1
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Balasco N, Ruggiero A, Smaldone G, Pecoraro G, Coppola L, Pirone L, Pedone EM, Esposito L, Berisio R, Vitagliano L. Structural studies of KCTD1 and its disease-causing mutant P20S provide insights into the protein function and misfunction. Int J Biol Macromol 2024; 277:134390. [PMID: 39111466 DOI: 10.1016/j.ijbiomac.2024.134390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/18/2024] [Accepted: 07/30/2024] [Indexed: 08/11/2024]
Abstract
Members of the KCTD protein family play key roles in fundamental physio-pathological processes including cancer, neurodevelopmental/neuropsychiatric, and genetic diseases. Here, we report the crystal structure of the KCTD1 P20S mutant, which causes the scalp-ear-nipple syndrome, and molecular dynamics (MD) data on the wild-type protein. Surprisingly, the structure unravels that the N-terminal region, which precedes the BTB domain (preBTB) and bears the disease-associated mutation, adopts a folded polyproline II (PPII) state. The KCTD1 pentamer is characterized by an intricate architecture in which the different subunits mutually exchange domains to generate a closed domain swapping motif. Indeed, the BTB of each chain makes peculiar contacts with the preBTB and the C-terminal domain (CTD) of an adjacent chain. The BTB-preBTB interaction consists of a PPII-PPII recognition motif whereas the BTB-CTD contacts are mediated by an unusual (+/-) helix discontinuous association. The inspection of the protein structure, along with the data emerged from the MD simulations, provides an explanation of the pathogenicity of the P20S mutation and unravels the role of the BTB-preBTB interaction in the insurgence of the disease. Finally, the presence of potassium bound to the central cavity of the CTD pentameric assembly provides insights into the role of KCTD1 in metal homeostasis.
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Affiliation(s)
- Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department Chemistry, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessia Ruggiero
- Institute of Molecular Biology and Pathology, CNR c/o Department Chemistry, Sapienza University of Rome, 00185 Rome, Italy
| | | | | | | | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy
| | - Emilia M Pedone
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy
| | - Luciana Esposito
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy.
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy.
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2
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Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins. Biomolecules 2022; 12:biom12091184. [PMID: 36139023 PMCID: PMC9496368 DOI: 10.3390/biom12091184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
The definition of the structural basis of the conformational preferences of the genetically encoded amino acid residues is an important yet unresolved issue of structural biology. In order to gain insights into this intricate topic, we here determined and compared the amino acid propensity scales for different (φ, ψ) regions of the Ramachandran plot and for different secondary structure elements. These propensities were calculated using the Chou–Fasman approach on a database of non-redundant protein chains retrieved from the Protein Data Bank. Similarities between propensity scales were evaluated by linear regression analyses. One of the most striking and unexpected findings is that distant regions of the Ramachandran plot may exhibit significantly similar propensity scales. On the other hand, contiguous regions of the Ramachandran plot may present anticorrelated propensities. In order to provide an interpretative background to these results, we evaluated the role that the local variability of protein backbone geometry plays in this context. Our analysis indicates that (dis)similarities of propensity scales between different regions of the Ramachandran plot are coupled with (dis)similarities in the local geometry. The concept that similarities of the propensity scales are dictated by the similarity of the NCαC angle and not necessarily by the similarity of the (φ, ψ) conformation may have far-reaching implications in the field.
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3
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Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human α-thrombin. Int J Biol Macromol 2021; 181:858-867. [PMID: 33864869 DOI: 10.1016/j.ijbiomac.2021.04.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/23/2022]
Abstract
The long-range communication between the two exosites of human α-thrombin (thrombin) tightly modulates the protein-effector interactions. Duplex/quadruplex aptamers represent an emerging class of very effective binders of thrombin. Among them, NU172 and HD22 aptamers are at the forefront of exosite I and II recognition, respectively. The present study investigates the simultaneous binding of these two aptamers by combining a structural and dynamics approach. The crystal structure of the ternary complex formed by the thrombin with NU172 and HD22_27mer provides a detailed view of the simultaneous binding of these aptamers to the protein, inspiring the design of novel bivalent thrombin inhibitors. The crystal structure represents the starting model for molecular dynamics studies, which point out the cooperation between the binding at the two exosites. In particular, the binding of an aptamer to its exosite reduces the intrinsic flexibility of the other exosite, that preferentially assumes conformations similar to those observed in the bound state, suggesting a predisposition to interact with the other aptamer. This behaviour is reflected in a significant increase of the anticoagulant activity of NU172 when the inactive HD22_27mer is bound to exosite II, providing a clear evidence of the synergic action of the two aptamers.
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4
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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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5
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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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6
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Balasco N, Vitagliano L, Merlino A, Verde C, Mazzarella L, Vergara A. The unique structural features of carbonmonoxy hemoglobin from the sub-Antarctic fish Eleginops maclovinus. Sci Rep 2019; 9:18987. [PMID: 31831781 PMCID: PMC6908587 DOI: 10.1038/s41598-019-55331-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/11/2019] [Indexed: 01/14/2023] Open
Abstract
Tetrameric hemoglobins (Hbs) are prototypical systems for the investigations of fundamental properties of proteins. Although the structure of these proteins has been known for nearly sixty years, there are many aspects related to their function/structure that are still obscure. Here, we report the crystal structure of a carbonmonoxy form of the Hb isolated from the sub-Antarctic notothenioid fish Eleginops maclovinus characterised by either rare or unique features. In particular, the distal site of the α chain results to be very unusual since the distal His is displaced from its canonical position. This displacement is coupled with a shortening of the highly conserved E helix and the formation of novel interactions at tertiary structure level. Interestingly, the quaternary structure is closer to the T-deoxy state of Hbs than to the R-state despite the full coordination of all chains. Notably, these peculiar structural features provide a rationale for some spectroscopic properties exhibited by the protein in solution. Finally, this unexpected structural plasticity of the heme distal side has been associated with specific sequence signatures of various Hbs.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Naples, Italy.
| | - Antonello Merlino
- Dept. Chemical Sciences, University of Napoli "Federico II", Via Cinthia, 80126, Naples, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Lelio Mazzarella
- Dept. Chemical Sciences, University of Napoli "Federico II", Via Cinthia, 80126, Naples, Italy
| | - Alessandro Vergara
- Dept. Chemical Sciences, University of Napoli "Federico II", Via Cinthia, 80126, Naples, Italy.
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7
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Smaldone G, Ruggiero A, Balasco N, Abuhammad A, Autiero I, Caruso D, Esposito D, Ferraro G, Gelardi ELM, Moreira M, Quareshy M, Romano M, Saaret A, Selvam I, Squeglia F, Troisi R, Kroon-Batenburg LMJ, Esposito L, Berisio R, Vitagliano L. The non-swapped monomeric structure of the arginine-binding protein from Thermotoga maritima. Acta Crystallogr F Struct Biol Commun 2019; 75:707-713. [PMID: 31702584 PMCID: PMC6839819 DOI: 10.1107/s2053230x1901464x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 01/07/2023] Open
Abstract
Domain swapping is a widespread oligomerization process that is observed in a large variety of protein families. In the large superfamily of substrate-binding proteins, non-monomeric members have rarely been reported. The arginine-binding protein from Thermotoga maritima (TmArgBP), a protein endowed with a number of unusual properties, presents a domain-swapped structure in its dimeric native state in which the two polypeptide chains mutually exchange their C-terminal helices. It has previously been shown that mutations in the region connecting the last two helices of the TmArgBP structure lead to the formation of a variety of oligomeric states (monomers, dimers, trimers and larger aggregates). With the aim of defining the structural determinants of domain swapping in TmArgBP, the monomeric form of the P235GK mutant has been structurally characterized. Analysis of this arginine-bound structure indicates that it consists of a closed monomer with its C-terminal helix folded against the rest of the protein, as typically observed for substrate-binding proteins. Notably, the two terminal helices are joined by a single nonhelical residue (Gly235). Collectively, the present findings indicate that extending the hinge region and conferring it with more conformational freedom makes the formation of a closed TmArgBP monomer possible. On the other hand, the short connection between the helices may explain the tendency of the protein to also adopt alternative oligomeric states (dimers, trimers and larger aggregates). The data reported here highlight the importance of evolutionary control to avoid the uncontrolled formation of heterogeneous and potentially harmful oligomeric species through domain swapping.
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Affiliation(s)
- Giovanni Smaldone
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- IRCCS SDN, Via Gianturco 113, 80143 Naples, Italy
| | - Alessia Ruggiero
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Nicole Balasco
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Areej Abuhammad
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Ida Autiero
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Daniela Caruso
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Università degli Studi della Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Davide Esposito
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Giarita Ferraro
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | | | - Miguel Moreira
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Mussa Quareshy
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Maria Romano
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Annica Saaret
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Irwin Selvam
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Flavia Squeglia
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Romualdo Troisi
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
| | - Loes M. J. Kroon-Batenburg
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Crystal and Structural Chemistry, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Luciana Esposito
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Rita Berisio
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Luigi Vitagliano
- AIC School Crystallographic Information Fiesta 2019, Naples, Italy
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
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8
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Balasco N, Smaldone G, Vigorita M, Del Vecchio P, Graziano G, Ruggiero A, Vitagliano L. The characterization of Thermotoga maritima Arginine Binding Protein variants demonstrates that minimal local strains have an important impact on protein stability. Sci Rep 2019; 9:6617. [PMID: 31036855 PMCID: PMC6488590 DOI: 10.1038/s41598-019-43157-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
The Ramachandran plot is a versatile and valuable tool that provides fundamental information for protein structure determination, prediction, and validation. The structural/thermodynamic effects produced by forcing a residue to adopt a conformation predicted to be forbidden were here explored using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model. Specifically, we mutated TmArgBP Gly52 that assumes a conformation believed to be strictly disallowed for non-Gly residues. Surprisingly, the crystallographic characterization of Gly52Ala TmArgBP indicates that the structural context forces the residue to adopt a non-canonical conformation never observed in any of the high-medium resolution PDB structures. Interestingly, the inspection of this high resolution structure demonstrates that only minor alterations occur. Nevertheless, experiments indicate that Gly52 replacements in TmArgBP produce destabilizations comparable to those observed upon protein truncation or dissection in domains. Notably, we show that force-fields commonly used in computational biology do not reproduce this non-canonical state. Using TmArgBP as model system we here demonstrate that the structural context may force residues to adopt conformations believed to be strictly forbidden and that barely detectable alterations produce major destabilizations. Present findings highlight the role of subtle strains in governing protein stability. A full understanding of these phenomena is essential for an exhaustive comprehension of the factors regulating protein structures.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, Italy
| | | | - Marilisa Vigorita
- Department of Science and Technology, University of Sannio, via Port'Arsa 11, Benevento, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, Napoli, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Port'Arsa 11, Benevento, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, Italy.
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, Italy.
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9
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Esposito L, Donnarumma F, Ruggiero A, Leone S, Vitagliano L, Picone D. Structure, stability and aggregation propensity of a Ribonuclease A-Onconase chimera. Int J Biol Macromol 2019; 133:1125-1133. [PMID: 31026530 DOI: 10.1016/j.ijbiomac.2019.04.164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/10/2019] [Accepted: 04/23/2019] [Indexed: 01/05/2023]
Abstract
Structural roles of loop regions are frequently overlooked in proteins. Nevertheless, they may be key players in the definition of protein topology and in the self-assembly processes occurring through domain swapping. We here investigate the effects on structure and stability of replacing the loop connecting the last two β-strands of RNase A with the corresponding region of the more thermostable Onconase. The crystal structure of this chimeric variant (RNaseA-ONC) shows that its terminal loop size better adheres to the topological rules for the design of stabilized proteins, proposed by Baker and coworkers [43]. Indeed, RNaseA-ONC displays a thermal stability close to that of RNase A, despite the lack of Pro at position 114, which, due to its propensity to favor a cis peptide bond, has been identified as an important stabilizing factor of the native protein. Accordingly, RNaseA-ONC is significantly more stable than RNase A variants lacking Pro114; RNaseA-ONC also displays a higher propensity to form oligomers in native conditions when compared to either RNase A or Onconase. This finding demonstrates that modifications of terminal loops should to be carefully controlled in terms of size and sequence to avoid unwanted and/or potentially harmful aggregation processes.
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Affiliation(s)
- Luciana Esposito
- CNR Istituto di Biostrutture e Bioimmagini, Via Mezzocannone 16, I-80134 Napoli, Italy.
| | - Federica Donnarumma
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II", Via Cintia, I-80126 Napoli, Italy
| | - Alessia Ruggiero
- CNR Istituto di Biostrutture e Bioimmagini, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Serena Leone
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II", Via Cintia, I-80126 Napoli, Italy
| | - Luigi Vitagliano
- CNR Istituto di Biostrutture e Bioimmagini, Via Mezzocannone 16, I-80134 Napoli, Italy.
| | - Delia Picone
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II", Via Cintia, I-80126 Napoli, Italy.
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10
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Ruggiero A, Smaldone G, Esposito L, Balasco N, Vitagliano L. Loop size optimization induces a strong thermal stabilization of the thioredoxin fold. FEBS J 2019; 286:1752-1764. [DOI: 10.1111/febs.14767] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/21/2018] [Accepted: 01/22/2019] [Indexed: 12/01/2022]
Affiliation(s)
| | | | | | - Nicole Balasco
- Institute of Biostructures and Bioimaging C.N.R. Naples Italy
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11
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Crystal structure of the ferric homotetrameric β 4 human hemoglobin. Biophys Chem 2018; 240:9-14. [DOI: 10.1016/j.bpc.2018.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/18/2018] [Accepted: 05/18/2018] [Indexed: 11/21/2022]
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12
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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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13
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Balasco N, Smaldone G, Ruggiero A, De Simone A, Vitagliano L. Local structural motifs in proteins: Detection and characterization of fragments inserted in helices. Int J Biol Macromol 2018; 118:1924-1930. [PMID: 30017977 DOI: 10.1016/j.ijbiomac.2018.07.047] [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: 06/08/2018] [Revised: 07/06/2018] [Accepted: 07/11/2018] [Indexed: 11/26/2022]
Abstract
The global/local fold of protein structures is stabilized by a variety of specific interactions. A primary role in this context is played by hydrogen bonds. In order to identify novel motifs in proteins, we searched Protein Data Bank structures looking for backbone H-bonds formed by NH groups of two (or more) consecutive residues with consecutive CO groups of distant residues in the sequence. The present analysis unravels the occurrence of recurrent structural motifs that, to the best of our knowledge, had not been characterized in literature. Indeed, these H-bonding patterns are found (i) in a specific parallel β-sheet capping, (ii) in linking of β-hairpins to α-helices, and (iii) in α-helix insertions. Interestingly, structural analyses of these motifs indicate that Gly residues frequently occupy prominent positions. The formation of these motifs is likely favored by the limited propensity of Gly to be embodied in helices/sheets. Of particular interest is the motif corresponding to insertions in helices that was detected in 1% of analyzed structures. Inserted fragments may assume different structures and aminoacid compositions and usually display diversified evolutionary conservation. Since inserted regions are physically separated from the rest of the protein structure, they represent hot spots for ad-hoc protein functionalization.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy.
| | | | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College South Kensington Campus, London SW7 2AZ, UK
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy.
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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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Dissection of Factors Affecting the Variability of the Peptide Bond Geometry and Planarity. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2617629. [PMID: 29164147 PMCID: PMC5661080 DOI: 10.1155/2017/2617629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/05/2017] [Indexed: 11/17/2022]
Abstract
Proteins frequently assume complex three-dimensional structures characterized by marginal thermodynamic stabilities. In this scenario, deciphering the folding code of these molecular giants with clay feet is a cumbersome task. Studies performed in last years have shown that the interplay between backbone geometry and local conformation has an important impact on protein structures. Although the variability of several geometrical parameters of protein backbone has been established, the role of the structural context in determining these effects has been hitherto limited to the valence bond angle τ (NCαC). We here investigated the impact of different factors on the observed variability of backbone geometry and peptide bond planarity. These analyses corroborate the notion that the local conformation expressed in terms of (ϕ, ψ) dihedrals plays a predominant role in dictating the variability of these parameters. The impact of secondary structure is limited to bond angles which involve atoms that are usually engaged in H-bonds and, therefore, more susceptible to the structural context. Present data also show that the nature of the side chain has a significant impact on angles such as NCαCβ and CβCαC. In conclusion, our analyses strongly support the use of variability of protein backbone geometry in structure refinement, validation, and prediction.
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