1
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Osterberg MK, Smith AK, Campbell C, Deredge DJ, Stemmler TL, Giedroc DP. Coupling of zinc and GTP binding drives G-domain folding in Acinetobacter baumannii ZigA. Biophys J 2024; 123:979-991. [PMID: 38459695 PMCID: PMC11052692 DOI: 10.1016/j.bpj.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
COG0523 proteins, also known as nucleotide-dependent metallochaperones, are a poorly understood class of small P-loop G3E GTPases. Multiple family members play critical roles in bacterial pathogen survival during an infection as part of the adaptive response to host-mediated "nutritional immunity." Our understanding of the structure, dynamics, and molecular-level function of COG0523 proteins, apart from the eukaryotic homolog, Zng1, remains in its infancy. Here, we use X-ray absorption spectroscopy to establish that Acinetobacter baumannii (Ab) ZigA coordinates ZnII using all three cysteines derived from the invariant CXCC motif to form an S3(N/O) coordination complex, a feature inconsistent with the ZnII-bound crystal structure of a distantly related COG0523 protein of unknown function from Escherichia coli, EcYjiA. The binding of ZnII and guanine nucleotides is thermodynamically linked in AbZigA, and this linkage is more favorable for the substrate GTP relative to the product GDP. Part of this coupling originates with nucleotide-induced stabilization of the G-domain tertiary structure as revealed by global thermodynamics measurements and hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS also reveals that the HDX behavior of the G2 (switch 1) loop is highly sensitive to nucleotide status and becomes more exchange labile in the GDP (product)-bound state. Significant long-range perturbation of local stability in both the G-domain and the C-terminal domain define a candidate binding pocket for a client protein that appears sensitive to nucleotide status (GDP versus GTP). We place these new insights into the structure, dynamics, and energetics of intermolecular metal transfer into the context of a model for AbZigA metallochaperone function.
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Affiliation(s)
| | - Ally K Smith
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Courtney Campbell
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana.
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2
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Smith AK, Deredge DJ. Optimization of hydrogen-deuterium exchange ensemble reweighting (HDXer) to aid the biophysical characterization of proteins. Biophys J 2023; 122:141a. [PMID: 36782642 DOI: 10.1016/j.bpj.2022.11.924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Ally K Smith
- University of Maryland Baltimore, Baltimore, MD, USA
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3
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Obi JO, McQueen L, Deredge DJ. Inter-domain coordination essential for dengue virus non-structural (5) NS5 interaction with stem loop a (SLA). Biophys J 2023; 122:220a. [PMID: 36783080 DOI: 10.1016/j.bpj.2022.11.1309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Juliet O Obi
- Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, MD, USA
| | - Linfah McQueen
- Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, MD, USA
| | - Daniel J Deredge
- School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
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4
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Sestok AE, Brown JB, Obi JO, O'Sullivan SM, Garcin ED, Deredge DJ, Smith AT. A fusion of the Bacteroides fragilis ferrous iron import proteins reveals a role for FeoA in stabilizing GTP-bound FeoB. J Biol Chem 2022; 298:101808. [PMID: 35271852 PMCID: PMC8980893 DOI: 10.1016/j.jbc.2022.101808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/25/2022] Open
Abstract
Iron is an essential element for nearly all organisms, and under anoxic and/or reducing conditions, Fe2+ is the dominant form of iron available to bacteria. The ferrous iron transport (Feo) system is the primary prokaryotic Fe2+ import machinery, and two constituent proteins (FeoA and FeoB) are conserved across most bacterial species. However, how FeoA and FeoB function relative to one another remains enigmatic. In this work, we explored the distribution of feoAB operons encoding a fusion of FeoA tethered to the N-terminal, G-protein domain of FeoB via a connecting linker region. We hypothesized that this fusion poises FeoA to interact with FeoB to affect function. To test this hypothesis, we characterized the soluble NFeoAB fusion protein from Bacteroides fragilis, a commensal organism implicated in drug-resistant infections. Using X-ray crystallography, we determined the 1.50-Å resolution structure of BfFeoA, which adopts an SH3-like fold implicated in protein–protein interactions. Using a combination of structural modeling, small-angle X-ray scattering, and hydrogen–deuterium exchange mass spectrometry, we show that FeoA and NFeoB interact in a nucleotide-dependent manner, and we mapped the protein–protein interaction interface. Finally, using guanosine triphosphate (GTP) hydrolysis assays, we demonstrate that BfNFeoAB exhibits one of the slowest known rates of Feo-mediated GTP hydrolysis that is not potassium-stimulated. Importantly, truncation of FeoA from this fusion demonstrates that FeoA–NFeoB interactions function to stabilize the GTP-bound form of FeoB. Taken together, our work reveals a role for FeoA function in the fused FeoAB system and suggests a function for FeoA among prokaryotes.
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Affiliation(s)
- Alex E Sestok
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA
| | - Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA
| | - Juliet O Obi
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, 21201 USA
| | - Sean M O'Sullivan
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA
| | - Elsa D Garcin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA; Laboratoire d'Information Génomique et Structurale, UMR7256, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, 21201 USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250 USA.
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5
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Kihn KC, Smith AK, Bradshaw R, Forrest LR, Deredge DJ. Modeling native state ensembles and macromolecular complexes using hydrogen-deuterium exchange ensemble reweighting. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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6
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Smith AK, Kihn KC, Deredge DJ. Optimizing hydrogen-deuterium exchange ensemble reweighting using candidate ensembles of calmodulin. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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7
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Kihn KC, Wilson T, Smith AK, Bradshaw RT, Wintrode PL, Forrest LR, Wilks A, Deredge DJ. Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting. Biophys J 2021; 120:5141-5157. [PMID: 34767787 PMCID: PMC8715216 DOI: 10.1016/j.bpj.2021.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/13/2021] [Accepted: 11/04/2021] [Indexed: 11/25/2022] Open
Abstract
The cytoplasmic heme binding protein from Pseudomonas aeruginosa, PhuS, plays two essential roles in regulating heme uptake and iron homeostasis. First, PhuS shuttles exogenous heme to heme oxygenase (HemO) for degradation and iron release. Second, PhuS binds DNA and modulates the transcription of the prrF/H small RNAs (sRNAs) involved in the iron-sparing response. Heme binding to PhuS regulates this dual function, as the unliganded form binds DNA, whereas the heme-bound form binds HemO. Crystallographic studies revealed nearly identical structures for apo- and holo-PhuS, and yet numerous solution-based measurements indicate that heme binding is accompanied by large conformational rearrangements. In particular, hydrogen-deuterium exchange mass spectrometry (HDX-MS) of apo- versus holo-PhuS revealed large differences in deuterium uptake, notably in α-helices 6, 7, and 8 (α6,7,8), which contribute to the heme binding pocket. These helices were mostly labile in apo-PhuS but largely protected in holo-PhuS. In contrast, in silico-predicted deuterium uptake levels of α6,7,8 from molecular dynamics (MD) simulations of the apo- and holo-PhuS structures are highly similar, consistent only with the holo-PhuS HDX-MS data. To rationalize this discrepancy between crystal structures, simulations, and observed HDX-MS, we exploit a recently developed computational approach (HDXer) that fits the relative weights of conformational populations within an ensemble of structures to conform to a target set of HDX-MS data. Here, a combination of enhanced sampling MD, HDXer, and dimensionality reduction analysis reveals an apo-PhuS conformational landscape in which α6, 7, and 8 are significantly rearranged compared to the crystal structure, including a loss of secondary structure in α6 and the displacement of α7 toward the HemO binding interface. Circular dichroism analysis confirms the loss of secondary structure, and the extracted ensembles of apo-PhuS and of heme-transfer-impaired H212R mutant, are consistent with known heme binding and transfer properties. The proposed conformational landscape provides structural insights into the modulation by heme of the dual function of PhuS.
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Affiliation(s)
- Kyle C Kihn
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Tyree Wilson
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Ally K Smith
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | | | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Angela Wilks
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
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8
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Aytenfisu AH, Deredge DJ, Klontz EH, Du J, Sundberg EJ, MacKerell AD. Antibody Modeling using Molecular Dynamics and Silcs Fragmaps. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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9
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Kihn KC, Wilson T, Bradshaw RT, Wintrode PL, Forrest LR, Wilks A, Deredge DJ. HDX-MS Guided Ensemble Reweighting Approach Characterizes a Large Conformational Rearrangement in the Cytoplasmic Heme Binding Protein PhuS. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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10
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Obi JO, Deredge DJ. A Combined HDX-MS and MD Simulation Approach to Identify Potential Druggable Regions in the NS5 Protein of the Dengue Virus Serotype 2. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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11
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Lee PS, Bradshaw RT, Marinelli F, Kihn K, Smith A, Wintrode PL, Deredge DJ, Faraldo-Gómez JD, Forrest LR. Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. Living J Comput Mol Sci 2021; 3:1521. [PMID: 36644498 PMCID: PMC9835200 DOI: 10.33011/livecoms.3.1.1521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Hydrogen-deuterium exchange (HDX) is a comprehensive yet detailed probe of protein structure and dynamics and, coupled to mass spectrometry, has become a powerful tool for investigating an increasingly large array of systems. Computer simulations are often used to help rationalize experimental observations of exchange, but interpretations have frequently been limited to simple, subjective correlations between microscopic dynamical fluctuations and the observed macroscopic exchange behavior. With this in mind, we previously developed the HDX ensemble reweighting approach and associated software, HDXer, to aid the objective interpretation of HDX data using molecular simulations. HDXer has two main functions; first, to compute H-D exchange rates that describe each structure in a candidate ensemble of protein structures, for example from molecular simulations, and second, to objectively reweight the conformational populations present in a candidate ensemble to conform to experimental exchange data. In this article, we first describe the HDXer approach, theory, and implementation. We then guide users through a suite of tutorials that demonstrate the practical aspects of preparing experimental data, computing HDX levels from molecular simulations, and performing ensemble reweighting analyses. Finally we provide a practical discussion of the capabilities and limitations of the HDXer methods including recommendations for a user's own analyses. Overall, this article is intended to provide an up-to-date, pedagogical counterpart to the software, which is freely available at https://github.com/Lucy-Forrest-Lab/HDXer.
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Affiliation(s)
- Paul Suhwan Lee
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Richard T. Bradshaw
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA,For correspondence: (RTB); (LRF)
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kyle Kihn
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Ally Smith
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Daniel J. Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - José D. Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucy R. Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA,For correspondence: (RTB); (LRF)
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12
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Centola G, Deredge DJ, Hom K, Ai Y, Dent AT, Xue F, Wilks A. Gallium(III)-Salophen as a Dual Inhibitor of Pseudomonas aeruginosa Heme Sensing and Iron Acquisition. ACS Infect Dis 2020; 6:2073-2085. [PMID: 32551497 DOI: 10.1021/acsinfecdis.0c00138] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic bacterium that causes life-threatening infections in immunocompromised patients. In infection, it uses heme as a primary iron source and senses the availability of exogenous heme through the heme assimilation system (Has), an extra cytoplasmic function σ-factor system. A secreted hemophore HasAp scavenges heme and, upon interaction with the outer-membrane receptor HasR, activates a signaling cascade, which in turn creates a positive feedback loop critical for sensing and adaptation within the host. The ability to sense and respond to heme as an iron source contributes to virulence. Consequently, the inhibition of this system will lead to a disruption in iron homeostasis, decreasing virulence. We have identified a salophen scaffold that successfully inhibits the activation of the Has signaling system while simultaneously targeting iron uptake via xenosiderophore receptors. We propose this dual mechanism wherein free Ga3+-salophen reduces growth through uptake and iron mimicry. A dual mechanism targeting extracellular heme signaling and uptake together with Ga3+-induced toxicity following active Ga3+salophen uptake provides a significant therapeutic advantage while reducing the propensity to develop resistance.
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Affiliation(s)
- Garrick Centola
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Daniel J. Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Yong Ai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Alecia T. Dent
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Angela Wilks
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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13
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Chea EE, Deredge DJ, Jones LM. Insights on the Conformational Ensemble of Cyt C Reveal a Compact State during Peroxidase Activity. Biophys J 2019; 118:128-137. [PMID: 31810655 DOI: 10.1016/j.bpj.2019.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/29/2019] [Accepted: 11/11/2019] [Indexed: 12/19/2022] Open
Abstract
Cytochrome c (cyt c) is known for its role in the electron transport chain but transitions to a peroxidase-active state upon exposure to oxidative species. The peroxidase activity ultimately results in the release of cyt c into the cytosol for the engagement of apoptosis. The accumulation of oxidative modifications that accompany the onset of the peroxidase function are well-characterized. However, the concurrent structural and conformational transitions of cyt c remain undercharacterized. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry is a protein footprinting technique used to structurally characterize proteins. FPOP coupled with native ion mobility separation shows that exposure to H2O2 results in the accumulation of a compact state of cyt c. Subsequent top-down fragmentation to localize FPOP modifications reveals changes in heme coordination between conformers. A time-resolved functional assay suggests that this compact conformer is peroxidase active. Altogether, combining FPOP, ion mobility separation, and top-down and bottom-up mass spectrometry allows us to discern individual conformations in solution and obtain a better understanding of the conformational ensemble and structural transitions of cyt c as it transitions from a respiratory role to a proapoptotic role.
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Affiliation(s)
- Emily E Chea
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland.
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14
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Taraban MB, Deredge DJ, Smith ME, Briggs KT, Li Y, Jiang ZX, Wintrode PL, Yu YB. Monitoring dendrimer conformational transition using 19 F and 1 H 2 O NMR. Magn Reson Chem 2019; 57:861-872. [PMID: 30746779 DOI: 10.1002/mrc.4849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/25/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
The conformational transition of a fluorinated amphiphilic dendrimer is monitored by the 1 H signal from water, alongside the 19 F signal from the dendrimer. High-field NMR data (chemical shift δ, self-diffusion coefficient D, longitudinal relaxation rate R1 , and transverse relaxation rate R2 ) for both dendrimer (19 F) and water (1 H) match each other in detecting the conformational transition. Among all parameters for both nuclei, the water proton transverse-relaxation rate R2 (1 H2 O) displays the highest relative scale of change upon conformational transition of the dendrimer. Hydrogen/deuterium-exchange mass spectrometry reveals that the compact form of the dendrimer has slower proton exchange with water than the extended form. This result suggests that the sensitivity of R2 (1 H2 O) toward dendrimer conformation originates, at least partially, from the difference in proton exchange efficiency between different dendrimer conformations. Finally, we also demonstrated that this conformational transition could be conveniently monitored using a low-field benchtop NMR spectrometer via R2 (1 H2 O). The 1 H2 O signal thus offers a simple way to monitor structural changes of macromolecules using benchtop time-domain NMR.
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Affiliation(s)
- Marc B Taraban
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Margaret E Smith
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Katharine T Briggs
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Yu Li
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zhong-Xing Jiang
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Yihua Bruce Yu
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
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15
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Deredge DJ, Wintrode PL. Remodeling KRAS. Structure 2019; 25:1323-1324. [PMID: 28877504 DOI: 10.1016/j.str.2017.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mutations in members of the RAS family of small GTPases have been associated with numerous human cancers. However, RAS family members are notoriously difficult to target. In this issue of Structure, Lu et al. (2017) examine the effects of two compounds with distinct chemical scaffolds on the structure and dynamics of an oncogenic KRAS mutant, thus highlighting the usefulness of HDX-MS for drug development.
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Affiliation(s)
- Daniel J Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 North Pine St., Baltimore, MD 21201, USA
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 North Pine St., Baltimore, MD 21201, USA.
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16
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Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Danté T Johnson
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Emily E Chea
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Jessica A Espino
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
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17
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Taraban MB, Deredge DJ, Smith ME, Briggs KT, Feng Y, Li Y, Jiang ZX, Wintrode PL, Yu YB. Conformational transition of a non-associative fluorinated amphiphile in aqueous solution. II. Conformational transition vs. supramolecular assembly. RSC Adv 2019; 9:1956-1966. [PMID: 35516151 PMCID: PMC9059749 DOI: 10.1039/c8ra08795d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/08/2019] [Indexed: 11/21/2022] Open
Abstract
Unlike many known amphiphiles, the fluorinated amphiphilic dendrimer studied in this work demonstrated a concentration-dependent conformational transition rather than micellization or assembly. Hydrophobic and hydrophilic interactions with water were suggested as the most probable driving force of this transition. This assumption was consistent with the observed 19F chemical shift changes of the dendrimer compared to a known micelle-forming fluorinated amphiphile. Since water is an important factor in the process, trends of the concentration-dependent changes in water proton transverse relaxation rate served as an indicator of structural changes and/or supramolecular assembly. The conformational transition process was also confirmed by ion-mobility mass-spectrometry. We suggested that structural features, namely, steric hindrances, prevented the micellization/assembly of the dendrimer of this study. This conclusion might inform the approach to develop novel unconventional amphiphiles. Conformational transition in non-associative fluorinated dendrimer—a way to novel unconventional amphiphiles.![]()
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Affiliation(s)
- Marc B. Taraban
- Department of Pharmaceutical Sciences
- School of Pharmacy
- University of Maryland
- Baltimore
- USA
| | - Daniel J. Deredge
- Department of Pharmaceutical Sciences
- School of Pharmacy
- University of Maryland
- Baltimore
- USA
| | - Margaret E. Smith
- Department of Pharmaceutical Sciences
- School of Pharmacy
- University of Maryland
- Baltimore
- USA
| | - Katharine T. Briggs
- Department of Pharmaceutical Sciences
- School of Pharmacy
- University of Maryland
- Baltimore
- USA
| | - Yue Feng
- Department of Pharmaceutical Sciences
- School of Pharmacy
- University of Maryland
- Baltimore
- USA
| | - Yu Li
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan
- China
| | | | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences
- School of Pharmacy
- University of Maryland
- Baltimore
- USA
| | - Yihua Bruce Yu
- Department of Pharmaceutical Sciences
- School of Pharmacy
- University of Maryland
- Baltimore
- USA
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18
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Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Danté T Johnson
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Emily E Chea
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Jessica A Espino
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
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Bradshaw RT, Nagarajan A, Adhikary S, Deredge DJ, Wintrode PL, Singh SK, Forrest LR. Neurotransmitter Transporter Conformational Dynamics using HDX-MS and Molecular Dynamics Simulation. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Deredge DJ, Huang W, Hui C, Moenne-Loccoz P, Wilks A, Wintrode P. Ligand Induced Allostery in Pseudomonas Aeruginosa Cytoplasmic Heme Binding Protein (Phus) Drives the Protein-Protein Interaction with Heme Oxygenase. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Baker JT, Deredge DJ, Datta K, LiCata VJ. Water Release upon DNA Binding by E. coli and T. aquaticus Pol I DNA Polymerases. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.482.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- John T. Baker
- Biological SciencesLouisiana State UniversityBaton RougeLA
| | | | - Kausiki Datta
- Biological SciencesLouisiana State UniversityBaton RougeLA
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Deredge DJ, Thompson GS, Jiang K, Patel S, Datta K, LiCata VJ. Klenow and Klentaq-DNA Binding: the ‘Glutamate Effect’ is Primarily an Osmotic Effect. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.2139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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