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Erba F, Mei G, Minicozzi V, Sabatucci A, Di Venere A, Maccarrone M. Conformational Dynamics of Lipoxygenases and Their Interaction with Biological Membranes. Int J Mol Sci 2024; 25:2241. [PMID: 38396917 PMCID: PMC10889196 DOI: 10.3390/ijms25042241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Lipoxygenases (LOXs) are a family of enzymes that includes different fatty acid oxygenases with a common tridimensional structure. The main functions of LOXs are the production of signaling compounds and the structural modifications of biological membranes. These features of LOXs, their widespread presence in all living organisms, and their involvement in human diseases have attracted the attention of the scientific community over the last decades, leading to several studies mainly focused on understanding their catalytic mechanism and designing effective inhibitors. The aim of this review is to discuss the state-of-the-art of a different, much less explored aspect of LOXs, that is, their interaction with lipid bilayers. To this end, the general architecture of six relevant LOXs (namely human 5-, 12-, and 15-LOX, rabbit 12/15-LOX, coral 8-LOX, and soybean 15-LOX), with different specificity towards the fatty acid substrates, is analyzed through the available crystallographic models. Then, their putative interface with a model membrane is examined in the frame of the conformational flexibility of LOXs, that is due to their peculiar tertiary structure. Finally, the possible future developments that emerge from the available data are discussed.
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Affiliation(s)
- Fulvio Erba
- Department of Clinical Science and Translational Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy;
| | - Giampiero Mei
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy;
| | - Velia Minicozzi
- Department of Physics and INFN, Tor Vergata University of Rome, Via Della Ricerca Scientifica 1, 00133 Rome, Italy;
| | - Annalaura Sabatucci
- Department of Biosciences and Technology for Food Agriculture and Environment, University of Teramo, Via Renato Balzarini 1, 64100 Teramo, Italy;
| | - Almerinda Di Venere
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy;
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito, 67100 L’Aquila, Italy
- European Center for Brain Research (CERC), Santa Lucia Foundation IRCCS, 00143 Rome, Italy
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2
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Lemler PM, Craft CL, Pollok CH, Regan TP, Vaccaro PH. Isolated and solvated chiroptical behavior in conformationally flexible butanamines. Chirality 2023; 35:586-618. [PMID: 37550220 DOI: 10.1002/chir.23570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 08/09/2023]
Abstract
The nonresonant optical activity of two highly flexible aliphatic amines, (2R)-3-methyl-2-butanamine (R-MBA) and (2R)-(3,3)-dimethyl-2-butanamine (R-DMBA), has been probed under isolated and solvated conditions to examine the roles of conformational isomerism and to explore the influence of extrinsic perturbations. The optical rotatory dispersion (ORD) measured in six solvents presented uniformly negative rotatory powers over the 320-590 nm region, with the long-wavelength magnitude of chiroptical response growing nearly monotonically as the dielectric constant of the surroundings diminished. The intrinsic specific optical rotation,α λ T (in deg dm-1 [g/mL]-1 ), extracted for ambient vapor-phase samples of R-MBA [-11.031(98) and -2.29 (11)] and R-DMBA [-9.434 (72) and -1.350 (48)] at 355 and 633 nm were best reproduced by counterintuitive solvents of high polarity (yet low polarizability) like acetonitrile and methanol. Attempts to interpret observed spectral signatures quantitatively relied on the linear-response frameworks of density-functional theory (B3LYP, cam-B3LYP, and dispersion-corrected analogs) and coupled-cluster theory (CCSD), with variants of the polarizable continuum model (PCM) deployed to account for the effects of implicit solvation. Building on the identification of several low-lying equilibrium geometries (nine for R-MBA and three for R-DMBA), ensemble-averaged ORD profiles were calculated at T = 300 K by means of the independent-conformer ansatz, which enabled response properties predicted for the optimized structure of each isomer to be combined through Boltzmann-weighted population fractions derived from corresponding relative internal-energy or free-energy values, the latter of which stemmed from composite CBS-APNO and G4 analyses. Although reasonable accord between theory and experiment was realized for the isolated (vapor-phase) species, the solution-phase results were less satisfactory and tended to degrade progressively as the solvent polarity increased. These trends were attributed to solvent-mediated changes in structural parameters and energy metrics for the transition states that separate and putatively isolate the equilibrium conformations supported by the ground electronic potential-energy surface, with the resulting displacement of barrier locations and/or decrease of barrier heights compromising the underlying premise of the independent-conformer ansatz.
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Affiliation(s)
- Paul M Lemler
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Intel Corporation, Hillsboro, Oregon, USA
| | - Clayton L Craft
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- United States Air Force Research Laboratory, Rome, New York, USA
| | - Corina H Pollok
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Organische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Thomas P Regan
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Patrick H Vaccaro
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
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3
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Stachowski TR, Fischer M. FLEXR: automated multi-conformer model building using electron-density map sampling. Acta Crystallogr D Struct Biol 2023; 79:354-367. [PMID: 37071395 PMCID: PMC10167668 DOI: 10.1107/s2059798323002498] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/13/2023] [Indexed: 04/19/2023] Open
Abstract
Protein conformational dynamics that may inform biology often lie dormant in high-resolution electron-density maps. While an estimated ∼18% of side chains in high-resolution models contain alternative conformations, these are underrepresented in current PDB models due to difficulties in manually detecting, building and inspecting alternative conformers. To overcome this challenge, we developed an automated multi-conformer modeling program, FLEXR. Using Ringer-based electron-density sampling, FLEXR builds explicit multi-conformer models for refinement. Thereby, it bridges the gap of detecting hidden alternate states in electron-density maps and including them in structural models for refinement, inspection and deposition. Using a series of high-quality crystal structures (0.8-1.85 Å resolution), we show that the multi-conformer models produced by FLEXR uncover new insights that are missing in models built either manually or using current tools. Specifically, FLEXR models revealed hidden side chains and backbone conformations in ligand-binding sites that may redefine protein-ligand binding mechanisms. Ultimately, the tool facilitates crystallographers with opportunities to include explicit multi-conformer states in their high-resolution crystallographic models. One key advantage is that such models may better reflect interesting higher energy features in electron-density maps that are rarely consulted by the community at large, which can then be productively used for ligand discovery downstream. FLEXR is open source and publicly available on GitHub at https://github.com/TheFischerLab/FLEXR.
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Affiliation(s)
- Timothy R Stachowski
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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4
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Stachowski TR, Nithianantham S, Vanarotti M, Lopez K, Fischer M. Pan-Hsp90 ligand binding reveals isoform-specific differences in plasticity and water networks. Protein Sci 2023; 32:e4629. [PMID: 36938943 PMCID: PMC10108437 DOI: 10.1002/pro.4629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/21/2023]
Abstract
Isoforms of heat shock protein 90 (HSP90) fold oncoproteins that facilitate all 10 hallmarks of cancer. However, its promise as a therapeutic target remains unfulfilled as there is still no FDA-approved drug targeting HSP90 in disease. Among the reasons hindering progress are side effects caused by pan-HSP90 inhibition. Selective targeting of the 4 isoforms is challenging due to high sequence and structural similarity. Surprisingly, while decades of drug discovery efforts have produced almost 400 human HSP90 structures, no single ligand has been structurally characterized across all 4 human isoforms to date, which could reveal structural differences to achieve selectivity. To better understand the HSP90 landscape relevant for ligand binding and design we take a 3-pronged approach. First, we solved the first complete set of structures of a single ligand bound to all 4 human isoforms. This enabled a systematic comparison of how side-chains and water networks respond to ligand binding across isoforms. Second, we expanded our analysis to publicly available, incomplete isoform-ligand series with distinct ligand chemistry. This highlighted general trends of protein and water mobility that differ among isoforms and impact ligand binding. Third, we further probed the Hsp90α conformational landscape for accommodating a congeneric series containing the purine scaffold common to HSP90 inhibitors. This revealed how minor ligand modifications flip ligand poses and perturb water and protein conformations. Taken together, this work illustrates how a systematic approach can shed new light on an "old" target and reveal hidden isoform-specific accommodations of congeneric ligands that may be exploited in ligand discovery and design.
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Affiliation(s)
- Timothy R Stachowski
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stanley Nithianantham
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Murugendra Vanarotti
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Karlo Lopez
- School of Natural Sciences, Mathematics, and Engineering, California State University, Bakersfield, CA, 93311, USA
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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5
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Su Z, Wu Y. Dissecting the general mechanisms of protein cage self-assembly by coarse-grained simulations. Protein Sci 2023; 32:e4552. [PMID: 36541820 PMCID: PMC9854185 DOI: 10.1002/pro.4552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/15/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
The development of artificial protein cages has recently gained massive attention due to their promising application prospect as novel delivery vehicles for therapeutics. These nanoparticles are formed through a process called self-assembly, in which individual subunits spontaneously arrange into highly ordered patterns via non-covalent but specific interactions. Therefore, the first step toward the design of novel engineered protein cages is to understand the general mechanisms of their self-assembling dynamics. Here we have developed a new computational method to tackle this problem. Our method is based on a coarse-grained model and a diffusion-reaction simulation algorithm. Using a tetrahedral cage as test model, we showed that self-assembly of protein cage requires of a seeding process in which specific configurations of kinetic intermediate states are identified. We further found that there is a critical concentration to trigger self-assembly of protein cages. This critical concentration allows that cages can only be successfully assembled under a persistently high concentration. Additionally, phase diagram of self-assembly has been constructed by systematically testing the model across a wide range of binding parameters. Finally, our simulations demonstrated the importance of protein's structural flexibility in regulating the dynamics of cage assembly. In summary, this study throws lights on the general principles underlying self-assembly of large cage-like protein complexes and thus provides insights to design new nanomaterials.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational BiologyAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Yinghao Wu
- Department of Systems and Computational BiologyAlbert Einstein College of MedicineBronxNew YorkUSA
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6
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Segawa K, Igarashi K, Murayama K. The Cys-Pro motifs in the intrinsically disordered regions of the transcription factor BACH1 mediate distinct and overlapping functions upon heme binding. FEBS Lett 2022; 596:1576-1585. [PMID: 35302665 DOI: 10.1002/1873-3468.14338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 11/09/2022]
Abstract
The function of the transcription factor BACH1 is regulated by heme binding to multiple Cys-Pro (CP) motifs within its intrinsically disordered regions. Here, biochemical analyses were conducted to reveal the individual functional roles of the CP motifs. Our findings revealed that four CP motifs in BACH1 individually contributed to the regulation of BACH1 activity by accepting heme in five- and six-coordination manner. The model structure around the bZip domain indicated that the CP motifs are in the N- and C-terminal heme-binding regions, which are approximately 9 nm apart, suggesting that spatial location is important for the individual function of the CP motifs. The presence of multiple CP motifs with distinct roles may ensure the multifaceted, strict regulation of BACH1 by heme.
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Affiliation(s)
- Kei Segawa
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Seiryo 2-1, Aoba, Sendai, 980-8575, Japan.,Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Asahigaoka 4-3-2, Hino, 191-8512, Tokyo, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo 2-1, Aoba, Sendai, 980-8575, Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Seiryo 2-1, Aoba, Sendai, 980-8575, Japan
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Samantray S, Olubiyi OO, Strodel B. The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans. Int J Mol Sci 2021; 22:11529. [PMID: 34768961 DOI: 10.3390/ijms222111529] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
The increasing recognition of the biochemical importance of glycosaminoglycans (GAGs) has in recent times made them the center of attention of recent research investigations. It became evident that subtle conformational factors play an important role in determining the relationship between the chemical composition of GAGs and their activity. Therefore, a thorough understanding of their structural flexibility is needed, which is addressed in this work by means of all-atom molecular dynamics (MD) simulations. Four major GAGs with different substitution patterns, namely hyaluronic acid as unsulphated GAG, heparan-6-sulphate, chondroitin-4-sulphate, and chondroitin-6-sulphate, were investigated to elucidate the influence of sulphation on the dynamical features of GAGs. Moreover, the effects of increasing NaCl and KCl concentrations were studied as well. Different structural parameters were determined from the MD simulations, in combination with a presentation of the free energy landscape of the GAG conformations, which allowed us to unravel the conformational fingerprints unique to each GAG. The largest effects on the GAG structures were found for sulphation at position 6, as well as binding of the metal ions in the absence of chloride ions to the carboxylate and sulphate groups, which both increase the GAG conformational flexibility.
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8
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Anandan A, Dunstan NW, Ryan TM, Mertens HDT, Lim KYL, Evans GL, Kahler CM, Vrielink A. Conformational flexibility of EptA driven by an interdomain helix provides insights for enzyme-substrate recognition. IUCrJ 2021; 8:732-746. [PMID: 34584735 PMCID: PMC8420757 DOI: 10.1107/s2052252521005613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Many pathogenic gram-negative bacteria have developed mechanisms to increase resistance to cationic antimicrobial peptides by modifying the lipid A moiety. One modification is the addition of phospho-ethano-lamine to lipid A by the enzyme phospho-ethano-lamine transferase (EptA). Previously we reported the structure of EptA from Neisseria, revealing a two-domain architecture consisting of a periplasmic facing soluble domain and a transmembrane domain, linked together by a bridging helix. Here, the conformational flexibility of EptA in different detergent environments is probed by solution scattering and intrinsic fluorescence-quenching studies. The solution scattering studies reveal the enzyme in a more compact state with the two domains positioned close together in an n-do-decyl-β-d-maltoside micelle environment and an open extended structure in an n-do-decyl-phospho-choline micelle environment. Intrinsic fluorescence quenching studies localize the domain movements to the bridging helix. These results provide important insights into substrate binding and the molecular mechanism of endotoxin modification by EptA.
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Affiliation(s)
- Anandhi Anandan
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Nicholas W. Dunstan
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Unit, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Katherine Y. L. Lim
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Genevieve L. Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Charlene M. Kahler
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
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Burevschi E, Sanz ME. Seven Conformations of the Macrocycle Cyclododecanone Unveiled by Microwave Spectroscopy. Molecules 2021; 26:molecules26175162. [PMID: 34500596 PMCID: PMC8433831 DOI: 10.3390/molecules26175162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/15/2021] [Accepted: 08/21/2021] [Indexed: 11/16/2022] Open
Abstract
The physicochemical properties and reactivity of macrocycles are critically shaped by their conformations. In this work, we have identified seven conformations of the macrocyclic ketone cyclododecanone using chirped-pulse Fourier transform microwave spectroscopy in combination with ab initio and density functional theory calculations. Cyclododecanone is strongly biased towards adopting a square configuration of the heavy atom framework featuring three C-C bonds per side. The substitution and effective structures of this conformation have been determined through the observation of its 13C isotopologues. The minimisation of transannular interactions and, to a lesser extent, HCCH eclipsed configurations drive conformational preferences. Our results contribute to a better understanding of the intrinsic forces mediating structural choices in macrocycles.
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Hibi T, Itoh T. Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity. J Biochem 2021; 169:15-23. [PMID: 33002140 DOI: 10.1093/jb/mvaa114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 09/24/2020] [Indexed: 11/13/2022] Open
Abstract
Urate oxidases (UOs) catalyze the cofactor-independent oxidation of uric acid, and an extensive water network in the active site has been suggested to play an essential role in the catalysis. For our present analysis of the structure and function of the water network, the crystal qualities of Bacillus sp. TB-90 urate oxidase were improved by controlled dehydration using the humid air and glue-coating method. After the dehydration, the P21212 crystals were transformed into the I222 space group, leading to an extension of the maximum resolution to 1.42 Å. The dehydration of the crystals revealed a significant change in the five-water-molecules' binding mode in the vicinity of the catalytic diad, indicating that these molecules are quasi-stable. The pH profile analysis of log(kcat) gave two pKa values: pKa1 at 6.07 ± 0.07 and pKa2 at 7.98 ± 0.13. The site-directed mutagenesis of K13, T73 and N276 involved in the formation of the active-site water network revealed that the activities of these mutant variants were significantly reduced. These structural and kinetic data suggest that the five quasi-stable water molecules play an essential role in the catalysis of the cofactor-independent urate oxidation by reducing the energy penalty for the substrate-binding or an on-off switching for the proton-relay rectification.
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Affiliation(s)
- Takao Hibi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Yoshida, Fukui 910-1195, Japan
| | - Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Yoshida, Fukui 910-1195, Japan
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11
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Pourjafar-Dehkordi D, Zacharias M. Influence of a Ser111-phosphorylation on Rab1b GTPase conformational dynamics studied by advanced sampling simulations. Proteins 2021; 89:1324-1332. [PMID: 34056776 DOI: 10.1002/prot.26153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/18/2021] [Accepted: 03/10/2021] [Indexed: 11/06/2022]
Abstract
Rab GTPases constitute the largest branch of the Ras protein superfamily that regulate intra-cellular membrane trafficking. Their signaling activity is mediated by the transition between an active GTP-bound state and an inactive GDP-bound state. In the inactive state the switch I and II segments adopt largely disordered flexible conformations, whereas in the active state these regions are in well-defined conformations. The switch I and II states are central for recognition of Rab GTPases by interacting partners. Phosphorylation of the Rab1b-GTPase at residue Ser111 (pS111) results in modulation of the signaling activity due to alterations of the protein interaction interface and also due to modulation of the conformational flexibility. We have studied the flexibility of native and pS111-Rab1b in complex with GTP or GDP using extensive Molecular Dynamics (MD) simulations and an advanced sampling method called DIhedral Angle-biasing potential Replica-Exchange Molecular dynamics (DIA-REMD). The DIA-REMD method promotes backbone and side chain dihedral transitions along a series of replica simulations in selected protein segments and through exchanges also improves sampling in an unbiased reference simulation. Application to the Rab1b system results in significantly enhanced sampling of different switch I/II conformational states in the GDP-bound Rab1b state. The pS111 modification is found to reduce the conformational flexibility even in the presence of GDP, which may influence signaling activities. The stabilizing effect can be attributed to the formation of additional surface salt bridges between Arg-residues and pS111 not present in the native structure. The DIA-REMD method could be a valuable approach for studying also other signaling proteins that contain flexible segments.
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Affiliation(s)
| | - Martin Zacharias
- Center for Functional Protein Assemblies, Technical University of Munich, Garching, Germany
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12
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Eche S, Kumar A, Sonela N, Gordon ML. Acquired HIV-1 Protease Conformational Flexibility Associated with Lopinavir Failure May Shape the Outcome of Darunavir Therapy after Antiretroviral Therapy Switch. Biomolecules 2021; 11:489. [PMID: 33805099 PMCID: PMC8064090 DOI: 10.3390/biom11040489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding the underlying molecular interaction during a therapy switch from lopinavir (LPV) to darunavir (DRV) is essential to achieve long-term virological suppression. We investigated the kinetic and structural characteristics of multidrug-resistant South African HIV-1 subtype C protease (HIV-1 PR) during therapy switch from LPV to DRV using enzyme activity and inhibition assay, fluorescence spectroscopy, and molecular dynamic simulation. The HIV-1 protease variants were from clinical isolates with a combination of drug resistance mutations; MUT-1 (M46I, I54V, V82A, and L10F), MUT-2 (M46I, I54V, L76V, V82A, L10F, and L33F), and MUT-3 (M46I, I54V, L76V, V82A, L90M, and F53L). Enzyme kinetics analysis shows an association between increased relative resistance to LPV and DRV with the progressive decrease in the mutant HIV-1 PR variants' catalytic efficiency. A direct relationship between high-level resistance to LPV and intermediate resistance to DRV with intrinsic changes in the three-dimensional structure of the mutant HIV-1 PR as a function of the multidrug-resistance mutation was observed. In silico analysis attributed these structural adjustments to the multidrug-resistance mutations affecting the LPV and DRV binding landscape. Though DRV showed superiority to LPV, as a lower concentration was needed to inhibit the HIV-1 PR variants, the inherent structural changes resulting from mutations selected during LPV therapy may dynamically shape the DRV treatment outcome after the therapy switch.
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Affiliation(s)
- Simeon Eche
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Ajit Kumar
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal (Westville Campus), Durban 4000, South Africa;
| | - Nelson Sonela
- School of Medicine, Physical and Natural Sciences, University of Rome Tor Vegata, 1-00133 Rome, Italy;
- Chantal Biya International Reference Center for Research on the Management and Prevention of HIV/AIDS (CIRCB), Yaoundé P.O. Box 3077, Cameroon
| | - Michelle L. Gordon
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa;
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13
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Takeda S, Koike R, Fujiwara I, Narita A, Miyata M, Ota M, Maéda Y. Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail. J Mol Biol 2021; 433:166891. [PMID: 33639213 DOI: 10.1016/j.jmb.2021.166891] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 12/19/2022]
Abstract
Twinfilin is a conserved actin regulator that interacts with actin capping protein (CP) via C terminus residues (TWtail) that exhibits sequence similarity with the CP interaction (CPI) motif of CARMIL. Here we report the crystal structure of TWtail in complex with CP. Our structure showed that although TWtail and CARMIL CPI bind CP to an overlapping surface via their middle regions, they exhibit different CP-binding modes at both termini. Consequently, TWtail and CARMIL CPI restrict the CP in distinct conformations of open and closed forms, respectively. Interestingly, V-1, which targets CP away from the TWtail binding site, also favors the open-form CP. Consistently, TWtail forms a stable ternary complex with CP and V-1, a striking contrast to CARMIL CPI, which rapidly dissociates V-1 from CP. Our results demonstrate that TWtail is a unique CP-binding motif that regulates CP in a manner distinct from CARMIL CPI.
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Affiliation(s)
- Shuichi Takeda
- Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Ryotaro Koike
- Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Ikuko Fujiwara
- Graduate School of Science, Osaka City University, Osaka, Osaka 558-8585, Japan
| | - Akihiro Narita
- Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, Osaka 558-8585, Japan; The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Osaka 558-8585, Japan
| | - Motonori Ota
- Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yuichiro Maéda
- Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
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14
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Li Q, Li M, Li C, Li X, Lu C, Tu X, Zhang Z, Zhang X. Halophilic to mesophilic adaptation of ubiquitin-like proteins. FEBS Lett 2020; 595:521-531. [PMID: 33301612 DOI: 10.1002/1873-3468.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/15/2020] [Accepted: 12/06/2020] [Indexed: 11/11/2022]
Abstract
Elucidating how proteins adapt from halophilic to mesophilic environments will enable a better understanding of protein evolution and folding. In this study, by directed evolution and site-directed mutagenesis of the halophilic ubiquitin-like protein (ULP) Samp2, we find that substitution of the prebiotic amino acid Asp31 by Gly is uniquely effective in the mesophilic adaptation of ULP. Sequence analysis shows that substitution of Asp/Glu in halophilic ULPs by Gly in mesophilic ULPs has higher occurrence than other substitutions, supporting the unique role of the substitution in the mesophilic adaptation of ULP. Molecular dynamic simulations indicate that the mesophilic adaptation might result from the effect of the substitution on the conformational flexibility of ULP.
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Affiliation(s)
- Quan Li
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Mengqing Li
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Cong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xinxin Li
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Chenghui Lu
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Xiaoming Tu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhiyong Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xuecheng Zhang
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
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15
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D’Onofrio M, Munari F, Assfalg M. Alpha-Synuclein-Nanoparticle Interactions: Understanding, Controlling and Exploiting Conformational Plasticity. Molecules 2020; 25:E5625. [PMID: 33260436 PMCID: PMC7731430 DOI: 10.3390/molecules25235625] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
Alpha-synuclein (αS) is an extensively studied protein due to its involvement in a group of neurodegenerative disorders, including Parkinson's disease, and its documented ability to undergo aberrant self-aggregation resulting in the formation of amyloid-like fibrils. In dilute solution, the protein is intrinsically disordered but can adopt multiple alternative conformations under given conditions, such as upon adsorption to nanoscale surfaces. The study of αS-nanoparticle interactions allows us to better understand the behavior of the protein and provides the basis for developing systems capable of mitigating the formation of toxic aggregates as well as for designing hybrid nanomaterials with novel functionalities for applications in various research areas. In this review, we summarize current progress on αS-nanoparticle interactions with an emphasis on the conformational plasticity of the biomolecule.
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Affiliation(s)
| | | | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (M.D.); (F.M.)
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16
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Abstract
Antibiotic resistance in clinically important bacteria can be mediated by target protection mechanisms, whereby a protein binds to the drug target and protects it from the inhibitory effects of the antibiotic. The most prevalent source of clinical resistance to the antibiotic fusidic acid (FA) is expression of the FusB family of proteins that bind to the drug target (Elongation factor G [EF-G]) and promote dissociation of EF-G from FA-stalled ribosome complexes. FusB binding causes changes in both the structure and conformational flexibility of EF-G, but which of these changes drives FA resistance was not understood. We present here detailed characterization of changes in the conformational flexibility of EF-G in response to FusB binding and show that these changes are responsible for conferring FA resistance. Binding of FusB to EF-G causes a significant change in the dynamics of domain III of EF-GC3 that leads to an increase in a minor, more disordered state of EF-G domain III. This is sufficient to overcome the steric block of transmission of conformational changes within EF-G by which FA prevents release of EF-G from the ribosome. This study has identified an antibiotic resistance mechanism mediated by allosteric effects on the dynamics of the drug target.
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Affiliation(s)
- Jennifer H Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT Leeds, United Kingdom;
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Arnout P Kalverda
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Antonio N Calabrese
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
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17
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Melero R, Sorzano COS, Foster B, Vilas JL, Martínez M, Marabini R, Ramírez-Aportela E, Sanchez-Garcia R, Herreros D, del Caño L, Losana P, Fonseca-Reyna YC, Conesa P, Wrapp D, Chacon P, McLellan JS, Tagare HD, Carazo JM. Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. IUCrJ 2020; 7:S2052252520012725. [PMID: 33063791 PMCID: PMC7553147 DOI: 10.1107/s2052252520012725] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/18/2020] [Indexed: 05/09/2023]
Abstract
Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results.
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Affiliation(s)
- Roberto Melero
- Centro Nacional de Biotecnologia–CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | | | - Brent Foster
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT 06520, USA
| | - José-Luis Vilas
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT 06520, USA
| | - Marta Martínez
- Centro Nacional de Biotecnologia–CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Roberto Marabini
- Centro Nacional de Biotecnologia–CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain
- Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente 11, 28049 Cantoblanco, Madrid, Spain
| | | | - Ruben Sanchez-Garcia
- Centro Nacional de Biotecnologia–CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - David Herreros
- Centro Nacional de Biotecnologia–CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Laura del Caño
- Centro Nacional de Biotecnologia–CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Patricia Losana
- Centro Nacional de Biotecnologia–CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | | | - Pablo Conesa
- Centro Nacional de Biotecnologia–CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Pablo Chacon
- Department of Biological Physical Chemistry, Instituto Rocasolano–CSIC, Calle de Serrano 119, 28006 Madrid, Spain
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hemant D. Tagare
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT 06520, USA
| | - Jose-Maria Carazo
- Centro Nacional de Biotecnologia–CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain
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18
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Metrick CM, Koenigsberg AL, Heldwein EE. Conserved Outer Tegument Component UL11 from Herpes Simplex Virus 1 Is an Intrinsically Disordered, RNA-Binding Protein. mBio 2020; 11:e00810-20. [PMID: 32371601 DOI: 10.1128/mBio.00810-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Herpesvirus virions contain a unique tegument layer sandwiched between the capsid and lipid envelope and composed of multiple copies of about two dozen viral proteins. However, little is known about the structure of the tegument or how it is assembled. Here, we show that a conserved tegument protein UL11 from herpes simplex virus 1, a prototypical alphaherpesvirus, is an intrinsically disordered protein that undergoes liquid-liquid phase separation in vitro. Through sequence analysis, we find intrinsically disordered regions of different lengths in all HSV-1 tegument proteins. We hypothesize that intrinsic disorder is a common characteristic of tegument proteins and propose a new model of tegument as a biomolecular condensate. A distinguishing morphological feature of all herpesviruses is the multiprotein tegument layer located between the nucleocapsid and lipid envelope of the virion. Tegument proteins play multiple roles in viral replication, including viral assembly, but we do not yet understand their individual functions or how the tegument is assembled and organized. UL11, the smallest tegument protein, is important for several distinct processes in replication, including efficient virion morphogenesis and cell-cell spread. However, the mechanistic understanding of its role in these and other processes is limited in part by the scant knowledge of its biochemical and structural properties. Here, we report that UL11 from herpes simplex virus 1 (HSV-1) is an intrinsically disordered, conformationally dynamic protein that undergoes liquid-liquid phase separation (LLPS) in vitro. Intrinsic disorder may underlie the ability of UL11 to exert multiple functions and bind multiple partners. Sequence analysis suggests that not only all UL11 homologs but also all HSV-1 tegument proteins contain intrinsically disordered regions of different lengths. The presence of intrinsic disorder, and potentially, the ability to form LLPS, may thus be a common feature of the tegument proteins. We hypothesize that tegument assembly may involve the formation of a biomolecular condensate, driven by the heterogeneous mixture of intrinsically disordered tegument proteins.
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19
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Asquith CRM, Laitinen T, Wells CI, Tizzard GJ, Zuercher WJ. New Insights into 4-Anilinoquinazolines as Inhibitors of Cardiac Troponin I-Interacting Kinase (TNNi3K). Molecules 2020; 25:E1697. [PMID: 32272798 DOI: 10.3390/molecules25071697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 11/16/2022] Open
Abstract
We report the synthesis of several related 4-anilinoquinazolines as inhibitors of cardiac troponin I-interacting kinase (TNNi3K). These close structural analogs of 3-((6,7-dimethoxyquinazolin-4-yl)amino)-4-(dimethylamino)-N-methylbenzenesulfonamide (GSK114) provide new understanding of structure-activity relationships between the 4-anilinoquinazoline scaffold and TNNi3K inhibition. Through a small focused library of inhibitors, we observed that the N-methylbenzenesulfonamide was driving the potency in addition to the more traditional quinazoline hinge-binding motif. We also identified a compound devoid of TNNi3K kinase activity due to the addition of a methyl group in the hinge binding region. This compound could serve as a negative control in the study of TNNi3K biology. Small molecule crystal structures of several quinazolines have been solved, supporting observations made about overall conformation and TNNi3K inhibition.
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20
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Loll B, Rückert C, Uchanska-Ziegler B, Ziegler A. Conformational Plasticity of HLA-B27 Molecules Correlates Inversely With Efficiency of Negative T Cell Selection. Front Immunol 2020; 11:179. [PMID: 32117305 PMCID: PMC7027375 DOI: 10.3389/fimmu.2020.00179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/23/2020] [Indexed: 01/07/2023] Open
Abstract
The development of autoimmune disorders is incompletely understood. Inefficient thymic T cell selection against self-peptides presented by major histocompatibility antigens (HLA in humans) may contribute to the emergence of auto-reactive effector cells, and molecular mimicry between foreign and self-peptides could promote T cell cross-reactivity. A pair of class I subtypes, HLA-B2705 and HLA-B2709, have previously been intensely studied, because they are distinguished from each other only by a single amino acid exchange at the floor of the peptide-binding groove, yet are differentially associated with the autoinflammatory disorder ankylosing spondylitis. Using X-ray crystallography in combination with ensemble refinement, we find that the non-disease-associated subtype HLA-B2709, when presenting the self-peptide pGR (RRRWHRWRL), exhibits elevated conformational dynamics, and the complex can also be recognized by T cells. Both features are not observed in case of the sequence-related self-peptide pVIPR (RRKWRRWHL) in complex with this subtype, and T cell cross-reactivity between pGR, pVIPR, and the viral peptide pLMP2 (RRRWRRLTV) is only rarely observed. The disease-associated subtype HLA-B2705, however, exhibits extensive conformational flexibility in case of the three complexes, all of which are also recognized by frequently occurring cross-reactive T cells. A comparison of the structural and dynamic properties of the six HLA-B27 complexes, together with their individual ability to interact with T cells, permits us to correlate the flexibility of HLA-B27 complexes with effector cell reactivity. The results suggest the existence of an inverse relationship between conformational plasticity of peptide-HLA-B27 complexes and the efficiency of negative selection of self-reactive cells within the thymus.
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Affiliation(s)
- Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Berlin, Germany,*Correspondence: Bernhard Loll
| | - Christine Rückert
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Berlin, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Berlin, Germany,Ziegler Biosolutions, Waldshut-Tiengen, Germany
| | - Andreas Ziegler
- Ziegler Biosolutions, Waldshut-Tiengen, Germany,Andreas Ziegler
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21
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Arcangeli C, Lico C, Baschieri S, Mancuso M. Characterization Of Blood-Brain Barrier Crossing And Tumor Homing Peptides By Molecular Dynamics Simulations. Int J Nanomedicine 2020; 14:10123-10136. [PMID: 31920308 PMCID: PMC6941700 DOI: 10.2147/ijn.s225793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/17/2019] [Indexed: 01/25/2023] Open
Abstract
Introduction The new frontier of tumor diagnosis and treatment relies on the development of delivery strategies capable of allowing the specific targeting of the diagnostic agents/chemotherapeutics, avoiding side effects. In the case of brain tumors, achieving this goal is made more difficult by the presence of the blood–brain barrier (BBB). Peptides have been revealed as excellent candidates for both BBB crossing and specific cancer homing. Nanoparticles (NPs), functionalized with BBB crossing and tumor homing (TH) peptides, are emerging as smart theranostic systems. However, there is still poor knowledge concerning the molecular structure and dynamical properties of these peptides, essential requirements for a suitable functionalization of the delivery systems themselves. Methods In this work, by means of molecular dynamics (MD) simulations, we have extensively characterized the structural and dynamical behavior of several peptides, known to be endowed of BBB crossing and TH properties. Results The simulations point out that, on the basis of their conformational dynamics, the peptides can be classified in two main groups: 1) peptides assuming a specific structural conformation, a feature that could be important for interacting with the molecular target but that may limit their use as functionalizing molecules and 2) highly flexible peptides whose interaction with the target may be independent of a particular structural conformation and that may represent good candidates for the functionalization of theranostic NP-based platforms. Discussion Such findings may be useful for the de novo designing of NP-based delivery systems. ![]()
Point your SmartPhone at the code above. If you have a QR code reader the video abstract will appear. Or use: https://youtu.be/wp8npbWb754
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Affiliation(s)
- Caterina Arcangeli
- Laboratory of Health and Environment, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Rome, Italy
| | - Chiara Lico
- Laboratory of Biotechnology, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Rome, Italy
| | - Selene Baschieri
- Laboratory of Biotechnology, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Rome, Italy
| | - Mariateresa Mancuso
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Rome, Italy
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22
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Ruggiu F, Yang S, Simmons RL, Casarez A, Jones AK, Li C, Jansen JM, Moser HE, Dean CR, Reck F, Lindvall M. Size Matters and How You Measure It: A Gram-Negative Antibacterial Example Exceeding Typical Molecular Weight Limits. ACS Infect Dis 2019; 5:1688-1692. [PMID: 31478369 DOI: 10.1021/acsinfecdis.9b00256] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Monobactam antibiotic 1 is active against Gram-negative bacteria even though it has a higher molecular weight (MW) than the limit of 600 Da typically applied in designing such compounds. On the basis of 2D NMR data, the compound is able to adopt a compact conformation. The dimensions, projection area, and dipole moment derived from this conformation are compatible with porin permeation, as are locations of polar groups upon superimposition to the crystal structure of ampicillin bound to E. coli OmpF porin. Minimum inhibitory concentration (MIC) shifts in a porin knock-out strain are also consistent with 1 predominately permeating through porins. In conclusion, we describe a carefully characterized case of a molecule outside default design parameters where MW does not adequately represent the 3D shape more directly related to permeability. Leveraging 3D design criteria would open up additional chemical space currently underutilized due to limitations perceived in 2D.
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Affiliation(s)
- Fiorella Ruggiu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Shengtian Yang
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Robert L. Simmons
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Anthony Casarez
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Adriana K. Jones
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cindy Li
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Johanna M. Jansen
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Heinz E. Moser
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Charles R. Dean
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mika Lindvall
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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23
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Kurkcuoglu Z, Bonvin AMJJ. Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems. Proteins 2019; 88:292-306. [PMID: 31441121 PMCID: PMC6973081 DOI: 10.1002/prot.25802] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 02/01/2023]
Abstract
Incorporating the dynamic nature of biomolecules in the modeling of their complexes is a challenge, especially when the extent and direction of the conformational changes taking place upon binding is unknown. Estimating whether the binding of a biomolecule to its partner(s) occurs in a conformational state accessible to its unbound form (“conformational selection”) and/or the binding process induces conformational changes (“induced‐fit”) is another challenge. We propose here a method combining conformational sampling using ClustENM—an elastic network‐based modeling procedure—with docking using HADDOCK, in a framework that incorporates conformational selection and induced‐fit effects upon binding. The extent of the applied deformation is estimated from its energetical costs, inspired from mechanical tensile testing on materials. We applied our pre‐ and post‐docking sampling of conformational changes to the flexible multidomain protein‐protein docking benchmark and a subset of the protein‐DNA docking benchmark. Our ClustENM‐HADDOCK approach produced acceptable to medium quality models in 7/11 and 5/6 cases for the protein‐protein and protein‐DNA complexes, respectively. The conformational selection (sampling prior to docking) has the highest impact on the quality of the docked models for the protein‐protein complexes. The induced‐fit stage of the pipeline (post‐sampling), however, improved the quality of the final models for the protein‐DNA complexes. Compared to previously described strategies to handle conformational changes, ClustENM‐HADDOCK performs better than two‐body docking in protein‐protein cases but worse than a flexible multidomain docking approach. However, it does show a better or similar performance compared to previous protein‐DNA docking approaches, which makes it a suitable alternative.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, the Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, the Netherlands
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24
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Van Agthoven JF, Shams H, Cochran FV, Alonso JL, Kintzing JR, Garakani K, Adair BD, Xiong JP, Mofrad MRK, Cochran JR, Arnaout MA. Structural Basis of the Differential Binding of Engineered Knottins to Integrins αVβ3 and α5β1. Structure 2019; 27:1443-1451.e6. [PMID: 31353240 DOI: 10.1016/j.str.2019.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/29/2019] [Accepted: 06/28/2019] [Indexed: 01/06/2023]
Abstract
Targeting both integrins αVβ3 and α5β1 simultaneously appears to be more effective in cancer therapy than targeting each one alone. The structural requirements for bispecific binding of ligand to integrins have not been fully elucidated. RGD-containing knottin 2.5F binds selectively to αVβ3 and α5β1, whereas knottin 2.5D is αVβ3 specific. To elucidate the structural basis of this selectivity, we determined the structures of 2.5F and 2.5D as apo proteins and in complex with αVβ3, and compared their interactions with integrins using molecular dynamics simulations. These studies show that 2.5D engages αVβ3 by an induced fit, but conformational selection of a flexible RGD loop accounts for high-affinity selective binding of 2.5F to both integrins. The contrasting binding of the highly flexible low-affinity linear RGD peptides to multiple integrins suggests that a "Goldilocks zone" of conformational flexibility of the RGD loop in 2.5F underlies its selective binding promiscuity to integrins.
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Affiliation(s)
- Johannes F Van Agthoven
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Hengameh Shams
- Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Frank V Cochran
- Departments of Bioengineering and Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - José L Alonso
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - James R Kintzing
- Departments of Bioengineering and Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Kiavash Garakani
- Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Brian D Adair
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Jian-Ping Xiong
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Mohammad R K Mofrad
- Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Jennifer R Cochran
- Departments of Bioengineering and Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - M Amin Arnaout
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA.
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25
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Landin EJB, Lovera S, de Fabritiis G, Kelm S, Mercier J, McMillan D, Sessions RB, Taylor RJ, Sands ZA, Joedicke L, Crump MP. The Aminotriazole Antagonist Cmpd-1 Stabilises a Distinct Inactive State of the Adenosine 2A Receptor. Angew Chem Int Ed Engl 2019; 58:9399-9403. [PMID: 31095849 DOI: 10.1002/anie.201902852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/03/2019] [Indexed: 11/06/2022]
Abstract
The widely expressed G-protein coupled receptors (GPCRs) are versatile signal transducer proteins that are attractive drug targets but structurally challenging to study. GPCRs undergo a number of conformational rearrangements when transitioning from the inactive to the active state but have so far been believed to adopt a fairly conserved inactive conformation. Using 19 F NMR spectroscopy and advanced molecular dynamics simulations we describe a novel inactive state of the adenosine 2A receptor which is stabilised by the aminotriazole antagonist Cmpd-1. We demonstrate that the ligand stabilises a unique conformation of helix V and present data on the putative binding mode of the compound involving contacts to the transmembrane bundle as well as the extracellular loop 2.
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Affiliation(s)
- Erik J B Landin
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS, Bristol, UK
| | - Silvia Lovera
- UCB Biopharma, 1 Chemin du Foriest, 1420, Braine l'Alleud, Belgium
| | - Gianni de Fabritiis
- Acellera, Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,ICREA, Passeig Lluis Companys 23, Barcelona, 08010, Spain
| | | | - Joël Mercier
- UCB Biopharma, 1 Chemin du Foriest, 1420, Braine l'Alleud, Belgium
| | | | - Richard B Sessions
- Biomedical Sciences, University of Bristol, University Walk, BS8 1TD, Bristol, UK
| | | | - Zara A Sands
- UCB Biopharma, 1 Chemin du Foriest, 1420, Braine l'Alleud, Belgium
| | | | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS, Bristol, UK
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26
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Kaur A, Gourav, Kumar S, Jaiswal N, Vashisht A, Kumar D, Gahlay GK, Mithu VS. NMR characterization of conformational fluctuations and noncovalent interactions of SUMO protein from Drosophila melanogaster (dSmt3). Proteins 2019; 87:658-667. [PMID: 30958586 DOI: 10.1002/prot.25690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/15/2019] [Accepted: 04/04/2019] [Indexed: 11/09/2022]
Abstract
Structural heterogeneity in the native-state ensemble of dSmt3, the only small ubiquitin-like modifier (SUMO) in Drosophila melanogaster, was investigated and compared with its human homologue SUMO1. Temperature dependence of amide proton's chemical shift was studied to identify amino acids possessing alternative structural conformations in the native state. Effect of small concentration of denaturant (1M urea) on this population was also monitored to assess the ruggedness of near-native energy landscape. Owing to presence of many such amino acids, especially in the β2 -loop-α region, the native state of dSmt3 seems more flexible in comparison to SUMO1. Information about backbone dynamics in ns-ps timescale was quantified from the measurement of 15 N-relaxation experiments. Furthermore, the noncovalent interaction of dSmt3 and SUMO1 with Daxx12 (Daxx729 DPEEIIVLSDSD740 ), a [V/I]-X-[V/I]-[V/I]-based SUMO interaction motif, was characterized using Bio-layer Interferometery and NMR spectroscopy. Daxx12 fits itself in the groove formed by β2 -loop-α structural region in both dSmt3 and SUMO1, but the binding is stronger with the former. Flexibility of β2 -loop-α region in dSmt3 is suspected to assist its interaction with Daxx12. Our results highlight the role of native-state flexibility in assisting noncovalent interactions of SUMO proteins especially in organisms where a single SUMO isoform has to tackle multiple substrates single handedly.
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Affiliation(s)
- Anupreet Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Gourav
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Sandeep Kumar
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Nancy Jaiswal
- Centre of Biomedical Research, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, Uttar Pradesh, India
| | - Ashutosh Vashisht
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Dinesh Kumar
- Centre of Biomedical Research, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, Uttar Pradesh, India
| | - Gagandeep K Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Venus S Mithu
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab, India
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27
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TranNgoc K, Pham N, Lee C, Jang SH. Cloning, Expression, and Characterization of a Psychrophilic Glucose 6-Phosphate Dehydrogenase from Sphingomonas sp. PAMC 26621. Int J Mol Sci 2019; 20:E1362. [PMID: 30889888 PMCID: PMC6471386 DOI: 10.3390/ijms20061362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 11/16/2022] Open
Abstract
Glucose 6-phosphate dehydrogenase (G6PD) (EC 1.1.1.363) is a crucial regulatory enzyme in the oxidative pentose phosphate pathway that provides reductive potential in the form of NADPH, as well as carbon skeletons for the synthesis of macromolecules. In this study, we report the cloning, expression, and characterization of G6PD (SpG6PD1) from a lichen-associated psychrophilic bacterium Sphingomonas sp. PAMC 26621. SpG6PD1 was expressed in Escherichia coli as a soluble protein, having optimum activity at pH 7.5⁻8.5 and 30 °C for NADP⁺ and 20 °C for NAD⁺. SpG6PD1 utilized both NADP⁺ and NAD⁺, with the preferential utilization of NADP⁺. A high Km value for glucose 6-phosphate and low activation enthalpy (ΔH‡) compared with the values of mesophilic counterparts indicate the psychrophilic nature of SpG6PD1. Despite the secondary structure of SpG6PD1 being maintained between 4⁻40 °C, its activity and tertiary structure were better preserved between 4⁻20 °C. The results of this study indicate that the SpG6PD1 that has a flexible structure is most suited to a psychrophilic bacterium that is adapted to a permanently cold habitat.
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Affiliation(s)
- Kiet TranNgoc
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, Korea.
| | - Nhung Pham
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, Korea.
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, Korea.
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, Korea.
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28
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Kothari S, Vippagunta RR. Predicting the Physical Stability of Amorphous Tenapanor Hydrochloride Using Local Molecular Structure Analysis, Relaxation Time Constants, and Molecular Modeling. Mol Pharm 2019; 16:943-951. [PMID: 30699296 DOI: 10.1021/acs.molpharmaceut.8b00853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational flexibility of organic molecules introduces more structural options for crystallization to occur but has potential complications, such as, reduced crystallization tendency and conformational polymorphism. Although a variety of energetically similar conformers could be anticipated, it is extremely difficult to predict the crystal conformation for conformationally flexible molecules. The present study investigates differences in thermodynamic parameters for the free base, c-FB, and an amorphous dihydrochloride salt, a-Di-HCl, of a conformationally flexible drug substance, tenapanor (RDX5791). A variety of complementary techniques such as, thermal analysis, powder X-ray diffraction (PXRD), and molecular modeling were used to assess the thermodynamic properties and the propensity of crystallization for a-FB and a-Di-HCl, tenapanor. Molecular modeling and total scattering measurements suggested that the a-Di-HCl salt exists in an open elongated state with local 1D stacking, which extends only to the first nearest neighbor, while the a-FB shows local stacking extending to the third nearest neighbor. The overall relaxation behavior, which typically is an indicator for physical stability, as measured by modulated temperature differential scanning calorimetry and PXRD suggested a nontypical dual relaxation process for the dihydrochloride salt form. The first relaxation was fast and occurred on warming from the quench conditions without any thermal annealing, while the second relaxation step followed a more traditional glass relaxation model, exhibiting an infinite relaxation time. Similar analysis for the a-FB suggested a comparatively shorter relaxation time (about 19 days) that results in its rapid crystallization. This observation is further validated with the extensive amount of physical stability data collected for the a-Di-HCl salt form of tenapanor under accelerated and stress stability conditions, as well as long-term storage for more than 3 years that show no change in its amorphous state.
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Affiliation(s)
- Sanjeev Kothari
- Pharmaceutical Chemistry and Formulations , Ardelyx , 34175 Ardenwood Blvd , Fremont , California 94555 , United States
| | - Radha R Vippagunta
- Pharmaceutical Chemistry and Formulations , Ardelyx , 34175 Ardenwood Blvd , Fremont , California 94555 , United States
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29
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Hetzke T, Vogel M, Gophane DB, Weigand JE, Suess B, Sigurdsson ST, Prisner TF. Influence of Mg 2+ on the conformational flexibility of a tetracycline aptamer. RNA 2019; 25:158-167. [PMID: 30337459 PMCID: PMC6298572 DOI: 10.1261/rna.068684.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/16/2018] [Indexed: 05/06/2023]
Abstract
The tetracycline-binding RNA aptamer (TC-aptamer) is a synthetic riboswitch that binds the antibiotic tetracycline (TC) with exceptionally high affinity. Although a crystal structure exists of the TC-bound state, little is known about the conformational dynamics and changes upon ligand binding. In this study, pulsed electron paramagnetic resonance techniques for measuring distances (PELDOR) in combination with rigid nitroxide spin labels (Çm spin label) were used to investigate the conformational flexibility of the TC-aptamer in the presence and absence of TC at different Mg2+ concentrations. TC was found to be the essential factor for stabilizing the tertiary structure at intermediate Mg2+ concentrations. At higher Mg2+ concentrations, Mg2+ alone is sufficient to stabilize the tertiary structure. In addition, the orientation of the two spin-labeled RNA helices with respect to each other was analyzed with orientation-selective PELDOR and compared to the crystal structure. These results demonstrate for the first time the unique value of the Çm spin label in combination with PELDOR to provide information about conformational flexibilities and orientations of secondary structure elements of biologically relevant RNAs.
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Affiliation(s)
- Thilo Hetzke
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Dnyaneshwar B Gophane
- Department of Chemistry, Science Institute, University of Iceland, 101 Reykjavik, Iceland
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 101 Reykjavik, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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30
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Ben-David M, Huang H, Sun MGF, Corbi-Verge C, Petsalaki E, Liu K, Gfeller D, Garg P, Tempel W, Sochirca I, Shifman JM, Davidson A, Min J, Kim PM, Sidhu SS. Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores. J Mol Biol 2019; 431:336-50. [PMID: 30471255 DOI: 10.1016/j.jmb.2018.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/04/2018] [Accepted: 11/14/2018] [Indexed: 11/21/2022]
Abstract
Hydrophobic cores are often viewed as tightly packed and rigid, but they do show some plasticity and could thus be attractive targets for protein design. Here we explored the role of different functional pressures on the core packing and ligand recognition of the SH3 domain from human Fyn tyrosine kinase. We randomized the hydrophobic core and used phage display to select variants that bound to each of three distinct ligands. The three evolved groups showed remarkable differences in core composition, illustrating the effect of different selective pressures on the core. Changes in the core did not significantly alter protein stability, but were linked closely to changes in binding affinity and specificity. Structural analysis and molecular dynamics simulations revealed the structural basis for altered specificity. The evolved domains had significantly reduced core volumes, which in turn induced increased backbone flexibility. These motions were propagated from the core to the binding surface and induced significant conformational changes. These results show that alternative core packing and consequent allosteric modulation of binding interfaces could be used to engineer proteins with novel functions.
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31
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Koenigsberg AL, Heldwein EE. The dynamic nature of the conserved tegument protein UL37 of herpesviruses. J Biol Chem 2018; 293:15827-15839. [PMID: 30166339 PMCID: PMC6187633 DOI: 10.1074/jbc.ra118.004481] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/26/2018] [Indexed: 12/26/2022] Open
Abstract
In all herpesviruses, the space between the capsid shell and the lipid envelope is occupied by the unique tegument layer composed of proteins that, in addition to structural roles, play many other roles in the viral replication. UL37 is a highly conserved tegument protein that has activities ranging from virion morphogenesis to directional capsid trafficking to manipulation of the host innate immune response and binds multiple partners. The N-terminal half of UL37 (UL37N) has a compact bean-shaped α-helical structure that contains a surface region essential for neuroinvasion. However, no biochemical or structural information is currently available for the C-terminal half of UL37 (UL37C) that mediates most of its interactions with multiple binding partners. Here, we show that the C-terminal half of UL37 from pseudorabies virus UL37C is a conformationally flexible monomer composed of an elongated folded core and an unstructured C-terminal tail. This elongated structure, along with that of its binding partner UL36, explains the nature of filamentous tegument structures bridging the capsid and the envelope. We propose that the dynamic nature of UL37 underlies its ability to perform diverse roles during viral replication.
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Affiliation(s)
- Andrea L Koenigsberg
- From the Department of Molecular Biology and Microbiology and Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts 02111
| | - Ekaterina E Heldwein
- From the Department of Molecular Biology and Microbiology and Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts 02111
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32
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Abstract
We present the accurate experimental structure of the steroid hormone β-estradiol obtained with high-resolution rotational spectroscopy under the solvent free, isolated, and cold conditions of a molecular jet. This is the first time that the rotational signature of a steroid hormone is reported. β-Estradiol is a primary female sex hormone and features a rigid steroidal ring system. Three conformers could be identified in the cold environment of a supersonic molecular jet, which only differ in the orientation of the two hydroxy groups attached to the steroidal backbone. The conformers are almost isoenergetic and have very similar rotational constants but still could be clearly resolved and assigned. The high sensitivity of the technique allowed us to record and identify all singly substituted 13 C isotopologues in natural abundance for the dominant conformer. The additional spectroscopic constants led to an accurate determination of its experimental molecular structure. Along with a previous comparison of β-estradiol structures in the solid state and the liquid phase, this study completes the investigations in all three main phases by providing the interaction free gas-phase structure.
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Affiliation(s)
- Sabrina Zinn
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, D-, 22607, Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-, 22761, Hamburg, Germany.,Christian-Albrechts-Universität zu Kiel, Institut für Physikalische Chemie, Max-Eyth-Str. 1, D-, 24118, Kiel, Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, D-, 22607, Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-, 22761, Hamburg, Germany.,Christian-Albrechts-Universität zu Kiel, Institut für Physikalische Chemie, Max-Eyth-Str. 1, D-, 24118, Kiel, Germany
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33
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Ströh LJ, Nagarathinam K, Krey T. Conformational Flexibility in the CD81-Binding Site of the Hepatitis C Virus Glycoprotein E2. Front Immunol 2018; 9:1396. [PMID: 29967619 PMCID: PMC6015841 DOI: 10.3389/fimmu.2018.01396] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/05/2018] [Indexed: 01/15/2023] Open
Abstract
Numerous antibodies have been described that potently neutralize a broad range of hepatitis C virus (HCV) isolates and the majority of these antibodies target the binding site for the cellular receptor CD81 within the major HCV glycoprotein E2. A detailed understanding of the major antigenic determinants is crucial for the design of an efficient vaccine that elicits high levels of such antibodies. In the past 6 years, structural studies have shed additional light on the way the host’s humoral immune system recognizes neutralization epitopes within the HCV glycoproteins. One of the most striking findings from these studies is that the same segments of the E2 polypeptide chain induce antibodies targeting distinct antigen conformations. This was demonstrated by several crystal structures of identical polypeptide segments bound to different antibodies, highlighting an unanticipated intrinsic structural flexibility that allows binding of antibodies with distinct paratope shapes following an “induced-fit” mechanism. This unprecedented flexibility extends to the entire binding site for the cellular receptor CD81, underlining the importance of dynamic analyses to understand (1) the interplay between HCV and the humoral immune system and (2) the relevance of this structural flexibility for virus entry. This review summarizes the current understanding how neutralizing antibodies target structurally flexible epitopes. We focus on differences and common features of the reported structures and discuss the implications of the observed structural flexibility for the viral replication cycle, the full scope of the interplay between the virus and the host immune system and—most importantly—informed vaccine design.
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Affiliation(s)
- Luisa J Ströh
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | | | - Thomas Krey
- Institute of Virology, Hannover Medical School, Hannover, Germany
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34
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Remesh SG, Armstrong AA, Mahan AD, Luo J, Hammel M. Conformational Plasticity of the Immunoglobulin Fc Domain in Solution. Structure 2018; 26:1007-1014.e2. [PMID: 29731233 DOI: 10.1016/j.str.2018.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/07/2018] [Accepted: 03/27/2018] [Indexed: 12/21/2022]
Abstract
Fragment crystallizable (Fc) region of immunoglobulin G (IgG) antibody binds to specific Fc receptors (FcγRs) to control antibody effector functions. Currently, engineered specific Fc-FcγR interactions are validated with a static conformation derived from the crystal structure. However, computational evidence suggests that the conformational variability of Fcs plays an important role in receptor recognition. Here we elucidate Fc flexibility of IgG1, IgG2, and IgG1 Fc with mutations (M255Y/S257T/T259E) in solution by small-angle X-ray scattering (SAXS). Measured SAXS profiles and experimental parameters show variations in flexibility between Fc isotypes. We develop and apply a modeling tool for an accurate conformational sampling of Fcs followed by SAXS fitting. Revealed conformational variability of the CH2 domain as low as 10 Å in displacement, illustrates the power of the atomistic modeling combined with SAXS. This inexpensive SAXS-based approach offers to improve the engineering of antibodies for tailoring Fc receptor interactions through altering and measuring Fc flexibility.
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Affiliation(s)
- Soumya G Remesh
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Andrew D Mahan
- Janssen BioTherapeutics, Janssen R&D, LLC, Spring House, PA 19477, USA
| | - Jinquan Luo
- Janssen BioTherapeutics, Janssen R&D, LLC, Spring House, PA 19477, USA.
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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35
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Kubota T, Tani O, Yamaguchi T, Namatame I, Sakashita H, Furukawa K, Yamasaki K. Crystal structures of FMN-bound and FMN-free forms of dihydroorotate dehydrogenase from Trypanosoma brucei. FEBS Open Bio 2018; 8:680-691. [PMID: 29632820 PMCID: PMC5881531 DOI: 10.1002/2211-5463.12403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 01/29/2023] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a flavin‐binding enzyme essential for pyrimidine biosynthesis, which converts dihydroorotate to orotate. Three‐dimensional structures of cytosolic DHODH of parasitic protozoa are of interest in drug discovery for neglected tropical diseases, especially because these enzymes possess significantly different structural and functional properties from the membrane‐associated human enzyme. The existing crystal structures of the flavin mononucleotide (FMN)‐bound DHODHs reveal a number of interactions stabilizing FMN. However, to understand the binding mechanism correctly, it is necessary to compare the structures of the FMN‐bound and FMN‐free forms, because the protein moiety of the former is not necessarily the same as the latter. Here, we prepared the FMN‐free DHODH of Trypanosoma brucei using an Escherichia coli overexpression system. Although this apoform lacks enzymatic activity, simple incubation with FMN activated the enzyme. It was stable enough to be crystallized, enabling us to determine its structure by X‐ray crystallography at 1.6 Å resolution. We also determined the FMN‐bound form at 1.8 Å resolution. Although the two structures have essentially the same scaffold, we observed flipping of a peptide‐bond plane in the vicinity of the FMN‐binding site, accompanied by an alternative hydrogen‐bonding pattern. Comparisons of B factors of the protein main chain revealed that binding of FMN decreased flexibility of most of the residues at the FMN‐binding site, but increased flexibility of a lid‐like loop structure over the active center. This increase was ascribed to a conformational change in an FMN‐contacting residue, Asn195, which induced a rearrangement of a hydrogen‐bond network of the residues comprising the lid.
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Affiliation(s)
- Tomomi Kubota
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Osamu Tani
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | | | | | - Hitoshi Sakashita
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Koji Furukawa
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Kazuhiko Yamasaki
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
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36
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Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ. Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification. Front Immunol 2018; 9:413. [PMID: 29545810 PMCID: PMC5840193 DOI: 10.3389/fimmu.2018.00413] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/14/2018] [Indexed: 12/18/2022] Open
Abstract
Antibodies can rapidly evolve in specific response to antigens. Affinity maturation drives this evolution through cycles of mutation and selection leading to enhanced antibody specificity and affinity. Elucidating the biophysical mechanisms that underlie affinity maturation is fundamental to understanding B-cell immunity. An emergent hypothesis is that affinity maturation reduces the conformational flexibility of the antibody's antigen-binding paratope to minimize entropic losses incurred upon binding. In recent years, computational and experimental approaches have tested this hypothesis on a small number of antibodies, often observing a decrease in the flexibility of the complementarity determining region (CDR) loops that typically comprise the paratope and in particular the CDR-H3 loop, which contributes a plurality of antigen contacts. However, there were a few exceptions and previous studies were limited to a small handful of cases. Here, we determined the structural flexibility of the CDR-H3 loop for thousands of recent homology models of the human peripheral blood cell antibody repertoire using rigidity theory. We found no clear delineation in the flexibility of naïve and antigen-experienced antibodies. To account for possible sources of error, we additionally analyzed hundreds of human and mouse antibodies in the Protein Data Bank through both rigidity theory and B-factor analysis. By both metrics, we observed only a slight decrease in the CDR-H3 loop flexibility when comparing affinity matured antibodies to naïve antibodies, and the decrease was not as drastic as previously reported. Further analysis, incorporating molecular dynamics simulations, revealed a spectrum of changes in flexibility. Our results suggest that rigidification may be just one of many biophysical mechanisms for increasing affinity.
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Affiliation(s)
- Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Adnan Sljoka
- Department of Informatics, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Nobuyuki Tsuchimura
- Department of Informatics, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan
| | - Naoki Katoh
- Department of Informatics, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jeffrey J Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States
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37
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Benning FMC, Sakiyama Y, Mazur A, Bukhari HST, Lim RYH, Maier T. High-Speed Atomic Force Microscopy Visualization of the Dynamics of the Multienzyme Fatty Acid Synthase. ACS Nano 2017; 11:10852-10859. [PMID: 29023094 DOI: 10.1021/acsnano.7b04216] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Multienzymes, such as the protein metazoan fatty acid synthase (FAS), are giant and highly dynamic molecular machines for critical biosynthetic processes. The molecular architecture of FAS was elucidated by static high-resolution crystallographic analysis, while electron microscopy revealed large-scale conformational variability in FAS with some correlation to functional states in catalysis. However, little is known about time scales of conformational dynamics, the trajectory of motions in individual FAS molecules, and the extent of coupling between catalysis and structural changes. Here, we present an experimental single-molecule approach to film immobilized or selectively tethered FAS in solution at different viewing angles and high spatiotemporal resolution using high-speed atomic force microscopy. Mobility of individual regions of the multienzyme is recognized in video sequences, and correlation of shape features implies a convergence of temporal resolution and velocity of FAS dynamics. Conformational variety can be identified and grouped by reference-free 2D class averaging, enabling the tracking of conformational transitions in movies. The approach presented here is suited for comprehensive studies of the dynamics of FAS and other multienzymes in aqueous solution at the single-molecule level.
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Affiliation(s)
- Friederike M C Benning
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Yusuke Sakiyama
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Adam Mazur
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Habib S T Bukhari
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Timm Maier
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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Matoba K, Mihara E, Tamura-Kawakami K, Miyazaki N, Maeda S, Hirai H, Thompson S, Iwasaki K, Takagi J. Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1. Cell Rep 2017; 18:32-40. [PMID: 28052259 DOI: 10.1016/j.celrep.2016.12.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/14/2016] [Accepted: 12/06/2016] [Indexed: 11/21/2022] Open
Abstract
LDL-receptor-related protein 6 (LRP6) is a single-pass membrane glycoprotein with a large modular ectodomain and forms a higher order signaling platform upon binding Wnt ligands on the cell surface. Although multiple crystal structures are available for fragments of the LRP6 ectodomain, we lack a consensus view on the overall molecular architecture of the full-length LRP6 and its dynamic aspects. Here, we used negative-stain electron microscopy to probe conformational states of the entire ectodomain of LRP6 in solution and found that the four-module ectodomain undergoes a large bending motion hinged at the junction between the second and the third modules. Importantly, the extent of inter-domain motion is modulated by evolutionarily conserved N-glycan chains proximal to the joint. We also found that the LRP6 ectodomain becomes highly compact upon complexation with the Wnt antagonist Dkk1, suggesting a potential role for the ectodomain conformational change in the regulation of receptor oligomerization and signaling.
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Sathiyamoorthy K, Vijayalakshmi J, Tirupati B, Fan L, Saper MA. Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution. J Biol Chem 2017; 292:17626-17642. [PMID: 28887305 DOI: 10.1074/jbc.m117.804997] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 08/13/2017] [Indexed: 11/06/2022] Open
Abstract
In many Gram-negative bacteria, the peptidoglycan synthase PBP1A requires the outer membrane lipoprotein LpoA for constructing a functional peptidoglycan required for bacterial viability. Previously, we have shown that the C-terminal domain of Haemophilus influenzae LpoA (HiLpoA) has a highly conserved, putative substrate-binding cleft between two α/β lobes. Here, we report a 2.0 Å resolution crystal structure of the HiLpoA N-terminal domain. Two subdomains contain tetratricopeptide-like motifs that form a concave groove, but their relative orientation differs by ∼45° from that observed in an NMR structure of the Escherichia coli LpoA N domain. We also determined three 2.0-2.8 Å resolution crystal structures containing four independent full-length HiLpoA molecules. In contrast to an elongated model previously suggested for E. coli LpoA, each HiLpoA formed a U-shaped structure with a different C-domain orientation. This resulted from both N-domain twisting and rotation of the C domain (up to 30°) at the end of the relatively immobile interdomain linker. Moreover, a previously predicted hinge between the lobes of the LpoA C domain exhibited variations of up to 12°. Small-angle X-ray scattering data revealed excellent agreement with a model calculated by normal mode analysis from one of the full-length HiLpoA molecules but even better agreement with an ensemble of this molecule and two of the partially extended normal mode analysis-predicted models. The different LpoA structures helped explain how an outer membrane-anchored LpoA can either withdraw from or extend toward the inner membrane-bound PBP1A through peptidoglycan gaps and hence regulate the synthesis of peptidoglycan necessary for bacterial viability.
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Affiliation(s)
| | | | | | - Lixin Fan
- the Small-Angle X-ray Scattering Core Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702
| | - Mark A Saper
- From the Program in Biophysics and .,the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-5606 and
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Li H, Sharma N, General IJ, Schreiber G, Bahar I. Dynamic Modulation of Binding Affinity as a Mechanism for Regulating Interferon Signaling. J Mol Biol 2017; 429:2571-2589. [PMID: 28648616 PMCID: PMC5545807 DOI: 10.1016/j.jmb.2017.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/15/2017] [Accepted: 06/16/2017] [Indexed: 12/22/2022]
Abstract
How structural dynamics affects cytokine signaling is under debate. Here, we investigated the dynamics of the type I interferon (IFN) receptor, IFNAR1, and its effect on signaling upon binding IFN and IFNAR2 using a combination of structure-based mechanistic studies, in situ binding, and gene induction assays. Our study reveals that IFNAR1 flexibility modulates ligand-binding affinity, which, in turn, regulates biological signaling. We identified the hinge sites and key interactions implicated in IFNAR1 inter-subdomain (SD1-SD4) movements. We showed that the predicted cooperative movements are essential to accommodate intermolecular interactions. Engineered disulfide bridges, computationally predicted to interfere with IFNAR1 dynamics, were experimentally confirmed. Notably, introducing disulfide bonds between subdomains SD2 and SD3 modulated IFN binding and activity in accordance with the relative attenuation of cooperative movements with varying distance from the hinge center, whereas locking the SD3-SD4 interface flexibility in favor of an extended conformer increased activity.
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Affiliation(s)
- Hongchun Li
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Nanaocha Sharma
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ignacio J General
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; School of Science and Technology, and CONICET, Universidad Nacional de San Martin, San Martin, Buenos Aires 1650, Argentina
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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Parker ML, Ramaswamy R, van Gordon K, Powell CJ, Bosch J, Boulanger MJ. The structure of Plasmodium falciparum 3D7_0606800 reveals a bi-lobed architecture that supports re-annotation as a Venus Flytrap protein. Protein Sci 2017; 26:1878-1885. [PMID: 28681555 DOI: 10.1002/pro.3218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/20/2017] [Accepted: 06/29/2017] [Indexed: 12/11/2022]
Abstract
Plasmodium falciparum, the causative agent of malaria, employs a diverse array of surface displayed proteins to promote dissemination and establish infection in the human host. Of these, Pf3D7_0606800 is highly immunogenic and has been designated a potential top 10 candidate for inclusion in a multicomponent malarial vaccine. The role of Pf3D7_0606800 in parasite biology, however, is unknown and its characterization has been complicated by a lack of sequence identity with proteins of known structure or function. Towards elucidating Pf3D7_0606800 function, we determined its structure to a resolution of 2.35 Å using selenium single wavelength anomalous dispersion. A bi-lobed architecture displays the core structural hallmarks of Venus Flytrap (VFT) proteins prompting us to re-annotate Pf3D7_0606800 as PfVFT1. Structural analysis further revealed an extended inter-lobe groove that, when interrogated by molecular docking, appears well suited to bind peptide-based ligands. Collectively, our structural characterization of the highly antigenic P. falciparum surface protein PfVFT1 provides intriguing functional insight and establishes a structural template that could prove valuable for malaria vaccine engineering studies.
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Affiliation(s)
- Michelle L Parker
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
| | - Raghavendran Ramaswamy
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
| | - Kyle van Gordon
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
| | - Cameron J Powell
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
| | - Jürgen Bosch
- Pediatric Pulmonology Division, Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio.,InterRayBio, LLC, Baltimore, Maryland
| | - Martin J Boulanger
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
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Vasiliauskaite I, Owsianka A, England P, Khan AG, Cole S, Bankwitz D, Foung SKH, Pietschmann T, Marcotrigiano J, Rey FA, Patel AH, Krey T. Conformational Flexibility in the Immunoglobulin-Like Domain of the Hepatitis C Virus Glycoprotein E2. mBio 2017; 8:e00382-17. [PMID: 28512091 PMCID: PMC5433095 DOI: 10.1128/mbio.00382-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/24/2017] [Indexed: 12/16/2022] Open
Abstract
The hepatitis C virus (HCV) glycoprotein E2 is the major target of neutralizing antibodies and is therefore highly relevant for vaccine design. Its structure features a central immunoglobulin (Ig)-like β-sandwich that contributes to the binding site for the cellular receptor CD81. We show that a synthetic peptide corresponding to a β-strand of this Ig-like domain forms an α-helix in complex with the anti-E2 antibody DAO5, demonstrating an inside-out flip of hydrophobic residues and a secondary structure change in the composite CD81 binding site. A detailed interaction analysis of DAO5 and cross-competing neutralizing antibodies with soluble E2 revealed that the Ig-like domain is trapped by different antibodies in at least two distinct conformations. DAO5 specifically captures retrovirus particles bearing HCV glycoproteins (HCVpp) and infectious cell culture-derived HCV particles (HCVcc). Infection of cells by DAO5-captured HCVpp can be blocked by a cross-competing neutralizing antibody, indicating that a single virus particle simultaneously displays E2 molecules in more than one conformation on its surface. Such conformational plasticity of the HCV E2 receptor binding site has important implications for immunogen design.IMPORTANCE Recent advances in the treatment of hepatitis C virus (HCV) infection with direct-acting antiviral drugs have enabled the control of this major human pathogen. However, due to their high costs and limited accessibility in combination with the lack of awareness of the mostly asymptomatic infection, there is an unchanged urgent need for an effective vaccine. The viral glycoprotein E2 contains regions that are crucial for virus entry into the host cell, and antibodies that bind to these regions can neutralize infection. One of the major targets of neutralizing antibodies is the central immunoglobulin (Ig)-like domain within E2. We show here that this Ig-like domain is conformationally flexible at the surface of infectious HCV particles and pseudoparticles. Our study provides novel insights into the interactions of HCV E2 with the humoral immune system that should aid future vaccine development.
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Affiliation(s)
- Ieva Vasiliauskaite
- Unité de Virologie Structurale, Department Virologie, Institut Pasteur, Paris, France
- CNRS UMR 3569, Paris, France
| | - Ania Owsianka
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Patrick England
- Plate-Forme de Biophysique Moléculaire, Institut Pasteur, Paris, France
- CNRS UMR 3528, Paris, France
| | - Abdul Ghafoor Khan
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Sarah Cole
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Dorothea Bankwitz
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Hannover, Germany
| | - Steven K H Foung
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Pietschmann
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Hannover, Germany
- German Center for Infection Research, Hannover-Braunschweig Site, Germany
| | - Joseph Marcotrigiano
- Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Felix A Rey
- Unité de Virologie Structurale, Department Virologie, Institut Pasteur, Paris, France
- CNRS UMR 3569, Paris, France
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Thomas Krey
- Unité de Virologie Structurale, Department Virologie, Institut Pasteur, Paris, France
- CNRS UMR 3569, Paris, France
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research, Hannover-Braunschweig Site, Germany
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43
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Tarry MJ, Haque AS, Bui KH, Schmeing TM. X-Ray Crystallography and Electron Microscopy of Cross- and Multi-Module Nonribosomal Peptide Synthetase Proteins Reveal a Flexible Architecture. Structure 2017; 25:783-793.e4. [PMID: 28434915 DOI: 10.1016/j.str.2017.03.014] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/02/2017] [Accepted: 03/23/2017] [Indexed: 10/19/2022]
Abstract
Nonribosomal peptide synthetases (NRPS) are macromolecular machines that produce peptides with diverse activities. Structural information exists for domains, didomains, and even modules, but little is known about higher-order organization. We performed a multi-technique study on constructs from the dimodular NRPS DhbF. We determined a crystal structure of a cross-module construct including the adenylation (A) and peptidyl carrier protein (PCP) domains from module 1 and the condensation domain from module 2, complexed with an adenosine-vinylsulfonamide inhibitor and an MbtH-like protein (MLP). The action of the inhibitor and the role of the MLP were investigated using adenylation reactions and isothermal titration calorimetry. In the structure, the PCP and A domains adopt a novel conformation, and noncovalent, cross-module interactions are limited. We calculated envelopes of dimodular DhbF using negative-stain electron microscopy. The data show large conformational variability between modules. Together, our results suggest that NRPSs lack a uniform, rigid supermodular architecture.
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Affiliation(s)
- Michael J Tarry
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
| | - Asfarul S Haque
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada.
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44
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Toth-Petroczy A, Palmedo P, Ingraham J, Hopf TA, Berger B, Sander C, Marks DS. Structured States of Disordered Proteins from Genomic Sequences. Cell 2016; 167:158-170.e12. [PMID: 27662088 DOI: 10.1016/j.cell.2016.09.010] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 07/08/2016] [Accepted: 09/06/2016] [Indexed: 12/22/2022]
Abstract
Protein flexibility ranges from simple hinge movements to functional disorder. Around half of all human proteins contain apparently disordered regions with little 3D or functional information, and many of these proteins are associated with disease. Building on the evolutionary couplings approach previously successful in predicting 3D states of ordered proteins and RNA, we developed a method to predict the potential for ordered states for all apparently disordered proteins with sufficiently rich evolutionary information. The approach is highly accurate (79%) for residue interactions as tested in more than 60 known disordered regions captured in a bound or specific condition. Assessing the potential for structure of more than 1,000 apparently disordered regions of human proteins reveals a continuum of structural order with at least 50% with clear propensity for three- or two-dimensional states. Co-evolutionary constraints reveal hitherto unseen structures of functional importance in apparently disordered proteins.
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Affiliation(s)
- Bradley C Doak
- a Department of Medicinal Chemistry, MIPS , Monash University , Parkville , Victoria , Australia
| | - Jan Kihlberg
- b Department of Chemistry - BMC , Uppsala University , Uppsala , Sweden
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46
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Kong L, Lee DE, Kadam RU, Liu T, Giang E, Nieusma T, Garces F, Tzarum N, Woods VL Jr, Ward AB, Li S, Wilson IA, Law M. Structural flexibility at a major conserved antibody target on hepatitis C virus E2 antigen. Proc Natl Acad Sci U S A 2016; 113:12768-73. [PMID: 27791120 DOI: 10.1073/pnas.1609780113] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Hepatitis C virus (HCV) is a major cause of liver disease, affecting over 2% of the world's population. The HCV envelope glycoproteins E1 and E2 mediate viral entry, with E2 being the main target of neutralizing antibody responses. Structural investigations of E2 have produced templates for vaccine design, including the conserved CD81 receptor-binding site (CD81bs) that is a key target of broadly neutralizing antibodies (bNAbs). Unfortunately, immunization with recombinant E2 and E1E2 rarely elicits sufficient levels of bNAbs for protection. To understand the challenges for eliciting bNAb responses against the CD81bs, we investigated the E2 CD81bs by electron microscopy (EM), hydrogen-deuterium exchange (HDX), molecular dynamics (MD), and calorimetry. By EM, we observed that HCV1, a bNAb recognizing the N-terminal region of the CD81bs, bound a soluble E2 core construct from multiple angles of approach, suggesting components of the CD81bs are flexible. HDX of multiple E2 constructs consistently indicated the entire CD81bs was flexible relative to the rest of the E2 protein, which was further confirmed by MD simulations. However, E2 has a high melting temperature of 84.8 °C, which is more akin to proteins from thermophilic organisms. Thus, recombinant E2 is a highly stable protein overall, but with an exceptionally flexible CD81bs. Such flexibility may promote induction of nonneutralizing antibodies over bNAbs to E2 CD81bs, underscoring the necessity of rigidifying this antigenic region as a target for rational vaccine design.
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47
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Singh W, Fields GB, Christov CZ, Karabencheva-Christova TG. Effects of Mutations on Structure-Function Relationships of Matrix Metalloproteinase-1. Int J Mol Sci 2016; 17:ijms17101727. [PMID: 27754420 PMCID: PMC5085758 DOI: 10.3390/ijms17101727] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 09/16/2016] [Accepted: 10/03/2016] [Indexed: 02/06/2023] Open
Abstract
Matrix metalloproteinase-1 (MMP-1) is one of the most widely studied enzymes involved in collagen degradation. Mutations of specific residues in the MMP-1 hemopexin-like (HPX) domain have been shown to modulate activity of the MMP-1 catalytic (CAT) domain. In order to reveal the structural and conformational effects of such mutations, a molecular dynamics (MD) study was performed of in silico mutated residues in the X-ray crystallographic structure of MMP-1 complexed with a collagen-model triple-helical peptide (THP). The results indicate an important role of the mutated residues in MMP-1 interactions with the THP and communication between the CAT and the HPX domains. Each mutation has a distinct impact on the correlated motions in the MMP-1•THP. An increased collagenase activity corresponded to the appearance of a unique anti-correlated motion and decreased correlated motions, while decreased collagenase activity corresponded both to increased and decreased anti-correlated motions.
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Affiliation(s)
- Warispreet Singh
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL 33458, USA.
- Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, FL 33458, USA.
| | - Christo Z Christov
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
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Ramaswamy R, Goomeshi Nobary S, Eyford BA, Pearson TW, Boulanger MJ. Structural characterization reveals a novel bilobed architecture for the ectodomains of insect stage expressed Trypanosoma brucei PSSA-2 and Trypanosoma congolense ISA. Protein Sci 2016; 25:2297-2302. [PMID: 27671214 DOI: 10.1002/pro.3053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 11/12/2022]
Abstract
African trypanosomiasis, caused by parasites of the genus Trypanosoma, is a complex of devastating vector-borne diseases of humans and livestock in sub-Saharan Africa. Central to the pathogenesis of African trypanosomes is their transmission by the arthropod vector, Glossina spp. (tsetse fly). Intriguingly, the efficiency of parasite transmission through the vector is reduced following depletion of Trypanosoma brucei Procyclic-Specific Surface Antigen-2 (TbPSSA-2). To investigate the underlying molecular mechanism of TbPSSA-2, we determined the crystal structures of its ectodomain and that of its homolog T. congolense Insect Stage Antigen (TcISA) to resolutions of 1.65 Å and 2.45 Å, respectively using single wavelength anomalous dispersion. Both proteins adopt a novel bilobed architecture with the individual lobes displaying rotational flexibility around the central tether that suggest a potential mechanism for coordinating a binding partner. In support of this hypothesis, electron density consistent with a bound peptide was observed in the inter-lob cleft of a TcISA monomer. These first reported structures of insect stage transmembrane proteins expressed by African trypanosomes provide potentially valuable insight into the interface between parasite and tsetse vector.
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Affiliation(s)
- Raghavendran Ramaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada, V8W 3P6
| | - Sarah Goomeshi Nobary
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada, V8W 3P6
| | - Brett A Eyford
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada, V8W 3P6.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Terry W Pearson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada, V8W 3P6
| | - Martin J Boulanger
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada, V8W 3P6
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Mei Y, Glover K, Su M, Sinha SC. Conformational flexibility of BECN1: Essential to its key role in autophagy and beyond. Protein Sci 2016; 25:1767-85. [PMID: 27414988 DOI: 10.1002/pro.2984] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/09/2016] [Accepted: 07/12/2016] [Indexed: 01/16/2023]
Abstract
BECN1 (Beclin 1), a highly conserved eukaryotic protein, is a key regulator of autophagy, a cellular homeostasis pathway, and also participates in vacuolar protein sorting, endocytic trafficking, and apoptosis. BECN1 is important for embryonic development, the innate immune response, tumor suppression, and protection against neurodegenerative disorders, diabetes, and heart disease. BECN1 mediates autophagy as a core component of the class III phosphatidylinositol 3-kinase complexes. However, the exact mechanism by which it regulates the activity of these complexes, or mediates its other diverse functions is unclear. BECN1 interacts with several diverse protein partners, perhaps serving as a scaffold or interaction hub for autophagy. Based on extensive structural, biophysical and bioinformatics analyses, BECN1 consists of an intrinsically disordered region (IDR), which includes a BH3 homology domain (BH3D); a flexible helical domain (FHD); a coiled-coil domain (CCD); and a β-α-repeated autophagy-specific domain (BARAD). Each of these BECN1 domains mediates multiple diverse interactions that involve concomitant conformational changes. Thus, BECN1 conformational flexibility likely plays a key role in facilitating diverse protein interactions. Further, BECN1 conformation and interactions are also modulated by numerous post-translational modifications. A better structure-based understanding of the interplay between different BECN1 conformational and binding states, and the impact of post-translational modifications will be essential to elucidating the mechanism of its multiple biological roles.
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Affiliation(s)
- Yang Mei
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - Karen Glover
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - Minfei Su
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - Sangita C Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050.
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Pastore A, Temussi P. When "IUPs" were "BAPs": How to study the nonconformation of intrinsically unfolded polyaminoacid chains. Biopolymers 2016; 100:592-600. [PMID: 23896858 DOI: 10.1002/bip.22363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 07/12/2013] [Indexed: 01/21/2023]
Abstract
Ideas often recur. It has been pointed out recently that proteins are not always the well-structured entities we have become accustomed to from crystallographic studies, but may be intrinsically unstructured or contain unstructured regions. This feature, far from making these proteins less interesting, is an essential requirement for their function. Fascinating though it may be, the concept of so-called intrinsically unfolded (or unordered) proteins (IUPs), also often referred to as intrinsically disordered proteins (IDPs), is not new: it directly links back to the 1970s when the attention of many structural biologists was focused on biologically active peptides, which like IUPs lack a specific defined conformation. The recurrent nature of this concept may now be of topical interest since it suggests the transfer, upon suitable adaptation, of old tools to develop new ideas. Here, we review some of the approaches that were developed for the study of peptides and discuss how they could inspire powerful new methodologies for the study of IUPs.
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Affiliation(s)
- Annalisa Pastore
- National Institute for Medical Research, The Ridgeway, London, NW7 1AA, United Kingdom
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