HDX-MS and MD simulations provide evidence for stabilization of the IgG1— FcγRIa (CD64a) immune complex through intermolecular glycoprotein bonds

The two major molecular switches in biology, kinases and GTPases, are both contained in the Parkinson’s Disease-related Leucine-rich repeat kinase 2 (LRRK2). Using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and Molecular Dynamics (MD) simulations, we generated a comprehensive dynamic allosteric portrait of the C-terminal domains of LRRK2 (LRRK2 RCKW). We identified two helices that shield the kinase domain and regulate LRRK2 conformation and function. One docking helix in COR-B (Dk-Helix) tethers the COR-B domain to the αC helix of the kinase domain and faces its Activation Loop, while the C-terminal helix (Ct-Helix) extends from the WD40 domain and interacts with both kinase lobes. The Ct-Helix and the N-terminus of the Dk-Helix create a “cap” that regulates the N-Lobe of the kinase domain. Our analyses reveal allosteric sites for pharmacological intervention and confirm the kinase domain as the central hub for conformational control.

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Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter

Nature Communications ◽

10.1038/s41467-020-20032-3 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Ruyu Jia ◽

Chloe Martens ◽

Mrinal Shekhar ◽

Shashank Pant ◽

Grant A. Pellowe ◽

...

Keyword(s):

Conformational Changes ◽

Conformational Transition ◽

Substrate Binding ◽

Conformational Dynamics ◽

Md Simulations ◽

Allosteric Coupling ◽

Exchange Mass Spectrometry ◽

Hydrogen Deuterium ◽

Deuterium Exchange Mass Spectrometry ◽

Hdx Ms

AbstractProton-coupled transporters use transmembrane proton gradients to power active transport of nutrients inside the cell. High-resolution structures often fail to capture the coupling between proton and ligand binding, and conformational changes associated with transport. We combine HDX-MS with mutagenesis and MD simulations to dissect the molecular mechanism of the prototypical transporter XylE. We show that protonation of a conserved aspartate triggers conformational transition from outward-facing to inward-facing state. This transition only occurs in the presence of substrate xylose, while the inhibitor glucose locks the transporter in the outward-facing state. MD simulations corroborate the experiments by showing that only the combination of protonation and xylose binding, and not glucose, sets up the transporter for conformational switch. Overall, we demonstrate the unique ability of HDX-MS to distinguish between the conformational dynamics of inhibitor and substrate binding, and show that a specific allosteric coupling between substrate binding and protonation is a key step to initiate transport.

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Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter

10.1101/2020.04.03.023564 ◽

2020 ◽

Author(s):

Ruyu Jia ◽

Chloe Martens ◽

Mrinal Shekhar ◽

Shashank Pant ◽

Grant A. Pellowe ◽

...

Keyword(s):

Conformational Changes ◽

Conformational Transition ◽

Substrate Binding ◽

Conformational Dynamics ◽

Md Simulations ◽

Allosteric Coupling ◽

Exchange Mass Spectrometry ◽

Hydrogen Deuterium ◽

Deuterium Exchange Mass Spectrometry ◽

Hdx Ms

AbstractProton-coupled transporters use transmembrane proton gradients to power active transport of nutrients inside the cell. High-resolution structures often fail to capture the coupling between proton and ligand binding, and conformational changes associated with transport. We combine HDX-MS with mutagenesis and MD simulations to dissect the molecular mechanism of the prototypical transporter XylE. We show that protonation of a conserved aspartate triggers conformational transition from outward-facing to inward-facing state. This transition only occurs in the presence of substrate xylose, while the inhibitor glucose locks the transporter in the outward-facing state. MD simulations corroborate the experiments by showing that only the combination of protonation and xylose binding, and not glucose, sets up the transporter for conformational switch. Overall, we demonstrate the unique ability of HDX-MS to distinguish between the conformational dynamics of inhibitor and substrate binding, and show that a specific allosteric coupling between substrate binding and protonation is a key step to initiate transport.

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Experimental Amyloidosis Induced by Immune Complex

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100066978 ◽

1971 ◽

Vol 29 ◽

pp. 582-583

Author(s):

A. Kawaoi

Keyword(s):

Immune Complex ◽

Systemic Amyloidosis ◽

Human Diseases ◽

Experimental Amyloidosis ◽

Freund’S Complete Adjuvant ◽

Freund's Complete Adjuvant ◽

Immunological Approach ◽

Experimentally Induced

Numbers of immunological approach have been made to the amyloidosis through the variety of predisposing human diseases and the experimentally induced animals by the greater number of agents. The results suggest an important role of impaired immunity involving both humoral and cell-mediated aspects.Recently the author has succeeded in producing amyloidosis in the rabbits and mice by the injections of immune complex of heat denatured DNA.The aim of this report is to demonstrate the details of the ultrastructure of the amyloidosis induced by heterologous insoluble immune complex. Eleven of twelve mice, dd strain, subcutaneously injected twice a week with Freund's complete adjuvant and four of seven animals intraperitonially injected developed systemic amyloidosis two months later from the initial injections. The spleens were electron microscopically observed.

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Ultrastructural study of cytoskeletal interactions with endosomes in macrophages by quickfreezing and deep-etching method

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100160431 ◽

1990 ◽

Vol 48 (3) ◽

pp. 576-577

Author(s):

Takeshi Baba ◽

Nobuki Shiozawa ◽

Masao Hotch ◽

Shinichi Ohno

Keyword(s):

Immune Complex ◽

Ultrastructural Study ◽

Fc Receptor ◽

Coated Pits ◽

Deep Etching ◽

Receptor Mediated Endocytosis ◽

Etching Method ◽

Quick Freezing

Endosomes are vesicular or tubular organelles that play important roles in transports of receptors and receptor―bound ligands during receptor-mediated endocytosis. The mechanisms of endocytic transports from clathrin-coated pits to lysosomes have been studied by many investigators. However, few studies were reported about the interactions between endosomes and cytoskeletons. In this study, Fc-receptor-mediated endocytosis in macrophages are investigated by quick-freezing and deep-etching (QF-DE) method combined with gold-labeled immune complex and “replica scraping method”.

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Localization of Immune Complexes in the Basement Membrane of the Ductuli Efferentes of the Rhesus Monkey

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s1431927600001963 ◽

1980 ◽

Vol 38 ◽

pp. 456-457

Author(s):

D. Marsh

Keyword(s):

Basement Membrane ◽

Fluorescence Microscopy ◽

Rhesus Monkey ◽

Immune Complex ◽

Immune Complexes ◽

Vas Deferens ◽

Frozen Sections ◽

Efferent Ducts ◽

Complex Deposition ◽

Sperm Antibodies

As a result of vasectomy, spermatozoa are confined to the epididymis and vas deferens, where they degenerate, releasing antigens that enter the circulation or are engulfed by macrophages. Multiple antigens of the sperm can elicit production of autoantibodies; circulating anti-sperm antibodies are found in a large percentage of vasectomized men, indicating the immunogenicity of the sperm. The increased prevalence of macrophages in the liomen of the rhesus monkey testicular efferent ducts after vasectomy led to further study of this region. Frozen sections were used for evaluation of immunopathological status by fluorescence microscopy with fluorescein-conjugated antibody. Subsequent granular deposits of immune complexes were revealed by positive immunofluorescence staining for complement. The immune complex deposition in the basement membrane surrounding the efferent ducts implies that this region is involved in antigen leakage (Fig. 1).

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Efficient Treatment of Fixed and Induced Dipolar Interactions

MRS Proceedings ◽

10.1557/proc-653-z7.22 ◽

2000 ◽

Vol 653 ◽

Author(s):

Celeste Sagui ◽

Thoma Darden

Keyword(s):

Molecular Dynamics ◽

Md Simulations ◽

Lagrangian Formalism ◽

Dipolar Interactions ◽

Time Step ◽

Efficient Treatment ◽

Particle Mesh Ewald ◽

Fixed Charges ◽

Self Consistency ◽

Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

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Immune Complex Analysis in Active Lyme Disease

Forum on Immunopathological Diseases and Therapeutics ◽

10.1615/forumimmundisther.2017019621 ◽

2016 ◽

Vol 7 (3-4) ◽

pp. 213-224

Author(s):

Steven E. Schutzer ◽

P. K. Coyle

Keyword(s):

Lyme Disease ◽

Immune Complex ◽

Complex Analysis

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Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

10.26434/chemrxiv.11365943.v1 ◽

2019 ◽

Author(s):

Dimitrios Kolokouris ◽

Iris Kalenderoglou ◽

Panagiotis Lagarias ◽

Antonios Kolocouris

Keyword(s):

Molecular Dynamic ◽

Lipid Bilayer ◽

Influenza A ◽

Md Simulations ◽

Membrane Curvature ◽

Buffer Size ◽

M2 Protein ◽

Dynamic Simulations ◽

Amphipathic Helices ◽

Drug Protein Binding

We studied by molecular dynamic (MD) simulations systems including the inwardclosed state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å2 or 20x20 Å2. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å2 lipids buffer in DMPC is needed when M2TM is used but 20x20 Å2 lipids buffer of the softer POPC; when M2AH is used all 10x10 Å2 lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å2 lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å2 lipids buffer and CHARMM36.

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A Hydrogen Bond Between Linear Tetrapyrrole and Conserved Aspartate Causes the Far-Red Shifted Absorption of Phytochrome Photoreceptors

10.26434/chemrxiv.12278780 ◽

2020 ◽

Author(s):

Egle Maximowitsch ◽

Tatiana Domratcheva

Keyword(s):

Hydrogen Bond ◽

Light Adaptation ◽

Positive Charge ◽

Pyrrole Ring ◽

Md Simulations ◽

Spectral Shift ◽

Specific Domain ◽

Study Guides ◽

Rational Engineering ◽

Tuning Mechanism

Photoswitching of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing (Pfr) states triggers light adaptation of plants, bacteria and other organisms. Using quantum chemistry, we elucidate the color-tuning mechanism of phytochromes and identify the origin of the Pfr-state red-shifted spectrum. Spectral variations are explained by resonance interactions of the protonated linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole ring D with the strictly conserved aspartate shifts the positive charge towards ring D thereby inducing the red spectral shift. Our MD simulations demonstrate that formation of the ring D–aspartate hydrogen bond depends on interactions between the chromophore binding domain (CBD) and phytochrome specific domain (PHY). Our study guides rational engineering of fluorescent phytochromes with a far-red shifted spectrum.

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