scholarly journals Evolution of polymer formation within the actin superfamily

2017 ◽  
Vol 28 (19) ◽  
pp. 2461-2469 ◽  
Author(s):  
Patrick R. Stoddard ◽  
Tom A. Williams ◽  
Ethan Garner ◽  
Buzz Baum
Keyword(s):  
Convergent Evolution ◽  
Atp Hydrolysis ◽  
Linear Polymers ◽  
Related Protein ◽  
Protein Families ◽  
Structure And Dynamics ◽  
Polymer Formation ◽  
Filament Structure ◽  
Related Proteins ◽  
Actin Superfamily

While many are familiar with actin as a well-conserved component of the eukaryotic cytoskeleton, it is less often appreciated that actin is a member of a large superfamily of structurally related protein families found throughout the tree of life. Actin-related proteins include chaperones, carbohydrate kinases, and other enzymes, as well as a staggeringly diverse set of proteins that use the energy from ATP hydrolysis to form dynamic, linear polymers. Despite differing widely from one another in filament structure and dynamics, these polymers play important roles in ordering cell space in bacteria, archaea, and eukaryotes. It is not known whether these polymers descended from a single ancestral polymer or arose multiple times by convergent evolution from monomeric actin-like proteins. In this work, we provide an overview of the structures, dynamics, and functions of this diverse set. Then, using a phylogenetic analysis to examine actin evolution, we show that the actin-related protein families that form polymers are more closely related to one another than they are to other nonpolymerizing members of the actin superfamily. Thus all the known actin-like polymers are likely to be the descendants of a single, ancestral, polymer-forming actin-like protein.

scholarly journals Plant dynamin-related protein families DRP1 and DRP2 in plant development

2010 ◽  
Vol 38 (3) ◽  
pp. 797-806 ◽  
Author(s):  
Sebastian Y. Bednarek ◽  
Steven K. Backues
Keyword(s):  
Plant Development ◽  
Membrane Trafficking ◽  
Cell Expansion ◽  
Cell Plate ◽  
Biological Knowledge ◽  
Related Protein ◽  
Protein Families ◽  
Cellular Processes ◽  
Domain Structures ◽  
Related Proteins

Two separate families of Arabidopsis dynamin-related proteins, DRP1 and DRP2, have been implicated in clathrin-mediated endocytosis and cell plate maturation during cytokinesis. The present review summarizes the current genetic, biochemical and cell biological knowledge about these two protein families, and suggests key directions for more fully understanding their roles and untangling their function in membrane trafficking. We focus particularly on comparing and contrasting these two protein families, which have very distinct domain structures and are independently essential for Arabidopsis development, yet which have been implicated in very similar cellular processes during cytokinesis and cell expansion.

scholarly journals Multiomics study of a heterotardigrade, Echinisicus testudo, suggests convergent evolution of anhydrobiosis-related proteins in Tardigrada

2020 ◽  
Author(s):  
Yumi Murai ◽  
Maho Yagi-Utsumi ◽  
Masayuki Fujiwara ◽  
Masaru Tomita ◽  
Koichi Kato ◽  
...  
Keyword(s):  
Water Content ◽  
Molecular Mechanism ◽  
Convergent Evolution ◽  
Structural Changes ◽  
Extreme Environments ◽  
Random Coil ◽  
Related Protein ◽  
Α Helix ◽  
Related Proteins

AbstractMany limno-terrestrial tardigrades can enter an ametabolic state upon desiccation, in which the animals can withstand extreme environments. To date, studies of the molecular mechanism have predominantly investigated the class Eutardigrada, and that in the Heterotardigrada, remains elusive. To this end, we report a multiomics study of the heterotardigrade Echiniscus testudo, which is one of the most desiccation-tolerant species. None of the previously identified tardigrade-specific anhydrobiosis-related genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families of novel abundant heat-soluble proteins and the proteins exhibited structural changes from random coil to α-helix as the water content decreased in vitro. These characteristics are analogous to those of anhydrobiosis-related protein in eutardigrades, while there is no conservation at the sequence level. Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada.

scholarly journals Improving Human Induced Pluripotent Stem Cell-Derived Megakaryocyte Differentiation and Platelet Production

2021 ◽  
Vol 22 (15) ◽  
pp. 8224
Author(s):  
Linda Krisch ◽  
Gabriele Brachtl ◽  
Sarah Hochmann ◽  
André Cronemberger Andrade ◽  
Michaela Oeller ◽  
...  
Keyword(s):  
Pluripotent Stem Cells ◽  
Iterative Process ◽  
Pluripotent Stem Cell ◽  
Induced Pluripotent Stem Cell ◽  
Mesoderm Induction ◽  
Related Protein ◽  
Media Composition ◽  
Platelet Production ◽  
Induced Pluripotent ◽  
Related Proteins

Several protocols exist for generating megakaryocytes (MKs) and platelets from human induced pluripotent stem cells (hiPSCs) with limited efficiency. We observed previously that mesoderm induction improved endothelial and stromal differentiation. We, therefore, hypothesized that a protocol modification prior to hemogenic endothelial cell (HEC) differentiation will improve MK progenitor (MKP) production and increase platelet output. We further asked if basic media composition affects MK maturation. In an iterative process, we first compared two HEC induction protocols. We found significantly more HECs using the modified protocol including activin A and CHIR99021, resulting in significantly increased MKs. MKs released comparable platelet amounts irrespective of media conditions. In a final validation phase, we obtained five-fold more platelets per hiPSC with the modified protocol (235 ± 84) compared to standard conditions (51 ± 15; p < 0.0001). The regenerative potency of hiPSC-derived platelets was compared to adult donor-derived platelets by profiling angiogenesis-related protein expression. Nineteen of 24 angiogenesis-related proteins were expressed equally, lower or higher in hiPSC-derived compared to adult platelets. The hiPSC-platelet’s coagulation hyporeactivity compared to adult platelets was confirmed by thromboelastometry. Further stepwise improvement of hiPSC-platelet production will, thus, permit better identification of platelet-mediated regenerative mechanisms and facilitate manufacture of sufficient amounts of functional platelets for clinical application.

scholarly journals Secreted Frizzled Related Proteins in Cardiovascular and Metabolic Diseases

2021 ◽  
Vol 12 ◽  
Author(s):  
Hua Guan ◽  
Jin Zhang ◽  
Jing Luan ◽  
Hao Xu ◽  
Zhenghao Huang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Metabolic Diseases ◽  
Structural Characteristics ◽  
Wnt Signaling Pathway ◽  
Secreted Protein ◽  
Related Protein ◽  
Disease Biomarkers ◽  
Protein Levels ◽  
Related Proteins

Abnormal gene expression and secreted protein levels are accompanied by extensive pathological changes. Secreted frizzled related protein (SFRP) family members are antagonistic inhibitors of the Wnt signaling pathway, and they were recently found to be involved in the pathogenesis of a variety of metabolic diseases, which has led to extensive interest in SFRPs. Previous reports highlighted the importance of SFRPs in lipid metabolism, obesity, type 2 diabetes mellitus and cardiovascular diseases. In this review, we provide a detailed introduction of SFRPs, including their structural characteristics, receptors, inhibitors, signaling pathways and metabolic disease impacts. In addition to summarizing the pathologies and potential molecular mechanisms associated with SFRPs, this review further suggests the potential future use of SFRPs as disease biomarkers therapeutic targets.

Dynamic lattice liquid (DLL) model in computer simulation of the structure and dynamics of polymer condensed systems

e-Polymers ◽  
2012 ◽  
Vol 12 (1) ◽  
Author(s):  
Anna Blim ◽  
Tomasz Kowalczyk
Keyword(s):  
Experimental Validation ◽  
Colloidal Particles ◽  
Excluded Volume ◽  
Linear Polymers ◽  
Simple Liquids ◽  
Structure And Dynamics ◽  
Polymer Liquids ◽  
Bottle Brush ◽  
Condensed Systems ◽  
Good Agreement

AbstractThis review presents the use of Dynamic Lattice Liquid (DLL) model proposed by Pakula and coworkers. In the model polymer liquids are represented as dense systems of macromolecules. The model fulfils requirements of the local continuity and excluded volume conditions. The use of the model for numerical simulations of simple liquids, colloidal particles systems, solutions of linear polymers, branched like bottle-brush or star shaped polymers is described. The use of simulations for the prediction of the properties of the systems and their experimental validation is described. The model is presented as an universal tool for investigation of different systems that provides good agreement between numerical and experimental results for a broad range of the systems and conditions.

Beclin 1, LC3, and p62 expression in paraquat-induced pulmonary fibrosis

2019 ◽  
Vol 38 (7) ◽  
pp. 794-802 ◽  
Author(s):  
G Xu ◽  
X Wang ◽  
H Yu ◽  
C Wang ◽  
Y Liu ◽  
...  
Keyword(s):  
Pulmonary Fibrosis ◽  
Light Chain ◽  
Lung Fibrosis ◽  
Beclin 1 ◽  
Related Protein ◽  
Protein Expressions ◽  
Hematoxylin And Eosin ◽  
Hematoxylin And Eosin Staining ◽  
Related Proteins

Paraquat (PQ) is a highly toxic herbicide to humans. Pulmonary fibrosis is one of the most typical features of PQ poisoning, which develops from several days to weeks after ingestion. However, the mechanism of fibrosis is still unclear. In this study, we aimed to determine expressions of autophagy-related markers Beclin 1, microtubule-associated protein light chain 3 (LC3), and p62 in PQ-poisoned lungs and to explore the role of autophagy in pulmonary fibrosis induced by PQ. We detected markers of lung fibrosis and expressions of autophagy-related protein in the specimens from eight fatal cases of PQ poisoning by hematoxylin and eosin staining, Masson’s trichrome staining, and immunohistochemistry. Based on the staining results of lung fibrosis, these cases were divided into two groups, fibrosis and non-fibrosis groups. The correlation between autophagy protein expressions and pulmonary fibrosis was examined. The results demonstrated that the autophagy-related proteins were significantly expressed in fibrosis group compared with the non-fibrosis group. There was a significantly positive correlation between these protein expressions and severity of lung fibrosis. In conclusion, autophagy dysfunction may be involved in lung fibrogenesis caused by PQ poisoning. This may be a promising clue for understanding the molecular mechanism underlying PQ-induced lung fibrosis and provide evidence for treating fibrosis by regulating the level of autophagy.

scholarly journals Ca2+-dependent regulation of vascular smooth-muscle caldesmon by S.100 and related smooth-muscle proteins

1991 ◽  
Vol 277 (3) ◽  
pp. 819-824 ◽  
Author(s):  
K Pritchard ◽  
S B Marston
Keyword(s):  
Smooth Muscle ◽  
Smooth Muscle Actin ◽  
Bovine Brain ◽  
Protein Yield ◽  
Muscle Actin ◽  
Muscle Proteins ◽  
Related Protein ◽  
Thin Filaments ◽  
S 100 ◽  
Related Proteins

1. We have investigated the ability of bovine brain S.100, and of three related proteins from sheep aorta smooth muscle, to confer Ca(2+)-sensitivity on thin filaments reconstituted from smooth-muscle actin, tropomyosin and caldesmon. 2. At 37 degrees C in pH 7.0 buffer containing 120 mM-KCl, approximately stoichiometric amounts of S.100 reversed caldesmon's inhibition of the activation of myosin MgATPase by smooth-muscle actin-tropomyosin. The [S.100] which reversed by 50% the inhibition by caldesmon (the E.C.50) was 2.5 microM when [caldesmon] = 2-3 microM in the assay mixture. When [KCl] was decreased to 70 mM, E.C.50 = 11.5 microM; at 25 degrees C in 70 mM-KCl, up to 20 microM-S.100 had no effect. When skeletal-muscle actin rather than smooth-muscle actin was used to reconstitute thin filaments, 20 microM-S.100 did reverse inhibition by caldesmon, at 25 degrees C in buffer containing 70 mM-KCl. This dependence on conditions is also characteristic of the calmodulin-caldesmon interaction. 3. These results suggested that S.100 or a related protein might interact with caldesmon in smooth muscle. We therefore attempted to prepare such a protein from sheep aorta. Three proteins were purified: an Mr-17,000 protein (yield 16 mg/kg), an abundant Mr-11,000 protein (yield 48 mg/kg), and an Mr-9000 protein (yield 4 mg/kg). Neither of the last two low-Mr proteins had any effect on activation of myosin MgATPase by reconstituted thin filaments. The protein of Mr 17,000 had Ca(2+)-sensitizing activity, and behaved exactly like brain calmodulin in the assay system.

scholarly journals Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families

2019 ◽  
Vol 47 (W1) ◽  
pp. W308-W314 ◽  
Author(s):  
Dmitry Suplatov ◽  
Daria Timonina ◽  
Yana Sharapova ◽  
Vytas Švedas
Keyword(s):  
Disulfide Bonds ◽  
Web Server ◽  
Bioinformatic Analysis ◽  
Protein Families ◽  
Sequence Alignments ◽  
Interactive Analysis ◽  
Functionally Diverse ◽  
Available Information ◽  
Related Proteins

Abstract Disulfide bonds play a significant role in protein stability, function or regulation but are poorly conserved among evolutionarily related proteins. The Yosshi can help to understand the role of S–S bonds by comparing sequences and structures of homologs with diverse properties and different disulfide connectivity patterns within a common structural fold of a superfamily, and assist to select the most promising hot-spots to improve stability of proteins/enzymes or modulate their functions by introducing naturally occurring crosslinks. The bioinformatic analysis is supported by the integrated Mustguseal web-server to construct large structure-guided sequence alignments of functionally diverse protein families that can include thousands of proteins based on all available information in public databases. The Yosshi+Mustguseal is a new integrated web-tool for a systematic homology-driven analysis and engineering of S–S bonds that facilitates a broader interpretation of disulfides not just as a factor of structural stability, but rather as a mechanism to implement functional diversity within a superfamily. The results can be downloaded as a content-rich PyMol session file or further studied online using the HTML5-based interactive analysis tools. Both web-servers are free and open to all users at https://biokinet.belozersky.msu.ru/yosshi and there is no login requirement.

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