scholarly journals Fibronectin Extra Domains tune cellular responses and confer topographically distinct features to fibril networks

2021 ◽  
Vol 134 (4) ◽  
pp. jcs252957 ◽  
Author(s):  
Georgios Efthymiou ◽  
Agata Radwanska ◽  
Anca-Ioana Grapa ◽  
Stéphanie Beghelli-de la Forest Divonne ◽  
Dominique Grall ◽  
...  
Keyword(s):  
Cellular Responses ◽  
Structural Features ◽  
Ph Homeostasis ◽  
Analysis Pipeline ◽  
The Matrix ◽  
Alternatively Spliced ◽  
And Function ◽  
Distinct Features ◽  
Functional Versatility ◽  
Cellular Fibronectin

ABSTRACTCellular fibronectin (FN; also known as FN1) variants harboring one or two alternatively spliced so-called extra domains (EDB and EDA) play a central bioregulatory role during development, repair processes and fibrosis. Yet, how the extra domains impact fibrillar assembly and function of the molecule remains unclear. Leveraging a unique biological toolset and image analysis pipeline for direct comparison of the variants, we demonstrate that the presence of one or both extra domains impacts FN assembly, function and physical properties of the matrix. When presented to FN-null fibroblasts, extra domain-containing variants differentially regulate pH homeostasis, survival and TGF-β signaling by tuning the magnitude of cellular responses, rather than triggering independent molecular switches. Numerical analyses of fiber topologies highlight significant differences in variant-specific structural features and provide a first step for the development of a generative model of FN networks to unravel assembly mechanisms and investigate the physical and functional versatility of extracellular matrix landscapes.This article has an associated First Person interview with the first author of the paper.

Electron microscopy and diffraction studies of polyimides

1983 ◽  
Vol 41 ◽  
pp. 28-29
Author(s):  
O.C. de Hodgins ◽  
K. R. Lawless ◽  
R. Anderson
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Structural Features ◽  
Inert Atmosphere ◽  
Polyimide Films ◽  
Resolution Electron ◽  
The Matrix ◽  
High Resolution Electron Microscope ◽  
Diffraction Patterns ◽  
Polymeric Samples

Commercial polyimide films have shown to be homogeneous on a scale of 5 to 200 nm. The observation of Skybond (SKB) 705 and PI5878 was carried out by using a Philips 400, 120 KeV STEM. The objective was to elucidate the structural features of the polymeric samples. The specimens were spun and cured at stepped temperatures in an inert atmosphere and cooled slowly for eight hours. TEM micrographs showed heterogeneities (or nodular structures) generally on a scale of 100 nm for PI5878 and approximately 40 nm for SKB 705, present in large volume fractions of both specimens. See Figures 1 and 2. It is possible that the nodulus observed may be associated with surface effects and the structure of the polymers be regarded as random amorphous arrays. Diffraction patterns of the matrix and the nodular areas showed different amorphous ring patterns in both materials. The specimens were viewed in both bright and dark fields using a high resolution electron microscope which provided magnifications of 100,000X or more on the photographic plates if desired.

kangaroo, a Mobile Element From Volvox carteri, Is a Member of a Newly Recognized Third Class of Retrotransposons

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1617-1630
Author(s):  
Leonard Duncan ◽  
Kristine Bouckaert ◽  
Fay Yeh ◽  
David L Kirk
Keyword(s):  
Genomic Structure ◽  
Mobile Element ◽  
Direct Repeat ◽  
Structural Features ◽  
Volvox Carteri ◽  
Developmentally Regulated ◽  
Closed Circle ◽  
Integration Mechanisms ◽  
And Function

Abstract Retrotransposons play an important role in the evolution of genomic structure and function. Here we report on the characterization of a novel retrotransposon called kangaroo from the multicellular green alga, Volvox carteri. kangaroo elements are highly mobile and their expression is developmentally regulated. They probably integrate via double-stranded, closed-circle DNA intermediates through the action of an encoded recombinase related to the λ-site-specific integrase. Phylogenetic analysis indicates that kangaroo elements are closely related to other unorthodox retrotransposons including PAT (from a nematode), DIRS-1 (from Dictyostelium), and DrDIRS1 (from zebrafish). PAT and kangaroo both contain split direct repeat (SDR) termini, and here we show that DIRS-1 and DrDIRS1 elements contain terminal features structurally related to SDRs. Thus, these mobile elements appear to define a third class of retrotransposons (the DIRS1 group) that are unified by common structural features, genes, and integration mechanisms, all of which differ from those of LTR and conventional non-LTR retrotransposons.

scholarly journals Cysteine-Free Proteins in the Immunobiology of Arthropod-Borne Diseases

2010 ◽  
Vol 2010 ◽  
pp. 1-10 ◽  
Author(s):  
J. Santiago Mejia ◽  
Erik N. Arthun ◽  
Richard G. Titus
Keyword(s):  
Plasmodium Falciparum ◽  
Amino Acid ◽  
Distribution Patterns ◽  
Structural Features ◽  
Structure And Function ◽  
Cysteine Residues ◽  
Distribution Analysis ◽  
And Function ◽  
Abundance And Distribution ◽  
Host Parasite

One approach to identify epitopes that could be used in the design of vaccines to control several arthropod-borne diseases simultaneously is to look for common structural features in the secretome of the pathogens that cause them. Using a novel bioinformatics technique, cysteine-abundance and distribution analysis, we found that many different proteins secreted by several arthropod-borne pathogens, includingPlasmodium falciparum, Borrelia burgdorferi, and eight species of Proteobacteria, are devoid of cysteine residues. The identification of three cysteine-abundance and distribution patterns in several families of proteins secreted by pathogenic and nonpathogenic Proteobacteria, and not found when the amino acid analyzed was tryptophan, provides evidence of forces restricting the content of cysteine residues in microbial proteins during evolution. We discuss these findings in the context of protein structure and function, antigenicity and immunogenicity, and host-parasite relationships.

scholarly journals Proteomic profiling of the mitochondrial ribosome identifies Atp25 as a composite mitochondrial precursor protein

2016 ◽  
Vol 27 (20) ◽  
pp. 3031-3039 ◽  
Author(s):  
Michael W. Woellhaf ◽  
Frederik Sommer ◽  
Michael Schroda ◽  
Johannes M. Herrmann
Keyword(s):  
Precursor Protein ◽  
Ribosomal Biogenesis ◽  
Proteomic Profiling ◽  
Mitochondrial Translation ◽  
Bacterial Ribosome ◽  
Mitochondrial Ribosome ◽  
Translation Apparatus ◽  
The Matrix ◽  
Processing Peptidase ◽  
And Function

Whereas the structure and function of cytosolic ribosomes are well characterized, we only have a limited understanding of the mitochondrial translation apparatus. Using SILAC-based proteomic profiling, we identified 13 proteins that cofractionated with the mitochondrial ribosome, most of which play a role in translation or ribosomal biogenesis. One of these proteins is a homologue of the bacterial ribosome-silencing factor (Rsf). This protein is generated from the composite precursor protein Atp25 upon internal cleavage by the matrix processing peptidase MPP, and in this respect, it differs from all other characterized mitochondrial proteins of baker’s yeast. We observed that cytosolic expression of Rsf, but not of noncleaved Atp25 protein, is toxic. Our results suggest that eukaryotic cells face the challenge of avoiding negative interference from the biogenesis of their two distinct translation machineries.

scholarly journals Proteolytic Events of Wound-Healing — Coordinated Interactions Among Matrix Metalloproteinases (MMPs), Integrins, and Extracellular Matrix Molecules

2001 ◽  
Vol 12 (5) ◽  
pp. 373-398 ◽  
Author(s):  
Bjorn Steffensen ◽  
Lari Häkkinen ◽  
Hannu Larjava
Keyword(s):  
Extracellular Matrix ◽  
Wound Healing ◽  
Matrix Metalloproteinases ◽  
Wound Repair ◽  
Enzyme Activation ◽  
Processing Enzymes ◽  
The Matrix ◽  
Signaling Receptors ◽  
State Of Rest ◽  
And Function

During wound-healing, cells are required to migrate rapidly into the wound site via a proteolytically generated pathway in the provisional matrix, to produce new extracellular matrix, and, subsequently, to remodel the newly formed tissue matrix during the maturation phase. Two classes of molecules cooperate closely to achieve this goal, namely, the matrix adhesion and signaling receptors, the integrins, and matrix-degrading and -processing enzymes, the matrix metalloproteinases (MMPs). There is now substantial experimental evidence that blocking key molecules of either group will prevent or seriously delay wound-healing. It has been known for some time now that cell adhesion by means of the integrins regulates the expression of MMPs. In addition, certain MMPs can bind to integrins or other receptors on the cell surface involved in enzyme activation, thereby providing a mechanism for localized matrix degradation. By proteolytically modifying the existing matrix molecules, the MMPs can then induce changes in cell behavior and function from a state of rest to migration. During wound repair, the expression of integrins and MMPs is simultaneously up-regulated. This review will focus on those aspects of the extensive knowledge of fibroblast and keratinocyte MMPs and integrins in biological processes that relate to wound-healing.

Abstract 250: Haploinsufficiency of Muscle-Enriched A-Type Lamin Interacting Protein (MLIP) Manifests as Enlarged Dilated Hearts

2012 ◽  
Vol 111 (suppl_1) ◽  
Author(s):  
Patrick Burgon ◽  
Julia Lockwood ◽  
Glenn Wells ◽  
Alexandre Blais
Keyword(s):  
Heart Development ◽  
Left Ventricular ◽  
Lamin A ◽  
Interacting Protein ◽  
Cellular Hypertrophy ◽  
Cellular Source ◽  
Alternatively Spliced ◽  
Normal Body Weight ◽  
Heart Size ◽  
And Function

Approximately 116 unique mutations in the lamin A/C gene have been described to date that are associated with dilated cardiomyopathy. We recently reported the discovery of MLIP through its interaction with lamin A/C. MLIP is expressed ubiquitously and most abundantly in heart, skeletal and smooth muscle of amniotes (mammals, reptiles and birds) and has no paralogous homologue suggesting no functional redundancy. The MLIP gene encodes at least seven, alternatively spliced, LMNA-interacting factors that possess several structural motifs not found in any other protein. The MLIP isoforms pattern of expression differs between each of the tissues with heart being the most heterogeneous. Down-regulation of lamin A/C expression by shRNA results in the up-regulation and mis-localization of MLIP. In addition to interacting and co-localizing with lamin A/C we also demonstrated that MLIP localizes to micro-domains in the nucleus with promyelocytic leukemia protein (PML) in close proximity to chromatin. MLIP's biological function still remains elusive. Eight week old hemizygous MLIP null mice develop enlarged hearts with a significant increase in heart to body weights (MLIP+/+ 5.62mg/g vs MLIP+/- 10.73mg/g, p<0.0001 n=7) with an overall 30% increase in the anterior-posterior ventricle length of MLIP hearts while maintaining a normal body weight (Figure). Echocardiographic analysis of MLIP+/- mice revealed that their hearts as having a significant (p3.93mm with a significant (p=0.011, n=12) reduction of left ventricular fractional shorting (LVFS) 31% when compare to littermate controls. Histological analysis of the hearts showed no overt phenotype other than an overall increase in the size of the MLIP+/- hearts. The cellular source for the increase in heart size and mass remains to be determined if it is the product of an increase in the number of cardiomyocytes due to aberrant hyperplasia or an increase in cardiomyocyte size through cellular hypertrophy. In conclusion, MLIP is a newly discovered lamin interacting protein that may serve as a transcriptional regulator that impact genes involved in heart development, growth and function and provides a new signaling paradigm.

Extracellular vesicle interplay in cardiovascular pathophysiology

2021 ◽  
Author(s):  
Sherin Saheera ◽  
Vivek P Jani ◽  
Kenneth W Witwer ◽  
Shelby Kutty
Keyword(s):  
Plasma Membrane ◽  
Cardiovascular System ◽  
Lipid Bilayer ◽  
Cellular Responses ◽  
Extracellular Vesicle ◽  
Cargo Proteins ◽  
And Function ◽  
Intercellular Communications ◽  
Rna And Dna

Extracellular vesicles (EVs) are nanosized lipid bilayer-delimited particles released from cells that mediate intercellular communications and play a pivotal role in various physiological and pathological processes. Subtypes of EVs may include plasma-membrane ectosomes or microvesicles and endosomal-origin exosomes, although functional distinctions remain unclear. EVs carry cargo proteins, nucleic acids (RNA and DNA), lipids, and metabolites. By presenting or transferring this cargo to recipient cells, EVs can trigger cellular responses. Here, we summarize what is known about EV biogenesis, composition, and function, with an emphasis on the role of EVs in cardiovascular system. Additionally, we provide an update on the function of EVs in cardiovascular pathophysiology, further highlighting their potential for diagnostic and therapeutic applications.

scholarly journals Structure and function of factor XI

Blood ◽  
2010 ◽  
Vol 115 (13) ◽  
pp. 2569-2577 ◽  
Author(s):  
Jonas Emsley ◽  
Paul A. McEwan ◽  
David Gailani
Keyword(s):  
Catalytic Domain ◽  
Structural Features ◽  
Factor Ix ◽  
Missense Mutations ◽  
Factor Xi ◽  
Disk Structure ◽  
Ligand Binding Sites ◽  
And Function ◽  
Insight Into

AbstractFactor XI (FXI) is the zymogen of an enzyme (FXIa) that contributes to hemostasis by activating factor IX. Although bleeding associated with FXI deficiency is relatively mild, there has been resurgence of interest in FXI because of studies indicating it makes contributions to thrombosis and other processes associated with dysregulated coagulation. FXI is an unusual dimeric protease, with structural features that distinguish it from vitamin K–dependent coagulation proteases. The recent availability of crystal structures for zymogen FXI and the FXIa catalytic domain have enhanced our understanding of structure-function relationships for this molecule. FXI contains 4 “apple domains” that form a disk structure with extensive interfaces at the base of the catalytic domain. The characterization of the apple disk structure, and its relationship to the catalytic domain, have provided new insight into the mechanism of FXI activation, the interaction of FXIa with the substrate factor IX, and the binding of FXI to platelets. Analyses of missense mutations associated with FXI deficiency have provided additional clues to localization of ligand-binding sites on the protein surface. Together, these data will facilitate efforts to understand the physiology and pathology of this unusual protease, and development of therapeutics to treat thrombotic disorders.

scholarly journals Mapping the glycosyltransferase fold landscape using interpretable deep learning

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rahil Taujale ◽  
Zhongliang Zhou ◽  
Wayland Yeung ◽  
Kelley W. Moremen ◽  
Sheng Li ◽  
...  
Keyword(s):  
Deep Learning ◽  
Secondary Structure ◽  
Structural Features ◽  
Functional Diversification ◽  
Sequence Structure ◽  
Cellular Processes ◽  
And Function ◽  
Deep Learning Model ◽  
Fold Prediction ◽  
Primary Sequence Alignment

AbstractGlycosyltransferases (GTs) play fundamental roles in nearly all cellular processes through the biosynthesis of complex carbohydrates and glycosylation of diverse protein and small molecule substrates. The extensive structural and functional diversification of GTs presents a major challenge in mapping the relationships connecting sequence, structure, fold and function using traditional bioinformatics approaches. Here, we present a convolutional neural network with attention (CNN-attention) based deep learning model that leverages simple secondary structure representations generated from primary sequences to provide GT fold prediction with high accuracy. The model learns distinguishing secondary structure features free of primary sequence alignment constraints and is highly interpretable. It delineates sequence and structural features characteristic of individual fold types, while classifying them into distinct clusters that group evolutionarily divergent families based on shared secondary structural features. We further extend our model to classify GT families of unknown folds and variants of known folds. By identifying families that are likely to adopt novel folds such as GT91, GT96 and GT97, our studies expand the GT fold landscape and prioritize targets for future structural studies.

scholarly journals In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1395
Author(s):  
Shahram Mesdaghi ◽  
David L. Murphy ◽  
Filomeno Sánchez Rodríguez ◽  
J. Javier Burgos-Mármol ◽  
Daniel J. Rigden
Keyword(s):  
Ab Initio ◽  
Rotational Symmetry ◽  
Domain Boundary ◽  
Pfam Domain ◽  
Transmembrane Proteins ◽  
Large Family ◽  
Data Bank ◽  
Structural Features ◽  
Structure And Function ◽  
And Function

Background: Recent strides in computational structural biology have opened up an opportunity to understand previously uncharacterised proteins.  The under-representation of transmembrane proteins in the Protein Data Bank highlights the need to apply new and advanced bioinformatics methods to shed light on their structure and function.  This study focuses on a family of transmembrane proteins containing the Pfam domain PF09335 ('SNARE_ASSOC'/ ‘VTT ‘/’Tvp38’). One prominent member, Tmem41b, has been shown to be involved in early stages of autophagosome formation and is vital in mouse embryonic development as well as being identified as a viral host factor of SARS-CoV-2. Methods: We used evolutionary covariance-derived information to construct and validate ab initio models, make domain boundary predictions and infer local structural features.  Results: The results from the structural bioinformatics analysis of Tmem41b and its homologues showed that they contain a tandem repeat that is clearly visible in evolutionary covariance data but much less so by sequence analysis.  Furthermore, cross-referencing of other prediction data with covariance analysis showed that the internal repeat features two-fold rotational symmetry.  Ab initio modelling of Tmem41b and homologues reinforces these structural predictions.  Local structural features predicted to be present in Tmem41b were also present in Cl-/H+ antiporters.  Conclusions: The results of this study strongly point to Tmem41b and its homologues being transporters for an as-yet uncharacterised substrate and possibly using H+ antiporter activity as its mechanism for transport.

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