A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway.
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Nils A. Berglund | Syma Khalid | Thomas J Piggot | Roland G Huber | Daniel A Holdbrook | Jan K Marzinek | Peter J Bond | Artur Schmidtchen | A. Schmidtchen | T. Piggot | D. Holdbrook | S. Khalid | P. Bond | Vasileios Kargas | Nils A Berglund | V. Kargas | R. G. Huber | J. Marzinek
[1] D. Spring,et al. The molecular basis of the host response to lipopolysaccharide , 2010, Nature Reviews Microbiology.
[2] K. Brandenburg,et al. Physical aspects of structure and function of membranes made from lipopolysaccharides and free lipid A , 1984 .
[3] Surbhi Leekha,et al. General Principles of Antimicrobial Therapy , 2011, Mayo Clinic proceedings.
[4] Berk Hess,et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .
[5] T. Harroun,et al. A MARTINI extension for Pseudomonas aeruginosa PAO1 lipopolysaccharide. , 2016, Journal of molecular graphics & modelling.
[6] R. Larson,et al. The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.
[7] N. Jain,et al. NMR spectral mapping of Lipid A molecular patterns affected by interaction with the innate immune receptor CD14. , 2009, Biochemical and biophysical research communications.
[8] K. Brandenburg. Fourier transform infrared spectroscopy characterization of the lamellar and nonlamellar structures of free lipid A and Re lipopolysaccharides from Salmonella minnesota and Escherichia coli. , 1993, Biophysical journal.
[9] M. V. Nogués,et al. Lipopolysaccharide Neutralization by Antimicrobial Peptides: A Gambit in the Innate Host Defense Strategy , 2012, Journal of Innate Immunity.
[10] Jie-Oh Lee,et al. The crystal structure of lipopolysaccharide binding protein reveals the location of a frequent mutation that impairs innate immunity. , 2013, Immunity.
[11] S. Khalid,et al. Molecular Dynamics Simulations Predict the Pathways via Which Pristine Fullerenes Penetrate Bacterial Membranes. , 2016, The journal of physical chemistry. B.
[12] F. Re,et al. Novel Roles in Human MD-2 of Phenylalanines 121 and 126 and Tyrosine 131 in Activation of Toll-like Receptor 4 by Endotoxin* , 2008, Journal of Biological Chemistry.
[13] T. Piggot,et al. Electroporation of the E. coli and S. Aureus membranes: molecular dynamics simulations of complex bacterial membranes. , 2011, The journal of physical chemistry. B.
[14] David A. Johnson,et al. Soluble CD14 Truncated at Amino Acid 152 Binds Lipopolysaccharide (LPS) and Enables Cellular Response to LPS (*) , 1995, The Journal of Biological Chemistry.
[15] Siewert J Marrink,et al. Martini Force Field Parameters for Glycolipids. , 2013, Journal of chemical theory and computation.
[16] K. Triantafilou,et al. Lipopolysaccharide recognition: CD14, TLRs and the LPS-activation cluster. , 2002, Trends in immunology.
[17] H. Jenssen,et al. Peptides and Peptidomimetics for Antimicrobial Drug Design , 2015, Pharmaceuticals.
[18] M. C. Hu,et al. Stimulation of macrophages and neutrophils by complexes of lipopolysaccharide and soluble CD14. , 1996, Journal of immunology.
[19] T. Kirikae,et al. Regulatory roles for CD14 and phosphatidylinositol in the signaling via toll-like receptor 4-MD-2. , 2000, Biochemical and biophysical research communications.
[20] A. Sali,et al. Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.
[21] Soo Jin Kim,et al. Reconstruction of LPS Transfer Cascade Reveals Structural Determinants within LBP, CD14, and TLR4‐MD2 for Efficient LPS Recognition and Transfer , 2017, Immunity.
[22] P. Tobias,et al. Mutational Analysis of Membrane and Soluble Forms of Human MD-2* , 2006, Journal of Biological Chemistry.
[23] Helgi I. Ingólfsson,et al. Computational Modeling of Realistic Cell Membranes , 2019, Chemical reviews.
[24] S. Paik,et al. Crystal Structure of CD14 and Its Implications for Lipopolysaccharide Signaling*♦ , 2005, Journal of Biological Chemistry.
[25] Yurii S. Moroz,et al. Isolated Toll-like Receptor Transmembrane Domains Are Capable of Oligomerization , 2012, PloS one.
[26] C. Janeway,et al. A human homologue of the Drosophila Toll protein signals activation of adaptive immunity , 1997, Nature.
[27] K. Brandenburg,et al. Conformation and supramolecular structure of lipid A. , 2010, Advances in experimental medicine and biology.
[28] J. Weiss,et al. Novel Roles of Lysines 122, 125, and 58 in Functional Differences between Human and Murine MD-21 , 2009, The Journal of Immunology.
[29] R. Ulevitch,et al. Lipopolysaccharide Is in Close Proximity to Each of the Proteins in Its Membrane Receptor Complex , 2001, The Journal of Biological Chemistry.
[30] R. Darveau,et al. CD14 Employs Hydrophilic Regions to “Capture” Lipopolysaccharides , 2000, The Journal of Immunology.
[31] R. Lins,et al. The Effect of Temperature, Cations, and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View. , 2012, Journal of chemical theory and computation.
[32] D. Koppel,et al. Lateral mobility in reconstituted membranes—comparisons with diffusion in polymers , 1980, Nature.
[33] F. Re,et al. Specific High Affinity Interactions of Monomeric Endotoxin·Protein Complexes with Toll-like Receptor 4 Ectodomain* , 2007, Journal of Biological Chemistry.
[34] N. Coussens,et al. Isolation of an endotoxin–MD-2 complex that produces Toll-like receptor 4-dependent cell activation at picomolar concentrations , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[35] Richard B. Sessions,et al. Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study , 2015, PLoS Comput. Biol..
[36] S. Zakharov,et al. Crystal structures of the OmpF porin: function in a colicin translocon , 2008, The EMBO journal.
[37] Thomas J Piggot,et al. The Structural Basis for Endotoxin-induced Allosteric Regulation of the Toll-like Receptor 4 (TLR4) Innate Immune Receptor* , 2013, The Journal of Biological Chemistry.
[38] J. Bajorath,et al. Identification of CD14 residues involved in specific lipopolysaccharide recognition , 1997, Infection and immunity.
[39] Wenjuan Jiang,et al. Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model. , 2015, The journal of physical chemistry. B.
[40] Richard H. Henchman,et al. Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force. , 2009, Journal of chemical theory and computation.
[41] Siewert J Marrink,et al. Martini Coarse-Grained Force Field: Extension to Carbohydrates. , 2009, Journal of chemical theory and computation.
[42] S. Akira,et al. Essential role of MD-2 in LPS responsiveness and TLR4 distribution , 2002, Nature Immunology.
[43] Bin Chen,et al. Solution NMR studies provide structural basis for endotoxin pattern recognition by the innate immune receptor CD14. , 2008, Biochemical and biophysical research communications.
[44] M. Parrinello,et al. Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.
[45] Liping Yu,et al. NMR Studies of Hexaacylated Endotoxin Bound to Wild-type and F126A Mutant MD-2 and MD-2·TLR4 Ectodomain Complexes* , 2012, The Journal of Biological Chemistry.
[46] D. Tieleman,et al. The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.
[47] T. McIntosh,et al. Lipopolysaccharide bilayer structure: effect of chemotype, core mutations, divalent cations, and temperature. , 1999, Biochemistry.
[48] C. Walsh,et al. Prospects for new antibiotics: a molecule-centered perspective , 2013, The Journal of Antibiotics.
[49] H. Nikaido. Molecular Basis of Bacterial Outer Membrane Permeability Revisited , 2003, Microbiology and Molecular Biology Reviews.
[50] S. Akira,et al. Pathogen Recognition by the Innate Immune System , 2011, International reviews of immunology.
[51] R. Ulevitch,et al. Structure and function of lipopolysaccharide binding protein. , 1990, Science.
[52] Hayyoung Lee,et al. The structural basis of lipopolysaccharide recognition by the TLR4–MD-2 complex , 2009, Nature.
[53] Yoshinori Nagai,et al. MD-2, a Molecule that Confers Lipopolysaccharide Responsiveness on Toll-like Receptor 4 , 1999, The Journal of experimental medicine.
[54] K. Miyake. Innate recognition of lipopolysaccharide by Toll-like receptor 4-MD-2. , 2004, Trends in microbiology.
[55] P. Pristovsek,et al. Essential Roles of Hydrophobic Residues in Both MD-2 and Toll-like Receptor 4 in Activation by Endotoxin* , 2009, Journal of Biological Chemistry.
[56] M. Wurfel,et al. Lipopolysaccharide (LPS)-binding protein accelerates the binding of LPS to CD14 , 1994, The Journal of experimental medicine.
[57] A. Solovyova,et al. Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis , 2016, Proceedings of the National Academy of Sciences.
[58] Satish K. Nair,et al. The Crystal Structure of Human Soluble CD14 Reveals a Bent Solenoid with a Hydrophobic Amino-Terminal Pocket , 2013, The Journal of Immunology.
[59] R. Ulevitch,et al. CD14, a receptor for complexes of lipopolysaccharide (LPS) and LPS binding protein. , 1990, Science.
[60] S. Khalid,et al. An Accurate In Vitro Model of the E. coli Envelope , 2015, Angewandte Chemie.
[61] Alireza Tafazzol,et al. Key residues in TLR4-MD2 tetramer formation identified by free energy simulations , 2019, PLoS Comput. Biol..
[62] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[63] Kate L. Irvine,et al. Energetics of Endotoxin Recognition in the Toll-Like Receptor 4 Innate Immune Response , 2015, Scientific Reports.
[64] K. Fukase,et al. Human MD-2 confers on mouse Toll-like receptor 4 species-specific lipopolysaccharide recognition. , 2001, International immunology.
[65] Sunhwan Jo,et al. Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. , 2013, Biophysical journal.
[66] M. Wurfel,et al. Targeted Deletion of the Lipopolysaccharide (LPS)-binding Protein Gene Leads to Profound Suppression of LPS Responses Ex Vivo, whereas In Vivo Responses Remain Intact , 1997, The Journal of experimental medicine.
[67] A. Schmidtchen,et al. Lipopolysaccharide interactions of C-terminal peptides from human thrombin. , 2013, Biomacromolecules.
[68] U. Zaehringer,et al. Reviewing and identifying amino acids of human, murine, canine and equine TLR4 / MD-2 receptor complexes conferring endotoxic innate immunity activation by LPS/lipid A, or antagonistic effects by Eritoran, in contrast to species-dependent modulation by lipid IVa , 2013, Computational and structural biotechnology journal.
[69] A. Schmidtchen,et al. Host Defense Peptides of Thrombin Modulate Inflammation and Coagulation in Endotoxin-Mediated Shock and Pseudomonas aeruginosa Sepsis , 2012, PloS one.
[70] Makiko Kobayashi,et al. Regulatory Roles for MD-2 and TLR4 in Ligand-Induced Receptor Clustering1 , 2006, The Journal of Immunology.
[71] J. Witztum,et al. Minimally Modified LDL Binds to CD14, Induces Macrophage Spreading via TLR4/MD-2, and Inhibits Phagocytosis of Apoptotic Cells* , 2003, The Journal of Biological Chemistry.
[72] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .
[73] Nils A. Berglund,et al. The role of protein-protein interactions in Toll-like receptor function. , 2015, Progress in biophysics and molecular biology.
[74] Hayyoung Lee,et al. Crystal Structure of the TLR4-MD-2 Complex with Bound Endotoxin Antagonist Eritoran , 2007, Cell.
[75] P. Bond,et al. The Structural Basis for Lipid and Endotoxin Binding in RP105-MD-1, and Consequences for Regulation of Host Lipopolysaccharide Sensitivity. , 2016, Structure.
[76] Y. Arakawa,et al. Crystallization of Synthetic Escherichia coli‐Type Lipid A , 1996, Microbiology and immunology.
[77] T. Kirkland,et al. A Region of Human CD14 Required for Lipopolysaccharide Binding (*) , 1995, The Journal of Biological Chemistry.
[78] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[79] T. Mogensen. Pathogen Recognition and Inflammatory Signaling in Innate Immune Defenses , 2009, Clinical Microbiology Reviews.
[80] A. Schmidtchen,et al. Proteolysis of Human Thrombin Generates Novel Host Defense Peptides , 2010, PLoS pathogens.