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Wang G, Qin J, Verderosa AD, Hor L, Santos-Martin C, Paxman JJ, Martin JL, Totsika M, Heras B. A Buried Water Network Modulates the Activity of the Escherichia coli Disulphide Catalyst DsbA. Antioxidants (Basel) 2023; 12:antiox12020380. [PMID: 36829940 PMCID: PMC9952396 DOI: 10.3390/antiox12020380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
The formation of disulphide bonds is an essential step in the folding of many proteins that enter the secretory pathway; therefore, it is not surprising that eukaryotic and prokaryotic organisms have dedicated enzymatic systems to catalyse this process. In bacteria, one such enzyme is disulphide bond-forming protein A (DsbA), a thioredoxin-like thiol oxidase that catalyses the oxidative folding of proteins required for virulence and fitness. A large body of work on DsbA proteins, particularly Escherichia coli DsbA (EcDsbA), has demonstrated the key role that the Cys30-XX-Cys33 catalytic motif and its unique redox properties play in the thiol oxidase activity of this enzyme. Using mutational and functional analyses, here we identify that a set of charged residues, which form an acidic groove on the non-catalytic face of the enzyme, further modulate the activity of EcDsbA. Our high-resolution structures indicate that these residues form a water-mediated proton wire that can transfer protons from the bulk solvent to the active site. Our results support the view that proton shuffling may facilitate the stabilisation of the buried Cys33 thiolate formed during the redox reaction and promote the correct direction of the EcDsbA-substrate thiol-disulphide exchange. Comparison with other proteins of the same class and proteins of the thioredoxin-superfamily in general suggest that a proton relay system appears to be a conserved catalytic feature among this widespread superfamily of proteins. Furthermore, this study also indicates that the acidic groove of DsbA could be a promising allosteric site to develop novel DsbA inhibitors as antibacterial therapeutics.
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Affiliation(s)
- Geqing Wang
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Correspondence: (G.W.); (B.H.)
| | - Jilong Qin
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Anthony D. Verderosa
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Lilian Hor
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Carlos Santos-Martin
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Jason J. Paxman
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Jennifer L. Martin
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Begoña Heras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Correspondence: (G.W.); (B.H.)
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Bochicchio A, Brandner AF, Engberg O, Huster D, Böckmann RA. Spontaneous Membrane Nanodomain Formation in the Absence or Presence of the Neurotransmitter Serotonin. Front Cell Dev Biol 2020; 8:601145. [PMID: 33330494 PMCID: PMC7734319 DOI: 10.3389/fcell.2020.601145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/06/2020] [Indexed: 11/23/2022] Open
Abstract
Detailed knowledge on the formation of biomembrane domains, their structure, composition, and physical characteristics is scarce. Despite its frequently discussed importance in signaling, e.g., in obtaining localized non-homogeneous receptor compositions in the plasma membrane, the nanometer size as well as the dynamic and transient nature of domains impede their experimental characterization. In turn, atomistic molecular dynamics (MD) simulations combine both, high spatial and high temporal resolution. Here, using microsecond atomistic MD simulations, we characterize the spontaneous and unbiased formation of nano-domains in a plasma membrane model containing phosphatidylcholine (POPC), palmitoyl-sphingomyelin (PSM), and cholesterol (Chol) in the presence or absence of the neurotransmitter serotonin at different temperatures. In the ternary mixture, highly ordered and highly disordered domains of similar composition coexist at 303 K. The distinction of domains by lipid acyl chain order gets lost at lower temperatures of 298 and 294 K, suggesting a phase transition at ambient temperature. By comparison of domain ordering and composition, we demonstrate how the domain-specific binding of the neurotransmitter serotonin results in a modified domain lipid composition and a substantial downward shift of the phase transition temperature. Our simulations thus suggest a novel mode of action of neurotransmitters possibly of importance in neuronal signal transmission.
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Affiliation(s)
- Anna Bochicchio
- Computational Biology, Department Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Astrid F Brandner
- Computational Biology, Department Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Oskar Engberg
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany.,Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Rainer A Böckmann
- Computational Biology, Department Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
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Abstract
The formation of disulfide bonds is critical to the folding of many extracytoplasmic proteins in all domains of life. With the discovery in the early 1990s that disulfide bond formation is catalyzed by enzymes, the field of oxidative folding of proteins was born. Escherichia coli played a central role as a model organism for the elucidation of the disulfide bond-forming machinery. Since then, many of the enzymatic players and their mechanisms of forming, breaking, and shuffling disulfide bonds have become understood in greater detail. This article summarizes the discoveries of the past 3 decades, focusing on disulfide bond formation in the periplasm of the model prokaryotic host E. coli.
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Putzu M, Gräter F, Elstner M, Kubař T. On the mechanism of spontaneous thiol–disulfide exchange in proteins. Phys Chem Chem Phys 2018; 20:16222-16230. [DOI: 10.1039/c8cp01325j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Free energy surfaces from QM/MM metadynamics on model peptides will be a basis to build reactive force field for reaction in proteins.
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Affiliation(s)
- Marina Putzu
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
- Center for Functional Nanostructures
| | - Frauke Gräter
- Interdisciplinary Center for Scientific Computing (IWR)
- Heidelberg University
- 69120 Heidelberg
- Germany
- Heidelberg Institute for Theoretical Studies
| | - Marcus Elstner
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
- Institute for Biological Interfaces (IBG-2)
| | - Tomáš Kubař
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
- Center for Functional Nanostructures
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Bertelshofer F, Sun L, Greiner G, Böckmann RA. GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules. Front Bioeng Biotechnol 2015; 3:186. [PMID: 26636074 PMCID: PMC4648074 DOI: 10.3389/fbioe.2015.00186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/30/2015] [Indexed: 11/16/2022] Open
Abstract
Knowledge about the electrostatic potential on the surface of biomolecules or biomembranes under physiological conditions is an important step in the attempt to characterize the physico-chemical properties of these molecules and, in particular, also their interactions with each other. Additionally, knowledge about solution electrostatics may also guide the design of molecules with specified properties. However, explicit water models come at a high computational cost, rendering them unsuitable for large design studies or for docking purposes. Implicit models with the water phase treated as a continuum require the numerical solution of the Poisson–Boltzmann equation (PBE). Here, we present a new flexible program for the numerical solution of the PBE, allowing for different geometries, and the explicit and implicit inclusion of membranes. It involves a discretization of space and the computation of the molecular surface. The PBE is solved using finite differences, the resulting set of equations is solved using a Gauss–Seidel method. It is shown for the example of the sucrose transporter ScrY that the implicit inclusion of a surrounding membrane has a strong effect also on the electrostatics within the pore region and, thus, needs to be carefully considered, e.g., in design studies on membrane proteins.
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Affiliation(s)
- Franziska Bertelshofer
- Computer Graphics Group, Department of Computer Science, University Erlangen-Nürnberg , Erlangen , Germany ; Computational Biology, Department of Biology, University Erlangen-Nürnberg , Erlangen , Germany
| | - Liping Sun
- Computational Biology, Department of Biology, University Erlangen-Nürnberg , Erlangen , Germany
| | - Günther Greiner
- Computer Graphics Group, Department of Computer Science, University Erlangen-Nürnberg , Erlangen , Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, University Erlangen-Nürnberg , Erlangen , Germany
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Who cares for the protons? Bioorg Med Chem 2012; 20:5453-60. [PMID: 22464682 DOI: 10.1016/j.bmc.2012.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/29/2012] [Accepted: 03/02/2012] [Indexed: 11/20/2022]
Abstract
It is tempting to use standard protonation states for the analysis of protein-ligand interactions. Two different pK(a) calculation methods, PROPKA (protein pK(a)) and MCCE (multi conformation continuum electrostatics), were applied to challenge this convenient behavior. As data basis, we selected five recently approved drugs for which structural information of the protein-drug complex is available. We analyzed the pK(a) calculations in terms of a measure termed BIPS (binary protonation states) recently introduced by us. Both methods agree in detecting the majority of the sites with atypical BIPS values. However, when using only one method, some of the atypcial BIPS value would have been missed. Therefore, we recommend using both methods to set such an interpretation on a solid basis.
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Kadokura H, Beckwith J. Mechanisms of oxidative protein folding in the bacterial cell envelope. Antioxid Redox Signal 2010; 13:1231-46. [PMID: 20367276 PMCID: PMC2959184 DOI: 10.1089/ars.2010.3187] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Disulfide-bond formation is important for the correct folding of a great number of proteins that are exported to the cell envelope of bacteria. Bacterial cells have evolved elaborate systems to promote the joining of two cysteines to form a disulfide bond and to repair misoxidized proteins. In the past two decades, significant advances have occurred in our understanding of the enzyme systems (DsbA, DsbB, DsbC, DsbG, and DsbD) used by the gram-negative bacterium Escherichia coli to ensure that correct pairs of cysteines are joined during the process of protein folding. However, a number of fundamental questions about these processes remain, especially about how they occur inside the cell. In addition, recent recognition of the increasing diversity among bacteria in the disulfide bond-forming capacity and in the systems for introducing disulfide bonds into proteins is raising new questions. We review here the marked progress in this field and discuss important questions that remain for future studies.
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Affiliation(s)
- Hiroshi Kadokura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan.
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Gatenby RA, Frieden BR. Coulomb interactions between cytoplasmic electric fields and phosphorylated messenger proteins optimize information flow in cells. PLoS One 2010; 5:e12084. [PMID: 20711447 PMCID: PMC2920310 DOI: 10.1371/journal.pone.0012084] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 07/14/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Normal cell function requires timely and accurate transmission of information from receptors on the cell membrane (CM) to the nucleus. Movement of messenger proteins in the cytoplasm is thought to be dependent on random walk. However, Brownian motion will disperse messenger proteins throughout the cytosol resulting in slow and highly variable transit times. We propose that a critical component of information transfer is an intracellular electric field generated by distribution of charge on the nuclear membrane (NM). While the latter has been demonstrated experimentally for decades, the role of the consequent electric field has been assumed to be minimal due to a Debye length of about 1 nanometer that results from screening by intracellular Cl- and K+. We propose inclusion of these inorganic ions in the Debye-Huckel equation is incorrect because nuclear pores allow transit through the membrane at a rate far faster than the time to thermodynamic equilibrium. In our model, only the charged, mobile messenger proteins contribute to the Debye length. FINDINGS Using this revised model and published data, we estimate the NM possesses a Debye-Huckel length of a few microns and find this is consistent with recent measurement using intracellular nano-voltmeters. We demonstrate the field will accelerate isolated messenger proteins toward the nucleus through Coulomb interactions with negative charges added by phosphorylation. We calculate transit times as short as 0.01 sec. When large numbers of phosphorylated messenger proteins are generated by increasing concentrations of extracellular ligands, we demonstrate they generate a self-screening environment that regionally attenuates the cytoplasmic field, slowing movement but permitting greater cross talk among pathways. Preliminary experimental results with phosphorylated RAF are consistent with model predictions. CONCLUSION This work demonstrates that previously unrecognized Coulomb interactions between phosphorylated messenger proteins and intracellular electric fields will optimize information transfer from the CM to the NM in cells.
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Affiliation(s)
- Robert A Gatenby
- Department of Radiology, Moffitt Cancer Center, Tampa, Florida, United States of America.
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