Structural Characterization of Pro-inflammatory and Anti-inflammatory Immunoglobulin G Fc Proteins

Immunoglobulin G (IgG) is central in mediating host defense due to its ability to target and eliminate invading pathogens. The fragment antigen binding (Fab) regions are responsible for antigen recognition; however the effector responses are encoded on the Fc region of IgG. IgG Fc displays considerable glycan heterogeneity, accounting for its complex effector functions of inflammation, modulation and immune suppression. Intravenous immunoglobulin G (IVIG) is pooled serum IgG from multiple donors and is used to treat individuals with autoimmune and inflammatory disorders such as rheumatoid arthritis and Kawasaki’s disease, respectively. It contains all the subtypes of IgG (IgG1-4) and over 120 glycovariants due to variation of an Asparagine 297-linked glycan on the Fc. The species identified as the activating component of IVIG is sialylated IgG Fc. Comparisons of wild type Fc and sialylated Fc X-ray crystal structures suggests that sialylation causes an increase in conformational flexibility, which may be important for its anti-inflammatory properties.

Although glycan modifications can promote the anti-inflammatory properties of the Fc, there are amino acid substitutions that cause Fcs to initiate an enhanced immune response. Mutations in the Fc can cause up to a 100-fold increase in binding affinity to activating Fc gamma receptors located on immune cells, and have been shown to enhance antibody dependent cell-mediated cytotoxicity. This is important in developing therapeutic antibodies against cancer and infectious diseases. Structural studies of mutant Fcs in complex with activating receptors gave insight into new protein-protein interactions that lead to an enhanced binding affinity.

Together these studies show how dynamic and diverse the Fc region is and how both protein and carbohydrate modifications can alter structure, leading to IgG Fc’s switch from a pro-inflammatory to an anti-inflammatory protein.

Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.

Studies of polysaccharides from three edible species of Nostoc (cyanobacteria) with different colony morphologies: Structural characterization and effect on the complement system of polysaccharides from Nostoc commune

The cyanobacterium Nostoc commune Vaucher produces quite complex extracellular polysaccharides. The cyanobacterium is nitrogen fixing, and on growing the cyanobacterium in media with and without nitrogen, different types of extracellular polysaccharides were obtained. These were also different from the polysaccharides present in N. commune collected in the field. High pH anion exchange chromatography (HPAEC) of weak acid hydrolysates of the culture-grown material demonstrated that, in this case, HPAEC was useful for comparison of the different polymers. The main differences between the polymers from the field group and the culture-grown samples were the presence of substantial amounts of arabinose, 2-O-methylglucose, and glucuronic acid in the latter. Methylation studies also revealed a difference in the branching points on the glucose units between the field and cultured samples, being 1,4,6 for the first and 1,3,6 for the latter. The field acidic fraction gave, on weak acid hydrolysis and separation on BioGel P2 and HPAEC, 12 oligosaccharide fractions that were isolated and studied by different mass spectroscopy techniques. The structures of the oligosaccharides were determined, and two different series that can originate from two repeating pentamers were identified: GlcAl-4/6GlcM1-4Ga11-4Glc1-4Xyl and GlcAl-4/6Glc1-4Ga11-4Glc1-4Xyl. The difference between these oligosaccharides lies in the methyl substituent on carbon 2 of the glucose unit next to the nonreducing glucuronic acid unit. The polysaccharides from field material were shown to have a strong effect on the complement system.

Structural characterization of mn implanted AlInN

AlInN/GaN thin films were implanted with Mn ions and subsequently annealed isochronically at 750 and 850 degrees C. X-ray diffraction and Rutherford backscattering spectroscopy (RBS) techniques were employed to study the microstructural properties of the implanted/annealed samples. The effect of annealing on implantation-induced strain in thin films has been studied in detail. The strain was found to increase with dose until it reached a saturation value and after that it started decreasing with a further increase in the dose. RBS measurements indicated the atomic diffusion of In, Al, Ga and Mn in implanted samples. The in- and out-diffusion of atoms has been observed after annealing at 750 degrees C and 850 degrees C, respectively. Strong decomposition of the samples took place when annealed at 850 degrees C.

Structural characterization of AlGaN/GaN superlattices by x-ray diffraction and Rutherford backscattering

We report on structural characterization of AlGaN/GaN superlattices grown on sapphire. The superlattice formation is evidenced by high-resolution x-ray diffraction and transmission electron microscopy. The high resolution x-ray diffraction spectra exhibit a pattern of satellite peaks. The in-plane lattice constants of the superlattices indicate the coherent growth of the AlGaN layer onto GaN. The average At composition in the superlattices is determined to be 0.08 by Rutherford backscattering spectroscopy. The average parallel and perpendicular elastic strains for the SLs are determined to be (e(parallel to)) = +0.25% and (e(perpendicular to)) = -0.17%. (c) 2006 Elsevier Ltd. All rights reserved.

High-precision determination of lattice constants and structural characterization of InN thin films

X-ray diffraction and Rutherford backscattering/channeling were used to characterize the crystalline quality of an InN layer grown on Al2O3(0001) Using metal-organic chemical-vapor deposition. A full width at half maximum of 0.27 degrees from an InN(0002) omega scan and a minimum yield of 23% from channeling measurements show that this 480-nm-thick InN layer grown at low temperature (450 degrees C) has a relatively good crystalline quality. High-resolution x-ray diffraction indicates that the InN layer contains a small fraction of cubic InN, besides the predominant hexagonal phase. From this InN sample, the lattice constants a=0.353 76 nm and c=0.570 64 nm for the hexagonal InN and a=0.4986 nm for the cubic InN were determined independently. 2 theta/omega-chi mapping and a pole figure measurement revealed that the crystallographic relationship among the cubic InN, the hexagonal InN, and the substrate is: InN[111]parallel to InN[0001]parallel to Al2O3[0001] and InN{110}parallel to InN{1120}parallel to Al2O3{1010}, and that the cubic InN is twinned. Photoluminescence measurements indicate that the band-gap energy of this sample is approximately 0.82 eV. (c) 2006 American Vacuum Society.

Structural characterization of epitaxial lateral overgrown GaN on patterned GaN/GaAs(001) substrates

Epitaxial lateral overgrown (ELO) cubic GaN (c-GaN) on SiO2 patterned GaN/GaAs(0 0 1) substrates by metalorganic vapor phase epitaxy was investigated using transmission electron microscopy and X-ray diffraction (XRD) measurements. The density of stacking faults (SFs) in ELO c-GaN was similar to6 x 10(8) cm(-2), while that in underlying GaN template was similar to5 x 10(9) cm(-2). XRD measurements showed that the full-width at half-maximum of c-GaN (0 0 2) rocking curve decreased from 33 to 17.8 arcmin, indicating the improved crystalline quality of ELO c-GaN. The mechanism of SF reduction in ELO c-GaN was also discussed. (C) 2002 Elsevier Science B.V. All rights reserved.

Structural characterization of stable amorphous silicon films

A kind of hydrogenated diphasic, silicon films has been prepared by a new regime of plasma enhanced chemical vapor deposition (PECVD) in the region adjacent to the phase transition from amorphous to crystalline state. The photoelectronic and microstructural properties of the films have been investigated by the constant photocurrent method (CPM), Raman scattering and nuclear magnetic resonance (NMR). Our experimental results and corresponding analyses showed that the diphasic films, incorporated with a subtle boron compensation, could gain both the fine photosensitivity and high stability, provided the crystalline fraction (f) was controlled in the range of 0 < f < 0.3. When compared with the conventional hydrogenated amorphous silicon (a-Si:H), the diphasic films are more ordered and robust in the microstructure, and have a less clustered phase in the Si-H bond configurations. (C) 2002 Elsevier Science Ltd. All rights reserved.