51
|
Synergism and Subadditivity of Verbascoside-Lignans and -Iridoids Binary Mixtures Isolated from Castilleja tenuiflora Benth. on NF-κB/AP-1 Inhibition Activity. Molecules 2021; 26:molecules26030547. [PMID: 33494340 PMCID: PMC7865359 DOI: 10.3390/molecules26030547] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 12/15/2022] Open
Abstract
Pharmacodynamic interactions between plant isolated compounds are important to understand the mode of action of an herbal extract to formulate or create better standardized extracts, phytomedicines, or phytopharmaceuticals. In this work, we propose binary mixtures using a leader compound to found pharmacodynamic interactions in inhibition of the NF-κB/AP-1 pathway using RAW-Blue™ cells. Eight compounds were isolated from Castilleja tenuiflora, four were new furofuran-type lignans for the species magnolin, eudesmin, sesamin, and kobusin. Magnolin (60.97%) was the most effective lignan inhibiting the NF-κB/AP-1 pathway, followed by eudesmin (56.82%), tenuifloroside (52.91%), sesamin (52.63%), and kobusin (45.45%). Verbascoside, a major compound contained in wild C. tenuiflora showed an inhibitory effect on NF-κB/AP-1. This polyphenol was chosen as a leader compound for binary mixtures. Verbacoside-aucubin and verbascoside-kobusin produced synergism, while verbascoside-tenuifloroside had subadditivity in all concentrations. Verbascoside-kobusin is a promising mixture to use on NF-κB/AP-1 related diseases and anti-inflammatory C. tenuiflora-based phytomedicines.
Collapse
|
52
|
McGuire BE, Hettle AG, Vickers C, King DT, Vocadlo DJ, Boraston AB. The structure of a family 110 glycoside hydrolase provides insight into the hydrolysis of α-1,3-galactosidic linkages in λ-carrageenan and blood group antigens. J Biol Chem 2020; 295:18426-18435. [PMID: 33127644 PMCID: PMC7939477 DOI: 10.1074/jbc.ra120.015776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Indexed: 11/30/2022] Open
Abstract
α-Linked galactose is a common carbohydrate motif in nature that is processed by a variety of glycoside hydrolases from different families. Terminal Galα1-3Gal motifs are found as a defining feature of different blood group and tissue antigens, as well as the building block of the marine algal galactan λ-carrageenan. The blood group B antigen and linear α-Gal epitope can be processed by glycoside hydrolases in family GH110, whereas the presence of genes encoding GH110 enzymes in polysaccharide utilization loci from marine bacteria suggests a role in processing λ-carrageenan. However, the structure-function relationships underpinning the α-1,3-galactosidase activity within family GH110 remain unknown. Here we focus on a GH110 enzyme (PdGH110B) from the carrageenolytic marine bacterium Pseudoalteromonas distincta U2A. We showed that the enzyme was active on Galα1-3Gal but not the blood group B antigen. X-ray crystal structures in complex with galactose and unhydrolyzed Galα1-3Gal revealed the parallel β-helix fold of the enzyme and the structural basis of its inverting catalytic mechanism. Moreover, an examination of the active site reveals likely adaptations that allow accommodation of fucose in blood group B active GH110 enzymes or, in the case of PdGH110, accommodation of the sulfate groups found on λ-carrageenan. Overall, this work provides insight into the first member of a predominantly marine clade of GH110 enzymes while also illuminating the structural basis of α-1,3-galactoside processing by the family as a whole.
Collapse
Affiliation(s)
- Bailey E McGuire
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Andrew G Hettle
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Chelsea Vickers
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Dustin T King
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - David J Vocadlo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
| |
Collapse
|
53
|
Design a synthetic glucose receptor using computational intelligence approach. J Mol Graph Model 2020; 103:107797. [PMID: 33246193 DOI: 10.1016/j.jmgm.2020.107797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/01/2020] [Accepted: 11/02/2020] [Indexed: 11/24/2022]
Abstract
The synthetic glucose receptors help to develop glucose sensors and alternative insulin therapies. Designing a glucose recognition molecule in an aqueous system remains a considerable challenge. Therefore, In-silico molecular screening hypothesis is proposed to overcome the difficulties found during the modeling of a molecule. The small organic compounds from compound databases are screened for glucose receptor modeling. Thereafter, the different computational models are designed that mimic natural glucose receptors based on screened compounds. The orientation and binding of glucose molecules within the developed receptor are predicted through the molecular interaction approach. The modeled receptors and receptor-glucose complex structures are used for geometry optimization and molecular dynamics computation. The docking results reveal that ZINC82047919, ZINC238094340, and ZINC238519600 compounds-based models provide better interactions with glucose and its orientation within the receptor cavity. The molecular dynamics simulation results showed that the receptor designed using compound ZINC238094340 is unable to hold the glucose and undergo significant conformation changes during simulation process. The receptor designed from ZINC238094340 and ZINC238519600 compounds is utilized as a reference glucose binding receptor in this study. The proposed computational approach is able to develop a novel glucose receptor and other glucose relative sugar molecules.
Collapse
|
54
|
Agostino M. Comprehensive analysis of carbohydrate-protein recognition in the Protein Data Bank. Carbohydr Res 2020; 498:108180. [PMID: 33096507 DOI: 10.1016/j.carres.2020.108180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 10/23/2022]
Abstract
Carbohydrate-protein interactions underpin wide-ranging aspects of biology. However, such interactions remain relatively unexplored in pharmaceutical and biotechnological applications, in part due to the challenges associated with their structural characterisation, both experimentally and computationally. Knowledge-based approaches have shown great success in the prediction of drug-protein and protein-protein interactions, although have not been comprehensively investigated for carbohydrate-protein interactions. In this work, carbohydrate-protein complexes from the Protein Data Bank were comprehensively obtained and analysed to identify patterns in how carbohydrate-protein interactions are mediated.
Collapse
Affiliation(s)
- Mark Agostino
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Bentley, Australia.
| |
Collapse
|
55
|
Hierarchical design of hyaluronic acid-peptide constructs for glioblastoma targeting: Combining insights from NMR and molecular dynamics simulations. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
56
|
Paul A, Frenkel-Pinter M, Escobar Alvarez D, Milordini G, Gazit E, Zacco E, Segal D. Tryptophan-galactosylamine conjugates inhibit and disaggregate amyloid fibrils of Aβ42 and hIAPP peptides while reducing their toxicity. Commun Biol 2020; 3:484. [PMID: 32879439 PMCID: PMC7468108 DOI: 10.1038/s42003-020-01216-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
Self-assembly of proteins into amyloid fibrils is a hallmark of various diseases, including Alzheimer's disease (AD) and Type-2 diabetes Mellitus (T2DM). Aggregation of specific peptides, like Aβ42 in AD and hIAPP in T2DM, causes cellular dysfunction resulting in the respective pathology. While these amyloidogenic proteins lack sequence homology, they all contain aromatic amino acids in their hydrophobic core that play a major role in their self-assembly. Targeting these aromatic residues by small molecules may be an attractive approach for inhibiting amyloid aggregation. Here, various biochemical and biophysical techniques revealed that a panel of tryptophan-galactosylamine conjugates significantly inhibit fibril formation of Aβ42 and hIAPP, and disassemble their pre-formed fibrils in a dose-dependent manner. They are also not toxic to mammalian cells and can reduce the cytotoxicity induced by Aβ42 and hIAPP aggregates. These tryptophan-galactosylamine conjugates can therefore serve as a scaffold for the development of therapeutics towards AD and T2DM.
Collapse
Affiliation(s)
- Ashim Paul
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Moran Frenkel-Pinter
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Daniela Escobar Alvarez
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Giulia Milordini
- The Maurice Wohl Clinical Neuroscience Institute, King's College London, Brixton, London, SE5 9RT, UK
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Elsa Zacco
- The Maurice Wohl Clinical Neuroscience Institute, King's College London, Brixton, London, SE5 9RT, UK.
- RNA Central Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, 16152, Genova, Italy.
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel.
- Sagol Interdisciplinary School of Neuroscience, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel.
| |
Collapse
|
57
|
Burman SSR, Nance ML, Jeliazkov JR, Labonte JW, Lubin JH, Biswas N, Gray JJ. Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37-45. Proteins 2020; 88:973-985. [PMID: 31742764 PMCID: PMC8589291 DOI: 10.1002/prot.25855] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/04/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023]
Abstract
Critical Assessment of PRediction of Interactions (CAPRI) rounds 37 through 45 introduced larger complexes, new macromolecules, and multistage assemblies. For these rounds, we used and expanded docking methods in Rosetta to model 23 target complexes. We successfully predicted 14 target complexes and recognized and refined near-native models generated by other groups for two further targets. Notably, for targets T110 and T136, we achieved the closest prediction of any CAPRI participant. We created several innovative approaches during these rounds. Since round 39 (target 122), we have used the new RosettaDock 4.0, which has a revamped coarse-grained energy function and the ability to perform conformer selection during docking with hundreds of pregenerated protein backbones. Ten of the complexes had some degree of symmetry in their interactions, so we tested Rosetta SymDock, realized its shortcomings, and developed the next-generation symmetric docking protocol, SymDock2, which includes docking of multiple backbones and induced-fit refinement. Since the last CAPRI assessment, we also developed methods for modeling and designing carbohydrates in Rosetta, and we used them to successfully model oligosaccharide-protein complexes in round 41. Although the results were broadly encouraging, they also highlighted the pressing need to invest in (a) flexible docking algorithms with the ability to model loop and linker motions and in (b) new sampling and scoring methods for oligosaccharide-protein interactions.
Collapse
Affiliation(s)
- Shourya S. Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Morgan L. Nance
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
| | | | - Jason W. Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Joseph H. Lubin
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Naireeta Biswas
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| |
Collapse
|
58
|
Kudo F, Kitayama Y, Miyanaga A, Hirayama A, Eguchi T. Biochemical and Structural Analysis of a Dehydrogenase, KanD2, and an Aminotransferase, KanS2, That Are Responsible for the Construction of the Kanosamine Moiety in Kanamycin Biosynthesis. Biochemistry 2020; 59:1470-1473. [DOI: 10.1021/acs.biochem.0c00204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yukinobu Kitayama
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Akane Hirayama
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| |
Collapse
|
59
|
Girardi NM, Thoden JB, Holden HM. Misannotations of the genes encoding sugar N-formyltransferases. Protein Sci 2020; 29:930-940. [PMID: 31867814 PMCID: PMC7096703 DOI: 10.1002/pro.3807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022]
Abstract
Tens of thousands of bacterial genome sequences are now known due to the development of rapid and inexpensive sequencing technologies. An important key in utilizing these vast amounts of data in a biologically meaningful way is to infer the function of the proteins encoded in the genomes via bioinformatics techniques. Whereas these approaches are absolutely critical to the annotation of gene function, there are still issues of misidentifications, which must be experimentally corrected. For example, many of the bacterial DNA sequences encoding sugar N-formyltransferases have been annotated as l-methionyl-tRNA transferases in the databases. These mistakes may be due in part to the fact that until recently the structures and functions of these enzymes were not well known. Herein we describe the misannotation of two genes, WP_088211966.1 and WP_096244125.1, from Shewanella spp. and Pseudomonas congelans, respectively. Although the proteins encoded by these genes were originally suggested to function as l-methionyl-tRNA transferases, we demonstrate that they actually catalyze the conversion of dTDP-4-amino-4,6-dideoxy-d-glucose to dTDP-4-formamido-4,6-dideoxy-d-glucose utilizing N10 -formyltetrahydrofolate as the carbon source. For this analysis, the genes encoding these enzymes were cloned and the corresponding proteins purified. X-ray structures of the two proteins were determined to high resolution and kinetic analyses were conducted. Both enzymes display classical Michaelis-Menten kinetics and adopt the characteristic three-dimensional structural fold previously observed for other sugar N-formyltransferases. The results presented herein will aid in the future annotation of these fascinating enzymes.
Collapse
|
60
|
Lansky S, Salama R, Shulami S, Lavid N, Sen S, Schapiro I, Shoham Y, Shoham G. Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein. J Mol Biol 2020; 432:2099-2120. [PMID: 32067952 DOI: 10.1016/j.jmb.2020.01.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/19/2020] [Accepted: 01/30/2020] [Indexed: 11/27/2022]
Abstract
ABC importers are membrane proteins responsible for the transport of nutrients into the cells of prokaryotes. Although the structures of ABC importers vary, all contain four conserved domains: two nucleotide-binding domains (NBDs), which bind and hydrolyze ATP, and two transmembrane domains (TMDs), which help translocate the substrate. ABC importers are also dependent on an additional protein component, a high-affinity substrate-binding protein (SBP) that specifically binds the target ligand for delivery to the appropriate ABC transporter. AbnE is a SBP belonging to the ABC importer for arabino-oligosaccharides in the Gram-positive thermophilic bacterium Geobacillus stearothermophilus. Using isothermal titration calorimetry (ITC), purified AbnE was shown to bind medium-sized arabino-oligosaccharides, in the range of arabino-triose (A3) to arabino-octaose (A8), all with Kd values in the nanomolar range. We describe herein the 3D structure of AbnE in its closed conformation in complex with a wide range of arabino-oligosaccharide substrates (A2-A8). These structures provide the basis for the detailed structural analysis of the AbnE-sugar complexes, and together with complementary quantum chemical calculations, site-specific mutagenesis, and isothermal titration calorimetry (ITC) experiments, provide detailed insights into the AbnE-substrate interactions involved. Small-angle X-ray scattering (SAXS) experiments and normal mode analysis (NMA) are used to study the conformational changes of AbnE, and these data, taken together, suggest clues regarding its binding mode to the full ABC importer.
Collapse
Affiliation(s)
- Shifra Lansky
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Smadar Shulami
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Noa Lavid
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel; Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel; Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Gil Shoham
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| |
Collapse
|
61
|
Wang X, Gao J. Atomic partial charge predictions for furanoses by random forest regression with atom type symmetry function. RSC Adv 2020; 10:666-673. [PMID: 35494472 PMCID: PMC9048215 DOI: 10.1039/c9ra09337k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 12/18/2019] [Indexed: 01/04/2023] Open
Abstract
Furanoses that are components for many important biomolecules have complicated conformational spaces due to the flexible ring and exo-cyclic moieties. Machine learning algorithms, which require descriptors as structural inputs, can be used to efficiently compute conformational adaptive (CA) charges to capture the electrostatic potential variations caused by the conformational changes in the molecular mechanics (MM) calculations. In the present study, we introduced atom type symmetry function (ATSF) developed based on atom centered symmetry function (ACSF) for describing conformations for furanoses, in which atoms were categorized by atom types defined by their properties or connectivity in classic molecular mechanics (MM) force field parameters to generate a suitable coordinate size. Random forest regression (RFR) models with ATSF showed improvements for predicting CA charges and dipole moments for furanoses compared to those with ACSF and atom name symmetry functions where atoms were categorized by their unique atom names. The CA charges predicted by RFR models with ATSF showed more comparable reproductions of the carbohydrate-water and carbohydrate-protein interactions computed with RESP charges individually derived from QM calculations than the ensemble-averaged atomic charge sets commonly employed in molecular mechanics force fields, suggesting that the predicted CA charges were capable of including electrostatic variations in their dynamic charge values. Improvements by ATSF showed that categorizing atoms by atom types introduced chemical structural perceptions to descriptors and produced a suitable coordinate size in ATSF to capture key structural features for furanoses. This categorizing scheme also allows ATSF to be readily adopted by other biomolecules thanks to the broad implementations of MM force fields.
Collapse
Affiliation(s)
- Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan China
| |
Collapse
|
62
|
Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain. Sci Rep 2019; 9:18918. [PMID: 31831756 PMCID: PMC6908686 DOI: 10.1038/s41598-019-53815-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/05/2019] [Indexed: 12/17/2022] Open
Abstract
Interactions between proteins and their small molecule ligands are of great importance for the process of drug design. Here we report an unbiased molecular dynamics simulation of systems containing hevein domain (HEV32) with N-acetylglucosamine mono-, di- or trisaccharide. Carbohydrate molecules were placed outside the binding site. Three of six simulations (6 × 2 μs) led to binding of a carbohydrate ligand into the binding mode in agreement with the experimentally determined structure. Unbinding was observed in one simulation (monosaccharide). There were no remarkable intermediates of binding for mono and disaccharide. Trisaccharide binding was initiated by formation of carbohydrate-aromatic CH/π interactions. Our results indicate that binding of ligands followed the model of conformational selection because the conformation of the protein ready for ligand binding was observed before the binding. This study extends the concept of docking by dynamics on carbohydrate-protein interactions.
Collapse
|
63
|
Nadaradjane AA, Quignot C, Traoré S, Andreani J, Guerois R. Docking proteins and peptides under evolutionary constraints in Critical Assessment of PRediction of Interactions rounds 38 to 45. Proteins 2019; 88:986-998. [PMID: 31746034 DOI: 10.1002/prot.25857] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 01/25/2023]
Abstract
Computational structural prediction of macromolecular interactions is a fundamental tool toward the global understanding of cellular processes. The Critical Assessment of PRediction of Interactions (CAPRI) community-wide experiment provides excellent opportunities for blind testing computational docking methods and includes original targets, thus widening the range of docking applications. Our participation in CAPRI rounds 38 to 45 enabled us to expand the way we include evolutionary information in structural predictions beyond our standard free docking InterEvDock pipeline. InterEvDock integrates a coarse-grained potential that accounts for interface coevolution based on joint multiple sequence alignments of two protein partners (co-alignments). However, even though such co-alignments could be built for none of the CAPRI targets in rounds 38 to 45, including host-pathogen and protein-oligosaccharide complexes and a redesigned interface, we identified multiple strategies that can be used to incorporate evolutionary constraints, which helped us to identify the most likely macromolecular binding modes. These strategies include template-based modeling where only local adjustments should be applied when query-template sequence identity is above 30% and larger perturbations are needed below this threshold; covariation-based structure prediction for individual protein partners; and the identification of evolutionarily conserved and structurally recurrent anchoring interface motifs. Overall, we submitted correct predictions among the top 5 models for 12 out of 19 interface challenges, including four High- and five Medium-quality predictions. Our top 20 models included correct predictions for three out of the five targets we missed in the top 5, including two targets for which misleading biological data led us to downgrade correct free docking models.
Collapse
Affiliation(s)
- Aravindan Arun Nadaradjane
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Chloé Quignot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Seydou Traoré
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| |
Collapse
|
64
|
Tommasone S, Allabush F, Tagger YK, Norman J, Köpf M, Tucker JHR, Mendes PM. The challenges of glycan recognition with natural and artificial receptors. Chem Soc Rev 2019; 48:5488-5505. [PMID: 31552920 DOI: 10.1039/c8cs00768c] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycans - simple or complex carbohydrates - play key roles as recognition determinants and modulators of numerous physiological and pathological processes. Thus, many biotechnological, diagnostic and therapeutic opportunities abound for molecular recognition entities that can bind glycans with high selectivity and affinity. This review begins with an overview of the current biologically and synthetically derived glycan-binding scaffolds that include antibodies, lectins, aptamers and boronic acid-based entities. It is followed by a more detailed discussion on various aspects of their generation, structure and recognition properties. It serves as the basis for highlighting recent key developments and technical challenges that must be overcome in order to fully deal with the specific recognition of a highly diverse and complex range of glycan structures.
Collapse
Affiliation(s)
- Stefano Tommasone
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | | | | | | | | | | | | |
Collapse
|
65
|
Adams LM, Andrews RJ, Hu QH, Schmit HL, Hati S, Bhattacharyya S. Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase. Biophys J 2019; 117:1269-1284. [PMID: 31542226 PMCID: PMC6818166 DOI: 10.1016/j.bpj.2019.08.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/27/2019] [Accepted: 08/28/2019] [Indexed: 01/08/2023] Open
Abstract
The effect of molecular crowding on the structure and function of Escherichia coli prolyl-transfer RNA synthetase (Ec ProRS), a member of the aminoacyl-transfer RNA synthetase family, has been investigated using a combined experimental and theoretical method. Ec ProRS is a multidomain enzyme; coupled-domain dynamics are essential for efficient catalysis. To gain insight into the mechanistic detail of the crowding effect, kinetic studies were conducted with varying concentrations and sizes of crowders. In parallel, spectroscopic and quantum chemical studies were employed to probe the "soft interactions" between crowders and protein side chains. Finally, the dynamics of the dimeric protein was examined in the presence of crowders using a long-duration (70 ns) classical molecular dynamic simulations. The results of the simulations revealed a shift in the conformational ensemble, which is consistent with the preferential exclusion of cosolutes. The "soft interactions" model of the crowding effect also explained the alteration in kinetic parameters. In summary, the study found that the effects of molecular crowding on both conformational dynamics and catalytic function are correlated in the multidomain Ec ProRS, an enzyme that is central to protein synthesis in all living cells. This study affirmed that large and small cosolutes have considerable impacts on the structure, dynamics, and function of modular proteins and therefore must be considered for stabilizing protein-based pharmaceuticals and industrial enzymes.
Collapse
Affiliation(s)
- Lauren M Adams
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Ryan J Andrews
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Quin H Hu
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Heidi L Schmit
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin.
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin.
| |
Collapse
|
66
|
Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases. Molecules 2019; 24:molecules24183215. [PMID: 31487855 PMCID: PMC6766793 DOI: 10.3390/molecules24183215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/15/2019] [Accepted: 08/23/2019] [Indexed: 12/23/2022] Open
Abstract
β-Glucosidases are enzymes with high importance for many industrial processes, catalyzing the last and limiting step of the conversion of lignocellulosic material into fermentable sugars for biofuel production. However, β-glucosidases are inhibited by high concentrations of the product (glucose), which limits the biofuel production on an industrial scale. For this reason, the structural mechanisms of tolerance to product inhibition have been the target of several studies. In this study, we performed in silico experiments, such as molecular dynamics (MD) simulations, free energy landscape (FEL) estimate, Poisson-Boltzmann surface area (PBSA), and grid inhomogeneous solvation theory (GIST) seeking a better understanding of the glucose tolerance and inhibition mechanisms of a representative GH1 β-glucosidase and a GH3 one. Our results suggest that the hydrophobic residues Y180, W350, and F349, as well the polar one D238 act in a mechanism for glucose releasing, herein called "slingshot mechanism", dependent also on an allosteric channel (AC). In addition, water activity modulation and the protein loop motions suggest that GH1 β-Glucosidases present an active site more adapted to glucose withdrawal than GH3, in consonance with the GH1s lower product inhibition. The results presented here provide directions on the understanding of the molecular mechanisms governing inhibition and tolerance to the product in β-glucosidases and can be useful for the rational design of optimized enzymes for industrial interests.
Collapse
|
67
|
Swietnicki W, Brzozowska E. In silico analysis of bacteriophage tail tubular proteins suggests a putative sugar binding site and a catalytic mechanism. J Mol Graph Model 2019; 92:8-16. [PMID: 31302501 DOI: 10.1016/j.jmgm.2019.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
Abstract
Bacteriophage base tailplate proteins were recently discovered to have hydrolytic activity towards disaccharides. The putative assignment of sugar binding sites was based on known lectin structures and identified residues a.a. 40-120 as the potential binding region for disaccharides [1]. To help verify the prediction, an in silico analysis was performed on the structure of a base tailplate protein gp31 from Klebsiella pneumoniae bacteriophage KP32 (PDB: 5MU4) which shows activity towards maltose but not trehalose [1]. Based on the information, a full surface docking was performed for both sugars which identified 2 regions different than originally predicted. The first region clearly favored maltose during the docking phase while the second one allowed for the energetically-equivalent binding of trehalose. To verify the assignment, a molecular dynamics simulation was performed to assess the stability of the docked substrates. MD simulations suggested that the first site included residues D131, D133, and E134, and was also superior for maltose binding while clearly disfavoring trehalose. Analysis of the putative catalytic mechanism suggested residues D131, D133 and E134 as critical for substrate binding. The residue D133 did participate in a stable substrate binding and was positioned near the scissile bond, potentially making it a catalytic residue. Catalytic residues were most likely D131 and D133, one of the two options proposed by Pyra et al. [1]. A comparison with known hydrolase mechanisms suggested that the enzyme most likely retains configuration during hydrolysis of maltose. The findings are discussed for other bacteriophage proteins regarding their potential specificities and catalytic mechanisms.
Collapse
Affiliation(s)
- Wieslaw Swietnicki
- L. Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Science, Department of Immunology and Infectious Diseases, ul. R. Weigla 12, 53-114, Wroclaw, PL, Poland.
| | - Ewa Brzozowska
- L. Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Science, Department of Immunology and Infectious Diseases, ul. R. Weigla 12, 53-114, Wroclaw, PL, Poland
| |
Collapse
|
68
|
Comegna D, Del Gatto A, Saviano M, Zaccaro L. On-Bead Peptoid Dimerization Induced by Incorporation of Glycosylated Bridging Units in Submonomer Solid-Phase Approach to Glycopeptoids. Org Lett 2019; 21:4454-4458. [PMID: 31150252 DOI: 10.1021/acs.orglett.9b01242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A study on submonomer solid-phase synthesis of S-glycopeptoids has been carried out by screening different parameters. Dimeric species, featuring glycosylated bridging amino monomers, were found under suitable conditions. These dimers arise from an on-resin cross-linking reaction occurring with the incorporation of a glycoamino submonomer into the growing chain and subsequent nucleophilic attack of the resulting secondary amine to a still unreacted bromoacetylated unit. The arising byproduct can be regarded as a novel dimeric peptoid type.
Collapse
Affiliation(s)
- Daniela Comegna
- Institute of Biostructures and Bioimaging-CNR , Via Mezzocannone 16 , 80134 Naples , Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging-CNR , Via Mezzocannone 16 , 80134 Naples , Italy.,Interdepartmental Center of Bioactive Peptide , University of Naples Federico II , Via Mezzocannone 16 , 80134 Naples , Italy
| | - Michele Saviano
- Interdepartmental Center of Bioactive Peptide , University of Naples Federico II , Via Mezzocannone 16 , 80134 Naples , Italy.,Institute of Crystallography-CNR , Via Amendola 122/O , 70126 Bari , Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging-CNR , Via Mezzocannone 16 , 80134 Naples , Italy.,Interdepartmental Center of Bioactive Peptide , University of Naples Federico II , Via Mezzocannone 16 , 80134 Naples , Italy
| |
Collapse
|
69
|
Chandravanshi M, Sharma A, Dasgupta P, Mandal SK, Kanaujia SP. Identification and characterization of ABC transporters for carbohydrate uptake in Thermus thermophilus HB8. Gene 2019; 696:135-148. [DOI: 10.1016/j.gene.2019.02.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/01/2019] [Indexed: 02/06/2023]
|
70
|
Li M, Müller C, Fröhlich K, Gorka O, Zhang L, Groß O, Schilling O, Einsle O, Jessen-Trefzer C. Detection and Characterization of a Mycobacterial L-Arabinofuranose ABC Transporter Identified with a Rapid Lipoproteomics Protocol. Cell Chem Biol 2019; 26:852-862.e6. [PMID: 31006617 DOI: 10.1016/j.chembiol.2019.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/23/2018] [Accepted: 03/01/2019] [Indexed: 02/06/2023]
Abstract
Nutrient uptake is essential for survival of organisms, and carbohydrates serve as a crucial carbon and energy source for most microorganisms. Given the importance of mycobacteria as human pathogens a detailed knowledge of carbohydrate uptake transporters is highly desirable, but currently available information is severely limited and mainly based on in silico analyses. Moreover, there is only very little data available on the in vitro characterization of carbohydrate transporters from mycobacterial species. To overcome these significant limitations there is a strong demand for innovative approaches to experimentally match substrates to ATP-binding cassette (ABC) transporters in a straightforward manner. Our study focuses on the model organism Mycobacterium smegmatis and identifies a mycobacterial ABC transport system based on a rapid label-free mass spectrometry lipoproteomics assay with broad applicability. Further validation and X-ray structure analyses reveal a highly selective mycobacterial L-arabinose uptake system.
Collapse
Affiliation(s)
- Miaomiao Li
- Department of Pharmaceutical Biology and Biotechnology, Faculty of Chemistry and Pharmacy, University of Freiburg, Stefan-Meier-Straße 19, 79104 Freiburg, Germany
| | - Christoph Müller
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Klemens Fröhlich
- Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 115A, 79106 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Albertstraße 19A, 79104 Freiburg, Germany
| | - Oliver Gorka
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 66, 79106 Freiburg, Germany
| | - Lin Zhang
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Olaf Groß
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 66, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 115A, 79106 Freiburg, Germany
| | - Oliver Einsle
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Claudia Jessen-Trefzer
- Department of Pharmaceutical Biology and Biotechnology, Faculty of Chemistry and Pharmacy, University of Freiburg, Stefan-Meier-Straße 19, 79104 Freiburg, Germany.
| |
Collapse
|
71
|
Bentley EP, Frey BB, Deniz AA. Physical Chemistry of Cellular Liquid-Phase Separation. Chemistry 2019; 25:5600-5610. [PMID: 30589142 PMCID: PMC6551525 DOI: 10.1002/chem.201805093] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/11/2018] [Indexed: 01/05/2023]
Abstract
Compartmentalization of biochemical processes is essential for cell function. Although membrane-bound organelles are well studied in this context, recent work has shown that phase separation is a key contributor to cellular compartmentalization through the formation of liquid-like membraneless organelles (MLOs). In this Minireview, the key mechanistic concepts that underlie MLO dynamics and function are first briefly discussed, including the relevant noncovalent interaction chemistry and polymer physical chemistry. Next, a few examples of MLOs and relevant proteins are given, along with their functions, which highlight the relevance of the above concepts. The developing area of active matter and non-equilibrium systems, which can give rise to unexpected effects in fluctuating cellular conditions, are also discussed. Finally, our thoughts for emerging and future directions in the field are discussed, including in vitro and in vivo studies of MLO physical chemistry and function.
Collapse
Affiliation(s)
- Emily P Bentley
- The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Benjamin B Frey
- The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Ashok A Deniz
- The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| |
Collapse
|
72
|
Hofmeister DL, Thoden JB, Holden HM. Investigation of a sugar N-formyltransferase from the plant pathogen Pantoea ananatis. Protein Sci 2019; 28:707-716. [PMID: 30666752 PMCID: PMC6423709 DOI: 10.1002/pro.3577] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/13/2019] [Accepted: 01/14/2019] [Indexed: 02/05/2023]
Abstract
Pantoea ananatis is a Gram-negative bacterium first recognized in 1928 as the causative agent of pineapple rot in the Philippines. Since then various strains of the organism have been implicated in the devastation of agriculturally important crops. Some strains, however, have been shown to function as non-pathogenic plant growth promoting organisms. To date, the factors that determine pathogenicity or lack thereof between the various strains are not well understood. All P. ananatis strains contain lipopolysaccharides, which differ with respect to the identities of their associated sugars. Given our research interest on the presence of the unusual sugar, 4-formamido-4,6-dideoxy-d-glucose, found on the lipopolysaccharides of Campylobacter jejuni and Francisella tularensis, we were curious as to whether other bacteria have the appropriate biosynthetic machinery to produce these unique carbohydrates. Four enzymes are typically required for their biosynthesis: a thymidylyltransferase, a 4,6-dehydratase, an aminotransferase, and an N-formyltransferase. Here, we report that the gene SAMN03097714_1080 from the P. ananatis strain NFR11 does, indeed, encode for an N-formyltransferase, hereafter referred to as PA1080c. Our kinetic analysis demonstrates that PA1080c displays classical Michaelis-Menten kinetics with dTDP-4-amino-4,6-dideoxy-d-glucose as the substrate and N10 -formyltetrahydrofolate as the carbon source. In addition, the X-ray structure of PA1080c, determined to 1.7 Å resolution, shows that the enzyme adopts the molecular architecture observed for other sugar N-formyltransferases. Analysis of the P. ananatis NFR11 genome suggests that the three other enzymes necessary for N-formylated sugar biosynthesis are also present. Intriguingly, those strains of P. ananatis that are non-pathogenic apparently do not contain these genes.
Collapse
Affiliation(s)
| | - James B. Thoden
- Department of BiochemistryUniversity of WisconsinMadisonWisconsin, 53706
| | - Hazel M. Holden
- Department of BiochemistryUniversity of WisconsinMadisonWisconsin, 53706
| |
Collapse
|
73
|
Sasaki M, Ryoson Y, Numata M, Fukuhara G. Oligosaccharide Sensing in Aqueous Media Using Porphyrin–Curdlan Conjugates: An Allosteric Signal-Amplification System. J Org Chem 2019; 84:6017-6027. [DOI: 10.1021/acs.joc.9b00040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mayuko Sasaki
- Department of Applied Chemistry, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
| | - Yuma Ryoson
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Munenori Numata
- Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
74
|
Substrate-assisted mechanism of catalytic hydrolysis of misaminoacylated tRNA required for protein synthesis fidelity. Biochem J 2019; 476:719-732. [PMID: 30718305 DOI: 10.1042/bcj20180910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/28/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
d-aminoacyl-tRNA-deacylase (DTD) prevents the incorporation of d-amino acids into proteins during translation by hydrolyzing the ester bond between mistakenly attached amino acids and tRNAs. Despite extensive study of this proofreading enzyme, the precise catalytic mechanism remains unknown. Here, a combination of biochemical and computational investigations has enabled the discovery of a new substrate-assisted mechanism of d-Tyr-tRNATyr hydrolysis by Thermus thermophilus DTD. Several functional elements of the substrate, misacylated tRNA, participate in the catalysis. During the hydrolytic reaction, the 2'-OH group of the А76 residue of d-Tyr-tRNATyr forms a hydrogen bond with a carbonyl group of the tyrosine residue, stabilizing the transition-state intermediate. Two water molecules participate in this reaction, attacking and assisting ones, resulting in a significant decrease in the activation energy of the rate-limiting step. The amino group of the d-Tyr aminoacyl moiety is unprotonated and serves as a general base, abstracting the proton from the assisting water molecule and forming a more nucleophilic ester-attacking species. Quantum chemical methodology was used to investigate the mechanism of hydrolysis. The DFT-calculated deacylation reaction is in full agreement with the experimental data. The Gibbs activation energies for the first and second steps were 10.52 and 1.05 kcal/mol, respectively, highlighting that the first step of the hydrolysis process is the rate-limiting step. Several amino acid residues of the enzyme participate in the coordination of the substrate and water molecules. Thus, the present work provides new insights into the proofreading details of misacylated tRNAs and can be extended to other systems important for translation fidelity.
Collapse
|
75
|
Zimmer J. Structural features underlying recognition and translocation of extracellular polysaccharides. Interface Focus 2019; 9:20180060. [PMID: 30842868 DOI: 10.1098/rsfs.2018.0060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2019] [Indexed: 12/31/2022] Open
Abstract
Essentially all living systems produce complex carbohydrates as an energy source, structural component, protective coat or adhesive for cell attachment. Many polysaccharides are displayed on the cell surface or are threaded through proteinaceous tunnels for degradation. Dictated by their chemical composition and mode of polymerization, the physical properties of complex carbohydrates differ substantially, from amphipathic water-insoluble polymers to highly hydrated hydrogel-forming macromolecules. Accordingly, diverse recognition and translocation mechanisms evolved to transport polysaccharides to their final destinations. This review will summarize and compare diverse polysaccharide transport mechanisms implicated in the biosynthesis and degradation of cell surface polymers in pro- and eukaryotes.
Collapse
Affiliation(s)
- Jochen Zimmer
- University of Virginia, 480 Ray C. Hunt Dr., Charlottesville, VA 22903, USA
| |
Collapse
|
76
|
Cova TF, Milne BF, Pais AA. Host flexibility and space filling in supramolecular complexation of cyclodextrins: A free-energy-oriented approach. Carbohydr Polym 2019; 205:42-54. [DOI: 10.1016/j.carbpol.2018.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 12/20/2022]
|
77
|
Frontera A, Bauzá A. closo-Carboranes as dual CH⋯π and BH⋯π donors: theoretical study and biological significance. Phys Chem Chem Phys 2019; 21:19944-19950. [DOI: 10.1039/c9cp03858b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this manuscript the ability ofcloso-carboranes to establish CH⋯π and BH⋯π interactions with several aromatic moieties exhibiting different electronic natures has been evaluated at the PBE0-D3/def2-TZVP level of theory.
Collapse
Affiliation(s)
- Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Antonio Bauzá
- Department of Chemistry University of Florida
- Gainesville
- USA
| |
Collapse
|
78
|
The Molecular Basis of Polysaccharide Sulfatase Activity and a Nomenclature for Catalytic Subsites in this Class of Enzyme. Structure 2018; 26:747-758.e4. [PMID: 29681469 DOI: 10.1016/j.str.2018.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/26/2018] [Accepted: 03/20/2018] [Indexed: 12/11/2022]
Abstract
Sulfatases play a biologically important role by cleaving sulfate groups from molecules. They can be identified on the basis of signature sequences within their primary structures, and the largest family, S1, has predictable features that contribute specifically to the recognition and catalytic removal of sulfate groups. However, despite advances in the prediction and understanding of S1 sulfatases, a major question regards the molecular determinants that drive substrate recognition beyond the targeted sulfate group. Here, through analysis of an endo-4S-ι-carrageenan sulfatase (PsS1_19A) from Pseudoalteromonas sp. PS47, particularly X-ray crystal structures in complex with intact substrates, we show that specific recognition of the substrate leaving group components, in this case carbohydrate, provides the enzyme with specificity for its substrate. On the basis of these results we propose a catalytic subsite nomenclature that we anticipate will form a general foundation for understanding and describing the molecular basis of substrate recognition by sulfatases.
Collapse
|
79
|
Jütten L, Ramírez-Gualito K, Weilhard A, Albrecht B, Cuevas G, Fernández-Alonso MD, Jiménez-Barbero J, Schlörer NE, Diaz D. Exploring the Role of Solvent on Carbohydrate-Aryl Interactions by Diffusion NMR-Based Studies. ACS OMEGA 2018; 3:536-543. [PMID: 31457911 PMCID: PMC6641296 DOI: 10.1021/acsomega.7b01630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/28/2017] [Indexed: 05/26/2023]
Abstract
Carbohydrate-protein interactions play an important role in many molecular recognition processes. An exquisite combination of multiple factors favors the interaction of the receptor with one specific type of sugar, whereas others are excluded. Stacking CH-aromatic interactions within the binding site provide a relevant contribution to the stabilization of the resulting sugar-protein complex. Being experimentally difficult to detect and analyze, the key CH-π interaction features have been very often dissected using a variety of techniques and simple model systems. In the present work, diffusion NMR spectroscopy has been employed to separate the components of sugar mixtures in different solvents on the basis of their differential ability to interact through CH-π interactions with one particular aromatic cosolute in solution. The experimental data show that the properties of the solvent did also influence the diffusion behavior of the sugars present in the mixture, inhibiting or improving their separation. Overall, the results showed that, for the considered monosaccharide derivatives, their diffusion coefficient values and, consequently, their apparent molecular sizes and/or shapes depend on the balance between solute/cosolute as well as solute/solvent interactions. Thus, in certain media and in the presence of the aromatic cosolute, the studied saccharides that are more suited to display CH-π interactions exhibited a lower diffusion coefficient than the noncomplexing sugars in the mixture. However, when dissolved in another medium, the interaction with the solvent strongly competes with that of the aromatic cosolute.
Collapse
Affiliation(s)
- Linda Jütten
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Karla Ramírez-Gualito
- Centro
de Nanociencias y Micro y Nanotecnología, Instituto Politécnico Nacional, Avenida Luis Enrique Erro S/N, Unidad Profesional
Adolfo López Mateos, Zacatenco, C.P. 07738 Ciudad de México, México
| | - Andreas Weilhard
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Benjamin Albrecht
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Gabriel Cuevas
- Instituto
de Química, Universidad Nacional Autónoma de México,
Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, C.P. 04510 Ciudad de México, México
| | | | - Jesús Jiménez-Barbero
- Centro
de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
- CIC
bioGUNE, Science and
Technology Park bld 801 A, 48160 Derio, Spain
- Basque Foundation
for Science, Ikerbasque, Maria Diaz de Haro 3, 48013 Bilbao, Spain
- Department
of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Spain
| | - Nils E. Schlörer
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Dolores Diaz
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
- Centro
de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| |
Collapse
|
80
|
Bi Y, Mann E, Whitfield C, Zimmer J. Architecture of a channel-forming O-antigen polysaccharide ABC transporter. Nature 2018; 553:361-365. [PMID: 29320481 PMCID: PMC5978415 DOI: 10.1038/nature25190] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/01/2017] [Indexed: 11/23/2022]
Abstract
O-antigens are cell surface polysaccharides of many Gram-negative pathogens that aid in escaping innate immune responses. A widespread O-antigen biosynthesis mechanism involves the synthesis of the lipid-anchored polymer on the cytosolic face of the inner membrane, followed by transport to the periplasmic side where it is ligated to the lipid A core to complete a lipopolysaccharide molecule. In this pathway, transport to the periplasm is mediated by an ATP-binding cassette (ABC) transporter, called Wzm-Wzt. Here we present the crystal structure of the Wzm-Wzt homologue from Aquifex aeolicus in an open conformation. The transporter forms a transmembrane channel that is sufficiently wide to accommodate a linear polysaccharide. Its nucleotide-binding domain and a periplasmic extension form 'gate helices' at the cytosolic and periplasmic membrane interfaces that probably serve as substrate entry and exit points. Site-directed mutagenesis of the gates impairs in vivo O-antigen secretion in the Escherichia coli prototype. Combined with a closed structure of the isolated nucleotide-binding domains, our structural and functional analyses suggest a processive O-antigen translocation mechanism, which stands in contrast to the classical alternating access mechanism of ABC transporters.
Collapse
Affiliation(s)
- Yunchen Bi
- Molecular Physiology and Biological Physics, University of Virginia
School of Medicine, Charlottesville, VA 22908, USA
| | - Evan Mann
- Department of Molecular and Cellular Biology, University of Guelph,
Guelph, Ontario, N1G 2W1, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph,
Guelph, Ontario, N1G 2W1, Canada
| | - Jochen Zimmer
- Molecular Physiology and Biological Physics, University of Virginia
School of Medicine, Charlottesville, VA 22908, USA
| |
Collapse
|
81
|
Stewart P, Renney CM, Mooibroek TJ, Ferheen S, Davis AP. Maltodextrin recognition by a macrocyclic synthetic lectin. Chem Commun (Camb) 2018; 54:8649-8652. [DOI: 10.1039/c8cc05074k] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This carbohydrate receptor achieves high affinities in water and shows an unusual preference for α-linked maltodextrins.
Collapse
Affiliation(s)
- Patrick Stewart
- School of Chemistry of the University of Bristol Cantock's Close
- Bristol
- UK
| | - Charles M. Renney
- School of Chemistry of the University of Bristol Cantock's Close
- Bristol
- UK
| | - Tiddo J. Mooibroek
- van’t Hoff Institute for Molecular Sciences
- University of Amsterdam
- Amsterdam
- The Netherlands
| | - Sadia Ferheen
- School of Chemistry of the University of Bristol Cantock's Close
- Bristol
- UK
| | - Anthony P. Davis
- School of Chemistry of the University of Bristol Cantock's Close
- Bristol
- UK
| |
Collapse
|
82
|
Aray Y, Aguilera-García R, Izquierdo DR. Exploring the nature of the H-bonds between the human class II MHC protein, HLA-DR1 (DRB*0101) and the influenza virus hemagglutinin peptide, HA306-318, using the quantum theory of atoms in molecules. J Biomol Struct Dyn 2017; 37:48-64. [PMID: 29246090 DOI: 10.1080/07391102.2017.1418432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The nature of the H-bonds between the human protein HLA-DR1 (DRB*0101) and the hemagglutinin peptide HA306-318 has been studied using the Quantum Theory of Atoms in Molecules for the first time. We have found four H-bond groups: one conventional CO··HN bond group and three nonconventional CO··HC, π··HC involving aromatic rings and HN··HCaliphatic groups. The calculated electron density at the determined H-bond critical points suggests the follow protein pocket binding trend: P1 (2,311) >> P9 (1.109) > P4 (0.950) > P6 (0.553) > P7 (0.213) which agrees and reveal the nature of experimental findings, showing that P1 produces by a long way the strongest binding of the HLA-DR1 human protein molecule with the peptide backbone as consequence of the vast number of H-bonds in the P1 area and at the same time the largest specific binding of the peptide Tyr308 residue with aromatic residues located at the binding groove floor. The present results suggest the topological analysis of the electronic density as a valuable tool that allows a non-arbitrary partition of the pockets binding energy via the calculated electron density at the determined critical points.
Collapse
Affiliation(s)
- Yosslen Aray
- a Facultad de Ciencias , Universidad de Ciencias Aplicadas y Ambientales, UDCA , Bogotá , Colombia
| | - Ricardo Aguilera-García
- a Facultad de Ciencias , Universidad de Ciencias Aplicadas y Ambientales, UDCA , Bogotá , Colombia
| | - Daniel R Izquierdo
- a Facultad de Ciencias , Universidad de Ciencias Aplicadas y Ambientales, UDCA , Bogotá , Colombia
| |
Collapse
|
83
|
Houser J, Kozmon S, Mishra D, Mishra SK, Romano PR, Wimmerová M, Koča J. Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL. PLoS One 2017; 12:e0189375. [PMID: 29232414 PMCID: PMC5726637 DOI: 10.1371/journal.pone.0189375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 11/20/2017] [Indexed: 11/19/2022] Open
Abstract
Protein-carbohydrate interactions are very often mediated by the stacking CH-π interactions involving the side chains of aromatic amino acids such as tryptophan (Trp), tyrosine (Tyr) or phenylalanine (Phe). Especially suitable for stacking is the Trp residue. Analysis of the PDB database shows Trp stacking for 265 carbohydrate or carbohydrate like ligands in 5 208 Trp containing motives. An appropriate model system to study such an interaction is the AAL lectin family where the stacking interactions play a crucial role and are thought to be a driving force for carbohydrate binding. In this study we present data showing a novel finding in the stacking interaction of the AAL Trp side chain with the carbohydrate. High resolution X-ray structure of the AAL lectin from Aleuria aurantia with α-methyl-l-fucoside ligand shows two possible Trp side chain conformations with the same occupation in electron density. The in silico data shows that the conformation of the Trp side chain does not influence the interaction energy despite the fact that each conformation creates interactions with different carbohydrate CH groups. Moreover, the PDB data search shows that the conformations are almost equally distributed across all Trp-carbohydrate complexes, which would suggest no substantial preference for one conformation over another.
Collapse
Affiliation(s)
- Josef Houser
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Stanislav Kozmon
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Deepti Mishra
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sushil K. Mishra
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, Wako, Saitama, Japan
| | - Patrick R. Romano
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Michaela Wimmerová
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail: (JK); (MW)
| | - Jaroslav Koča
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail: (JK); (MW)
| |
Collapse
|