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Guanidinium binding to proteins: The intriguing effects on the D1 and D2 domains of Thermotoga maritima Arginine Binding Protein and a comprehensive analysis of the Protein Data Bank. Int J Biol Macromol 2020; 163:375-385. [PMID: 32629051 DOI: 10.1016/j.ijbiomac.2020.06.290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 06/30/2020] [Indexed: 10/23/2022]
Abstract
Thermotoga maritima Arginine Binding Protein has been extensively characterized because of its peculiar features and its possible use as a biosensor. In this characterization, deletion of the C-terminal helix to obtain the monomeric protein TmArgBP20-233 and dissection of the monomer in its two domains, D1 and D2, have been performed. In the present study the stability of these three forms against guanidinium chloride is investigated by means of circular dichroism and differential scanning calorimetry measurements. All three proteins show a high conformational stability; moreover, D1 shows an unusual behavior in the presence of low concentrations of guanidinium chloride. This finding has led us to investigate a possible binding interaction by means of isothermal titration calorimetry and X-ray crystallography; the results indicate that D1 is able to bind the guanidinium ion (GuH+), due to its similarity with the arginine terminal moiety. The analysis of the structural and dynamic properties of the D1-GuH+ complex indicates that the protein binds the ligand through multiple and diversified interactions. An exhaustive survey of the binding modes of GuH+ to proteins indicates that this is a rather common feature. These observations provide interesting insights into the effects that GuH+ is able to induce in protein structures.
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2
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Smaldone G, Ruggiero A, Balasco N, Vitagliano L. Development of a Protein Scaffold for Arginine Sensing Generated through the Dissection of the Arginine-Binding Protein from Thermotoga maritima. Int J Mol Sci 2020; 21:ijms21207503. [PMID: 33053818 PMCID: PMC7589609 DOI: 10.3390/ijms21207503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
Arginine is one of the most important nutrients of living organisms as it plays a major role in important biological pathways. However, the accumulation of arginine as consequence of metabolic defects causes hyperargininemia, an autosomal recessive disorder. Therefore, the efficient detection of the arginine is a field of relevant biomedical/biotechnological interest. Here, we developed protein variants suitable for arginine sensing by mutating and dissecting the multimeric and multidomain structure of Thermotoga maritima arginine-binding protein (TmArgBP). Indeed, previous studies have shown that TmArgBP domain-swapped structure can be manipulated to generate simplified monomeric and single domain scaffolds. On both these stable scaffolds, to measure tryptophan fluorescence variations associated with the arginine binding, a Phe residue of the ligand binding pocket was mutated to Trp. Upon arginine binding, both mutants displayed a clear variation of the Trp fluorescence. Notably, the single domain scaffold variant exhibited a good affinity (~3 µM) for the ligand. Moreover, the arginine binding to this variant could be easily reverted under very mild conditions. Atomic-level data on the recognition process between the scaffold and the arginine were obtained through the determination of the crystal structure of the adduct. Collectively, present data indicate that TmArgBP scaffolds represent promising candidates for developing arginine biosensors.
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Affiliation(s)
- Giovanni Smaldone
- IRCCS SDN, Via Emanuele Gianturco, 113 80143 Naples, Italy
- Correspondence: (G.S.); (A.R.)
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Naples, Italy; (N.B.); (L.V.)
- Correspondence: (G.S.); (A.R.)
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Naples, Italy; (N.B.); (L.V.)
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16. I-80134 Naples, Italy; (N.B.); (L.V.)
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3
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Abstract
Ca2+ regulation in living systems occurs via specific structural alterations, subtle or drastic, in the Ca2+-binding domains of sensor proteins. Sensor proteins perform designated nonredundant roles within the dense network of Ca2+-binding proteins. A detailed understanding of the structural changes in calcium sensor proteins due to Ca2+ spikes that vary spatially, temporally, and in magnitude would provide better insights into the mechanism of Ca2+ sensing. This chapter describes a method to study various stages during apo to the holo transition of Ca2+-binding proteins by Trp-mediated scanning of individual EF-hand motifs. We describe the applicability of this procedure to caldendrin, which is a neuronal Ca2+-binding protein and to integrin-binding protein. Tryptophan mutants of full-length caldendrin were designed to reveal local structural changes in each EF-hand of the protein. This method, referred to as "EF-hand scanning tryptophan mutagenesis," not only allows the identification of canonical and noncanonical EF-hands using very low concentrations of protein but also enables visualization of the hierarchical filling of Ca2+ into the canonical EF-hands.
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Affiliation(s)
- Uday Kiran
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
- Leibniz Group 'Dendritic Organelles and Synaptic Function', University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology, ZMNH, Hamburg, Germany
| | - Yogendra Sharma
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
| | - Asima Chakraborty
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India.
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4
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Smaldone G, Balasco N, Vigorita M, Ruggiero A, Cozzolino S, Berisio R, Del Vecchio P, Graziano G, Vitagliano L. Domain communication in Thermotoga maritima Arginine Binding Protein unraveled through protein dissection. Int J Biol Macromol 2018; 119:758-769. [PMID: 30059738 DOI: 10.1016/j.ijbiomac.2018.07.172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022]
Abstract
Substrate binding proteins represent a large protein family that plays fundamental roles in selective transportation of metabolites across membrane. The function of these proteins relies on the relative motions of their two domains. Insights into domain communication in this class of proteins have been here collected using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model system. TmArgBP was dissected into two domains (D1 and D2) that were exhaustively characterized using a repertoire of different experimental and computational techniques. Indeed, stability, crystalline structure, ability to recognize the arginine substrate, and dynamics of the two individual domains have been here studied. Present data demonstrate that, although in the parent protein both D1 and D2 cooperate for the arginine anchoring; only D1 is intrinsically able to bind the substrate. The implications of this finding on the mechanism of arginine binding and release by TmArgBP have been discussed. Interestingly, both D1 and D2 retain the remarkable thermal/chemical stability of the parent protein. The analysis of the structural and dynamic properties of TmArgBP and of the individual domains highlights possible routes of domain communication. Finally, this study generated two interesting molecular tools, the two stable isolated domains that could be used in future investigations.
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Affiliation(s)
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Marilisa Vigorita
- Department of Sciences and Technologies, Università del Sannio, via Port'arsa 11, 82100 Benevento, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Serena Cozzolino
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Giuseppe Graziano
- Department of Sciences and Technologies, Università del Sannio, via Port'arsa 11, 82100 Benevento, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
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5
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Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:952-962. [PMID: 29860047 DOI: 10.1016/j.bbapap.2018.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/11/2018] [Accepted: 05/28/2018] [Indexed: 11/21/2022]
Abstract
Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. As the intrinsic stability of TmArgBP allows for extensive protein manipulations, we here dissected its structure in two parts: its main body deprived of the swapping fragment (TmArgBP20-233) and the C-terminal peptide corresponding to the helical swapping element. Both elements have been characterized independently or in combination using a repertoire of biophysical/structural techniques. Present investigations clearly indicate that TmArgBP20-233 represents a better scaffold for arginine sensing compared to the wild-type protein. Moreover, our data demonstrate that the ligand-free and the ligand-bound forms respond very differently to this helix deletion. This drastic perturbation has an important impact on the ligand-bound form of TmArgBP20-233 stability whereas it barely affects its ligand-free state. The crystallographic structures of these forms provide a rationale to this puzzling observation. Indeed, the arginine-bound state is very rigid and virtually unchanged upon protein truncation. On the other hand, the flexible ligand-free TmArgBP20-233 is able to adopt a novel state as a consequence of the helix deletion. Therefore, the flexibility of the ligand-free form endows this state with a remarkable robustness upon severe perturbations. In this scenario, TmArgBP dissection highlights an intriguing connection between destabilizing/stabilizing effects and the overall flexibility that could operate also in other proteins.
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Turner K, Joel S, Feliciano J, Feltus A, Pasini P, Wynn D, Dau P, Dikici E, Deo SK, Daunert S. Transcriptional regulatory proteins as biosensing tools. Chem Commun (Camb) 2018; 53:6820-6823. [PMID: 28492634 DOI: 10.1039/c6cc09512g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed sensing systems employing different classes of transcriptional regulatory proteins genetically and chemically modified to incorporate a fluorescent reporter molecule for detection of arsenic, hydroxylated polychlorinated biphenyls (OH-PCBs), and cyclic AMP (cAMP). These are the first examples of optical sensing systems based on transcriptional regulatory proteins.
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Affiliation(s)
- Kendrick Turner
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
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Donaldson T, Iozzino L, Deacon LJ, Billones H, Ausili A, D'Auria S, Dattelbaum JD. Engineering a switch-based biosensor for arginine using a Thermotoga maritima periplasmic binding protein. Anal Biochem 2017; 525:60-66. [PMID: 28259516 DOI: 10.1016/j.ab.2017.02.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/26/2017] [Accepted: 02/28/2017] [Indexed: 11/26/2022]
Abstract
The Thermotoga maritima arginine-binding protein (TmArgBP) has been modified to create a reagentless fluorescent protein biosensor. Two design methods for biosensor construction are compared: 1) solvent accessibility of environmentally-sensitive probes and 2) fluorescence deactivation due to photo-induced electron transfer (PET). Nine single cysteine TmArgBP mutants were created and labeled with three different environmentally sensitive fluorescent probes. These mutants demonstrated limited changes in fluorescence emission upon the addition of arginine. In contrast, the PET-based biosensor provides significant enhancements over the traditional approach and provides a fluorescence quenching mechanism that was capable of providing quantitative detection of arginine. Site-directed mutagenesis of TmArgBP was used to create attachment points for the fluorescent probe (K145C) and for an internal aromatic residue (D18X) to serve as the PET quencher. Both tyrosine and tryptophan, but not phenylalanine, were able to quench the emission of the fluorescent probe by more than 80% upon the addition of arginine. The dissociation constant for arginine ranged from 0.87 to 1.5 μM across the different sensors. This PET-based strategy provides a simple and broadly applicable approach for the analytical detection of small molecules that may be applied to any protein that exhibits conformational switching in a ligand dependent manner.
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Affiliation(s)
- Teraya Donaldson
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA
| | - Luisa Iozzino
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA; Laboratory for Molecular Sensing, ISA-CNR, Via Roma 64, 83100 Avellino, Italy
| | - Lindsay J Deacon
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA
| | - Hilbert Billones
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA
| | - Alessio Ausili
- Laboratory for Molecular Sensing, ISA-CNR, Via Roma 64, 83100 Avellino, Italy
| | - Sabato D'Auria
- Laboratory for Molecular Sensing, ISA-CNR, Via Roma 64, 83100 Avellino, Italy
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Smaldone G, Vigorita M, Ruggiero A, Balasco N, Dattelbaum JD, D'Auria S, Del Vecchio P, Graziano G, Vitagliano L. Proline 235 plays a key role in the regulation of the oligomeric states of Thermotoga maritima Arginine Binding Protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:814-24. [PMID: 27087545 DOI: 10.1016/j.bbapap.2016.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/06/2016] [Accepted: 04/11/2016] [Indexed: 10/22/2022]
Abstract
The Arginine Binding Protein isolated from Thermotoga maritima (TmArgBP) is a protein endowed with several peculiar properties. We have previously shown that TmArgBP dimerization is a consequence of the swapping of the C-terminal helix. Here we explored the structural determinants of TmArgBP domain swapping and oligomerization. In particular, we report a mutational analysis of the residue Pro235, which is located in the hinge region of the swapping dimer. This residue was either replaced with a Gly-Lys dipeptide (TmArgBP(P235GK)) or a Gly residue (TmArgBP(P235G)). Different forms of these mutants were generated and extensively characterized using biophysical techniques. For both TmArgBP(P235GK) and TmArgBP(P235G) mutants, the occurrence of multiple oligomerization states (monomers, dimers and trimers) was detected. The formation of well-folded monomeric forms for these mutants indicates that the dimerization through C-terminal domain swapping observed in wild-type TmArgBP is driven by conformational restraints imposed by the presence of Pro235 in the hinge region. Molecular dynamics studies corroborate this observation by showing that Gly235 assumes conformational states forbidden for Pro residues in the TmArgBP(P235G) monomer. Unexpectedly, the trimeric forms present: (a) peculiar circular dichroism spectra, (b) a great susceptibility to heating, and (c) the ability to bind the Thioflavin T dye. The present findings clearly demonstrate that single-point mutations have an important impact on the TmArgBP oligomerization process. In a wider context, they also indicate that proteins endowed with an intrinsic propensity to swap have an easy access to states with altered structural and, possibly, functional properties.
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Affiliation(s)
| | - Marilisa Vigorita
- Department of Sciences and Technologies, Università del Sannio, Via Port'arsa 11, Benevento 82100, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy; DiSTABiF, Second University of Naples, Caserta 81100, Italy
| | | | - Sabato D'Auria
- Institute of Food Science, CNR, Via Roma, 64, Avellino, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Napoli, Italy
| | - Giuseppe Graziano
- Department of Sciences and Technologies, Università del Sannio, Via Port'arsa 11, Benevento 82100, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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9
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Lipska AG, Sieradzan AK, Krupa P, Mozolewska MA, D’Auria S, Liwo A. Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field. J Mol Model 2015; 21:64. [DOI: 10.1007/s00894-015-2609-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/08/2015] [Indexed: 11/30/2022]
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10
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Preferential interactions between protein and arginine: Effects of arginine on tertiary conformational and colloidal stability of protein solution. Int J Pharm 2015; 478:753-61. [DOI: 10.1016/j.ijpharm.2014.12.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 12/08/2014] [Accepted: 12/16/2014] [Indexed: 01/01/2023]
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11
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Ruggiero A, Dattelbaum JD, Staiano M, Berisio R, D'Auria S, Vitagliano L. A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima. PLoS One 2014; 9:e96560. [PMID: 24832102 PMCID: PMC4022495 DOI: 10.1371/journal.pone.0096560] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/09/2014] [Indexed: 01/08/2023] Open
Abstract
The arginine binding protein from Thermatoga maritima (TmArgBP), a substrate binding protein (SBP) involved in the ABC system of solute transport, presents a number of remarkable properties. These include an extraordinary stability to temperature and chemical denaturants and the tendency to form multimeric structures, an uncommon feature among SBPs involved in solute transport. Here we report a biophysical and structural characterization of the TmArgBP dimer. Our data indicate that the dimer of the protein is endowed with a remarkable stability since its full dissociation requires high temperature as well as SDS and urea at high concentrations. In order to elucidate the atomic level structural properties of this intriguing protein, we determined the crystallographic structures of the apo and the arginine-bound forms of TmArgBP using MAD and SAD methods, respectively. The comparison of the liganded and unliganded models demonstrates that TmArgBP tertiary structure undergoes a very large structural re-organization upon arginine binding. This transition follows the Venus Fly-trap mechanism, although the entity of the re-organization observed in TmArgBP is larger than that observed in homologous proteins. Intriguingly, TmArgBP dimerizes through the swapping of the C-terminal helix. This dimer is stabilized exclusively by the interactions established by the swapping helix. Therefore, the TmArgBP dimer combines a high level of stability and conformational freedom. The structure of the TmArgBP dimer represents an uncommon example of large tertiary structure variations amplified at quaternary structure level by domain swapping. Although the biological relevance of the dimer needs further assessments, molecular modelling suggests that the two TmArgBP subunits may simultaneously interact with two distinct ABC transporters. Moreover, the present protein structures provide some clues about the determinants of the extraordinary stability of the biomolecule. The availability of an accurate 3D model represents a powerful tool for the design of new TmArgBP suited for biotechnological applications.
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Affiliation(s)
| | - Jonathan D Dattelbaum
- Department of Chemistry, University of Richmond, Richmond, Virginia, United States of America
| | - Maria Staiano
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
| | - Sabato D'Auria
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
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