IN SILICO ANALYSIS OF ACRAL PEELING SKIN SYNDROME: A PROTEOMIC APPROACH

ABSTRACTObjective: Acral peeling skin syndrome (APSS), a rare genetic disorder, indicated by the continuous blistering and shedding of the outer epidermallayers. Transglutaminase 5 (TGM5), a calcium-dependent TGM, present in the epidermis has been implicated as the cause of APSS. An attempt hasbeen made to compare in silico the wild and mutant form of TGM5 and its implication on its interaction with involucrin (IVL).Methods: Comparative modeling was performed using MAESTRO for proteins TGM5 and IVL using templates from the protein databank. Generatedmodel was later refined using side chain refinement and loop refinement. Three-dimensional (3D) structure of TGM5 and IVL was analyzed inPROCHECK, VERIFY3D, and ERRAT was used to assess the reliability of the 3D model. IMPACT package from Schrödinger was used to generate abinding site for calcium ion which is essential for functioning of protein. Energy minimization for the modelled structures was performed usingIMPACT module of Schrodinger. Subsequently, wild type and mutated models of TGM5 was used for performing docking studies with IVL.Results: The structures for TGM5 and IVL were modeled and energy minimized using Schrödinger suite. Conserved calcium binding domain formedby three asparagine residues (N224, N226 and N229) and alanine (A221) corresponding to TGM3 was found in TGM5 at positions 226, 229, 231,and 234. Identification of probable active site for TGM5 was predicted using SiteMap program in Schrödinger. 17 cysteine residues are present inwild type structure of TGM5 and in mutated form G113C, the probability of forming an extra disulfide increases. With the mutation occurring at113 position formation of disulfide bond between C113 and Cys306 increases manifold. This hypothesis was confirmed by the fact that root-meansquaredistance valueofenergyminimized mutatedTGM5whencomparedtonativeTGM5on aligning all561atomswasfoundtobe 0.141 indicatingachange of overallstructureof protein.Conclusion: The mutation G113C is increasing the dynamic nature of the protein to increase as the probability of the formation of disulfide bondincreases.Keywords: Skin, Acral peeling skin syndrome, Glutaminase, Involucrin, Mutation, Interaction

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 angstrom resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 angstrom resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.Peer reviewe

Molecular Dynamics Simulations on the Elastic Properties of Polypropylene Bionanocomposite Reinforced with Cellulose Nanofibrils

Cellulose-reinforced polypropylene bionanocomposites can show improved elastic properties over their pure polypropylene counterparts. We have used equilibrium and non-equilibrium molecular dynamics (MD) simulations to study the elastic properties of polypropylene bionanocomposite systems composed of cellulose nanofibrils (CNF), polypropylene (PP) matrix, and maleic anhydride (MAH) coupling agent. The components of the bionanocomposite were parametrized for compatibility with the AMBER14SB force fields. The elastic properties of pure PP systems converge for the chains with at least 20 monomers. The ratio of cellulose in CNF-PP bionanocomposites strongly affects their elastic properties. The elastic modulus of CNF-PP bionanocomposites shows small improvement when the adhesion between hydrophobic and hydrophilic components is facilitated by a MAH coupling agent. The results demonstrate how fully-atomistic MD simulations can be systematically used to evaluate the elastic properties of CNF-PP bionanocomposites and to make predictions that are in agreement with experiments

Observe while it happens : catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations

Organisms use photo-receptors to react to light. The first step is usually the absorption of a photon by a prosthetic group embedded inside the photo-receptor, often a conjugated chromophore. The electronic changes in the chromophore induced by photo-absorption can trigger a cascade of structural or chemical transformations that culminate into a response to light. Understanding how these proteins have evolved to mediate their activation process has remained challenging because the required time and spacial resolutions are notoriously difficult to achieve experimentally. Therefore, mechanistic insights into photoreceptor activation have been predominantly obtained with computer simulations. Here we briefly outline the challenges associated with such computations and review the progress made in this field.peerReviewe

Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of Bacteriophytochrome

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra.peerReviewe

The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization

Photoactivation of bacteriophytochrome involves a cis–trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications.peerReviewe

Orthotropic liver transplantation for intractable neurological manifestations of Wilson′s disease

Wilson′s disease (WD) is an inherited autosomal recessive disorder characterized by copper accumulation and toxicity, affecting mainly the liver and brain. Orthotopic liver transplantation (OLT) is the definitive therapy for patients with WD. Acute fulminant hepatic failure and decompensated cirrhosis are well-established indications for OLT. Patients with severe neurologic impairment can also be benefited by OLT. Here, we present a patient who underwent OLT for isolated neurological WD

A case of acute graft-versus-host disease in postliver transplantation

Graft-versus-host disease (GVHD) after liver transplantation, although rare, is well documented in liver transplant recipients. In this syndrome, donor T lymphocytes transferred with the graft are activated by alloantigens expressed by host antigen-presenting cells and initiate an immune response against recipient tissues, especially skin, gastrointestinal tract, and hemopoietic tissue. A descriptive study of clinical case and the management includes investigations, diagnosis, and treatment of GVHD. Diagnosis of the GVHD was based on combination of clinical features and histological features on skin biopsy. Possible differential diagnosis was ruled out on the basis of laboratory investigations. Empirical treatment with continuous immunosuppressant and antibiotics were continued. There was a transient response to the treatment with resurgence of the features culminating in multiple organ dysfunction leading to death. This first case of this rare complication in the experience of our institute of nearly one hundred and twenty liver transplantation amounts to the incidence of approximately 0.8%. This is in alignment with the worldwide incidence. The rarity of this complication coupled with fair incidence of infective complications of liver transplantation mimicking it clinically makes the diagnosis of GVHD more difficult until sought after proactively. Moreover, the balance between the immunosuppression and superadded infection thereof with ill-defined and ill-studied treatment options makes the treatment of the complication more difficult thus justifying its high mortality across the world. Although GVHD is a rare complication of LT and the mortality rate remains very high, clinical features represent an important tool for early diagnosis. The prognosis remains poor, and further research is needed to clarify the pathogenesis of GVHD and to provide new therapy

The Evolving Landscape of Exosomes in Neurodegenerative Diseases : Exosomes Characteristics and a Promising Role in Early Diagnosis

Neurodegenerative diseases (ND) remains to be one of the biggest burdens on healthcare systems and serves as a leading cause of disability and death. Alzheimer’s disease (AD) is among the most common of such disorders, followed by Parkinson’s disease (PD). The basic molecular details of disease initiation and pathology are still under research. Only recently, the role of exosomes has been linked to the initiation and progression of these neurodegenerative diseases. Exosomes are small bilipid layer enclosed extracellular vesicles, which were once considered as a cellular waste and functionless. These nano-vesicles of 30–150 nm in diameter carry specific proteins, lipids, functional mRNAs, and high amounts of non-coding RNAs (miRNAs, lncRNAs, and circRNAs). As the exosomes content is known to vary as per their originating and recipient cells, these vesicles can be utilized as a diagnostic biomarker for early disease detection. Here we review exosomes, their biogenesis, composition, and role in neurodegenerative diseases. We have also provided details for their characterization through an array of available techniques. Their updated role in neurodegenerative disease pathology is also discussed. Finally, we have shed light on a novel field of salivary exosomes as a potential candidate for early diagnosis in neurodegenerative diseases and compared the biomarkers of salivary exosomes with other blood/cerebrospinal fluid (CSF) based exosomes within these neurological ailmentsValiderad;2021;Nivå 2;2021-01-13 (johcin)</p