scholarly journals Endosomal Recycling Defects and Neurodevelopmental Disorders

Cells ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 148
Author(s):  
Shinji Saitoh
Keyword(s):  
Membrane Proteins ◽  
Neurodegenerative Disorders ◽  
Neurodevelopmental Disorders ◽  
Protein Complexes ◽  
Future Perspectives ◽  
Recycling Process ◽  
Pathogenic Variants ◽  
Endosomal Recycling ◽  
Human Disorders ◽  
Relationship Of

The quality and quantity of membrane proteins are precisely and dynamically maintained through an endosomal recycling process. This endosomal recycling is executed by two protein complexes: retromer and recently identified retriever. Defects in the function of retromer or retriever cause dysregulation of many membrane proteins and result in several human disorders, including neurodegenerative disorders such as Alzheimer’s disease and Parkinson´s disease. Recently, neurodevelopmental disorders caused by pathogenic variants in genes associated with retriever were identified. This review focuses on the two recycling complexes and discuss their biological and developmental roles and the consequences of defects in endosomal recycling, especially in the nervous system. We also discuss future perspectives of a possible relationship of the dysfunction of retromer and retriever with neurodevelopmental disorders.

scholarly journals Deformable elastic network refinement for low-resolution macromolecular crystallography

2014 ◽  
Vol 70 (9) ◽  
pp. 2241-2255 ◽  
Author(s):  
Gunnar F. Schröder ◽  
Michael Levitt ◽  
Axel T. Brunger
Keyword(s):  
Membrane Proteins ◽  
Crystal Structures ◽  
Protein Complexes ◽  
Macromolecular Crystallography ◽  
Future Perspectives ◽  
Low Resolution ◽  
Molecular Flexibility ◽  
Elastic Network ◽  
Mosaic Spread ◽  
Refinement Method

Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

scholarly journals Fast Diffusion of the Unassembled PetC1-GFP Protein in the Cyanobacterial Thylakoid Membrane

Life ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 15
Author(s):  
Radek Kaňa ◽  
Gábor Steinbach ◽  
Roman Sobotka ◽  
György Vámosi ◽  
Josef Komenda
Keyword(s):  
Membrane Proteins ◽  
Single Molecule ◽  
Protein Interactions ◽  
Thylakoid Membrane ◽  
Protein Complexes ◽  
Correlation Spectroscopy ◽  
Membrane Microdomains ◽  
Fast Diffusion ◽  
Light Harvesting Complexes ◽  
Term Survival

Biological membranes were originally described as a fluid mosaic with uniform distribution of proteins and lipids. Later, heterogeneous membrane areas were found in many membrane systems including cyanobacterial thylakoids. In fact, cyanobacterial pigment–protein complexes (photosystems, phycobilisomes) form a heterogeneous mosaic of thylakoid membrane microdomains (MDs) restricting protein mobility. The trafficking of membrane proteins is one of the key factors for long-term survival under stress conditions, for instance during exposure to photoinhibitory light conditions. However, the mobility of unbound ‘free’ proteins in thylakoid membrane is poorly characterized. In this work, we assessed the maximal diffusional ability of a small, unbound thylakoid membrane protein by semi-single molecule FCS (fluorescence correlation spectroscopy) method in the cyanobacterium Synechocystis sp. PCC6803. We utilized a GFP-tagged variant of the cytochrome b6f subunit PetC1 (PetC1-GFP), which was not assembled in the b6f complex due to the presence of the tag. Subsequent FCS measurements have identified a very fast diffusion of the PetC1-GFP protein in the thylakoid membrane (D = 0.14 − 2.95 µm2s−1). This means that the mobility of PetC1-GFP was comparable with that of free lipids and was 50–500 times higher in comparison to the mobility of proteins (e.g., IsiA, LHCII—light-harvesting complexes of PSII) naturally associated with larger thylakoid membrane complexes like photosystems. Our results thus demonstrate the ability of free thylakoid-membrane proteins to move very fast, revealing the crucial role of protein–protein interactions in the mobility restrictions for large thylakoid protein complexes.

scholarly journals mCSM-membrane: predicting the effects of mutations on transmembrane proteins

2020 ◽  
Vol 48 (W1) ◽  
pp. W147-W153 ◽  
Author(s):  
Douglas E V Pires ◽  
Carlos H M Rodrigues ◽  
David B Ascher
Keyword(s):  
Membrane Proteins ◽  
Single Point ◽  
Point Mutations ◽  
Web Server ◽  
Protein Coding ◽  
Pathogenic Variants ◽  
Model Protein ◽  
Matthew’S Correlation Coefficient ◽  
Membrane Protein Stability ◽  
User Friendly

Abstract Significant efforts have been invested into understanding and predicting the molecular consequences of mutations in protein coding regions, however nearly all approaches have been developed using globular, soluble proteins. These methods have been shown to poorly translate to studying the effects of mutations in membrane proteins. To fill this gap, here we report, mCSM-membrane, a user-friendly web server that can be used to analyse the impacts of mutations on membrane protein stability and the likelihood of them being disease associated. mCSM-membrane derives from our well-established mutation modelling approach that uses graph-based signatures to model protein geometry and physicochemical properties for supervised learning. Our stability predictor achieved correlations of up to 0.72 and 0.67 (on cross validation and blind tests, respectively), while our pathogenicity predictor achieved a Matthew's Correlation Coefficient (MCC) of up to 0.77 and 0.73, outperforming previously described methods in both predicting changes in stability and in identifying pathogenic variants. mCSM-membrane will be an invaluable and dedicated resource for investigating the effects of single-point mutations on membrane proteins through a freely available, user friendly web server at http://biosig.unimelb.edu.au/mcsm_membrane.

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

scholarly journals Dynamic Relationship of Focal Contacts and Hemidesmosome Protein Complexes in Live Cells

2010 ◽  
Vol 130 (6) ◽  
pp. 1624-1635 ◽  
Author(s):  
Toshiyuki Ozawa ◽  
Daisuke Tsuruta ◽  
Jonathan C.R. Jones ◽  
Masamitsu Ishii ◽  
Kazuo Ikeda ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Live Cells ◽  
Dynamic Relationship ◽  
Focal Contacts ◽  
Relationship Of

scholarly journals Periprotein lipidomes of Saccharomyces cerevisiae provide a flexible environment for conformational changes of membrane proteins

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Joury S van 't Klooster ◽  
Tan-Yun Cheng ◽  
Hendrik R Sikkema ◽  
Aike Jeucken ◽  
Branch Moody ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Small Molecules ◽  
Conformational Changes ◽  
Direct Detection ◽  
Protein Complexes ◽  
Lateral Diffusion ◽  
Low Ph ◽  
Lipid Particles ◽  
High Degree

Yeast tolerates a low pH and high solvent concentrations. The permeability of the plasma membrane (PM) for small molecules is low and lateral diffusion of proteins is slow. These findings suggest a high degree of lipid order, which raises the question of how membrane proteins function in such an environment. The yeast PM is segregated into the Micro-Compartment-of-Can1 (MCC) and Pma1 (MCP), which have different lipid compositions. We extracted proteins from these microdomains via stoichiometric capture of lipids and proteins in styrene-maleic-acid-lipid-particles (SMALPs). We purified SMALP-lipid-protein complexes by chromatography and quantitatively analyzed periprotein lipids located within the diameter defined by one SMALP. Phospholipid and sterol concentrations are similar for MCC and MCP, but sphingolipids are enriched in MCP. Ergosterol is depleted from this periprotein lipidome, whereas phosphatidylserine is enriched relative to the bulk of the plasma membrane. Direct detection of PM lipids in the 'periprotein space' supports the conclusion that proteins function in the presence of a locally disordered lipid state.

scholarly journals Monitoring mitochondrial translation by pulse SILAC

2021 ◽  
Author(s):  
Koshi Imami ◽  
Matthias Selbach ◽  
Yasushi Ishihama
Keyword(s):  
Oxidative Stress ◽  
Amino Acids ◽  
Membrane Proteins ◽  
Translational Regulation ◽  
Isotope Labeling ◽  
Protein Complexes ◽  
Complex Iii ◽  
Mitochondrial Translation ◽  
Mitochondrial Ribosomes ◽  
Hydrophobic Nature

SummaryMitochondrial ribosomes are specialized to translate the 13 membrane proteins encoded in the mitochondrial genome, but it is challenging to quantify mitochondrial translation products due to their hydrophobic nature. Here, we introduce a proteomic method that combines biochemical isolation of mitochondria with pulse stable isotope labeling by amino acids in cell culture (pSILAC). Our method provides the highest protein coverage (quantifying 12 out of the 13 inner-membrane proteins; average 2-fold improvement over previous studies) with the shortest measurement time. We applied this method to uncover the global picture of (post)translational regulation of both mitochondrial- and nuclear-encoded proteins involved in the assembly of protein complexes that mediate oxidative phosphorylation (OXPHOS). The results allow us to infer the assembly order of complex components and/or partners, as exemplified by complex III. This method should be applicable to study mitochondrial translation programs in many contexts, including oxidative stress and mitochondrial disease.

Dual oxidase (DUOX) system genes defects in Children with Congenital Hypothyroidism

Endocrinology ◽  
2021 ◽  
Author(s):  
Fengqi Wang ◽  
Li Xiaole ◽  
Ruixin Ma ◽  
Dehua Zhao ◽  
Shiguo Liu
Keyword(s):  
Congenital Hypothyroidism ◽  
Functional Domain ◽  
Target Region ◽  
Pathogenic Variants ◽  
Significant Difference ◽  
Ef Hand ◽  
Dual Oxidase ◽  
Variation Rate ◽  
Relationship Of

Abstract Purpose The objectives of this study were to analyze the distribution of Dual oxidase (DUOX) system genes (containing DUOX2, DUOX1, DUOXA2 and DUOXA1) variants in children with congenital hypothyroidism and their phenotypes. Methods Target region sequencing technology was performed on DUOX system genes among 606 congenital hypothyroidism (CH) subjects covering all the exon and intron regions. Detailed clinical data were collected for statistical analysis. Results A total of 95 suspected pathogenic variants were detected in the DUOX system genes, showing a 39.11% rate in variant carrying (237/606). DUOX2 was with the highest rate in this study. There were statistical difference in maximum adjusted dose and current dose of L-T4 between the DUOX system genes non-mutated group with the mutated group (p<0.001; p<0.001). The cases in DUOX system genes mutated group were more likely to develop into transient CH (χ 2 = 23.155, p<0.001) and more likely to manifested as goiter or gland-in-situ (χ 2 = 66.139, p<0.001). In addition, there was no significant difference in clinical characteristics between DUOX system genes mono-allelic and non mono-allelic. Although 20% of the variants affected the functional domain regions (EF hand, and FAD and NADPH binding sites), there was no significant effect on the phenotype severity whether the variation is located in the functional domain regions. Conclusions Our results showed the high variation rate of DUOX2 in the DUOX system genes among the Chinese CH patients. And the complex genotype-phenotype relationship of DUOX system genes broadened the understanding of CH phenotype spectrum.

Endocrine Disruptors and Neurobehavioral Disorders

2017 ◽  
Author(s):  
Heather B. Patisaul ◽  
Scott M. Belcher
Keyword(s):  
Endocrine Disruption ◽  
Neurodegenerative Disorders ◽  
Neurodevelopmental Disorders ◽  
Environmental Pollutants ◽  
Autism Spectrum ◽  
Organophosphate Pesticides ◽  
Hyperactivity Disorder ◽  
Experimental Systems ◽  
Neural Disorders ◽  
The Brain

This chapter focuses on the role environmental pollutants are playing in the rapidly rising rate of neurodevelopmental disorders in children. The available EDC data are summarized and analyzed in relation to whether or not evidence supports a role for EDCs as contributing to neural disorders. The distinction between endocrine disruption and neurotoxicity is established by focusing on the differences between toxicants, toxins, and altered endocrine/neuroendocrine effects in organizational alterations of the brain. Evidence from experimental systems demonstrating effects of EDCs on the developing brain and the potential roles for EDCs as bad actors in rising rates of autism spectrum disorder (ASD), and attention deficit hyperactivity disorder (ADHD) are presented in detail. Additional impacts of EDCs on neurodegenerative disorders, including Parkinsons’s disease, are reviewed. The mechanisms of rotenone and paraquat neurodegeneration are compared and contrasted with the evidence and mechanisms of actions for organochlorine and organophosphate pesticides in Parkinsons’s disease.

Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development

2020 ◽  
Vol 60 (1) ◽  
pp. 51-71 ◽  
Author(s):  
Javier García-Nafría ◽  
Christopher G. Tate
Keyword(s):  
Membrane Proteins ◽  
G Protein ◽  
Rational Design ◽  
Protein Complexes ◽  
Host Cells ◽  
X Ray ◽  
X Ray Crystallography ◽  
Receptor Modulation ◽  
Lipid Environment ◽  
Drug Receptors

Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein–coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiological heteromeric receptors in a lipid environment have uncovered the molecular basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR–G protein complexes from three different classes of GPCRs have now been determined by cryo-EM. These structures give detailed insights into molecular interactions with drugs, GPCR–G protein selectivity, how accessory membrane proteins alter receptor–ligand pharmacology, and the mechanism by which HIV uses GPCRs to enter host cells.

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