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Ma X, Zhang Y, Zhu L, Wu Y, Li J, Huang K, Xu W. Aptamer and Thiol Co-Regulated Color-Shifting Fluorophores via Dynamic Through-Bond/Space Conjugation for Constructing Ratiometric RNA Sensor. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401437. [PMID: 38932671 DOI: 10.1002/smll.202401437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Fluorophores with color-shifting characteristics have attracted enormous research interest in the quantitative application of RNA sensors. It reports here a simple synthesis, luminescent properties, and co-transcription ability of de-conjugated triphenylmethane leucomalachite green (LMG). This novel clusteroluminescence fluorophore is rapidly synthesized from malachite green (MG) in reductive transcription system containing dithiothreitol, emitting fluorescence in the UV region through space conjugation. The co-transcribed MG RNA aptamer (MGA) bound to the ligand, resulting in red fluorescence from the through-bond conjugation. Given the equilibrated color-shifting fluorophores, they are rationally employed in a 3WJ-based rolling circle transcription switch, with the target-aptamer acting as an activator to achieve steric allosterism. This one-pot system allows the target to compete continuously for allosteric sites, and the activated transcription switches continue to amplify MGA forward, achieving accurate Aflatoxin 1 quantification at the picomolar level in 1 h. Due to the programmability of this RNA sensor, the design method of target-competitive aptamers is standardized, making it universally applicable.
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Affiliation(s)
- Xuan Ma
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Yifan Wu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Jun Li
- College of Food Science, Hebei Normal University of Science and Technology, Hebei, 066004, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
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2
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Bernetti M, Bosio S, Bresciani V, Falchi F, Masetti M. Probing allosteric communication with combined molecular dynamics simulations and network analysis. Curr Opin Struct Biol 2024; 86:102820. [PMID: 38688074 DOI: 10.1016/j.sbi.2024.102820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
Understanding the allosteric mechanisms within biomolecules involved in diseases is of paramount importance for drug discovery. Indeed, characterizing communication pathways and critical hotspots in signal transduction can guide a rational approach to leverage allosteric modulation for therapeutic purposes. While the atomistic signatures of allosteric processes are difficult to determine experimentally, computational methods can be a remarkable resource. Network analysis built on Molecular Dynamics simulation data is particularly suited in this respect and is gradually becoming of routine use. Herein, we collect the recent literature in the field, discussing different aspects and available options for network construction and analysis. We further highlight interesting refinements and extensions, eventually providing our perspective on this topic.
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Affiliation(s)
- Mattia Bernetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.
| | - Stefano Bosio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/Stefano__Bosio
| | - Veronica Bresciani
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/V_Bresciani
| | - Federico Falchi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
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3
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Read BJ, Mitchell JBO, da Silva RG. Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release. Commun Chem 2024; 7:77. [PMID: 38582930 PMCID: PMC10998830 DOI: 10.1038/s42004-024-01165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
Heavy-isotope substitution into enzymes slows down bond vibrations and may alter transition-state barrier crossing probability if this is coupled to fast protein motions. ATP phosphoribosyltransferase from Acinetobacter baumannii is a multi-protein complex where the regulatory protein HisZ allosterically enhances catalysis by the catalytic protein HisGS. This is accompanied by a shift in rate-limiting step from chemistry to product release. Here we report that isotope-labelling of HisGS has no effect on the nonactivated reaction, which involves negative activation heat capacity, while HisZ-activated HisGS catalytic rate decreases in a strictly mass-dependent fashion across five different HisGS masses, at low temperatures. Surprisingly, the effect is not linked to the chemical step, but to fast motions governing product release in the activated enzyme. Disruption of a specific enzyme-product interaction abolishes the isotope effects. Results highlight how altered protein mass perturbs allosterically modulated thermal motions relevant to the catalytic cycle beyond the chemical step.
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Affiliation(s)
- Benjamin J Read
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - John B O Mitchell
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK.
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4
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McCullagh M, Zeczycki TN, Kariyawasam CS, Durie CL, Halkidis K, Fitzkee NC, Holt JM, Fenton AW. What is allosteric regulation? Exploring the exceptions that prove the rule! J Biol Chem 2024; 300:105672. [PMID: 38272229 PMCID: PMC10897898 DOI: 10.1016/j.jbc.2024.105672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
"Allosteric" was first introduced to mean the other site (i.e., a site distinct from the active or orthosteric site), an adjective for "regulation" to imply a regulatory outcome resulting from ligand binding at another site. That original idea outlines a system with two ligand-binding events at two distinct locations on a macromolecule (originally a protein system), which defines a four-state energy cycle. An allosteric energy cycle provides a quantifiable allosteric coupling constant and focuses our attention on the unique properties of the four equilibrated protein complexes that constitute the energy cycle. Because many observed phenomena have been referenced as "allosteric regulation" in the literature, the goal of this work is to use literature examples to explore which systems are and are not consistent with the two-ligand thermodynamic energy cycle-based definition of allosteric regulation. We emphasize the need for consistent language so comparisons can be made among the ever-increasing number of allosteric systems. Building on the mutually exclusive natures of an energy cycle definition of allosteric regulation versus classic two-state models, we conclude our discussion by outlining how the often-proposed Rube-Goldberg-like mechanisms are likely inconsistent with an energy cycle definition of allosteric regulation.
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Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Konstantine Halkidis
- Department of Hematologic Malignancies and Cellular Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Jo M Holt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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5
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Wu N, Barahona M, Yaliraki SN. Allosteric communication and signal transduction in proteins. Curr Opin Struct Biol 2024; 84:102737. [PMID: 38171189 DOI: 10.1016/j.sbi.2023.102737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Allostery is one of the cornerstones of biological function, as it plays a fundamental role in regulating protein activity. The modelling of allostery has gradually moved from a conformation-based framework, linked to structural changes, to dynamics-based allostery, whereby the effects of ligand binding propagate via signal transduction from the allosteric site to other regions of the protein via inter-residue interactions. Characterising such allosteric signalling pathways, which do not necessarily lead to conformational changes, has been pursued experimentally and complemented by computational analysis of protein networks to detect subtle dynamic propagation paths. Considering allostery from the perspective of signal transduction broadens the understanding of allosteric mechanisms, underscores the importance of protein topology, and can provide insights into allosteric drug design.
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Affiliation(s)
- Nan Wu
- Department of Chemistry, Imperial College London, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, United Kingdom. https://twitter.com/@CMPHImperial
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6
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Read B, Cadzow AF, Alphey MS, Mitchell JBO, da Silva RG. Crystal Structure, Steady-State, and Pre-Steady-State Kinetics of Acinetobacter baumannii ATP Phosphoribosyltransferase. Biochemistry 2024; 63:230-240. [PMID: 38150593 PMCID: PMC10795190 DOI: 10.1021/acs.biochem.3c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/23/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023]
Abstract
The first step of histidine biosynthesis in Acinetobacter baumannii, the condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate to produce N1-(5-phospho-β-d-ribosyl)-ATP (PRATP) and pyrophosphate, is catalyzed by the hetero-octameric enzyme ATP phosphoribosyltransferase, a promising target for antibiotic design. The catalytic subunit, HisGS, is allosterically activated upon binding of the regulatory subunit, HisZ, to form the hetero-octameric holoenzyme (ATPPRT), leading to a large increase in kcat. Here, we present the crystal structure of ATPPRT, along with kinetic investigations of the rate-limiting steps governing catalysis in the nonactivated (HisGS) and activated (ATPPRT) forms of the enzyme. A pH-rate profile showed that maximum catalysis is achieved above pH 8.0. Surprisingly, at 25 °C, kcat is higher when ADP replaces ATP as substrate for ATPPRT but not for HisGS. The HisGS-catalyzed reaction is limited by the chemical step, as suggested by the enhancement of kcat when Mg2+ was replaced by Mn2+, and by the lack of a pre-steady-state burst of product formation. Conversely, the ATPPRT-catalyzed reaction rate is determined by PRATP diffusion from the active site, as gleaned from a substantial solvent viscosity effect. A burst of product formation could be inferred from pre-steady-state kinetics, but the first turnover was too fast to be directly observed. Lowering the temperature to 5 °C allowed observation of the PRATP formation burst by ATPPRT. At this temperature, the single-turnover rate constant was significantly higher than kcat, providing additional evidence for a step after chemistry limiting catalysis by ATPPRT. This demonstrates allosteric activation by HisZ accelerates the chemical step.
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Affiliation(s)
- Benjamin
J. Read
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Andrew F. Cadzow
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Magnus S. Alphey
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - John B. O. Mitchell
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Rafael G. da Silva
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
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7
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Knight AL, Widjaja V, Lisi GP. Temperature as a modulator of allosteric motions and crosstalk in mesophilic and thermophilic enzymes. Front Mol Biosci 2023; 10:1281062. [PMID: 37877120 PMCID: PMC10591084 DOI: 10.3389/fmolb.2023.1281062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Mesophilic and thermophilic enzyme counterparts are often studied to understand how proteins function under harsh conditions. To function well outside of standard temperature ranges, thermophiles often tightly regulate their structural ensemble through intra-protein communication (via allostery) and altered interactions with ligands. It has also become apparent in recent years that the enhancement or diminution of allosteric crosstalk can be temperature-dependent and distinguish thermophilic enzymes from their mesophilic paralogs. Since most studies of allostery utilize chemical modifications from pH, mutations, or ligands, the impact of temperature on allosteric function is comparatively understudied. Here, we discuss the biophysical methods, as well as critical case studies, that dissect temperature-dependent function of mesophilic-thermophilic enzyme pairs and their allosteric regulation across a range of temperatures.
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Affiliation(s)
| | | | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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8
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Gheeraert A, Lesieur C, Batista VS, Vuillon L, Rivalta I. Connected Component Analysis of Dynamical Perturbation Contact Networks. J Phys Chem B 2023; 127:7571-7580. [PMID: 37641933 PMCID: PMC10493978 DOI: 10.1021/acs.jpcb.3c04592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/02/2023] [Indexed: 08/31/2023]
Abstract
Describing protein dynamical networks through amino acid contacts is a powerful way to analyze complex biomolecular systems. However, due to the size of the systems, identifying the relevant features of protein-weighted graphs can be a difficult task. To address this issue, we present the connected component analysis (CCA) approach that allows for fast, robust, and unbiased analysis of dynamical perturbation contact networks (DPCNs). We first illustrate the CCA method as applied to a prototypical allosteric enzyme, the imidazoleglycerol phosphate synthase (IGPS) enzyme from Thermotoga maritima bacteria. This approach was shown to outperform the clustering methods applied to DPCNs, which could not capture the propagation of the allosteric signal within the protein graph. On the other hand, CCA reduced the DPCN size, providing connected components that nicely describe the allosteric propagation of the signal from the effector to the active sites of the protein. By applying the CCA to the IGPS enzyme in different conditions, i.e., at high temperature and from another organism (yeast IGPS), and to a different enzyme, i.e., a protein kinase, we demonstrated how CCA of DPCNs is an effective and transferable tool that facilitates the analysis of protein-weighted networks.
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Affiliation(s)
- Aria Gheeraert
- Laboratoire
de Mathématiques (LAMA), Université
Savoie Mont Blanc, CNRS, 73376 Le Bourget du Lac, France
- Dipartimento
di Chimica Industriale “Toso Montanari”, Alma Mater
Studiorum, Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Claire Lesieur
- Univ.
Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole
Centrale de Lyon, Ampère UMR5005, Villeurbanne 69622, France
- Institut
Rhônalpin des Systèmes Complexes, IXXI-ENS-Lyon, Lyon 69007, France
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Laurent Vuillon
- Laboratoire
de Mathématiques (LAMA), Université
Savoie Mont Blanc, CNRS, 73376 Le Bourget du Lac, France
- Institut
Rhônalpin des Systèmes Complexes, IXXI-ENS-Lyon, Lyon 69007, France
| | - Ivan Rivalta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Alma Mater
Studiorum, Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
- ENS
de Lyon,
CNRS, Laboratoire de Chimie UMR 5182, 69364 Lyon, France
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