU0134992.
Kharade SV, Kurata H, Bender AM, Blobaum AL, Figueroa EE, Duran A, Kramer M, Days E, Vinson P, Flores D, Satlin LM, Meiler J, Weaver CD, Lindsley CW, Hopkins CR, Denton JS
(2018) Mol Pharmacol 94: 926-937
MeSH Terms: Animals, Binding Sites, Diuretics, Electrolytes, HEK293 Cells, Humans, Male, Models, Molecular, Molecular Docking Simulation, Molecular Structure, Mutagenesis, Site-Directed, Potassium Channels, Inwardly Rectifying, Rats, Small Molecule Libraries, Substrate Specificity
Show Abstract · Added April 10, 2019
The inward rectifier potassium (Kir) channel Kir4.1 () carries out important physiologic roles in epithelial cells of the kidney, astrocytes in the central nervous system, and stria vascularis of the inner ear. Loss-of-function mutations in lead to EAST/SeSAME syndrome, which is characterized by epilepsy, ataxia, renal salt wasting, and sensorineural deafness. Although genetic approaches have been indispensable for establishing the importance of Kir4.1 in the normal function of these tissues, the availability of pharmacological tools for acutely manipulating the activity of Kir4.1 in genetically normal animals has been lacking. We therefore carried out a high-throughput screen of 76,575 compounds from the Vanderbilt Institute of Chemical Biology library for small-molecule modulators of Kir4.1. The most potent inhibitor identified was 2-(2-bromo-4-isopropylphenoxy)--(2,2,6,6-tetramethylpiperidin-4-yl)acetamide (VU0134992). In whole-cell patch-clamp electrophysiology experiments, VU0134992 inhibits Kir4.1 with an IC value of 0.97 M and is 9-fold selective for homomeric Kir4.1 over Kir4.1/5.1 concatemeric channels (IC = 9 M) at -120 mV. In thallium (Tl) flux assays, VU0134992 is greater than 30-fold selective for Kir4.1 over Kir1.1, Kir2.1, and Kir2.2; is weakly active toward Kir2.3, Kir6.2/SUR1, and Kir7.1; and is equally active toward Kir3.1/3.2, Kir3.1/3.4, and Kir4.2. This potency and selectivity profile is superior to Kir4.1 inhibitors amitriptyline, nortriptyline, and fluoxetine. Medicinal chemistry identified components of VU0134992 that are critical for inhibiting Kir4.1. Patch-clamp electrophysiology, molecular modeling, and site-directed mutagenesis identified pore-lining glutamate 158 and isoleucine 159 as critical residues for block of the channel. VU0134992 displayed a large free unbound fraction () in rat plasma ( = 0.213). Consistent with the known role of Kir4.1 in renal function, oral dosing of VU0134992 led to a dose-dependent diuresis, natriuresis, and kaliuresis in rats. Thus, VU0134992 represents the first in vivo active tool compound for probing the therapeutic potential of Kir4.1 as a novel diuretic target for the treatment of hypertension.
Copyright © 2018 by The American Society for Pharmacology and Experimental Therapeutics.
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MeSH Terms
Using two-site binding models to analyze microscale thermophoresis data.
Tso SC, Chen Q, Vishnivetskiy SA, Gurevich VV, Iverson TM, Brautigam CA
(2018) Anal Biochem 540-541: 64-75
MeSH Terms: Adenosine Monophosphate, Algorithms, Animals, Aptamers, Nucleotide, Binding Sites, Cattle, Kinetics, Models, Molecular, Monte Carlo Method, Mutagenesis, Site-Directed, Phytic Acid, Protein Binding, Recombinant Proteins, beta-Arrestin 2
Show Abstract · Added March 14, 2018
The emergence of microscale thermophoresis (MST) as a technique for determining the dissociation constants for bimolecular interactions has enabled these quantities to be measured in systems that were previously difficult or impracticable. However, most models for analyses of these data featured the assumption of a simple 1:1 binding interaction. The only model widely used for multiple binding sites was the Hill equation. Here, we describe two new MST analytic models that assume a 1:2 binding scheme: the first features two microscopic binding constants (K(1) and K(2)), while the other assumes symmetry in the bivalent molecule, culminating in a model with a single macroscopic dissociation constant (K) and a single factor (α) that accounts for apparent cooperativity in the binding. We also discuss the general applicability of the Hill equation for MST data. The performances of the algorithms on both real and simulated data are assessed, and implementation of the algorithms in the MST analysis program PALMIST is discussed.
Copyright © 2017 Elsevier Inc. All rights reserved.
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2 Members
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14 MeSH Terms
Proteolytic processing of lysyl oxidase-like-2 in the extracellular matrix is required for crosslinking of basement membrane collagen IV.
López-Jiménez AJ, Basak T, Vanacore RM
(2017) J Biol Chem 292: 16970-16982
MeSH Terms: Amino Acid Oxidoreductases, Basement Membrane, Collagen Type IV, Extracellular Matrix, HEK293 Cells, Humans, Mutagenesis, Site-Directed, Protein Domains, Protein Processing, Post-Translational, Proteolysis
Show Abstract · Added November 3, 2017
Lysyl oxidase-like-2 (LOXL2) is an enzyme secreted into the extracellular matrix that crosslinks collagens by mediating oxidative deamination of lysine residues. Our previous work demonstrated that this enzyme crosslinks the 7S domain, a structural domain that stabilizes collagen IV scaffolds in the basement membrane. Despite its relevant role in extracellular matrix biosynthesis, little is known about the structural requirements of LOXL2 that enable collagen IV crosslinking. In this study, we demonstrate that LOXL2 is processed extracellularly by serine proteases, generating a 65-kDa form lacking the first two scavenger receptor cysteine-rich domains. Site-specific mutagenesis to prevent proteolytic processing generated a full-length enzyme that is active toward a soluble substrate, but fails to crosslink insoluble collagen IV within the extracellular matrix. In contrast, the processed form of LOXL2 binds to collagen IV and crosslinks the 7S domain. Together, our data demonstrate that proteolytic processing is an important event that allows LOXL2-mediated crosslinking of basement membrane collagen IV.
© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
1 Communities
1 Members
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10 MeSH Terms
cytochrome P450 46A1 (CYP46A1) activation by neuroactive compounds.
Mast N, Anderson KW, Johnson KM, Phan TTN, Guengerich FP, Pikuleva IA
(2017) J Biol Chem 292: 12934-12946
MeSH Terms: Acetylcholine, Allosteric Regulation, Amino Acid Substitution, Anti-HIV Agents, Aspartic Acid, Benzoxazines, Binding Sites, Biocatalysis, Cholesterol 24-Hydroxylase, Deuterium Exchange Measurement, Enzyme Activation, Glutamic Acid, Ligands, Models, Molecular, Molecular Docking Simulation, Mutagenesis, Site-Directed, Mutation, Nerve Tissue Proteins, Peptide Fragments, Protein Conformation, Recombinant Fusion Proteins, gamma-Aminobutyric Acid
Show Abstract · Added March 14, 2018
Cytochrome P450 46A1 (CYP46A1, cholesterol 24-hydroxylase) is the enzyme responsible for the majority of cholesterol elimination from the brain. Previously, we found that the anti-HIV drug efavirenz (EFV) can pharmacologically activate CYP46A1 in mice. Herein, we investigated whether CYP46A1 could also be activated by endogenous compounds, including major neurotransmitters. experiments with purified recombinant CYP46A1 indicated that CYP46A1 is activated by l-glutamate (l-Glu), l-aspartate, γ-aminobutyric acid, and acetylcholine, with l-Glu eliciting the highest increase (3-fold) in CYP46A1-mediated cholesterol 24-hydroxylation. We also found that l-Glu and other activating neurotransmitters bind to the same site on the CYP46A1 surface, which differs from the EFV-binding site. The other principal differences between EFV and l-Glu in CYP46A1 activation include an apparent lack of l-Glu binding to the P450 active site and different pathways of signal transduction from the allosteric site to the active site. EFV and l-Glu similarly increased the CYP46A1 , the rate of the "fast" phase of the enzyme reduction by the redox partner NADPH-cytochrome P450 oxidoreductase, and the amount of P450 reduced. Spectral titrations with cholesterol, in the presence of EFV or l-Glu, suggest that water displacement from the heme iron can be affected in activator-bound CYP46A1. Moreover, EFV and l-Glu synergistically activated CYP46A1. Collectively, our data, along with those from previous cell culture and studies by others, suggest that l-Glu-induced CYP46A1 activation is of physiological relevance.
© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
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1 Members
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22 MeSH Terms
Structural and biochemical analyses reveal insights into covalent flavinylation of the Complex II homolog quinol:fumarate reductase.
Starbird CA, Maklashina E, Sharma P, Qualls-Histed S, Cecchini G, Iverson TM
(2017) J Biol Chem 292: 12921-12933
MeSH Terms: Amino Acid Substitution, Biocatalysis, Crystallography, X-Ray, Enzyme Stability, Escherichia coli, Escherichia coli Proteins, Flavin-Adenine Dinucleotide, Gene Deletion, Glutamic Acid, Hot Temperature, Models, Molecular, Molecular Docking Simulation, Mutagenesis, Site-Directed, Mutation, Oxidoreductases, Protein Conformation, Protein Denaturation, Protein Interaction Domains and Motifs, Protein Multimerization, Protein Processing, Post-Translational, Protein Subunits, Recombinant Proteins, Structural Homology, Protein, Succinate Dehydrogenase
Show Abstract · Added April 1, 2019
The Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the QFR FrdA subunit. Using a Δ strain, we show that the requirement for the assembly factor depends on the cellular redox environment. We next identified residues important for the covalent attachment and selected the FrdA residue, which contributes to proton shuttling during fumarate reduction, for detailed biophysical and structural characterization. We found that QFR complexes containing FrdA have a structure similar to that of the WT flavoprotein, but lack detectable substrate binding and turnover. In the context of the isolated FrdA subunit, the anticipated assembly intermediate during covalent flavinylation, FrdA variants had stability similar to that of WT FrdA, contained noncovalent FAD, and displayed a reduced capacity to interact with SdhE. However, small-angle X-ray scattering (SAXS) analysis of WT FrdA cross-linked to SdhE suggested that the FrdA residue is unlikely to contribute directly to the FrdA-SdhE protein-protein interface. We also found that no auxiliary factor is absolutely required for flavinylation, indicating that the covalent flavinylation is autocatalytic. We propose that multiple factors, including the SdhE assembly factor and bound dicarboxylates, stimulate covalent flavinylation by preorganizing the active site to stabilize the quinone-methide intermediate.
© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
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MeSH Terms
Implications of the differing roles of the β1 and β3 transmembrane and cytoplasmic domains for integrin function.
Lu Z, Mathew S, Chen J, Hadziselimovic A, Palamuttam R, Hudson BG, Fässler R, Pozzi A, Sanders CR, Zent R
(2016) Elife 5:
MeSH Terms: Amino Acid Substitution, Cell Adhesion, Cells, Cultured, Epithelial Cells, Humans, Integrin alpha1, Integrin beta1, Integrin beta3, Mutagenesis, Site-Directed, Mutant Proteins, Platelet Membrane Glycoprotein IIb, Protein Binding, Protein Multimerization
Show Abstract · Added March 26, 2017
Integrins are transmembrane receptors composed of α and β subunits. Although most integrins contain β1, canonical activation mechanisms are based on studies of the platelet integrin, αIIbβ3. Its inactive conformation is characterized by the association of the αIIb transmembrane and cytosolic domain (TM/CT) with a tilted β3 TM/CT that leads to activation when disrupted. We show significant structural differences between β1 and β3 TM/CT in bicelles. Moreover, the 'snorkeling' lysine at the TM/CT interface of β subunits, previously proposed to regulate αIIbβ3 activation by ion pairing with nearby lipids, plays opposite roles in β1 and β3 integrin function and in neither case is responsible for TM tilt. A range of affinities from almost no interaction to the relatively high avidity that characterizes αIIbβ3 is seen between various α subunits and β1 TM/CTs. The αIIbβ3-based canonical model for the roles of the TM/CT in integrin activation and function clearly does not extend to all mammalian integrins.
1 Communities
3 Members
1 Resources
13 MeSH Terms
ML418: The First Selective, Sub-Micromolar Pore Blocker of Kir7.1 Potassium Channels.
Swale DR, Kurata H, Kharade SV, Sheehan J, Raphemot R, Voigtritter KR, Figueroa EE, Meiler J, Blobaum AL, Lindsley CW, Hopkins CR, Denton JS
(2016) ACS Chem Neurosci 7: 1013-23
MeSH Terms: Animals, Dose-Response Relationship, Drug, HEK293 Cells, Humans, Membrane Potentials, Models, Molecular, Mutagenesis, Site-Directed, Mutation, Patch-Clamp Techniques, Potassium, Potassium Channel Blockers, Potassium Channels, Inwardly Rectifying, Structure-Activity Relationship, Time Factors, Transfection
Show Abstract · Added April 8, 2017
The inward rectifier potassium (Kir) channel Kir7.1 (KCNJ13) has recently emerged as a key regulator of melanocortin signaling in the brain, electrolyte homeostasis in the eye, and uterine muscle contractility during pregnancy. The pharmacological tools available for exploring the physiology and therapeutic potential of Kir7.1 have been limited to relatively weak and nonselective small-molecule inhibitors. Here, we report the discovery in a fluorescence-based high-throughput screen of a novel Kir7.1 channel inhibitor, VU714. Site-directed mutagenesis of pore-lining amino acid residues identified glutamate 149 and alanine 150 as essential determinants of VU714 activity. Lead optimization with medicinal chemistry generated ML418, which exhibits sub-micromolar activity (IC50 = 310 nM) and superior selectivity over other Kir channels (at least 17-fold selective over Kir1.1, Kir2.1, Kir2.2, Kir2.3, Kir3.1/3.2, and Kir4.1) except for Kir6.2/SUR1 (equally potent). Evaluation in the EuroFins Lead Profiling panel of 64 GPCRs, ion-channels, and transporters for off-target activity of ML418 revealed a relatively clean ancillary pharmacology. While ML418 exhibited low CLHEP in human microsomes which could be modulated with lipophilicity adjustments, it showed high CLHEP in rat microsomes regardless of lipophilicity. A subsequent in vivo PK study of ML418 by intraperitoneal (IP) administration (30 mg/kg dosage) revealed a suitable PK profile (Cmax = 0.20 μM and Tmax = 3 h) and favorable CNS distribution (mouse brain/plasma Kp of 10.9 to support in vivo studies. ML418, which represents the current state-of-the-art in Kir7.1 inhibitors, should be useful for exploring the physiology of Kir7.1 in vitro and in vivo.
1 Communities
2 Members
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15 MeSH Terms