1
|
Marques HM. The inorganic chemistry of the cobalt corrinoids - an update. J Inorg Biochem 2023; 242:112154. [PMID: 36871417 DOI: 10.1016/j.jinorgbio.2023.112154] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B12, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B12-dependent enzymes is also given for the reader's convenience.
Collapse
Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
| |
Collapse
|
2
|
Ogden DS, Moradi M. Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.29.518406. [PMID: 36482979 PMCID: PMC9727763 DOI: 10.1101/2022.11.29.518406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Severe acute respiratory syndrome (SARS) coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) derive transmissibility from spike protein activation in the receptor binding domain (RBD) and binding to the host cell angiotensin converting enzyme 2 (ACE2). However, the mechanistic details that describe the large-scale conformational changes associated with spike protein activation or deactivation are still somewhat unknown. Here, we have employed an extensive set of nonequilibrium all-atom molecular dynamics (MD) simulations, utilizing a novel protocol, for the SARS-CoV-1 (CoV-1) and SARS-CoV-2 (CoV-2) prefusion spike proteins in order to characterize the conformational pathways associated with the active-to-inactive transition. Our results indicate that both CoV-1 and CoV-2 spike proteins undergo conformational transitions along pathways unique to each protein. We have identified a number of key residues that form various inter-domain saltbridges, suggesting a multi-stage conformational change along the pathways. We have also constructed the free energy profiles along the transition pathways for both CoV-1 and CoV-2 spike proteins. The CoV-2 spike protein must overcome larger free energy barriers to undergo conformational changes towards protein activation or deactivation, when compared to CoV-1.
Collapse
|
3
|
Native Cell Environment Constrains Loop Structure in the Escherichia coli Cobalamin Transporter BtuB. Biophys J 2020; 119:1550-1557. [PMID: 32946767 DOI: 10.1016/j.bpj.2020.08.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 11/23/2022] Open
Abstract
The extracellular loops of bacterial outer membrane (OM) transporters are thought to sample a range of conformations in the apo state but to undergo a gating motion and assume a more defined conformation upon the binding of substrate. Here, we use pulse electron paramagnetic resonance to examine the conformations of the extracellular loops of BtuB, the Escherichia coli TonB-dependent vitamin B12 transporter, in whole cells. Unlike previous measurements carried out in vitro, the loops assume well-defined configurations in situ that closely match the in surfo crystal structures. Moreover, there is no evidence that the loops undergo significant gating motions upon the binding of substrate. The results demonstrate that the structure of BtuB is dependent upon an intact native OM environment, in which a critical component is likely to be the extracellular lipopolysaccharide. In general, this work indicates that measurements on OM proteins in reconstituted membrane systems may not reflect the native state of the protein in vivo.
Collapse
|
4
|
Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli. PLoS Comput Biol 2020; 16:e1008024. [PMID: 32609716 PMCID: PMC7360065 DOI: 10.1371/journal.pcbi.1008024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/14/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
Vitamin B12 (or cobalamin) is an enzymatic cofactor essential both for mammals and bacteria. However, cobalamin can be synthesized only by few microorganisms so most bacteria need to take it up from the environment through the TonB-dependent transport system. The first stage of cobalamin import to E. coli cells occurs through the outer-membrane receptor called BtuB. Vitamin B12 binds with high affinity to the extracellular side of the BtuB protein. BtuB forms a β-barrel with inner luminal domain and extracellular loops. To mechanically allow for cobalamin passage, the luminal domain needs to partially unfold with the help of the inner-membrane TonB protein. However, the mechanism of cobalamin permeation is unknown. Using all-atom molecular dynamics, we simulated the transport of cobalamin through the BtuB receptor embedded in an asymmetric and heterogeneous E. coli outer-membrane. To enhance conformational sampling of the BtuB loops, we developed the Gaussian force-simulated annealing method (GF-SA) and coupled it with umbrella sampling. We found that cobalamin needs to rotate in order to permeate through BtuB. We showed that the mobility of BtuB extracellular loops is crucial for cobalamin binding and transport and resembles an induced-fit mechanism. Loop mobility depends not only on the position of cobalamin but also on the extension of luminal domain. We provided atomistic details of cobalamin transport through the BtuB receptor showing the essential role of the mobility of BtuB extracellular loops. A similar TonB-dependent transport system is used also by many other compounds, such as haem and siderophores, and importantly, can be hijacked by natural antibiotics. Our work could have implications for future delivery of antibiotics to bacteria using this transport system.
Collapse
|
5
|
Lundquist KP, Gumbart JC. Presence of substrate aids lateral gate separation in LptD. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183025. [PMID: 31351059 DOI: 10.1016/j.bbamem.2019.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/25/2019] [Accepted: 07/14/2019] [Indexed: 10/26/2022]
Abstract
Lipopolysaccharides (LPS) provide the outer membrane (OM) of Gram-negative bacteria with a strong protective barrier. The periplasm-spanning Lpt machinery is responsible for the transport of LPS molecules across the periplasm, culminating in insertion by the outer-membrane proteins LptD and LptE. In order to elucidate the mechanisms of LPS insertion by LptDE, we performed over 14 microseconds of equilibrium molecular dynamics simulations. Bilayer-dependent differences in the fluctuations and secondary structure of LptD's extracellular loops are observed for a pure DMPE membrane vs. a model of the OM. Furthermore, LptD's periplasmic N-terminal domain is highly dynamic, which may help to maintain the integrity of the periplasm-spanning complex amidst relative motion of the inner-membrane and outer-membrane anchored domains. In addition, our simulations demonstrate that binding of LPS substrate activates a switching between the associated and dissociated states of two lumenal loops at the interface between the β-barrel and the N-terminal domain as well as LptD's lateral gate on the microsecond timescale, neither of which is observed for the apo state. Placement of a substrate LPS molecule also causes an increase in the average separation of the LptD lateral gate strands and a lowering of the energetic barrier to lateral gate opening.
Collapse
Affiliation(s)
- Karl P Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30313, United States of America
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30313, United States of America.
| |
Collapse
|
6
|
Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
7
|
Pavlova A, Parks JM, Gumbart JC. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations. J Chem Theory Comput 2018; 14:784-798. [PMID: 29334459 DOI: 10.1021/acs.jctc.7b01236] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co3+, Co2+, and Co1+, and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.
Collapse
Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| |
Collapse
|
8
|
Sikora A, Joseph B, Matson M, Staley JR, Cafiso DS. Allosteric Signaling Is Bidirectional in an Outer-Membrane Transport Protein. Biophys J 2017; 111:1908-1918. [PMID: 27806272 DOI: 10.1016/j.bpj.2016.09.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/14/2016] [Accepted: 09/23/2016] [Indexed: 11/19/2022] Open
Abstract
In BtuB, the Escherichia coli TonB-dependent transporter for vitamin B12, substrate binding to the extracellular surface unfolds a conserved energy coupling motif termed the Ton box into the periplasm. This transmembrane signaling event facilitates an interaction between BtuB and the inner-membrane protein TonB. In this study, continuous-wave and pulse electron paramagnetic resonance in a native outer-membrane preparation demonstrate that signaling also occurs from the periplasmic to the extracellular surface in BtuB. The binding of a TonB fragment to the periplasmic interface alters the configuration of the second extracellular loop and partially dissociates a spin-labeled substrate analog. Moreover, mutants in the periplasmic Ton box that are transport-defective alter the binding site for vitamin B12 in BtuB. This work demonstrates that the Ton box and the extracellular substrate binding site are allosterically coupled in BtuB, and that TonB binding may initiate a partial round of transport.
Collapse
Affiliation(s)
- Arthur Sikora
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Benesh Joseph
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Morgan Matson
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Jacob R Staley
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia.
| |
Collapse
|
9
|
Balusek C, Gumbart JC. Role of the Native Outer-Membrane Environment on the Transporter BtuB. Biophys J 2017; 111:1409-1417. [PMID: 27705764 DOI: 10.1016/j.bpj.2016.08.033] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 08/22/2016] [Accepted: 08/26/2016] [Indexed: 11/19/2022] Open
Abstract
BtuB is a TonB-dependent transporter that permits the high-affinity binding and transport of cobalamin (CBL), or vitamin B12, across the asymmetric outer membrane (OM) of Gram-negative bacteria. It has been shown that Ca2+ binding is necessary for high-affinity binding of CBL to BtuB, and earlier simulations suggested that calcium ions serve to stabilize key substrate-binding extracellular loops. However, those simulations did not account for the lipopolysaccharides in the OM. To illuminate the roles of both Ca2+ and lipopolysaccharides in protein functionality, we performed simulations of apo and Ca2+-loaded BtuB in symmetric and asymmetric bilayers. The simulations reveal that the oligosaccharides of LPS stabilize the extracellular loops to some degree, apparently obviating the need for Ca2+. However, it is shown that Ca2+ ions stabilize a key substrate-binding loop to an even greater degree, as well as reposition specific CBL-binding residues, bringing them closer to the organization found in the CBL-bound structure. These results indicate the importance of including realistic membrane models when simulating outer-membrane proteins.
Collapse
Affiliation(s)
- Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
| |
Collapse
|
10
|
Hickman SJ, Cooper REM, Bellucci L, Paci E, Brockwell DJ. Gating of TonB-dependent transporters by substrate-specific forced remodelling. Nat Commun 2017; 8:14804. [PMID: 28429713 PMCID: PMC5413942 DOI: 10.1038/ncomms14804] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/31/2017] [Indexed: 12/21/2022] Open
Abstract
Membrane proteins play vital roles in inside-out and outside-in signal transduction by responding to inputs that include mechanical stimuli. Mechanical gating may be mediated by the membrane or by protein(s) but evidence for the latter is scarce. Here we use force spectroscopy, protein engineering and bacterial growth assays to investigate the effects of force on complexes formed between TonB and TonB-dependent transporters (TBDT) from Gram-negative bacteria. We confirm the feasibility of protein-only mediated mechanical gating by demonstrating that the interaction between TonB and BtuB (a TBDT) is sufficiently strong under force to create a channel through the TBDT. In addition, by comparing the dimensions of the force-induced channel in BtuB and a second TBDT (FhuA), we show that the mechanical properties of the interaction are perfectly tuned to their function by inducing formation of a channel whose dimensions are tailored to the ligand.
Collapse
Affiliation(s)
- Samuel J Hickman
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Rachael E M Cooper
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Luca Bellucci
- NEST, Istituto Nanoscienze-CNR, Piazza San Silvestro, 12-56127 Pisa, Italy
| | - Emanuele Paci
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| |
Collapse
|
11
|
Pietra F. Uptake of Organohalide Pollutants, and Release of Partially Dehalogenated Products, by NpRdhA, a 'Base-Off' Cob(II)alamin-Dependent Reductive Dehalogenase from a Deep Sea Bacterium. A Molecular Dynamics Investigation. Chem Biodivers 2016; 12:1945-53. [PMID: 26663844 DOI: 10.1002/cbdv.201500195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Indexed: 11/12/2022]
Abstract
This work shows that, during MD aided by external tiny random forces, 3-bromo-4-hydroxybenzoic acid (LHB), the product of reductive dehalogenation of 3,5-dibromo-4-hydroxybenzoic acid (LBB) by the corrin-based marine enzyme NpRdhA, is expelled along mainly the wide channel that connects the corrin to the external medium. In accordance, unbiased MD showed that LBB migrates relatively rapidly from the external medium to the inside of the channel, finally getting to the corrin active center of NpRdhA. The LBB pose, with bromide head and carboxylate tail nearly equidistant from the corrin Co ion, does not fit the results of previous automatic docking. Either the experimental structure of the NpRdhA-LBB complex, or a quantum-mechanical study of LBB at the corrin active site, are therefore urged.
Collapse
Affiliation(s)
- Francesco Pietra
- Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, IT-55100 Lucca, (phone/fax: +39-0583-417336).
| |
Collapse
|
12
|
Schmidt TH, Raunest M, Fischer N, Reith D, Kandt C. Computer simulations suggest direct and stable tip to tip interaction between the outer membrane channel TolC and the isolated docking domain of the multidrug RND efflux transporter AcrB. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1419-26. [PMID: 27045078 DOI: 10.1016/j.bbamem.2016.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 01/16/2023]
Abstract
One way by which bacteria achieve antibiotics resistance is preventing drug access to its target molecule for example through an overproduction of multi-drug efflux pumps of the resistance nodulation division (RND) protein super family of which AcrAB-TolC in Escherichia coli is a prominent example. Although representing one of the best studied efflux systems, the question of how AcrB and TolC interact is still unclear as the available experimental data suggest that either both proteins interact in a tip to tip manner or do not interact at all but are instead connected by a hexamer of AcrA molecules. Addressing the question of TolC-AcrB interaction, we performed a series of 100 ns - 1 µs-molecular dynamics simulations of membrane-embedded TolC in presence of the isolated AcrB docking domain (AcrB(DD)). In 5/6 simulations we observe direct TolC-AcrB(DD) interaction that is only stable on the simulated time scale when both proteins engage in a tip to tip manner. At the same time we find TolC opening and closing freely on extracellular side while remaining closed at the inner periplasmic bottleneck region, suggesting that either the simulated time is too short or additional components are required to unlock TolC.
Collapse
Affiliation(s)
- Thomas H Schmidt
- Department of Membrane Biochemistry, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Martin Raunest
- MLL Münchner Leukämielabor GmbH, Max-Lebsche-Platz 31, 81377 München, Germany
| | - Nadine Fischer
- Berlin-Chemie AG, Glienicker Weg 125, 12489 Berlin, Germany
| | - Dirk Reith
- Bonn-Rhein-Sieg University of Applied Sciences, Department of Electrical/Mechanical Engineering and Tech.Journalism, Grantham-Allee 20, 53757 Sankt Augustin, Germany
| | - Christian Kandt
- Bonn-Rhein-Sieg University of Applied Sciences, Department of Electrical/Mechanical Engineering and Tech.Journalism, Grantham-Allee 20, 53757 Sankt Augustin, Germany.
| |
Collapse
|
13
|
Pavlova A, Hwang H, Lundquist K, Balusek C, Gumbart JC. Living on the edge: Simulations of bacterial outer-membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1753-9. [PMID: 26826270 DOI: 10.1016/j.bbamem.2016.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 01/06/2023]
Abstract
Gram-negative bacteria are distinguished in part by a second, outer membrane surrounding them. This membrane is distinct from others, possessing an outer leaflet composed not of typical phospholipids but rather large, highly charged molecules known as lipopolysaccharides. Therefore, modeling the structure and dynamics of proteins embedded in the outer membrane requires careful consideration of their native environment. In this review, we examine how simulations of such outer-membrane proteins have evolved over the last two decades, culminating most recently in detailed, highly accurate atomistic models of the outer membrane. We also draw attention to how the simulations have coupled with experiments to produce novel insights unattainable through a single approach. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Collapse
Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Karl Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States.
| |
Collapse
|
14
|
Malki I, Simenel C, Wojtowicz H, Cardoso de Amorim G, Prochnicka-Chalufour A, Hoos S, Raynal B, England P, Chaffotte A, Delepierre M, Delepelaire P, Izadi-Pruneyre N. Interaction of a partially disordered antisigma factor with its partner, the signaling domain of the TonB-dependent transporter HasR. PLoS One 2014; 9:e89502. [PMID: 24727671 PMCID: PMC3984077 DOI: 10.1371/journal.pone.0089502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/21/2014] [Indexed: 11/21/2022] Open
Abstract
Bacteria use diverse signaling pathways to control gene expression in response to external stimuli. In Gram-negative bacteria, the binding of a nutrient is sensed by an outer membrane transporter. This signal is then transmitted to an antisigma factor and subsequently to the cytoplasm where an ECF sigma factor induces expression of genes related to the acquisition of this nutrient. The molecular interactions involved in this transmembrane signaling are poorly understood and structural data on this family of antisigma factor are rare. Here, we present the first structural study of the periplasmic domain of an antisigma factor and its interaction with the transporter. The study concerns the signaling in the heme acquisition system (Has) of Serratia marcescens. Our data support unprecedented partially disordered periplasmic domain of an anti-sigma factor HasS in contact with a membrane-mimicking environment. We solved the 3D structure of the signaling domain of HasR transporter and identified the residues at the HasS-HasR interface. Their conservation in several bacteria suggests wider significance of the proposed model for the understanding of bacterial transmembrane signaling.
Collapse
Affiliation(s)
- Idir Malki
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Catherine Simenel
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Halina Wojtowicz
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Gisele Cardoso de Amorim
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Ada Prochnicka-Chalufour
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Sylviane Hoos
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, Paris, France
| | - Bertrand Raynal
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, Paris, France
| | - Patrick England
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, Paris, France
| | - Alain Chaffotte
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Muriel Delepierre
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Philippe Delepelaire
- Institut de Biologie Physico-Chimique, CNRS Université Paris-Diderot UMR 7099, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| |
Collapse
|
15
|
A Microscopic View of the Mechanisms of Active Transport Across the Cellular Membrane. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63378-1.00004-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
16
|
Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, Buchanan SK. Structural insight into the biogenesis of β-barrel membrane proteins. Nature 2013; 501:385-90. [PMID: 23995689 PMCID: PMC3779476 DOI: 10.1038/nature12521] [Citation(s) in RCA: 327] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 08/01/2013] [Indexed: 11/17/2022]
Abstract
β-barrel membrane proteins are essential for nutrient import, signaling, motility, and survival. In Gram-negative bacteria, the β-barrel assembly machinery (BAM) complex is responsible for the biogenesis of β-barrel membrane proteins, with homologous complexes found in mitochondria and chloroplasts. Here we describe the structure of BamA, the central and essential component of the BAM complex, from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. BamA consists of a large periplasmic domain attached to a 16-strand transmembrane β-barrel domain. Three structural features speak to the mechanism by which BamA catalyzes β-barrel assembly. First, the interior cavity is accessible in one BamA structure and conformationally closed in the other. Second, an exterior rim of the β-barrel has a distinctly narrowed hydrophobic surface, locally destabilizing the outer membrane. And third, the β-barrel can undergo lateral opening, evocatively suggesting a route from the interior cavity in BamA into the outer membrane.
Collapse
Affiliation(s)
- Nicholas Noinaj
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Piggot TJ, Holdbrook DA, Khalid S. Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:284-93. [DOI: 10.1016/j.bbamem.2012.08.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/02/2012] [Accepted: 08/23/2012] [Indexed: 11/25/2022]
|
18
|
Shaikh S, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E. Visualizing functional motions of membrane transporters with molecular dynamics simulations. Biochemistry 2013; 52:569-87. [PMID: 23298176 PMCID: PMC3560430 DOI: 10.1021/bi301086x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 12/21/2012] [Indexed: 01/08/2023]
Abstract
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.
Collapse
Affiliation(s)
- Saher
A. Shaikh
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jing Li
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Giray Enkavi
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Po-Chao Wen
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Zhijian Huang
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| |
Collapse
|
19
|
Enkavi G, Li J, Mahinthichaichan P, Wen PC, Huang Z, Shaikh SA, Tajkhorshid E. Simulation studies of the mechanism of membrane transporters. Methods Mol Biol 2013; 924:361-405. [PMID: 23034756 DOI: 10.1007/978-1-62703-017-5_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Membrane transporters facilitate active transport of their specific substrates, often against their electrochemical gradients across the membrane, through coupling the process to various sources of cellular energy, for example, ATP binding and hydrolysis in primary transporters, and pre-established electrochemical gradient of molecular species other than the substrate in the case of secondary transporters. In order to provide efficient energy-coupling mechanisms, membrane transporters have evolved into molecular machines in which stepwise binding, translocation, and transformation of various molecular species are closely coupled to protein conformational changes that take the transporter from one functional state to another during the transport cycle. Furthermore, in order to prevent the formation of leaky states and to be able to pump the substrate against its electrochemical gradient, all membrane transporters use the widely-accepted "alternating access mechanism," which ensures that the substrate is only accessible from one side of the membrane at a given time, but relies on complex and usually global protein conformational changes that differ for each family of membrane transporters. Describing the protein conformational changes of different natures and magnitudes is therefore at the heart of mechanistic studies of membrane transporters. Here, using a number of membrane transporters from diverse families, we present common protocols used in setting up and performing molecular dynamics simulations of membrane transporters and in analyzing the results, in order to characterize relevant motions of the system. The emphasis will be on highlighting how optimal design of molecular dynamics simulations combined with mechanistically oriented analysis can shed light onto key functionally relevant protein conformational changes in this family of membrane proteins.
Collapse
Affiliation(s)
- Giray Enkavi
- Department of Biochemistry, Center for Biophysics and Computational Biology, College of Medicine, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | | | | | | | | |
Collapse
|
20
|
Koch DC, Raunest M, Harder T, Kandt C. Unilateral access regulation: ground state dynamics of the Pseudomonas aeruginosa outer membrane efflux duct OprM. Biochemistry 2012; 52:178-87. [PMID: 23234291 DOI: 10.1021/bi3014714] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acting as an efflux duct in the MexA-MexB-OprM multidrug efflux pump, OprM plays a major role in the antibiotic resistance capability of Pseudomonas aeruginosa, trafficking substrates through the outer cell membrane. Whereas the available crystal structures showed restricted OprM access on both ends, the underlying gating mechanism is not yet fully understood. To gain insight into the functional mechanism of OprM access regulation, we conducted a series of five independent, unbiased molecular dynamics simulations, computing 200 ns dynamics samples of the wild-type protein in a phospholipid membrane/150 mM NaCl water environment. On the extracellular side, OprM opens and closes freely under the simulated conditions, suggesting the absence of a gating mechanism on this side of the isolated protein. On the periplasmic side, we observe an opening of the tip regions at Val408 and to a lesser degree Asp416 located 1.5 nm further into the channel, leading to OprM end conformations being up to 3 and 1.4 times, respectively, more open than the asymmetric crystal structure. If our simulations are correct, our findings imply that periplasmic gating involves only the Asp416 region and that in vivo additional components, absent in our simulation, might be required for periplasmic gating if the observed opening trend near Asp416 is not negligible. In addition to that ,we identified in each monomer a previously unreported sodium binding site in the channel interior coordinated by Asp171 and Asp230 whose functional role remains to be investigated.
Collapse
Affiliation(s)
- Dennis C Koch
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences (LIMES) Institute, University of Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany
| | | | | | | |
Collapse
|
21
|
Noinaj N, Easley NC, Oke M, Mizuno N, Gumbart J, Boura E, Steere AN, Zak O, Aisen P, Tajkhorshid E, Evans RW, Gorringe AR, Mason AB, Steven AC, Buchanan SK. Structural basis for iron piracy by pathogenic Neisseria. Nature 2012; 483:53-8. [PMID: 22327295 PMCID: PMC3292680 DOI: 10.1038/nature10823] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 01/09/2012] [Indexed: 11/20/2022]
Abstract
Neisseria are obligate human pathogens causing bacterial meningitis, septicaemia and gonorrhoea. Neisseria require iron for survival and can extract it directly from human transferrin for transport across the outer membrane. The transport system consists of TbpA, an integral outer membrane protein, and TbpB, a co-receptor attached to the cell surface; both proteins are potentially important vaccine and therapeutic targets. Two key questions driving Neisseria research are how human transferrin is specifically targeted, and how the bacteria liberate iron from transferrin at neutral pH. To address these questions, we solved crystal structures of the TbpA-transferrin complex and of the corresponding co-receptor TbpB. We characterized the TbpB-transferrin complex by small-angle X-ray scattering and the TbpA-TbpB-transferrin complex by electron microscopy. Our studies provide a rational basis for the specificity of TbpA for human transferrin, show how TbpA promotes iron release from transferrin, and elucidate how TbpB facilitates this process.
Collapse
Affiliation(s)
- Nicholas Noinaj
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Raunest M, Kandt C. Locked on one side only: ground state dynamics of the outer membrane efflux duct TolC. Biochemistry 2012; 51:1719-29. [PMID: 22313049 DOI: 10.1021/bi201814s] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Playing a major role in the expulsion of antibiotics and the secretion of cell toxins in conjunction with inner membrane transporters of three protein superfamilies, the outer membrane channel TolC occurs in at least two states blocking or permitting the passage of substrates. The details of the underlying gating mechanism are not fully understood. Addressing the questions of extracellular access control and periplasmic gating mechanism, we conducted a series of independent, unbiased 150-300 ns molecular dynamics simulations of wild-type TolC in a phospholipid membrane/150 mM NaCl water environment. We find that TolC opens and closes freely on the extracellular side, suggesting the absence of a gating mechanism on this side in the isolated protein. On the periplasmic side, we observe the outer periplasmic bottleneck region adopting in all simulations a conformation more open than the TolC wild-type crystal structures until in one run the successive binding of two sodium ions induces the transition to a conformation more closed than any of the available TolC X-ray structures. Concurrent with a heightened sodium residence probability near Asp374, the inner periplasmic bottleneck region at Asp374 remains closed throughout the simulations unless all NaCl is removed from the system, inducing a reopening of the outer and inner bottleneck. Our findings suggest that TolC is locked only on the periplasmic side in a sodium-dependent manner.
Collapse
Affiliation(s)
- Martin Raunest
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life and Medical Sciences Center, University of Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany
| | | |
Collapse
|
23
|
Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter. J Mol Biol 2011; 415:128-42. [PMID: 22094314 DOI: 10.1016/j.jmb.2011.10.049] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 10/26/2011] [Accepted: 10/31/2011] [Indexed: 11/23/2022]
Abstract
Autotransporters are secreted proteins produced by pathogenic Gram-negative bacteria. They consist of a membrane-embedded β-domain and an extracellular passenger domain that is sometimes cleaved and released from the cell surface. We solved the structures of three noncleavable mutants of the autotransporter EspP to examine how it promotes asparagine cyclization to cleave its passenger. We found that cyclization is facilitated by multiple factors. The active-site asparagine is sterically constrained to conformations favorable for cyclization, while electrostatic interactions correctly orient the carboxamide group for nucleophilic attack. During molecular dynamics simulations, water molecules were observed to enter the active site and to form hydrogen bonds favorable for increasing the nucleophilicity of the active-site asparagine. When the activated asparagine attacks its main-chain carbonyl carbon, the resulting oxyanion is stabilized by a protonated glutamate. Upon cleavage, this proton could be transferred to the leaving amine group, helping overcome a significant energy barrier. Together, these findings provide insight into factors important for asparagine cyclization, a mechanism broadly used for protein cleavage.
Collapse
|
24
|
Piggot TJ, Holdbrook DA, Khalid S. Electroporation of the E. coli and S. Aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes. J Phys Chem B 2011; 115:13381-8. [DOI: 10.1021/jp207013v] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas J. Piggot
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Daniel A. Holdbrook
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| |
Collapse
|
25
|
Clardy SM, Allis DG, Fairchild TJ, Doyle RP. Vitamin B12in drug delivery: breaking through the barriers to a B12bioconjugate pharmaceutical. Expert Opin Drug Deliv 2010; 8:127-40. [DOI: 10.1517/17425247.2011.539200] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
26
|
Marino N, Rabideau AE, Doyle RP. Trifluoracetic acid-assisted crystallization of vitamin B12 results in protonation of the phosphate group of the nucleotide loop: insight into the influence of crystal packing forces on vitamin B12 structures. Inorg Chem 2010; 50:220-30. [PMID: 21128680 DOI: 10.1021/ic101810v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In the course of experiments concerning our ongoing project on the synthesis of vitamin B(12) (cyanocobalamin, CNCbl) bioconjugates for drug-delivery purposes, we observed the formation of well-shaped red parallelepipeds from a concentrated aqueous solution of the HPLC-purified vitamin. The X-ray structural investigation (MoK(α)) at 98 K on these crystals revealed a CNCbl-TFA salt of formula [CNCbl(H)](TFAc)·14H(2)O (1, where TFA = trifluoracetic acid; TFAc(-) = trifluoracetate anion), in which a proton transfer from the trifluoracetic acid to the phosphate-O4P oxygen atoms is observed. 1 crystallizes in the standard orthorhombic P2(1)2(1)2(1) space group, a = 16.069(2) Å, b = 20.818(2) Å, c = 24.081(2) Å, Z = 4. The final full-matrix least-squares refinements on F(2) converged with R(1) = 4.1% for the 18957 significant reflections, a very low crystallographic residual for cobalamins, which facilitated the analysis of the extensive network of hydrogen bonds within the lattice. To the best of our knowledge, this is the first cobalamin structure to show protonation of the phosphate group of the cobalamin nucleotide loop. In this work, the crystal structure of 1 is analyzed and compared to other CNCbls reported in the literature, namely, CNCbl·3PrOH·12H(2)O (2, PrOH = propyl alcohol), CNCbl·acetone·20H(2)O (3), CNCbl·2LiCl·10.2H(2)O (4), and CNCbl·2KCl·10.6H(2)O (5). The analysis confirmed that protonation of the phosphate leaves the major CNCbl structural parameters unaffected, so that 1 can be considered an "unmodified" Cbl solvate. However, comparison between 1-5 led to interesting findings. In fact, although the cobalt(III) coordination sphere in 1-5 is similar, significant differences could be noted in the upward fold angle of the corrin macrocycle, a parameter commonly related to the steric hindrance of the axial lower "α" nucleotide-base and the electronic trans influence of the upper "β" substituent. This suggests that crystal-packing forces may influence the corrin deformation as well. Herein we explore, on the basis of the newly acquired structure and reported crystallographic data, whether the incongruities among 1-5 have to be attributed to random crystal packing effects or if it is possible to associate them with specific crystal packing (clusters).
Collapse
Affiliation(s)
- Nadia Marino
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100, USA
| | | | | |
Collapse
|
27
|
Allis DG, Fairchild TJ, Doyle RP. The binding of vitamin B12 to transcobalamin(II); structural considerations for bioconjugate design—a molecular dynamics study. MOLECULAR BIOSYSTEMS 2010; 6:1611-8. [DOI: 10.1039/c003476b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|