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Galano‐Frutos JJ, Sancho J. Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable. Protein Sci 2024; 33:e4905. [PMID: 38284492 PMCID: PMC10804899 DOI: 10.1002/pro.4905] [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: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/30/2024]
Abstract
Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.
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Affiliation(s)
- Juan José Galano‐Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
- Aragon Health Research Institute (IIS Aragón)ZaragozaSpain
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2
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Seal S, Banerjee N, Mahato R, Kundu T, Sinha D, Chakraborty T, Sinha D, Sau K, Chatterjee S, Sau S. Serine 106 preserves the tertiary structure, function, and stability of a cyclophilin from Staphylococcus aureus. J Biomol Struct Dyn 2023; 41:1479-1494. [PMID: 34967275 DOI: 10.1080/07391102.2021.2021992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
SaCyp, a staphylococcal cyclophilin involved in both protein folding and pathogenesis, has a Ser residue at position 106 and a Trp residue at position 136. While Ser 106 of SaCyp aligned with a cyclosporin A (CsA) binding Ala residue, its Trp 136 aligned with a Trp or a Phe residue of most other cyclophilins. To demonstrate the exact roles of Ser 106 and Trp 136 in SaCyp, we have elaborately studied rCyp[S106A] and rCyp[W136A], two-point mutants of a recombinant SaCyp (rCyp) harboring an Ala substitution at positions 106 and 136, respectively. Of the mutants, rCyp[W136A] showed the rCyp-like CsA binding affinity and peptidyl-prolyl cis-trans isomerase (PPIase) activity. Conversely, the PPIase activity, CsA binding affinity, stability, tertiary structure, surface hydrophobicity, and Trp accessibility of rCyp[S106A] notably differed from those of rCyp. The computational experiments also reveal that the structure, dimension, and fluctuation of SaCyp are not identical to those of SaCyp[S106A]. Furthermore, Ser at position 106 of SaCyp, compared to Ala at the same position, formed a higher number of non-covalent bonds with CsA. Collectively, Ser 106 is an indispensable residue for SaCyp that keeps its tertiary structure, function, and stability intact.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Rohit Mahato
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Tanmoy Kundu
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | - Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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Conde-Giménez M, Galano-Frutos JJ, Galiana-Cameo M, Mahía A, Victor BL, Salillas S, Velázquez-Campoy A, Brito RMM, Gálvez JA, Díaz-de-Villegas MD, Sancho J. Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase. Int J Mol Sci 2022; 23:ijms23094502. [PMID: 35562892 PMCID: PMC9100405 DOI: 10.3390/ijms23094502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 11/17/2022] Open
Abstract
Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ΔΔGb values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme.
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Affiliation(s)
- María Conde-Giménez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Juan José Galano-Frutos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - María Galiana-Cameo
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Alejandro Mahía
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Bruno L. Victor
- Coimbra Chemistry Center-Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal; (B.L.V.); (R.M.M.B.)
| | - Sandra Salillas
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- CIBER de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rui M. M. Brito
- Coimbra Chemistry Center-Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal; (B.L.V.); (R.M.M.B.)
| | - José Antonio Gálvez
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain;
| | - María D. Díaz-de-Villegas
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain;
- Correspondence: (M.D.D.-d.-V.); (J.S.)
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- Correspondence: (M.D.D.-d.-V.); (J.S.)
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Conde-Giménez M, Sancho J. Unravelling the Complex Denaturant and Thermal-Induced Unfolding Equilibria of Human Phenylalanine Hydroxylase. Int J Mol Sci 2021; 22:ijms22126539. [PMID: 34207146 PMCID: PMC8234983 DOI: 10.3390/ijms22126539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022] Open
Abstract
Human phenylalanine hydroxylase (PAH) is a metabolic enzyme involved in the catabolism of L-Phe in liver. Loss of conformational stability and decreased enzymatic activity in PAH variants result in the autosomal recessive disorder phenylketonuria (PKU), characterized by developmental and psychological problems if not treated early. One current therapeutic approach to treat PKU is based on pharmacological chaperones (PCs), small molecules that can displace the folding equilibrium of unstable PAH variants toward the native state, thereby rescuing the physiological function of the enzyme. Understanding the PAH folding equilibrium is essential to develop new PCs for different forms of the disease. We investigate here the urea and the thermal-induced denaturation of full-length PAH and of a truncated form lacking the regulatory and the tetramerization domains. For either protein construction, two distinct transitions are seen in chemical denaturation followed by fluorescence emission, indicating the accumulation of equilibrium unfolding intermediates where the catalytic domains are partly unfolded and dissociated from each other. According to analytical centrifugation, the chemical denaturation intermediates of either construction are not well-defined species but highly polydisperse ensembles of protein aggregates. On the other hand, each protein construction similarly shows two transitions in thermal denaturation measured by fluorescence or differential scanning calorimetry, also indicating the accumulation of equilibrium unfolding intermediates. The similar temperatures of mid denaturation of the two constructions, together with their apparent lack of response to protein concentration, indicate the catalytic domains are unfolded in the full-length PAH thermal intermediate, where they remain associated. That the catalytic domain unfolds in the first thermal transition is relevant for the choice of PCs identified in high throughput screening of chemical libraries using differential scanning fluorimetry.
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Affiliation(s)
- María Conde-Giménez
- Departamento de Bioquímica y Biología Molecular y Celular, Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50009 Zaragoza, Spain;
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50009 Zaragoza, Spain;
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- Correspondence:
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5
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Chakraborty T, Polley S, Sinha D, Seal S, Sinha D, Mitra SK, Hazra J, Sau K, Pal M, Sau S. Structurally distinct unfolding intermediates formed from a staphylococcal capsule-producing enzyme retained NADPH binding activity. J Biomol Struct Dyn 2021; 40:9126-9143. [PMID: 33977860 DOI: 10.1080/07391102.2021.1924269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
CapF, a capsule-producing enzyme expressed by Staphylococcus aureus, binds NADPH and exists as a dimer in the aqueous solution. Many other capsule-producing virulent bacteria also express CapF orthologs. To understand the folding-unfolding mechanism of S. aureus CapF, herein a recombinant CapF (rCapF) was individually investigated using urea and guanidine hydrochloride (GdnCl). Unfolding of rCapF by both the denaturants was reversible but proceeded via the synthesis of a different number of intermediates. While two dimeric intermediates (rCapF4 and rCapF5) were formed at 0.5 M and 1.5 M GdnCl, three dimeric intermediates (rCapF1, rCapF2, and rCapF3) were produced at 1 M, 2 M, and 3 M urea, respectively. rCapF5 showed 3.6 fold less NADPH binding activity, whereas other intermediates retained full NADPH binding activity. Compared to rCapF, all of the intermediates (except rCapF3) had a compressed shape. Conversely, rCapF3 possessed a native protein-like shape. The maximum shape loss was in rCapF4 though its secondary structure remained unperturbed. Additionally, the tertiary structure and hydrophobic surface area of the intermediates neither matched with each other nor with those of the native rCapF. Of the four Trp residues in rCapF, one or more Trp residues in the intermediates may have higher solvent accessibility. Using sequence alignment and a tertiary structural model of CapF, we have demonstrated that the region around Trp 137 of CapF may be most sensitive to unfolding, whereas the NADPH binding motif carrying region at the N-terminal end of this protein may be resistant to unfolding, particularly at the low denaturant concentrations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Sudip K Mitra
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Joyita Hazra
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Mahadeb Pal
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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W196 and the β-Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6673661. [PMID: 33510840 PMCID: PMC7822688 DOI: 10.1155/2021/6673661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023]
Abstract
The human apoptosis-inducing factor (hAIF) is a moonlight flavoprotein involved in mitochondrial respiratory complex assembly and caspase-independent programmed cell death. These functions might be modulated by its redox-linked structural transition that enables hAIF to act as a NAD(H/+) redox sensor. Upon reduction with NADH, hAIF undergoes a conformational reorganization in two specific insertions—the flexible regulatory C-loop and the 190-202 β-harpin—promoting protein dimerization and the stabilization of a long-life charge transfer complex (CTC) that modulates its monomer-dimer equilibrium and its protein interaction network in healthy mitochondria. In this regard, here, we investigated the precise function of the β-hairpin in the AIF conformation landscape related to its redox mechanism, by analyzing the role played by W196, a key residue in the interaction of this motif with the regulatory C-loop. Mutations at W196 decrease the compactness and stability of the oxidized hAIF, indicating that the β-hairpin and C-loop coupling contribute to protein stability. Kinetic studies complemented with computational simulations reveal that W196 and the β-hairpin conformation modulate the low efficiency of hAIF as NADH oxidoreductase, contributing to configure its active site in a noncompetent geometry for hydride transfer and to stabilize the CTC state by enhancing the affinity for NAD+. Finally, the β-hairpin motif contributes to define the conformation of AIF's interaction surfaces with its physiological partners. These findings improve our understanding on the molecular basis of hAIF's cellular activities, a crucial aspect for clarifying its associated pathological mechanisms and developing new molecular therapies.
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7
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Sinha D, Sinha D, Dutta A, Chakraborty T, Mondal R, Seal S, Poddar A, Chatterjee S, Sau S. Alternative Sigma Factor of Staphylococcus aureus Interacts with the Cognate Antisigma Factor Primarily Using Its Domain 3. Biochemistry 2021; 60:135-151. [PMID: 33406357 DOI: 10.1021/acs.biochem.0c00881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
σB, an alternative sigma factor, is usually employed to tackle the general stress response in Staphylococcus aureus and other Gram-positive bacteria. This protein, involved in S. aureus-mediated pathogenesis, is typically blocked by RsbW, an antisigma factor having serine kinase activity. σB, a σ70-like sigma factor, harbors three conserved domains designated σB2, σB3, and σB4. To better understand the interaction between RsbW and σB or its domains, we have studied their recombinant forms, rRsbW, rσB, rσB2, rσB3, and rσB4, using different probes. The results show that none of the rσB domains, unlike rσB, showed binding to a cognate DNA in the presence of a core RNA polymerase. However, both rσB2 and rσB3, like rσB, interacted with rRsbW, and the order of their rRsbW binding affinity looks like rσB > rσB3 > rσB2. Furthermore, the reaction between rRsbW and rσB or rσB3 was exothermic and occurred spontaneously. rRsbW and rσB3 also associate with each other at a stoichiometry of 2:1, and different types of noncovalent bonds might be responsible for their interaction. A structural model of the RsbW-σB3 complex that has supported our experimental results indicated the binding of rσB3 at the putative dimeric interface of RsbW. A genetic study shows that the tentative dimer-forming region of RsbW is crucial for preserving its rσB binding ability, serine kinase activity, and dimerization ability. Additionally, a urea-induced equilibrium unfolding study indicated a notable thermodynamic stabilization of σB3 in the presence of RsbW. Possible implications of the stabilization data in drug discovery were discussed at length.
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Affiliation(s)
- Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | - Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, Kolkata, West Bengal 700054, India
| | - Tushar Chakraborty
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | - Rajkrishna Mondal
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland 797112, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | - Asim Poddar
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
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8
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Sinha D, Sinha D, Banerjee N, Rai P, Seal S, Chakraborty T, Chatterjee S, Sau S. A conserved arginine residue in a staphylococcal anti-sigma factor is required to preserve its kinase activity, structure, and stability. J Biomol Struct Dyn 2020; 40:4972-4986. [PMID: 33356973 DOI: 10.1080/07391102.2020.1864475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
RsbW, σB, and RsbV, encoded by Staphylococcus aureus and related bacteria, act as an anti-sigma factor, an sigma factor, and an anti-anti-sigma factor, respectively. The interaction between RsbW and σB blocks the transcription initiation activity of the latter protein. RsbW also functions as a serine kinase and phosphorylates RsbV in the presence of ATP. Our modeling study indicates that the RsbW-RsbV complex is stabilized by twenty-four intermolecular non-covalent bonds. Of the bond-forming RsbW residues, Arg 23, and Glu 49 are conserved residues. To understand the roles of Arg 23 in RsbW, rRsbW[R23A], a recombinant S. aureus RsbW (rRsbW) harboring Arg to Ala change at position 23, was investigated using various probes. The results reveal that rRsbW[R23A], like rRsbW, exists as the dimers in the aqueous solution. However, rRsbW[R23A], unlike rRsbW, neither interacted with a chimeric RsbV (rRsbV) nor formed the phosphorylated rRsbV in the presence of ATP. Furthermore, the tertiary structure and hydrophobic surface area of rRsbW[R23A] matched little with those of rRsbW. Conversely, both rRsbW[R23A] and rRsbW showed interaction with a recombinant σB (rσB). rRsbW and rRsbW[R23A] were also unfolded via the formation of at least one intermediate in the presence of urea. However, the thermodynamic stability of rRsbW significantly differed from that of rRsbW[R23A]. Our molecular dynamics (MD) simulation study also reveals the substantial change of structure, dimension, and stability of RsbW due to the above mutation. The ways side chain of critical Arg 23 contributes to maintaining the tertiary structure, and stability of RsbW was elaborately discussed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Priya Rai
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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9
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Lo SY, Goulet DL, Fraaz U, Siemann S. Effect of pH and denaturants on the fold and metal status of anthrax lethal factor. Arch Biochem Biophys 2020; 692:108547. [PMID: 32828796 DOI: 10.1016/j.abb.2020.108547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 01/26/2023]
Abstract
Anthrax lethal factor (LF) is a critical component of the anthrax toxin, and functions intracellularly as a zinc-dependent endopeptidase targeting proteins involved in maintaining critical host signaling pathways. To reach the cytoplasm, LF requires to be unfolded and guided through the narrow protective antigen pore in a pH-dependent process. The current study sought to address the question as to whether LF is capable of retaining its metal ion when exposed to a low-pH environment (similar to that found in late endosomes) and an unfolding stress (induced by urea). Using a combination of tryptophan fluorescence spectroscopy and chelation studies, we show that a decrease in the pH value (from 7.0 to 5.0) leads to a pronounced shift in the onset of structural alterations in LF to lower urea concentrations. More importantly, the enzyme was found to retain its Zn2+ ion beyond the unfolding transitions monitored by Trp fluorescence, a finding indicative of tight metal binding to LF in a non-native state. In addition, an analysis of red-edge excitation shift (REES) spectra suggests the protein to maintain residual structure (a feature necessary for metal binding) even at very high denaturant concentrations. Furthermore, studies using the chromophoric chelator 4-(2-pyridylazo)resorcinol (PAR) revealed LF's Zn2+ ion to become accessible to complexation at urea concentrations in between those required to cause structural changes and metal dissociation. This phenomenon likely originates from the conversion of a PAR-inaccessible (closed) to a PAR-accessible (open) state of LF at intermediate denaturant concentrations.
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Affiliation(s)
- Suet Y Lo
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - Danica L Goulet
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - Usama Fraaz
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - Stefan Siemann
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada.
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10
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Sinha D, Chakraborty T, Sinha D, Poddar A, Chattopadhyaya R, Sau S. Understanding the structure, stability, and anti-sigma factor-binding thermodynamics of an anti-anti-sigma factor from Staphylococcus aureus. J Biomol Struct Dyn 2020; 39:6539-6552. [PMID: 32755297 DOI: 10.1080/07391102.2020.1801511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | - Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Asim Poddar
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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11
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Antileishmanial activity evaluation of thiazolidine-2,4-dione against Leishmania infantum and Leishmania braziliensis. Parasitol Res 2020; 119:2263-2274. [PMID: 32462293 DOI: 10.1007/s00436-020-06706-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/05/2020] [Indexed: 01/04/2023]
Abstract
Leishmaniasis is responsible for approximately 65,000 annual deaths. Despite the mortality data, drugs available for the treatment of patients are insufficient and have moderate therapeutic efficacy in addition to serious adverse effects, which makes the development of new drugs urgent. To achieve this goal, the integration of kinetic and DSF assays against parasitic validated targets, along with phenotypic assays, can help the identification and optimization of bioactive compounds. Pteridine reductase 1 (PTR1), a validated target in Leishmania sp., is responsible for the reduction of folate and biopterin to tetrahydrofolate and tetrahydrobiopterin, respectively, both of which are essential for cell growth. In addition to the in vitro evaluation of 16 thiazolidine-2,4-dione derivatives against Leishmania major PTR1 (LmPTR1), using the differential scanning fluorimetry (ThermoFluor®), phenotypic assays were employed to evaluate the compound effect over Leishmania braziliensis (MHOM/BR/75/M2903) and Leishmania infantum (MHOM/BR/74/PP75) promastigotes viability. The ThermoFluor® results show that thiazolidine-2,4-dione derivatives have micromolar affinity to the target and equivalent activity on Leishmania cells. 2b is the most potent compound against L. infantum (EC50 = 23.45 ± 4.54 μM), whereas 2a is the most potent against L. braziliensis (EC50 = 44.16 ± 5.77 μM). This result suggests that lipophilic substituents on either-meta and/or-para positions of the benzylidene ring increase the potency against L. infantum. On the other hand, compound 2c (CE50 = 49.22 ± 7.71 μM) presented the highest selectivity index.
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12
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González A, Casado J, Chueca E, Salillas S, Velázquez-Campoy A, Sancho J, Lanas Á. Small Molecule Inhibitors of the Response Regulator ArsR Exhibit Bactericidal Activity against Helicobacter pylori. Microorganisms 2020; 8:microorganisms8040503. [PMID: 32244717 PMCID: PMC7232201 DOI: 10.3390/microorganisms8040503] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/19/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori is considered the most prevalent bacterial pathogen in humans. The increasing antibiotic resistance evolved by this microorganism has raised alarm bells worldwide due to the significant reduction in the eradication rates of traditional standard therapies. A major challenge in this antibiotic resistance crisis is the identification of novel microbial targets whose inhibitors can overcome the currently circulating resistome. In the present study, we have validated the use of the essential response regulator ArsR as a novel and promising therapeutic target against H. pylori infections. A high-throughput screening of a repurposing chemical library using a fluorescence-based thermal shift assay identified several ArsR binders. At least four of these low-molecular weight compounds noticeably inhibited the DNA binding activity of ArsR and showed bactericidal effects against antibiotic-resistant strains of H. pylori. Among the ArsR inhibitors, a human secondary bile acid, lithocholic acid, quickly destroyed H. pylori cells and exhibited partial synergistic action in combination with clarithromycin or levofloxacin, while the antimicrobial effect of this compound against representative members of the normal human microbiota such as Escherichia coli and Staphylococcus epidermidis appeared irrelevant. Our results enhance the battery of novel therapeutic tools against refractory infections caused by multidrug-resistant H. pylori strains.
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Affiliation(s)
- Andrés González
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Correspondence: ; Tel.: +34-976-762807
| | - Javier Casado
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Eduardo Chueca
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Sandra Salillas
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Monforte de Lemos 3-5, 28029 Madrid, Spain
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), Government of Aragon, Ranillas 1-D, 50018 Zaragoza, Spain
| | - Javier Sancho
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Ángel Lanas
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Monforte de Lemos 3-5, 28029 Madrid, Spain
- Digestive Diseases Service, University Clinic Hospital Lozano Blesa, San Juan Bosco 15, 50009 Zaragoza, Spain
- Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
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13
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Galano-Frutos JJ, García-Cebollada H, Sancho J. Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when. Brief Bioinform 2019; 22:3-19. [PMID: 31813950 DOI: 10.1093/bib/bbz146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/22/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical-chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80-85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore's law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants.
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Affiliation(s)
- Juan J Galano-Frutos
- Protein Folding and Molecular Design (ProtMol)' group at BIFI, University of Zaragoza
| | | | - Javier Sancho
- Protein Folding and Molecular Design (ProtMol)' group at BIFI, University of Zaragoza
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14
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Galano-Frutos JJ, Sancho J. Accurate Calculation of Barnase and SNase Folding Energetics Using Short Molecular Dynamics Simulations and an Atomistic Model of the Unfolded Ensemble: Evaluation of Force Fields and Water Models. J Chem Inf Model 2019; 59:4350-4360. [PMID: 31513394 DOI: 10.1021/acs.jcim.9b00430] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
As proteins perform most cellular functions, quantitative understanding of protein energetics is required to gain control of biological phenomena. Accurate models of native proteins can be obtained experimentally, but the lack of equally fine models of unfolded ensembles impedes the calculation of protein folding energetics from first principles. Here, we show that an atomistic unfolded ensemble model, consisting of a few dozen conformations built from a protein sequence, can be used in conjunction with an X-ray structure of its native state to calculate accurately by difference the changes in enthalpy and heat capacity of the polypeptide upon folding. The calculation is done using molecular dynamics simulations, popular force fields, and water models, and for the two model proteins studied (barnase and SNase), the results agree within error or are very close to their experimentally determined properties. The enthalpy sampling of the unfolded ensemble is done through short 2 ns simulations that do not significantly modify the representative distribution of Rg of the starting conformations. The impressive accuracy obtained opens the possibility to investigate quantitatively systems or phenomena not amenable to experiment and paves the way for addressing the calculation of protein conformational stability (i.e., the change in Gibbs energy upon folding), a central goal of structural biology. So far, these calculated enthalpy and heat capacity changes, combined with the experimentally determined melting temperatures of the corresponding protein, allow us to reproduce the stability curves of both barnase and SNase.
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Affiliation(s)
- Juan José Galano-Frutos
- Department of Biochemistry and Molecular and Cellular Biology , University of Zaragoza , Pedro Cerbuna 12 , Zaragoza 50009 , Spain.,Biocomputation and Complex Systems Physics Institute (Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC) , University of Zaragoza , Mariano Esquillor s/n, Edificio I + D , Zaragoza 50018 , Spain
| | - Javier Sancho
- Department of Biochemistry and Molecular and Cellular Biology , University of Zaragoza , Pedro Cerbuna 12 , Zaragoza 50009 , Spain.,Biocomputation and Complex Systems Physics Institute (Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC) , University of Zaragoza , Mariano Esquillor s/n, Edificio I + D , Zaragoza 50018 , Spain.,Aragon Health Research Institute (IIS Aragón) , Avda. San Juan Bosco 13 , Zaragoza 50009 , Spain
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15
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Mazurenko S, Stourac J, Kunka A, Nedeljkovic S, Bednar D, Prokop Z, Damborsky J. CalFitter: a web server for analysis of protein thermal denaturation data. Nucleic Acids Res 2019; 46:W344-W349. [PMID: 29762722 PMCID: PMC6031030 DOI: 10.1093/nar/gky358] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/24/2018] [Indexed: 01/26/2023] Open
Abstract
Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.
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Affiliation(s)
- Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Sava Nedeljkovic
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
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16
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Pérez-Amigot D, Taleb V, Boneta S, Anoz-Carbonell E, Sebastián M, Velázquez-Campoy A, Polo V, Martínez-Júlvez M, Medina M. Towards the competent conformation for catalysis in the ferredoxin-NADP + reductase from the Brucella ovis pathogen. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148058. [PMID: 31394095 DOI: 10.1016/j.bbabio.2019.148058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/19/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023]
Abstract
Brucella ovis encodes a bacterial subclass 1 ferredoxin-NADP(H) reductase (BoFPR) that, by similarity with other FPRs, is expected either to deliver electrons from NADPH to the redox-based metabolism and/or to oxidize NADPH to regulate the soxRS regulon that protects bacteria against oxidative damage. Such potential roles for the pathogen survival under infection conditions make of interest to understand and to act on the BoFPR mechanism. Here, we investigate the NADP+/H interaction and NADPH oxidation by hydride transfer (HT) to BoFPR. Crystal structures of BoFPR in free and in complex with NADP+ hardly differ. The latter shows binding of the NADP+ adenosine moiety, while its redox-reactive nicotinamide protrudes towards the solvent. Nonetheless, pre-steady-state kinetics show formation of a charge-transfer complex (CTC-1) prior to the hydride transfer, as well as conversion of CTC-1 into a second charge-transfer complex (CTC-2) concomitantly with the HT event. Thus, during catalysis nicotinamide and flavin reacting rings stack. Kinetic data also identify the HT itself as the rate limiting step in the reduction of BoFPR by NADPH, as well as product release limiting the overall reaction. Using all-atom molecular dynamics simulations with a thermal effect approach we are able to visualise a potential transient catalytically competent interaction of the reacting rings. Simulations indicate that the architecture of the FAD folded conformation in BoFPR might be key in catalysis, pointing to its adenine as an element to orient the reactive atoms in conformations competent for HT.
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Affiliation(s)
- Daniel Pérez-Amigot
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Víctor Taleb
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Sergio Boneta
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Aragon Institute for Health Research (IIS-Aragon), Zaragoza 50009, Spain; Biomedical Research Networking Center in Digestive and Hepatic Diseases (CIBERehd), Madrid, Spain; Fundacion ARAID, Government of Aragon, Zaragoza 50018, Spain
| | - Víctor Polo
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
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17
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Villanueva R, Romero-Tamayo S, Laplaza R, Martínez-Olivan J, Velázquez-Campoy A, Sancho J, Ferreira P, Medina M. Redox- and Ligand Binding-Dependent Conformational Ensembles in the Human Apoptosis-Inducing Factor Regulate Its Pro-Life and Cell Death Functions. Antioxid Redox Signal 2019; 30:2013-2029. [PMID: 30450916 DOI: 10.1089/ars.2018.7658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aims: The human apoptosis-inducing factor (hAIF) supports OXPHOS biogenesis and programmed cell death, with missense mutations producing neurodegenerative phenotypes. hAIF senses the redox environment of cellular compartments, stabilizing a charge transfer complex (CTC) dimer that modulates the protein interaction network. In this context, we aimed to evaluate the subcellular pH, CTC formation, and pathogenic mutations effects on hAIF stability, and a thermal denaturation high-throughput screening (HTS) assay to discover AIF binders. Results: Apoptotic hAIFΔ1-101 is not stable at intermembrane mitochondrial space (IMS) pH, but the 77-101 residues confer stability to the mitochondrial isoform. hAIF and its CTC populate different conformational ensembles with redox switch to the CTC producing a less stable and compact protein. The pathogenic G308E, ΔR201, and E493V mutations modulate hAIF stability; particularly, ΔR201 causes a population shift to a less stable conformation that remodels active site structure and dynamics. We have identified new molecules that modulate the hAIF reduced nicotinamide adenine dinucleotide (NADH)/oxidized nicotinamide adenine dinucleotide (NAD+) association/dissociation equilibrium and regulate its catalytic efficiency. Innovation: Biophysical methods allow evaluating the regulation of hAIF functional ensembles and to develop an HTS assay to discover small molecules that might modulate hAIF stability and activities. Conclusions: The mitochondrial soluble 54-77 portion stabilizes hAIF at the IMS pH. NADH-redox-linked conformation changes course with strong NAD+ binding and protein dimerization, but they produce a negative impact in overall hAIF stability. Loss of functionality in the R201 deletion is due to distortion of the active site architecture. We report molecules that may serve as leads in the development of hAIF bioactive compounds.
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Affiliation(s)
- Raquel Villanueva
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Silvia Romero-Tamayo
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Ruben Laplaza
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,2 Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan Martínez-Olivan
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,3 Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.,4 Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,5 Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Javier Sancho
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,4 Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Patricia Ferreira
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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18
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Seal S, Polley S, Sau S. A staphylococcal cyclophilin carries a single domain and unfolds via the formation of an intermediate that preserves cyclosporin A binding activity. PLoS One 2019; 14:e0210771. [PMID: 30925148 PMCID: PMC6440624 DOI: 10.1371/journal.pone.0210771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 03/18/2019] [Indexed: 12/22/2022] Open
Abstract
Cyclophilin (Cyp), a peptidyl-prolyl cis-trans isomerase (PPIase), acts as a virulence factor in many bacteria including Staphylococcus aureus. The enzymatic activity of Cyp is inhibited by cyclosporin A (CsA), an immunosuppressive drug. To precisely determine the unfolding mechanism and the domain structure of Cyp, we have investigated a chimeric S. aureus Cyp (rCyp) using various probes. Our limited proteolysis and the consequent analysis of the proteolytic fragments indicate that rCyp is composed of one domain with a short flexible tail at the C-terminal end. We also show that the urea-induced unfolding of both rCyp and rCyp-CsA is completely reversible and proceeds via the synthesis of at least one stable intermediate. Both the secondary structure and the tertiary structure of each intermediate appears very similar to those of the corresponding native protein. Conversely, the hydrophobic surface areas of the intermediates are comparatively less. Further analyses reveal no loss of CsA binding activity in rCyp intermediate. The thermodynamic stability of rCyp was also significantly increased in the presence of CsA, recommending that this protein could be employed to screen new CsA derivatives in the future.
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Affiliation(s)
- Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail:
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19
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Biswas A, Ghosh S, Sinha D, Dutta A, Seal S, Bagchi A, Sau S. Dimerization ability, denaturation mechanism, and the stability of a staphylococcal phage repressor and its two domains. Int J Biol Macromol 2019; 124:903-914. [DOI: 10.1016/j.ijbiomac.2018.11.263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022]
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20
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Olloqui-Sariego JL, Díaz-Quintana A, De la Rosa MÁ, Calvente JJ, Márquez I, Díaz-Moreno I, Andreu R. Protein crosslinking improves the thermal resistance of plastocyanin immobilized on a modified gold electrode. Bioelectrochemistry 2018; 124:127-132. [DOI: 10.1016/j.bioelechem.2018.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/13/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
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21
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Olloqui-Sariego JL, Márquez I, Frutos-Beltrán E, Díaz-Moreno I, De la Rosa MA, Calvente JJ, Andreu R, Díaz-Quintana A. Key Role of the Local Hydrophobicity in the East Patch of Plastocyanins on Their Thermal Stability and Redox Properties. ACS OMEGA 2018; 3:11447-11454. [PMID: 31459248 PMCID: PMC6645426 DOI: 10.1021/acsomega.8b01612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/06/2018] [Indexed: 06/10/2023]
Abstract
Understanding the molecular basis of the thermal stability and functionality of redox proteins has important practical applications. Here, we show a distinct thermal dependence of the spectroscopic and electrochemical properties of two plastocyanins from the thermophilic cyanobacterium Phormidium laminosum and their mesophilic counterpart from Synechocystis sp. PCC 6803, despite the similarity of their molecular structures. To explore the origin of these differences, we have mimicked the local hydrophobicity in the east patch of the thermophilic protein by replacing a valine of the mesophilic plastocyanin by isoleucine. Interestingly, the resulting mutant approaches the thermal stability, redox thermodynamics, and dynamic coupling of the flexible site motions of the thermophilic protein, indicating the existence of a close connection between the hydrophobic packing of the east patch region of plastocyanin and the functional control and stability of the oxidized and reduced forms of the protein.
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Affiliation(s)
- José Luis Olloqui-Sariego
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Inmaculada Márquez
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Estrella Frutos-Beltrán
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Miguel A. De la Rosa
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Juan José Calvente
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Rafael Andreu
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Antonio Díaz-Quintana
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
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22
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Mahapa A, Mandal S, Sinha D, Sau S, Sau K. Determining the Roles of a Conserved α-Helix in a Global Virulence Regulator from Staphylococcus aureus. Protein J 2018; 37:103-112. [PMID: 29464485 DOI: 10.1007/s10930-018-9762-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
SarA, a pleiotropic transcription regulator, is encoded by Staphylococcus aureus, a pathogenic bacterium. The expression of many virulence and non-virulence genes in S. aureus is modulated by this regulator. Structural studies have shown it to be a winged-helix DNA-binding protein carrying two monomers. Each SarA monomer is composed of five α-helices (α1-α5), three β-strands (β1-β3) and multiple loops. The putative DNA binding region of SarA is constituted with α3, α4, β2, and β3, whereas, its dimerization seems to occur using α1, α2, and α5. Interestingly, many SarA-like proteins are dimeric and use three or more helices for their dimerization. To clearly understand the roles of helix α1 in the dimerization, we have constructed and purified a SarA mutant (Δα1) that lacks helix α1. Our in-depth studies with Δα1 indicate that the helix α1 is critical for preserving the structure, DNA binding activity and thermodynamic stability of SarA. However, the helix has little affected its dimerization ability. Possible reasons for such anomaly have been discussed at length.
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Affiliation(s)
- Avisek Mahapa
- Department of Biotechnology, Haldia Institute of Technology, PO-HIT, Dist-Purba, Medinipur, 721657, West Bengal, India
| | - Sukhendu Mandal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India.
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, PO-HIT, Dist-Purba, Medinipur, 721657, West Bengal, India.
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23
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Alanine substitution mutations in the DNA binding region of a global staphylococcal virulence regulator affect its structure, function, and stability. Int J Biol Macromol 2018; 113:1221-1232. [DOI: 10.1016/j.ijbiomac.2018.03.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 03/02/2018] [Accepted: 03/11/2018] [Indexed: 12/11/2022]
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Synergistic Effects of Copper Sites on Apparent Stability of Multicopper Oxidase, Fet3p. Int J Mol Sci 2018; 19:ijms19010269. [PMID: 29337899 PMCID: PMC5796215 DOI: 10.3390/ijms19010269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/19/2017] [Accepted: 01/12/2018] [Indexed: 11/16/2022] Open
Abstract
Saccharomyces cerevisiae Fet3p is a multicopper oxidase that contains three cupredoxin-like domains and four copper ions located in three distinct metal sites (T1 in domain 3; T2 and the binuclear T3 at the interface between domains 1 and 3). To probe the role of the copper sites in Fet3p thermodynamic stability, we performed urea-induced unfolding experiments with holo-, apo- and three partially-metallated (T1, T2 and T1/T2 sites depleted of copper) forms of Fet3p. Using a combination of spectroscopic probes (circular dichroism, fluorescence intensity and maximum, 8-anilinonaphthalene-1-sulfonic acid (ANS) emission, oxidase activity and blue color), we reveal that all forms of Fet3p unfold in a four-state reaction with two partially-folded intermediates. Using phase diagrams, it emerged that Fet3p with all copper sites filled had a significantly higher stability as compared to the combined contributions of the individual copper sites. Hence, there is long-range inter-domain communication between distal copper sites that contribute to overall Fet3p stability.
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25
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Betancor-Fernández I, Timson DJ, Salido E, Pey AL. Natural (and Unnatural) Small Molecules as Pharmacological Chaperones and Inhibitors in Cancer. Handb Exp Pharmacol 2018; 245:155-190. [PMID: 28993836 DOI: 10.1007/164_2017_55] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mutations causing single amino acid exchanges can dramatically affect protein stability and function, leading to disease. In this chapter, we will focus on several representative cases in which such mutations affect protein stability and function leading to cancer. Mutations in BRAF and p53 have been extensively characterized as paradigms of loss-of-function/gain-of-function mechanisms found in a remarkably large fraction of tumours. Loss of RB1 is strongly associated with cancer progression, although the molecular mechanisms by which missense mutations affect protein function and stability are not well known. Polymorphisms in NQO1 represent a remarkable example of the relationships between intracellular destabilization and inactivation due to dynamic alterations in protein ensembles leading to loss of function. We will review the function of these proteins and their dysfunction in cancer and then describe in some detail the effects of the most relevant cancer-associated single amino exchanges using a translational perspective, from the viewpoints of molecular genetics and pathology, protein biochemistry and biophysics, structural, and cell biology. This will allow us to introduce several representative examples of natural and synthetic small molecules applied and developed to overcome functional, stability, and regulatory alterations due to cancer-associated amino acid exchanges, which hold the promise for using them as potential pharmacological cancer therapies.
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Affiliation(s)
- Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, UK
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, 18071, Spain.
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26
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Scott HL, Westerfield JM, Barrera FN. Determination of the Membrane Translocation pK of the pH-Low Insertion Peptide. Biophys J 2017; 113:869-879. [PMID: 28834723 DOI: 10.1016/j.bpj.2017.06.065] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/13/2017] [Accepted: 06/28/2017] [Indexed: 01/13/2023] Open
Abstract
The pH-low insertion peptide (pHLIP) is a leading peptide technology to target the extracellular acidosis that characterizes solid tumors. The pHLIP binds to lipid membranes, and responds to acidification by undergoing a coupled folding/membrane insertion process. In the final transmembrane state, the C terminus of pHLIP gets exposed to the cytoplasm of the target cell, providing a means to translocate membrane-impermeable drug cargoes across the plasma membrane of cancer cells. There exists a need to develop improved pHLIP variants to target tumors with greater efficiency. Characterization of such variants typically relies on determining the pK parameter, the pH midpoint of peptide insertion into the lipid bilayer. Here we report that the value of the pK can be strongly dependent on the method used for its determination. Membrane insertion of pHLIP involves at least four intermediate states, which are believed to be linked to the staggered titration of key acidic residues. We propose that some spectroscopic methods are influenced more heavily by specific membrane folding intermediates, and as a result yield different pK values. To address this potential problem, we have devised an assay to independently monitor the environment of the two termini of pHLIP. This approach provides insights into the conformation pHLIP adopts immediately before the establishment of the transmembrane configuration. Additionally, our data indicate that the membrane translocation of the C terminus of pHLIP, the folding step more directly relevant to drug delivery, occurs at more acidic pH values than previously considered. Consequently, such a pK difference could have substantial ramifications for assessing the translocation of drug cargoes conjugated to pHLIP.
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Affiliation(s)
- Haden L Scott
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
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27
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Neira JL, Cámara-Artigas A. Trifluoroethanol-induced conformational transition of the C-terminal sterile alpha motif (SAM) of human p73. Arch Biochem Biophys 2017; 619:1-9. [DOI: 10.1016/j.abb.2017.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 01/03/2023]
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28
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Polley S, Seal S, Mahapa A, Jana B, Biswas A, Mandal S, Sinha D, Sau K, Sau S. Identification and characterization of a cyclosporin binding cyclophilin from Staphylococcus aureus Newman. Bioinformation 2017; 13:78-85. [PMID: 28584448 PMCID: PMC5450249 DOI: 10.6026/97320630013078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/04/2017] [Indexed: 01/24/2023] Open
Abstract
Cyclophilins, a class of peptidyl-prolyl cis-trans isomerase (PPIase) enzymes, are inhibited by cyclosporin A (CsA), an
immunosuppressive drug. Staphylococcus aureus Newman, a pathogenic bacterium, carries a gene for encoding a putative cyclophilin
(SaCyp). SaCyp shows significant homology with other cyclophilins at the sequence level. A three-dimensional model structure of
SaCyp harbors a binding site for CsA. To verify whether SaCyp possesses both the PPIase activity and the CsA binding ability, we
have purified and investigated a recombinant SaCyp (rCyp) using various in vitro tools. Our RNase T1 refolding assay indicates that
rCyp has a substantial extent of PPIase activity. rCyp that exists as a monomer in the aqueous solution is truly a cyclophilin as its
catalytic activity specifically shows sensitivity to CsA. rCyp appears to bind CsA with a reasonably high affinity. Additional
investigations reveal that binding of CsA to rCyp alters its structure and shape to some extent. Both rCyp and rCyp-CsA are unfolded
via the formation of at least one intermediate in the presence of guanidine hydrochloride. Unfolding study also indicates that there is
substantial extent of thermodynamic stabilization of rCyp in the presence of CsA as well. The data suggest that rCyp may be exploited
to screen the new antimicrobial agents in the future.
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Affiliation(s)
- Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Avisek Mahapa
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Biswanath Jana
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Anindya Biswas
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Sukhendu Mandal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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29
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Halim AAA, Zaroog MS, Kadir HA, Tayyab S. Alcohol-induced structural transitions in the acid-denatured Bacillus licheniformis α-amylase. JOURNAL OF SAUDI CHEMICAL SOCIETY 2017. [DOI: 10.1016/j.jscs.2014.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Motamedi-Shad N, Jagger AM, Liedtke M, Faull SV, Nanda AS, Salvadori E, Wort JL, Kay CW, Heyer-Chauhan N, Miranda E, Perez J, Ordóñez A, Haq I, Irving JA, Lomas DA. An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour. Biochem J 2016; 473:3269-90. [PMID: 27407165 PMCID: PMC5264506 DOI: 10.1042/bcj20160159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 11/30/2022]
Abstract
Serpins are important regulators of proteolytic pathways with an antiprotease activity that involves a conformational transition from a metastable to a hyperstable state. Certain mutations permit the transition to occur in the absence of a protease; when associated with an intermolecular interaction, this yields linear polymers of hyperstable serpin molecules, which accumulate at the site of synthesis. This is the basis of many pathologies termed the serpinopathies. We have previously identified a monoclonal antibody (mAb4B12) that, in single-chain form, blocks α1-antitrypsin (α1-AT) polymerisation in cells. Here, we describe the structural basis for this activity. The mAb4B12 epitope was found to encompass residues Glu32, Glu39 and His43 on helix A and Leu306 on helix I. This is not a region typically associated with the serpin mechanism of conformational change, and correspondingly the epitope was present in all tested structural forms of the protein. Antibody binding rendered β-sheet A - on the opposite face of the molecule - more liable to adopt an 'open' state, mediated by changes distal to the breach region and proximal to helix F. The allosteric propagation of induced changes through the molecule was evidenced by an increased rate of peptide incorporation and destabilisation of a preformed serpin-enzyme complex following mAb4B12 binding. These data suggest that prematurely shifting the β-sheet A equilibrium towards the 'open' state out of sequence with other changes suppresses polymer formation. This work identifies a region potentially exploitable for a rational design of ligands that is able to dynamically influence α1-AT polymerisation.
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Affiliation(s)
- Neda Motamedi-Shad
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Alistair M. Jagger
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Maximilian Liedtke
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
| | - Sarah V. Faull
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Arjun Scott Nanda
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Enrico Salvadori
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
- London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, U.K
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - Joshua L. Wort
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Christopher W.M. Kay
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
- London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, U.K
| | - Narinder Heyer-Chauhan
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Elena Miranda
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, Rome 00185, Italy
| | - Juan Perez
- Departamento de Biologia Celular, Genetica y Fisiologia, Facultad de Ciencias, Campus Teatinos, Universidad de Malaga, Malaga 29071, Spain
| | - Adriana Ordóñez
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Imran Haq
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - James A. Irving
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - David A. Lomas
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
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31
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Rodríguez-Cárdenas Á, Rojas AL, Conde-Giménez M, Velázquez-Campoy A, Hurtado-Guerrero R, Sancho J. Streptococcus pneumoniae TIGR4 Flavodoxin: Structural and Biophysical Characterization of a Novel Drug Target. PLoS One 2016; 11:e0161020. [PMID: 27649488 PMCID: PMC5029806 DOI: 10.1371/journal.pone.0161020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/28/2016] [Indexed: 12/30/2022] Open
Abstract
Streptococcus pneumoniae (Sp) strain TIGR4 is a virulent, encapsulated serotype that causes bacteremia, otitis media, meningitis and pneumonia. Increased bacterial resistance and limited efficacy of the available vaccine to some serotypes complicate the treatment of diseases associated to this microorganism. Flavodoxins are bacterial proteins involved in several important metabolic pathways. The Sp flavodoxin (Spfld) gene was recently reported to be essential for the establishment of meningitis in a rat model, which makes SpFld a potential drug target. To facilitate future pharmacological studies, we have cloned and expressed SpFld in E. coli and we have performed an extensive structural and biochemical characterization of both the apo form and its active complex with the FMN cofactor. SpFld is a short-chain flavodoxin containing 146 residues. Unlike the well-characterized long-chain apoflavodoxins, the Sp apoprotein displays a simple two-state thermal unfolding equilibrium and binds FMN with moderate affinity. The X-ray structures of the apo and holo forms of SpFld differ at the FMN binding site, where substantial rearrangement of residues at the 91-100 loop occurs to permit cofactor binding. This work will set up the basis for future studies aiming at discovering new potential drugs to treat S. pneumoniae diseases through the inhibition of SpFld.
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Affiliation(s)
- Ángela Rodríguez-Cárdenas
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Adriana L. Rojas
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - María Conde-Giménez
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain
- Fundación ARAID, Government of Aragón, Zaragoza, Spain
| | - Ramón Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain
- Fundación ARAID, Government of Aragón, Zaragoza, Spain
- * E-mail: (RHG); (JS)
| | - Javier Sancho
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain
- * E-mail: (RHG); (JS)
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32
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Neira JL, Hornos F, Bacarizo J, Cámara-Artigás A, Gómez J. The Monomeric Species of the Regulatory Domain of Tyrosine Hydroxylase Has a Low Conformational Stability. Biochemistry 2016; 55:3418-31. [PMID: 27224548 DOI: 10.1021/acs.biochem.6b00135] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine hydroxylase (TyrH) catalyzes the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine, the first step in the synthesis of catecholamine neurotransmitters. The protein contains a 159-residue regulatory domain (RD) at its N-terminus that forms dimers in solution; the N-terminal region of RDTyrH (residues 1-71) is absent in the solution structure of the domain. We have characterized the conformational stability of two species of RDTyrH (one containing the N-terminal region and another lacking the first 64 residues) to clarify how that N-terminal region modulates the conformational stability of RD. Under the conditions used in this study, the RD species lacking the first 64 residues is a monomer at pH 7.0, with a small conformational stability at 25 °C (4.7 ± 0.8 kcal mol(-1)). On the other hand, the entire RDTyrH is dimeric at physiological pH, with an estimated dissociation constant of 1.6 μM, as determined by zonal gel filtration chromatography; dimer dissociation was spectroscopically silent to circular dichroism but not to fluoresecence. Both RD species were disordered below physiological pH, but the acquisition of secondary native-like structure occurs at pHs lower than those measured for the attainment of tertiary native- and compactness-like arrangements.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain.,Biocomputation and Complex Systems Physics Institute , 50009 Zaragoza, Spain
| | - Felipe Hornos
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain
| | - Julio Bacarizo
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Ana Cámara-Artigás
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Javier Gómez
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain
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33
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Bedouelle H. Principles and equations for measuring and interpreting protein stability: From monomer to tetramer. Biochimie 2016; 121:29-37. [DOI: 10.1016/j.biochi.2015.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/17/2015] [Indexed: 11/28/2022]
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34
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Estrada J, Echenique P, Sancho J. Predicting stabilizing mutations in proteins using Poisson-Boltzmann based models: study of unfolded state ensemble models and development of a successful binary classifier based on residue interaction energies. Phys Chem Chem Phys 2015; 17:31044-54. [PMID: 26530878 DOI: 10.1039/c5cp04348d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In many cases the stability of a protein has to be increased to permit its biotechnological use. Rational methods of protein stabilization based on optimizing electrostatic interactions have provided some fine successful predictions. However, the precise calculation of stabilization energies remains challenging, one reason being that the electrostatic effects on the unfolded state are often neglected. We have explored here the feasibility of incorporating Poisson-Boltzmann model electrostatic calculations performed on representations of the unfolded state as large ensembles of geometrically optimized conformations calculated using the ProtSA server. Using a data set of 80 electrostatic mutations experimentally tested in two-state proteins, the predictive performance of several such models has been compared to that of a simple one that considers an unfolded structure of non-interacting residues. The unfolded ensemble models, while showing correlation between the predicted stabilization values and the experimental ones, are worse than the simple model, suggesting that the ensembles do not capture well the energetics of the unfolded state. A more attainable goal is classifying potential mutations as either stabilizing or non-stabilizing, rather than accurately calculating their stabilization energies. To implement a fast classification method that can assist in selecting stabilizing mutations, we have used a much simpler electrostatic model based only on the native structure and have determined its precision using different stabilizing energy thresholds. The binary classifier developed finds 7 true stabilizing mutants out of every 10 proposed candidates and can be used as a robust tool to propose stabilizing mutations.
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Affiliation(s)
- Jorge Estrada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Mariano Esquillor s/n, Edificio I+D, 50018, Zaragoza, Spain
| | - Pablo Echenique
- Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Mariano Esquillor s/n, Edificio I+D, 50018, Zaragoza, Spain and Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006, Madrid, Spain
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Mariano Esquillor s/n, Edificio I+D, 50018, Zaragoza, Spain
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An antibody raised against a pathogenic serpin variant induces mutant-like behaviour in the wild-type protein. Biochem J 2015; 468:99-108. [PMID: 25738741 PMCID: PMC4422257 DOI: 10.1042/bj20141569] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A monoclonal antibody (mAb) that binds to a transient intermediate may act as a catalyst for the corresponding reaction; here we show this principle can extend on a macro molecular scale to the induction of mutant-like oligomerization in a wild-type protein. Using the common pathogenic E342K (Z) variant of α1-antitrypsin as antigen–whose native state is susceptible to the formation of a proto-oligomeric intermediate–we have produced a mAb (5E3) that increases the rate of oligomerization of the wild-type (M) variant. Employing ELISA, gel shift, thermal stability and FRET time-course experiments, we show that mAb5E3 does not bind to the native state of α1-antitrypsin, but recognizes a cryptic epitope in the vicinity of the post-helix A loop and strand 4C that is revealed upon transition to the polymerization intermediate, and which persists in the ensuing oligomer. This epitope is not shared by loop-inserted monomeric conformations. We show the increased amenity to polymerization by either the pathogenic E342K mutation or the binding of mAb5E3 occurs without affecting the energetic barrier to polymerization. As mAb5E3 also does not alter the relative stability of the monomer to intermediate, it acts in a manner similar to the E342K mutant, by facilitating the conformational interchange between these two states. We show that a monoclonal antibody can act as a ‘molecular template’ in aberrant protein oligomerization, and the transient intermediate of α1-antitrypsin, a key to the molecular mechanism of disease pathogenesis, expresses a cryptic epitope also present in the oligomer.
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Vassall KA, Jenkins AD, Bamm VV, Harauz G. Thermodynamic Analysis of the Disorder-to-α-Helical Transition of 18.5-kDa Myelin Basic Protein Reveals an Equilibrium Intermediate Representing the Most Compact Conformation. J Mol Biol 2015; 427:1977-92. [DOI: 10.1016/j.jmb.2015.03.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/11/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
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Lo SY, Säbel CE, Mapletoft JP, Siemann S. Influence of chemical denaturants on the activity, fold and zinc status of anthrax lethal factor. Biochem Biophys Rep 2015; 1:68-77. [PMID: 29124135 PMCID: PMC5668564 DOI: 10.1016/j.bbrep.2015.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 11/17/2022] Open
Abstract
Anthrax lethal factor (LF) is a zinc-dependent endopeptidase which, through a process facilitated by protective antigen, translocates to the host cell cytosol in a partially unfolded state. In the current report, the influence of urea and guanidine hydrochloride (GdnHCl) on LF׳s catalytic function, fold and metal binding was assessed at neutral pH. Both urea and GdnHCl were found to inhibit LF prior to the onset of unfolding, with the inhibition by the latter denaturant being a consequence of its ionic strength. With the exception of demetallated LF (apoLF) in urea, unfolding, as monitored by tryptophan fluorescence spectroscopy, was found to follow a two-state (native to unfolded) mechanism. Analysis of the metal status of LF with 4-(2-pyridylazoresorcinol) (PAR) following urea or GdnHCl exposure suggests the enzyme to be capable of maintaining its metal ion passed the observed unfolding transition in a chelator-inaccessible form. Although an increase in the concentration of the denaturants eventually allowed the chelator access to the protein׳s zinc ion, such process is not correlated with the release of the metal ion. Indeed, significant dissociation of the zinc ion from LF was not observed even at 6 M urea, and only high concentrations of GdnHCl (>3 M) were capable of inducing the release of the metal ion from the protein. Hence, the current study demonstrates not only the propensity of LF to tightly bind its zinc ion beyond the spectroscopically determined unfolding transition, but also the utility of PAR as a structural probe. Lethal factor (LF) is strongly inhibited by guanidine hydrochloride. Except of apoLF in urea, unfolding follows a two-state mechanism. LF shields and retains its zinc ion in an unfolded state. Pyridylazoresorcinol is a useful probe to assess metal accessibility and release.
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Key Words
- 4-(2-pyridylazo)resorcinol
- CD, circular dichroism
- Chemical denaturants
- DPA, dipicolinic acid
- EDTA, ethylenediaminetetraacetic acid
- EF, edema factor
- LF, anthrax lethal factor
- Lethal factor
- MWCO, molecular weight cut-off
- PA, protective antigen
- PAR, 4-(2-pyridylazo)resorcinol
- Protein folding
- S-pNA, lethal factor substrate
- SASA, solvent-accessible surface area
- SOD, superoxide dismutase
- Tryptophan fluorescence
- Zinc
- ZnLF, zinc-containing lethal factor
- cps, counts per second
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Affiliation(s)
- Suet Y. Lo
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Crystal E. Säbel
- Bharti School of Engineering, Laurentian University, Sudbury, Ontario, Canada
| | | | - Stefan Siemann
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
- Correspondence to: Department of Chemistry and Biochemistry, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario, Canada P3E 2C6. Tel.: +1 705 675 1151; fax: +1 705 675 4844.
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Lamazares E, Clemente I, Bueno M, Velázquez-Campoy A, Sancho J. Rational stabilization of complex proteins: a divide and combine approach. Sci Rep 2015; 5:9129. [PMID: 25774740 PMCID: PMC4360737 DOI: 10.1038/srep09129] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/19/2015] [Indexed: 11/09/2022] Open
Abstract
Increasing the thermostability of proteins is often crucial for their successful use as analytic, synthetic or therapeutic tools. Most rational thermostabilization strategies were developed on small two-state proteins and, unsurprisingly, they tend to fail when applied to the much more abundant, larger, non-fully cooperative proteins. We show that the key to stabilize the latter is to know the regions of lower stability. To prove it, we have engineered apoflavodoxin, a non-fully cooperative protein on which previous thermostabilizing attempts had failed. We use a step-wise combination of structure-based, rationally-designed, stabilizing mutations confined to the less stable structural region, and obtain variants that, according to their van't Hoff to calorimetric enthalpy ratios, exhibit fully-cooperative thermal unfolding with a melting temperature of 75°C, 32 degrees above the lower melting temperature of the non-cooperative wild type protein. The ideas introduced here may also be useful for the thermostabilization of complex proteins through formulation or using specific stabilizing ligands (e.g. pharmacological chaperones).
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Affiliation(s)
- Emilio Lamazares
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Isabel Clemente
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Bueno
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain [3] Fundación ARAID, Gobierno de Aragón, Spain
| | - Javier Sancho
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
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Wang I, Kowalski MP, Langley AR, Rodriguez R, Balasubramanian S, Hsu STD, Krude T. Nucleotide contributions to the structural integrity and DNA replication initiation activity of noncoding y RNA. Biochemistry 2014; 53:5848-63. [PMID: 25151917 DOI: 10.1021/bi500470b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Noncoding Y RNAs are small stem-loop RNAs that are involved in different cellular processes, including the regulation of DNA replication. An evolutionarily conserved small domain in the upper stem of vertebrate Y RNAs has an essential function for the initiation of chromosomal DNA replication. Here we provide a structure-function analysis of this essential RNA domain under physiological conditions. Solution state nuclear magnetic resonance and far-ultraviolet circular dichroism spectroscopy show that the upper stem domain of human Y1 RNA adopts a locally destabilized A-form helical structure involving eight Watson-Crick base pairs. Within this helix, two G:C base pairs are highly stable even at elevated temperatures and therefore may serve as clamps to maintain the local structure of the helix. These two stable G:C base pairs frame three unstable base pairs, which are located centrally between them. Systematic substitution mutagenesis results in a disruption of the ordered A-form helical structure and in the loss of DNA replication initiation activity, establishing a positive correlation between folding stability and function. Our data thus provide a structural basis for the evolutionary conservation of key nucleotides in this RNA domain that are essential for the functionality of noncoding Y RNAs during the initiation of DNA replication.
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Affiliation(s)
- Iren Wang
- Institute of Biological Chemistry, Academia Sinica , 128, Section 2, Academia Road, Taipei 11529, Taiwan
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Inhibitor-induced conformational stabilization and structural alteration of a mip-like peptidyl prolyl cis-trans isomerase and its C-terminal domain. PLoS One 2014; 9:e102891. [PMID: 25072141 PMCID: PMC4114562 DOI: 10.1371/journal.pone.0102891] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/25/2014] [Indexed: 02/05/2023] Open
Abstract
FKBP22, an Escherichia coli-encoded PPIase (peptidyl-prolyl cis-trans isomerase) enzyme, shares substantial identity with the Mip-like pathogenic factors, caries two domains, exists as a dimer in solution and binds some immunosuppressive drugs (such as FK506 and rapamycin) using its C-terminal domain (CTD). To understand the effects of these drugs on the structure and stability of the Mip-like proteins, rFKBP22 (a chimeric FKBP22) and CTD+ (a CTD variant) have been studied in the presence and absence of rapamycin using different probes. We demonstrated that rapamycin binding causes minor structural alterations of rFKBP22 and CTD+. Both the proteins (equilibrated with rapamycin) were unfolded via the formation of intermediates in the presence of urea. Further study revealed that thermal unfolding of both rFKBP22 and rapamycin-saturated rFKBP22 occurred by a three-state mechanism with the synthesis of intermediates. Intermediate from the rapamycin-equilibrated rFKBP22 was formed at a comparatively higher temperature. All intermediates carried substantial extents of secondary and tertiary structures. Intermediate resulted from the thermal unfolding of rFKBP22 existed as the dimers in solution, carried an increased extent of hydrophobic surface and possessed relatively higher rapamycin binding activity. Despite the formation of intermediates, both the thermal and urea-induced unfolding reactions were reversible in nature. Unfolding studies also indicated the considerable stabilization of both proteins by rapamycin binding. The data suggest that rFKBP22 or CTD+ could be exploited to screen the rapamycin-like inhibitors in the future.
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Thomas S, Bakkes PJ, Smits SHJ, Schmitt L. Equilibrium folding of pro-HlyA from Escherichia coli reveals a stable calcium ion dependent folding intermediate. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1500-10. [PMID: 24865936 DOI: 10.1016/j.bbapap.2014.05.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/13/2014] [Accepted: 05/16/2014] [Indexed: 11/17/2022]
Abstract
HlyA from Escherichia coli is a member of the repeats in toxin (RTX) protein family, produced by a wide range of Gram-negative bacteria and secreted by a dedicated Type 1 Secretion System (T1SS). RTX proteins are thought to be secreted in an unfolded conformation and to fold upon secretion by Ca(2+) binding. However, the exact mechanism of secretion, ion binding and folding to the correct native state remains largely unknown. In this study we provide an easy protocol for high-level pro-HlyA purification from E. coli. Equilibrium folding studies, using intrinsic tryptophan fluorescence, revealed the well-known fact that Ca(2+) is essential for stability as well as correct folding of the whole protein. In the absence of Ca(2+), pro-HlyA adopts a non-native conformation. Such molecules could however be rescued by Ca(2+) addition, indicating that these are not dead-end species and that Ca(2+) drives pro-HlyA folding. More importantly, pro-HlyA unfolded via a two-state mechanism, whereas folding was a three-state process. The latter is indicative of the presence of a stable folding intermediate. Analysis of deletion and Trp mutants revealed that the first folding transition, at 6-7M urea, relates to Ca(2+) dependent structural changes at the extreme C-terminus of pro-HlyA, sensed exclusively by Trp914. Since all Trp residues of HlyA are located outside the RTX domain, our results demonstrate that Ca(2+) induced folding is not restricted to the RTX domain. Taken together, Ca(2+) binding to the pro-HlyA RTX domain is required to drive the folding of the entire protein to its native conformation.
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Affiliation(s)
- Sabrina Thomas
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Patrick J Bakkes
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany.
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Martínez-Oliván J, Rozado-Aguirre Z, Arias-Moreno X, Angarica VE, Velázquez-Campoy A, Sancho J. Low-density lipoprotein receptor is a calcium/magnesium sensor - role of LR4 and LR5 ion interaction kinetics in low-density lipoprotein release in the endosome. FEBS J 2014; 281:2638-58. [PMID: 24720672 DOI: 10.1111/febs.12811] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/25/2014] [Accepted: 04/08/2014] [Indexed: 11/28/2022]
Abstract
The low-density lipoprotein receptor (LDLR) captures circulating lipoproteins and delivers them in the endosome for degradation. Its function is essential for cholesterol homeostasis, and mutations in the LDLR are the major cause of familiar hypercholesterolemia. The release of LDL is usually attributed to endosome acidification. As the pH drops, the affinity of the LDLR/LDL complex is reduced, whereas the strength of a self-complex formed between two domains of the receptor (i.e. the LDL binding domain and the β-propeller domain) increases. However, an alternative model states that, as a consequence of a drop in both pH and Ca(2+) concentration, the LDLR binding domain is destabilized in the endosome, which weakens the LDLR/LDL complex, thus liberating the LDL particles. In the present study, we test a key underlying assumption of the second model, namely that the lipoprotein binding repeats of the receptor (specifically repeats 4 and 5, LR4 and LR5) rapidly sense endosomal changes in Ca(2+) concentration. Our kinetic and thermodynamic analysis of Ca(2+) and Mg(2+) binding to LR4 and LR5, as well as to the tandem of the two (LR4-5), shows that both repeats spontaneously release Ca(2+) in a time scale much shorter than endosomal delivery of LDL, thus acting as Ca(2+) sensors that become unfolded under endosomal conditions. Our analysis additionally explains the lower Ca(2+) affinity of repeat LR4, compared to LR5, as arising from a very slow Ca(2+) binding reaction in the former, most likely related to the lower conformational stability of apolipoprotein LR4, compared to apolipoprotein LR5, as determined from thermal unfolding experiments and molecular dynamics simulations.
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Affiliation(s)
- Juan Martínez-Oliván
- Biocomputation and Complex Systems Physics Institute (BIFI) - Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Spain
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Zhang F, Hu C, Dong Y, Lin MS, Liu J, Jiang X, Ge Y, Guo Y. The impact of V30A mutation on transthyretin protein structural stability and cytotoxicity against neuroblastoma cells. Arch Biochem Biophys 2013; 535:120-7. [DOI: 10.1016/j.abb.2013.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 11/16/2022]
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Simeonov A. Recent developments in the use of differential scanning fluorometry in protein and small molecule discovery and characterization. Expert Opin Drug Discov 2013; 8:1071-82. [PMID: 23738712 DOI: 10.1517/17460441.2013.806479] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Despite tremendous advances in the application of biophysical methods in drug discovery, the preponderance of instruments and techniques still require sophisticated analyses by dedicated personnel and/or large amounts of frequently hard-to-produce proteins. A technique which carries the promise of simplicity and relatively low protein consumption is the differential scanning fluorometry (DSF). This technique monitors protein through the use of environmentally sensitive fluorescent dye, in a temperature-ramp regime by observing the gradual exposure to the solvent of otherwise buried hydrophobic faces of protein domains. AREAS COVERED This review describes recent developments in the field of DSF. This article pays a particular emphasis on the advances published during the 2010 - 2013 period. EXPERT OPINION There has been a significant diversification of DSF applications beyond initial small molecule discovery into areas such as protein therapeutic development, formulation studies and various mechanistic investigations. This serves as a further indication of the broad penetration of the technique. In the small molecule arena, DSF has expanded toward sophisticated co-dependency MOA tests, demonstrating the wealth of information which the technique can provide. Importantly, the first public deposition of a large screening dataset may enable the use of thermal stabilization data in refining in silico models for small molecule binding.
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Affiliation(s)
- Anton Simeonov
- National Institutes of Health, National Center for Advancing Translational Sciences, Division of Discovery Innovation, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA.
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