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Levengood JD, Potoyan D, Penumutchu S, Kumar A, Wang Y, Hansen AL, Kutluay S, Roche J, Tolbert BS. Thermodynamic Coupling of the tandem RRM domains of hnRNP A1 underlie its Pleiotropic RNA Binding Functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553700. [PMID: 37645738 PMCID: PMC10462124 DOI: 10.1101/2023.08.17.553700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The functional properties of RNA-binding proteins (RBPs) require allosteric regulation through inter-domain communication. Despite the foundational importance of allostery to biological regulation, almost no studies have been conducted to describe the biophysical nature by which inter-domain communication manifests in RBPs. Here, we show through high-pressure studies with hnRNP A1 that inter-domain communication is vital for the unique stability of its N- terminal domain containing a tandem of RNA Recognition Motifs (RRMs). Despite high sequence similarity and nearly identical tertiary structures, the two RRMs exhibit drastically different stability under pressure. RRM2 unfolds completely under high-pressure as an individual domain, but when appended to RRM1, it remains stable. Variants in which inter-domain communication is disrupted between the tandem RRMs show a large decrease in stability under pressure. Carrying these mutations over to the full-length protein for in vivo experiments revealed that the mutations affected the ability of the disordered C-terminus to engage in protein-protein interactions and more importantly, they also influenced the RNA binding capacity. Collectively, this work reveals that thermodynamic coupling between the tandem RRMs of hnRNP A1 accounts for its allosteric regulatory functions.
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An Y, Sedinkin SL, Venditti V. Solution NMR methods for structural and thermodynamic investigation of nanoparticle adsorption equilibria. NANOSCALE ADVANCES 2022; 4:2583-2607. [PMID: 35769933 PMCID: PMC9195484 DOI: 10.1039/d2na00099g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/07/2022] [Indexed: 05/09/2023]
Abstract
Characterization of dynamic processes occurring at the nanoparticle (NP) surface is crucial for developing new and more efficient NP catalysts and materials. Thus, a vast amount of research has been dedicated to developing techniques to characterize sorption equilibria. Over recent years, solution NMR spectroscopy has emerged as a preferred tool for investigating ligand-NP interactions. Indeed, due to its ability to probe exchange dynamics over a wide range of timescales with atomic resolution, solution NMR can provide structural, kinetic, and thermodynamic information on sorption equilibria involving multiple adsorbed species and intermediate states. In this contribution, we review solution NMR methods for characterizing ligand-NP interactions, and provide examples of practical applications using these methods as standalone techniques. In addition, we illustrate how the integrated analysis of several NMR datasets was employed to elucidate the role played by support-substrate interactions in mediating the phenol hydrogenation reaction catalyzed by ceria-supported Pd nanoparticles.
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Affiliation(s)
- Yeongseo An
- Department of Chemistry, Iowa State University Hach Hall, 2438 Pammel Drive Ames Iowa 50011 USA +1-515-294-7550 +1-515-294-1044
| | - Sergey L Sedinkin
- Department of Chemistry, Iowa State University Hach Hall, 2438 Pammel Drive Ames Iowa 50011 USA +1-515-294-7550 +1-515-294-1044
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University Hach Hall, 2438 Pammel Drive Ames Iowa 50011 USA +1-515-294-7550 +1-515-294-1044
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University Ames Iowa 50011 USA
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Solution structure ensemble of human obesity-associated protein FTO reveals druggable surface pockets at the interface between the N- and C-terminal domain. J Biol Chem 2022; 298:101907. [PMID: 35398093 PMCID: PMC9065727 DOI: 10.1016/j.jbc.2022.101907] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 12/17/2022] Open
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An engineered construct of cFLIP provides insight into DED1 structure and interactions. Structure 2022; 30:229-239.e5. [PMID: 34800372 PMCID: PMC8818036 DOI: 10.1016/j.str.2021.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/24/2021] [Accepted: 10/22/2021] [Indexed: 02/05/2023]
Abstract
Cellular FLICE-like inhibitory protein (cFLIP) is a member of the Death Domain superfamily with pivotal roles in many cellular processes and disease states, including cancer and autoimmune disorders. In the context of the death-inducing signaling complex (DISC), cFLIP isoforms regulate extrinsic apoptosis by controlling procaspase-8 activation. The function of cFLIP is mediated through a series of protein-protein interactions, engaging the two N-terminal death effector domains (DEDs). Here, we solve the structure of an engineered DED1 domain of cFLIP using solution nuclear magnetic resonance (NMR) and we define the interaction with FADD and calmodulin, protein-protein interactions that regulate the function of cFLIP in the DISC. cFLIP DED1 assumes a canonical DED fold characterized by six α helices and is able to bind calmodulin and FADD through two separate interfaces. Our results clearly demonstrate the role of DED1 in the cFLIP/FADD association and contribute to the understanding of the assembly of DISC filaments.
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Purslow JA, Thimmesch JN, Sivo V, Nguyen TT, Khatiwada B, Dotas RR, Venditti V. A Single Point Mutation Controls the Rate of Interconversion Between the g + and g - Rotamers of the Histidine 189 χ2 Angle That Activates Bacterial Enzyme I for Catalysis. Front Mol Biosci 2021; 8:699203. [PMID: 34307459 PMCID: PMC8295985 DOI: 10.3389/fmolb.2021.699203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Enzyme I (EI) of the bacterial phosphotransferase system (PTS) is a master regulator of bacterial metabolism and a promising target for development of a new class of broad-spectrum antibiotics. The catalytic activity of EI is mediated by several intradomain, interdomain, and intersubunit conformational equilibria. Therefore, in addition to its relevance as a drug target, EI is also a good model for investigating the dynamics/function relationship in multidomain, oligomeric proteins. Here, we use solution NMR and protein design to investigate how the conformational dynamics occurring within the N-terminal domain (EIN) affect the activity of EI. We show that the rotameric g+-to-g− transition of the active site residue His189 χ2 angle is decoupled from the state A-to-state B transition that describes a ∼90° rigid-body rearrangement of the EIN subdomains upon transition of the full-length enzyme to its catalytically competent closed form. In addition, we engineered EIN constructs with modulated conformational dynamics by hybridizing EIN from mesophilic and thermophilic species, and used these chimeras to assess the effect of increased or decreased active site flexibility on the enzymatic activity of EI. Our results indicate that the rate of the autophosphorylation reaction catalyzed by EI is independent from the kinetics of the g+-to-g− rotameric transition that exposes the phosphorylation site on EIN to the incoming phosphoryl group. In addition, our work provides an example of how engineering of hybrid mesophilic/thermophilic chimeras can assist investigations of the dynamics/function relationship in proteins, therefore opening new possibilities in biophysics.
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Affiliation(s)
- Jeffrey A Purslow
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | | | - Valeria Sivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università Degli Studi Della Campania, Caserta, Italy
| | - Trang T Nguyen
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | | | - Rochelle R Dotas
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, IA, United States.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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