1
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Niu Y, Chen SJ, Klauda JB. Simulations of naïve and KLA-activated macrophage plasma membrane models. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184242. [PMID: 37866689 DOI: 10.1016/j.bbamem.2023.184242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/25/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
Macrophages (MAs), which play vital roles in human immune responses and lipid metabolisms, are implicated in the development and progression of atherosclerosis, a major contributor to cardiovascular diseases. Specifically, the abnormal lipid metabolism of oxidized low-density lipids (oxLDLs) in MAs is believed to be a crucial factor. However, the precise mechanism by which the MA membrane contributes to this altered lipid metabolism remains unclear. Lipidomic studies have revealed significant differences in membrane composition between various MA phenotypes. This study serves to provide and characterize complex realistic computational models for naïve (M0) and Kdo2-lipid A-activated (M1) state MA. Analyses of surface area per lipid (SA/lip), area compressibility modulus (KA), carbon‑hydrogen order parameter (SCH), electron density profile (EDP), tilt angles, two-dimension radial distribution functions (2D RDFs), mean squared displacement (MSD), hydrogen bonds (H-bonds), lipid clustering, and lipid wobble were conducted for both models. Results indicate that the M1 state MA membrane is more tightly packed, with increased chain order across lipid species, and forms PSM-DOPG-CHOL and PSM-SLPC-CHOL clusters. Importantly, the bilayer thicknesses reported for the models are in good agreement with experimental data for the thicknesses of transmembrane regions for MA integral proteins. These findings validate the described models as physiologically accurate for future computational studies of MA membranes and their residing proteins.
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Affiliation(s)
- Yueqi Niu
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Si Jia Chen
- Medical Scientist Training Program, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, MD 20742, USA.
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2
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Liao C, Santoscoy MC, Craft J, Anderson C, Soupir ML, Jarboe LR. Allelic variation of Escherichia coli outer membrane protein A: Impact on cell surface properties, stress tolerance and allele distribution. PLoS One 2022; 17:e0276046. [PMID: 36227900 PMCID: PMC9560509 DOI: 10.1371/journal.pone.0276046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Outer membrane protein A (OmpA) is one of the most abundant outer membrane proteins of Gram-negative bacteria and is known to have patterns of sequence variations at certain amino acids-allelic variation-in Escherichia coli. Here we subjected seven exemplar OmpA alleles expressed in a K-12 (MG1655) ΔompA background to further characterization. These alleles were observed to significantly impact cell surface charge (zeta potential), cell surface hydrophobicity, biofilm formation, sensitivity to killing by neutrophil elastase, and specific growth rate at 42°C and in the presence of acetate, demonstrating that OmpA is an attractive target for engineering cell surface properties and industrial phenotypes. It was also observed that cell surface charge and biofilm formation both significantly correlate with cell surface hydrophobicity, a cell property that is increasingly intriguing for bioproduction. While there was poor alignment between the observed experimental values relative to the known sequence variation, differences in hydrophobicity and biofilm formation did correspond to the identity of residue 203 (N vs T), located within the proposed dimerization domain. The relative abundance of the (I, δ) allele was increased in extraintestinal pathogenic E. coli (ExPEC) isolates relative to environmental isolates, with a corresponding decrease in (I, α) alleles in ExPEC relative to environmental isolates. The (I, α) and (I, δ) alleles differ at positions 203 and 251. Variations in distribution were also observed among ExPEC types and phylotypes. Thus, OmpA allelic variation and its influence on OmpA function warrant further investigation.
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Affiliation(s)
- Chunyu Liao
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | - Miguel C. Santoscoy
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
| | - Julia Craft
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Chiron Anderson
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Michelle L. Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Laura R. Jarboe
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
- * E-mail:
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3
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Matos R, Amorim I, Magalhães A, Haesebrouck F, Gärtner F, Reis CA. Adhesion of Helicobacter Species to the Human Gastric Mucosa: A Deep Look Into Glycans Role. Front Mol Biosci 2021; 8:656439. [PMID: 34026832 PMCID: PMC8138122 DOI: 10.3389/fmolb.2021.656439] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/22/2021] [Indexed: 12/15/2022] Open
Abstract
Helicobacter species infections may be associated with the development of gastric disorders, such as gastritis, peptic ulcers, intestinal metaplasia, dysplasia and gastric carcinoma. Binding of these bacteria to the gastric mucosa occurs through the recognition of specific glycan receptors expressed by the host epithelial cells. This review addresses the state of the art knowledge on these host glycan structures and the bacterial adhesins involved in Helicobacter spp. adhesion to gastric mucosa colonization. Glycans are expressed on every cell surface and they are crucial for several biological processes, including protein folding, cell signaling and recognition, and host-pathogen interactions. Helicobacter pylori is the most predominant gastric Helicobacter species in humans. The adhesion of this bacterium to glycan epitopes present on the gastric epithelial surface is a crucial step for a successful colonization. Major adhesins essential for colonization and infection are the blood-group antigen-binding adhesin (BabA) which mediates the interaction with fucosylated H-type 1 and Lewis B glycans, and the sialic acid-binding adhesin (SabA) which recognizes the sialyl-Lewis A and X glycan antigens. Since not every H. pylori strain expresses functional BabA or SabA adhesins, other bacterial proteins are most probably also involved in this adhesion process, including LabA (LacdiNAc-binding adhesin), which binds to the LacdiNAc motif on MUC5AC mucin. Besides H. pylori, several other gastric non-Helicobacter pylori Helicobacters (NHPH), mainly associated with pigs (H. suis) and pets (H. felis, H. bizzozeronii, H. salomonis, and H. heilmannii), may also colonize the human stomach and cause gastric disease, including gastritis, peptic ulcers and mucosa-associated lymphoid tissue (MALT) lymphoma. These NHPH lack homologous to the major known adhesins involved in colonization of the human stomach. In humans, NHPH infection rate is much lower than in the natural hosts. Differences in the glycosylation profile between gastric human and animal mucins acting as glycan receptors for NHPH-associated adhesins, may be involved. The identification and characterization of the key molecules involved in the adhesion of gastric Helicobacter species to the gastric mucosa is important to understand the colonization and infection strategies displayed by different members of this genus.
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Affiliation(s)
- Rita Matos
- Instituto de Investigação e Inovação Em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS), Porto, Portugal
| | - Irina Amorim
- Instituto de Investigação e Inovação Em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS), Porto, Portugal
| | - Ana Magalhães
- Instituto de Investigação e Inovação Em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Fátima Gärtner
- Instituto de Investigação e Inovação Em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Celso A. Reis
- Instituto de Investigação e Inovação Em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS), Porto, Portugal
- Faculdade de Medicina da Universidade do Porto (FMUP), Porto, Portugal
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4
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Le Guennec L, Coureuil M, Nassif X, Bourdoulous S. Strategies used by bacterial pathogens to cross the blood-brain barrier. Cell Microbiol 2019; 22:e13132. [PMID: 31658405 DOI: 10.1111/cmi.13132] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/11/2019] [Accepted: 10/13/2019] [Indexed: 12/15/2022]
Abstract
The skull, spine, meninges, and cellular barriers at the blood-brain and the blood-cerebrospinal fluid interfaces well protect the brain and meningeal spaces against microbial invasion. However, once in the bloodstream, a range of pathogenic bacteria is able to reach the brain and cause meningitis. Despite advances in antibacterial therapy, bacterial meningitis remains one of the most important infectious diseases worldwide. The most common causative bacteria in children and adults are Streptococcus pneumoniae and Neisseria meningitidis associated with high morbidity and mortality, while among neonates, most cases of bacterial meningitis are due to group B Streptococcus and Escherichia coli. Here we summarise our current knowledge on the strategies used by these bacterial pathogens to survive in the bloodstream, to colonise the brain vasculature and to cross the blood-brain barrier.
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Affiliation(s)
- Loic Le Guennec
- Inserm (Institut National de la Sante et de la Recherche Medicale), U1016, Institut Cochin, Paris, France.,CNRS (Centre National de la recherche Scientifique), UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Mathieu Coureuil
- Inserm (Institut National de la Sante et de la Recherche Medicale), unité U1151, Institut-Necker-Enfants-Malades, Paris, France.,CNRS (Centre National de la recherche Scientifique), UMR 8253, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, Paris, France
| | - Xavier Nassif
- Inserm (Institut National de la Sante et de la Recherche Medicale), unité U1151, Institut-Necker-Enfants-Malades, Paris, France.,CNRS (Centre National de la recherche Scientifique), UMR 8253, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Necker Enfants Malades, Paris, France
| | - Sandrine Bourdoulous
- Inserm (Institut National de la Sante et de la Recherche Medicale), U1016, Institut Cochin, Paris, France.,CNRS (Centre National de la recherche Scientifique), UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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5
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Liao C, Liang X, Yang F, Soupir ML, Howe AC, Thompson ML, Jarboe LR. Allelic Variation in Outer Membrane Protein A and Its Influence on Attachment of Escherichia coli to Corn Stover. Front Microbiol 2017; 8:708. [PMID: 28515712 PMCID: PMC5413513 DOI: 10.3389/fmicb.2017.00708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 04/05/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding the genetic factors that govern microbe-sediment interactions in aquatic environments is important for water quality management and reduction of waterborne disease outbreaks. Although chemical properties of bacteria have been identified that contribute to initiation of attachment, the outer membrane proteins that contribute to these chemical properties still remain unclear. In this study we explored the attachment of 78 Escherichia coli environmental isolates to corn stover, a representative agricultural residue. Outer membrane proteome analysis led to the observation of amino acid variations, some of which had not been previously described, in outer membrane protein A (OmpA) at 10 distinct locations, including each of the four extracellular loops, three of the eight transmembrane segments, the proline-rich linker and the dimerization domain. Some of the polymorphisms within loops 1, 2, and 3 were found to significantly co-occur. Grouping of sequences according to the outer loop polymorphisms revealed five distinct patterns that each occur in at least 5% of our isolates. The two most common patterns, I and II, are encoded by 33.3 and 20.5% of these isolates and differ at each of the four loops. Statistically significant differences in attachment to corn stover were observed among isolates expressing different versions of OmpA and when different versions of OmpA were expressed in the same genetic background. Most notable was the increased corn stover attachment associated with a loop 3 sequence of SNFDGKN relative to the standard SNVYGKN sequence. These results provide further insight into the allelic variation of OmpA and implicate OmpA in contributing to attachment to corn stover.
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Affiliation(s)
- Chunyu Liao
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA
| | - Xiao Liang
- Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | - Fan Yang
- Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | - Michelle L Soupir
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA.,Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | - Adina C Howe
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA.,Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | | | - Laura R Jarboe
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA.,Department of Chemical and Biological Engineering, Iowa State UniversityAmes, IA, USA
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6
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Hare NJ, Lee LY, Loke I, Britton WJ, Saunders BM, Thaysen-Andersen M. Mycobacterium tuberculosis Infection Manipulates the Glycosylation Machinery and the N-Glycoproteome of Human Macrophages and Their Microparticles. J Proteome Res 2016; 16:247-263. [PMID: 27760463 DOI: 10.1021/acs.jproteome.6b00685] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tuberculosis (TB) remains a prevalent and lethal infectious disease. The glycobiology associated with Mycobacterium tuberculosis infection of frontline alveolar macrophages is still unresolved. Herein, we investigated the regulation of protein N-glycosylation in human macrophages and their secreted microparticles (MPs) used for intercellular communication upon M. tb infection. LC-MS/MS-based proteomics and glycomics were performed to monitor the regulation of glycosylation enzymes and receptors and the N-glycome in in vitro-differentiated macrophages and in isolated MPs upon M. tb infection. Infection promoted a dramatic regulation of the macrophage proteome. Most notably, significant infection-dependent down-regulation (4-26 fold) of 11 lysosomal exoglycosidases, e.g., β-galactosidase, β-hexosaminidases and α-/β-mannosidases, was observed. Relative weak infection-driven transcriptional regulation of these exoglycosidases and a stronger augmentation of the extracellular hexosaminidase activity demonstrated that the lysosome-centric changes may originate predominantly from infection-induced secretion of the lysosomal content. The macrophages showed heterogeneous N-glycan profiles and displayed significant up-regulation of complex-type glycosylation and concomitant down-regulation of paucimannosylation upon infection. Complementary intact N-glycopeptide analysis supported a subcellular-specific manipulation of the glycosylation machinery and altered glycosylation patterns of lysosomal N-glycoproteins within infected macrophages. Interestingly, the corresponding macrophage-derived MPs displayed unique N-glycome and proteome signatures supporting a preferential packaging from plasma membranes. The MPs were devoid of infection-dependent N-glycosylation signatures, but interestingly displayed increased levels of the glyco-initiating oligosaccharyltransferase complex and associated α-glucosidases that correlated with increased formation, N-glycan precursor levels and N-glycan density of infected MPs. In conclusion, this system-wide study provides new insight into the host- and pathogen-driven N-glycoproteome manipulation of macrophages in TB.
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Affiliation(s)
- Nathan J Hare
- Tuberculosis Research Program, Centenary Institute, Discipline of Medicine, Infectious Diseases and Immunology, Sydney Medical School, The University of Sydney , Newtown, NSW 2042, Australia
| | - Ling Y Lee
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, NSW 2109, Australia
| | - Ian Loke
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, NSW 2109, Australia
| | - Warwick J Britton
- Tuberculosis Research Program, Centenary Institute, Discipline of Medicine, Infectious Diseases and Immunology, Sydney Medical School, The University of Sydney , Newtown, NSW 2042, Australia
| | - Bernadette M Saunders
- Tuberculosis Research Program, Centenary Institute, Discipline of Medicine, Infectious Diseases and Immunology, Sydney Medical School, The University of Sydney , Newtown, NSW 2042, Australia.,School of Life Sciences, University of Technology Sydney , Sydney, NSW 2007, Australia
| | - Morten Thaysen-Andersen
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, NSW 2109, Australia
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7
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Yang M, Angles d’Ortoli T, Säwén E, Jana M, Widmalm G, MacKerell AD. Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations. Phys Chem Chem Phys 2016; 18:18776-94. [PMID: 27346493 PMCID: PMC4945446 DOI: 10.1039/c6cp02970a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The conformation of saccharides in solution is challenging to characterize in the context of a single well-defined three-dimensional structure. Instead, they are better represented by an ensemble of conformations associated with their structural diversity and flexibility. In this study, we delineate the conformational heterogeneity of five trisaccharides via a combination of experimental and computational techniques. Experimental NMR measurements target conformationally sensitive parameters, including J couplings and effective distances around the glycosidic linkages, while the computational simulations apply the well-calibrated additive CHARMM carbohydrate force field in combination with efficient enhanced sampling molecular dynamics simulation methods. Analysis of conformational heterogeneity is performed based on sampling of discreet states as defined by dihedral angles, on root-mean-square differences of Cartesian coordinates and on the extent of volume sampled. Conformational clustering, based on the glycosidic linkage dihedral angles, shows that accounting for the full range of sampled conformations is required to reproduce the experimental data, emphasizing the utility of the molecular simulations in obtaining an atomic detailed description of the conformational properties of the saccharides. Results show the presence of differential conformational preferences as a function of primary sequence and glycosidic linkage types. Significant differences in conformational ensembles associated with the anomeric configuration of a single glycosidic linkage reinforce the impact of such changes on the conformational properties of carbohydrates. The present structural insights of the studied trisaccharides represent a foundation for understanding the range of conformations adopted in larger oligosaccharides and how these molecules encode their conformational heterogeneity into the monosaccharide sequence.
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Affiliation(s)
- Mingjun Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - Thibault Angles d’Ortoli
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Elin Säwén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Madhurima Jana
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
- Department of Chemistry, National Institute of Technology Rourkela, Odisha, India 769008
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
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8
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Yang M, Huang J, MacKerell AD. Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension. J Chem Theory Comput 2016; 11:2855-67. [PMID: 26082676 PMCID: PMC4463548 DOI: 10.1021/acs.jctc.5b00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 12/17/2022]
Abstract
![]()
Replica exchange (REX) is a powerful
computational tool for overcoming
the quasi-ergodic sampling problem of complex molecular systems. Recently,
several multidimensional extensions of this method have been developed
to realize exchanges in both temperature and biasing potential space
or the use of multiple biasing potentials to improve sampling efficiency.
However, increased computational cost due to the multidimensionality
of exchanges becomes challenging for use on complex systems under
explicit solvent conditions. In this study, we develop a one-dimensional
(1D) REX algorithm to concurrently combine the advantages of overall
enhanced sampling from Hamiltonian solute scaling and the specific
enhancement of collective variables using Hamiltonian biasing potentials.
In the present Hamiltonian replica exchange method, termed HREST-BP,
Hamiltonian solute scaling is applied to the solute subsystem, and
its interactions with the environment to enhance overall conformational
transitions and biasing potentials are added along selected collective
variables associated with specific conformational transitions, thereby
balancing the sampling of different hierarchical degrees of freedom.
The two enhanced sampling approaches are implemented concurrently
allowing for the use of a small number of replicas (e.g., 6 to 8)
in 1D, thus greatly reducing the computational cost in complex system
simulations. The present method is applied to conformational sampling
of two nitrogen-linked glycans (N-glycans) found
on the HIV gp120 envelope protein. Considering the general importance
of the conformational sampling problem, HREST-BP represents an efficient
procedure for the study of complex saccharides, and, more generally,
the method is anticipated to be of general utility for the conformational
sampling in a wide range of macromolecular systems.
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Affiliation(s)
- Mingjun Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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9
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Yang M, MacKerell AD. Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM). J Chem Theory Comput 2016; 11:788-99. [PMID: 25705140 DOI: 10.1021/ct500993h] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Oligosaccharides and polysaccharides exert numerous functional roles in biology through their structural diversity and conformational properties. To investigate their conformational properties using computational methods, Hamiltonian replica exchange (H-REX) combined with two-dimensional grid-based correction maps as biasing potentials (bpCMAP) significantly improves the sampling efficiency about glycosidic linkages. In the current study, we extend the application of H-REX with bpCMAP to complex saccharides and establish systematic procedures for bpCMAP construction, determination of replica distribution, and data analysis. Our main findings are that (1) the bpCMAP for each type of glycosidic linkage can be constructed from the corresponding disaccharide using gas-phase umbrella sampling simulations, (2) the replica distribution can be conveniently determined following the exact definition of the average acceptance ratio based on the assigned distribution of biasing potentials, and (3) the extracted free energy surface (or potential of mean force (PMF)) can be improved using the weighted histogram analysis method (WHAM) allowing for the inclusion of data from the excited state replicas in the calculated probability distribution. The method is applied to a branched N-glycan found on the HIV gp120 protein, and a linear N-glycan. Considering the general importance of N-glycans and the wide appreciation of the sampling problem, the present method represents an efficient procedure for the conformational sampling of complex oligo- and polysaccharides under explicit solvent conditions. More generally, the use of WHAM is anticipated to be of general utility for the calculation of PMFs from H-REX simulations in a wide range of macromolecular systems.
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Affiliation(s)
- Mingjun Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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10
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Chang AC, Krishnan S, Prasadarao NV. The effects of cytotoxic necrotizing factor 1 expression in the uptake of Escherichia coli K1 by macrophages and the onset of meningitis in newborn mice. Virulence 2016; 7:806-18. [PMID: 27221788 DOI: 10.1080/21505594.2016.1192730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Macrophages are a permissive niche for E. coli K1 multiplication for which the interaction of the bacterial outer membrane protein A and its cognate receptor CD64 are critical. Using in vitro immunofluorescence and live microscopy with ex vivo macrophage cultures from RFP-Lifeact mice, we show that cytotoxic necrotizing factor 1 (CNF1) secreted by E. coli K1 sequesters cellular actin toward microspike formation, thereby limiting actin availability for OmpA-mediated bacterial invasion. Surprisingly, the observed effects of CNF1 occur despite the absence of 67-kDa laminin receptor in macrophages. Concomitantly, the CNF1 deletion mutant of E. coli K1 (Δcnf1) invades macrophages and the brains of newborn mice in greater numbers compared to wild-type. However, the Δcnf1 strain induces less severe pathology in the brain. These results suggest a novel role for CNF1 in limiting E. coli K1 entry into macrophages while exacerbating disease severity in the brains of newborn mice.
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Affiliation(s)
- Alexander C Chang
- a Division of Infectious Diseases and Department of Pediatrics , Children's Hospital Los Angeles , Los Angeles , CA , USA
| | - Subramanian Krishnan
- a Division of Infectious Diseases and Department of Pediatrics , Children's Hospital Los Angeles , Los Angeles , CA , USA
| | - Nemani V Prasadarao
- a Division of Infectious Diseases and Department of Pediatrics , Children's Hospital Los Angeles , Los Angeles , CA , USA.,b Department of Surgery , Children's Hospital Los Angeles , Los Angeles , CA , USA.,c Keck School of Medicine , University of Southern California , Los Angeles , CA , USA
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11
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Doran KS, Fulde M, Gratz N, Kim BJ, Nau R, Prasadarao N, Schubert-Unkmeir A, Tuomanen EI, Valentin-Weigand P. Host-pathogen interactions in bacterial meningitis. Acta Neuropathol 2016; 131:185-209. [PMID: 26744349 PMCID: PMC4713723 DOI: 10.1007/s00401-015-1531-z] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 12/26/2022]
Abstract
Bacterial meningitis is a devastating disease occurring worldwide with up to half of the survivors left with permanent neurological sequelae. Due to intrinsic properties of the meningeal pathogens and the host responses they induce, infection can cause relatively specific lesions and clinical syndromes that result from interference with the function of the affected nervous system tissue. Pathogenesis is based on complex host–pathogen interactions, some of which are specific for certain bacteria, whereas others are shared among different pathogens. In this review, we summarize the recent progress made in understanding the molecular and cellular events involved in these interactions. We focus on selected major pathogens, Streptococcus pneumonia, S. agalactiae (Group B Streptococcus), Neisseria meningitidis, and Escherichia coli K1, and also include a neglected zoonotic pathogen, Streptococcus suis. These neuroinvasive pathogens represent common themes of host–pathogen interactions, such as colonization and invasion of mucosal barriers, survival in the blood stream, entry into the central nervous system by translocation of the blood–brain and blood–cerebrospinal fluid barrier, and induction of meningeal inflammation, affecting pia mater, the arachnoid and subarachnoid spaces.
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12
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Chenoweth AM, Trist HM, Tan PS, Wines BD, Hogarth PM. The high-affinity receptor for IgG, FcγRI, of humans and non-human primates. Immunol Rev 2015; 268:175-91. [DOI: 10.1111/imr.12366] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alicia M. Chenoweth
- Centre for Biomedicine; Burnet Institute; Melbourne Vic. Australia
- Department of Immunology; Monash University; Melbourne Vic. Australia
| | - Halina M. Trist
- Centre for Biomedicine; Burnet Institute; Melbourne Vic. Australia
| | - Peck-Szee Tan
- Centre for Biomedicine; Burnet Institute; Melbourne Vic. Australia
| | - Bruce D. Wines
- Centre for Biomedicine; Burnet Institute; Melbourne Vic. Australia
- Department of Immunology; Monash University; Melbourne Vic. Australia
- Department of Pathology; University of Melbourne; Melbourne Vic. Australia
| | - P. Mark Hogarth
- Centre for Biomedicine; Burnet Institute; Melbourne Vic. Australia
- Department of Immunology; Monash University; Melbourne Vic. Australia
- Department of Pathology; University of Melbourne; Melbourne Vic. Australia
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13
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Krishnan S, Chang AC, Hodges J, Couraud PO, Romero IA, Weksler B, Nicholson BA, Nolan LK, Prasadarao NV. Serotype O18 avian pathogenic and neonatal meningitis Escherichia coli strains employ similar pathogenic strategies for the onset of meningitis. Virulence 2015; 6:777-86. [PMID: 26407066 DOI: 10.1080/21505594.2015.1091914] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Neonatal meningitis Escherichia coli K1 (NMEC) are thought to be transmitted from mothers to newborns during delivery or by nosocomial infections. However, the source of E. coli K1 causing these infections is not clear. Avian pathogenic E. coli (APEC) have the potential to cause infection in humans while human E. coli have potential to cause colibacillosis in poultry, suggesting that these strains may lack host specificity. APEC strains are capable of causing meningitis in newborn rats; however, it is unclear whether these bacteria use similar mechanisms to that of NMEC to establish disease. Using four representative APEC and NMEC strains that belong to serotype O18, we demonstrate that these strains survive in human serum similar to that of the prototypic NMEC strain E44, a derivative of RS218. These bacteria also bind and enter both macrophages and human cerebral microvascular endothelial cells (HCMEC/D3) with similar frequency as that of E44. The amino acid sequences of the outer membrane protein A (OmpA), an important virulence factor in the pathogenesis of meningitis, are identical within these representative APEC and NMEC strains. Further, these strains also require FcγRI-α chain (CD64) and Ecgp96 as receptors for OmpA in macrophages and HCMEC/D3, respectively, to bind and enter these cells. APEC and NMEC strains induce meningitis in newborn mice with varying degree of pathology in the brains as assessed by neutrophil recruitment and neuronal apoptosis. Together, these results suggest that serotype O18 APEC strains utilize similar pathogenic mechanisms as those of NMEC strains in causing meningitis.
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Affiliation(s)
- Subramanian Krishnan
- a Division of Infectious Diseases and Department of Pediatrics; Children's Hospital Los Angeles , CA USA
| | - Alexander C Chang
- a Division of Infectious Diseases and Department of Pediatrics; Children's Hospital Los Angeles , CA USA
| | - Jacqueline Hodges
- a Division of Infectious Diseases and Department of Pediatrics; Children's Hospital Los Angeles , CA USA
| | - Pierre-Olivier Couraud
- b Inserm; Institut Cochin, Paris, France; Université Paris Descartes; Sorbonne Paris Cité , Paris , France
| | - Ignacio A Romero
- c Department of Life ; Health and Chemical Sciences; Open University ; Milton Keynes , UK
| | - Babette Weksler
- d Division of Hematology and Medical Oncology; Weill Cornell Medical College ; New York , NY USA
| | - Bryon A Nicholson
- e Department of Veterinary Microbiology and Preventive Medicine ; College of Veterinary Medicine; Iowa State University ; Ames , IA USA
| | - Lisa K Nolan
- e Department of Veterinary Microbiology and Preventive Medicine ; College of Veterinary Medicine; Iowa State University ; Ames , IA USA
| | - Nemani V Prasadarao
- a Division of Infectious Diseases and Department of Pediatrics; Children's Hospital Los Angeles , CA USA.,f Department of Surgery ; Children's Hospital Los Angeles; University of Southern California ; Los Angeles , CA USA
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