scholarly journals Chemomechanical Simulation of Microtubule Dynamics With Explicit Lateral Bond Dynamics

2021 ◽  
Vol 9 ◽  
Author(s):  
Matthias Schmidt ◽  
Jan Kierfeld
Keyword(s):  
Structural Features ◽  
Microtubule Dynamics ◽  
Bond Rupture ◽  
Computationally Efficient ◽  
Hydrolysis Process ◽  
Hydrolysis Rates ◽  
Microscopic Features ◽  
Hydrolysis Of ◽  
Insight Into ◽  
Chemomechanical Model

We introduce and parameterize a chemomechanical model of microtubule dynamics on the dimer level, which is based on the allosteric tubulin model and includes attachment, detachment and hydrolysis of tubulin dimers as well as stretching of lateral bonds, bending at longitudinal junctions, and the possibility of lateral bond rupture and formation. The model is computationally efficient such that we reach sufficiently long simulation times to observe repeated catastrophe and rescue events at realistic tubulin concentrations and hydrolysis rates, which allows us to deduce catastrophe and rescue rates. The chemomechanical model also allows us to gain insight into microscopic features of the GTP-tubulin cap structure and microscopic structural features triggering microtubule catastrophes and rescues. Dilution simulations show qualitative agreement with experiments. We also explore the consequences of a possible feedback of mechanical forces onto the hydrolysis process and the GTP-tubulin cap structure.

Hydrolysis Dynamics of Diquat in Aquatic Environment

2014 ◽  
Vol 608-609 ◽  
pp. 1079-1083
Author(s):  
Juan Ying Peng ◽  
Ren Bin Yang
Keyword(s):  
Ground Water ◽  
River Water ◽  
Critical Factor ◽  
Order Reaction ◽  
Deionized Water ◽  
Activation Entropy ◽  
First Order ◽  
Hydrolysis Process ◽  
Hydrolysis Rates ◽  
Hydrolysis Of

The hydrolysis of diquat in deionized water, river water, and ground water were studied by incubation at 25°C and hydrolysis of diquat at different temperature (10°C, 25°C, and 35°C) in pH9 were investigated in the paper. The degradation was followed by GC. The experimental results indicated that the kinetics process of diquat can be described by the first-order reaction law, the hydrolysis rates of diquat in deionized water, river water, and ground water were almost the same; the pH was a critical factor of the rate of the degradation of diquat in aqueous solutions,diquat was stable in acid water and neutral water, but its hydrolysis easily took place in basic water; the higher temperture was helpful for the hydrolysis process during the range from 283k to 308k in basic water, the activation energy of hydrolysis for diquat was 25.89kJ/mol, activation entropy was –191.81 J/mol.K, and the temperature coefficient was 1.52.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools

2019 ◽  
Vol 16 (2) ◽  
pp. 159-172 ◽  
Author(s):  
Elaheh Kashani-Amin ◽  
Ozra Tabatabaei-Malazy ◽  
Amirhossein Sakhteman ◽  
Bagher Larijani ◽  
Azadeh Ebrahim-Habibi
Keyword(s):  
Systematic Review ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Web Of Science ◽  
Secondary Structure Prediction ◽  
Structural Information ◽  
Protein Secondary Structure ◽  
Structural Features ◽  
Prediction Tools ◽  
Insight Into

Background: Prediction of proteins’ secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. Objective: A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Methods: Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. Results: Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. Conclusion: This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.

The Oxford Handbook of the Brazilian Economy

2018 ◽  
Keyword(s):  
Direct Investment ◽  
Global Economy ◽  
Iron Ore ◽  
Structural Features ◽  
Economic Importance ◽  
Closed Economy ◽  
Current Characteristics ◽  
Insight Into ◽  
Contemporary Context ◽  
Over Time

Brazil constitutes a globally vital but troubled economy. It accounts for the largest GDP in Latin America and ranks among the world’s largest exporters of critical commodities including iron ore, soya, coffee, and beef. In recent years Brazil’s global economic importance has been magnified by a surge in both outward and inward foreign direct investment. This has served to further internationalize what has been historically a relatively closed economy. The purpose of this Handbook is to offer real insight into the Brazil’s economic development in contemporary context, understanding its most salient characteristics and analyzing its structural features across various dimensions. At a more granular level, this volume accomplishes the following tasks. First, it provides an understanding of the economy’s evolution over time and the connection of its current characteristics to this evolution. Second, it analyzes Brazil’s broader place in the global economy, and considers the ways in which this role has changed, and is likely to change, over coming years. Third, reflecting contemporary concerns, the volume offers an understanding, not only of how one of the world’s key economies has developed and transformed itself, but also of the ways in which this process has yet to be completed. The volume thus analyzes the current challenges facing the Brazilian economy and the kinds of issues that need to be tackled for these to be addressed.

scholarly journals Cold-Active β-Galactosidases: Insight into Cold Adaption Mechanisms and Biotechnological Exploitation

Marine Drugs ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. 43
Author(s):  
Marco Mangiagalli ◽  
Marina Lotti
Keyword(s):  
Low Temperature ◽  
Molecular Mechanisms ◽  
Building Blocks ◽  
Cold Active ◽  
Cold Adaption ◽  
Glycosyl Donor ◽  
Pharmaceutical Industries ◽  
Biotechnological Processes ◽  
Hydrolysis Of ◽  
Insight Into

β-galactosidases (EC 3.2.1.23) catalyze the hydrolysis of β-galactosidic bonds in oligosaccharides and, under certain conditions, transfer a sugar moiety from a glycosyl donor to an acceptor. Cold-active β-galactosidases are identified in microorganisms endemic to permanently low-temperature environments. While mesophilic β-galactosidases are broadly studied and employed for biotechnological purposes, the cold-active enzymes are still scarcely explored, although they may prove very useful in biotechnological processes at low temperature. This review covers several issues related to cold-active β-galactosidases, including their classification, structure and molecular mechanisms of cold adaptation. Moreover, their applications are discussed, focusing on the production of lactose-free dairy products as well as on the valorization of cheese whey and the synthesis of glycosyl building blocks for the food, cosmetic and pharmaceutical industries.

scholarly journals Cryo-EM structure of amyloid fibrils formed by the entire low complexity domain of TDP-43

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qiuye Li ◽  
W. Michael Babinchak ◽  
Witold K. Surewicz
Keyword(s):  
Amyloid Fibrils ◽  
Low Complexity ◽  
Structural Features ◽  
Protein Fragments ◽  
Hydrophobic Residues ◽  
Backbone Conformation ◽  
Hydrophobic Amino Acids ◽  
Insight Into ◽  
Lateral Sclerosis

AbstractAmyotrophic lateral sclerosis and several other neurodegenerative diseases are associated with brain deposits of amyloid-like aggregates formed by the C-terminal fragments of TDP-43 that contain the low complexity domain of the protein. Here, we report the cryo-EM structure of amyloid formed from the entire TDP-43 low complexity domain in vitro at pH 4. This structure reveals single protofilament fibrils containing a large (139-residue), tightly packed core. While the C-terminal part of this core region is largely planar and characterized by a small proportion of hydrophobic amino acids, the N-terminal region contains numerous hydrophobic residues and has a non-planar backbone conformation, resulting in rugged surfaces of fibril ends. The structural features found in these fibrils differ from those previously found for fibrils generated from short protein fragments. The present atomic model for TDP-43 LCD fibrils provides insight into potential structural perturbations caused by phosphorylation and disease-related mutations.

Insight into the structural features of Zhaotong lignite using multiple techniques

Fuel ◽  
2015 ◽  
Vol 153 ◽  
pp. 176-182 ◽  
Author(s):  
Zhan-Ku Li ◽  
Xian-Yong Wei ◽  
Hong-Lei Yan ◽  
Zhi-Min Zong
Keyword(s):  
Structural Features ◽  
Insight Into

scholarly journals Structural basis for distinct inflammasome complex assembly by human NLRP1 and CARD8

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qin Gong ◽  
Kim Robinson ◽  
Chenrui Xu ◽  
Phuong Thao Huynh ◽  
Kelvin Han Chung Chong ◽  
...  
Keyword(s):  
Cell Death ◽  
Inner Core ◽  
Inflammatory Diseases ◽  
Structural Features ◽  
Structural Basis ◽  
Cultured Human Cells ◽  
Structural Insight ◽  
Sensor Proteins ◽  
Insight Into

AbstractNod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 undergo unique auto-proteolysis-dependent activation and are implicated in auto-inflammatory diseases; however, their mechanisms of activation are not understood. Here we report the structural basis of how the activating domains (FIINDUPA-CARD) of NLRP1 and CARD8 self-oligomerize to assemble distinct inflammasome complexes. Recombinant FIINDUPA-CARD of NLRP1 forms a two-layered filament, with an inner core of oligomerized CARD surrounded by an outer ring of FIINDUPA. Biochemically, self-assembled NLRP1-CARD filaments are sufficient to drive ASC speck formation in cultured human cells—a process that is greatly enhanced by NLRP1-FIINDUPA which forms oligomers in vitro. The cryo-EM structures of NLRP1-CARD and CARD8-CARD filaments, solved here at 3.7 Å, uncover unique structural features that enable NLRP1 and CARD8 to discriminate between ASC and pro-caspase-1. In summary, our findings provide structural insight into the mechanisms of activation for human NLRP1 and CARD8 and reveal how highly specific signaling can be achieved by heterotypic CARD interactions within the inflammasome complexes.

THE WATER-SOLUBLE POLYSACCHARIDES OF DERMATOPHYTES: IV. GALACTOMANNANS I FROM TRICHOPHYTON GRANULOSUM, TRICHOPHYTON INTERDIGITALE, MICROSPORUM QUINCKEANUM, TRICHOPHYTON RUBRUM, AND TRICHOPHYTON SCHÖNLEINII

1965 ◽  
Vol 43 (1) ◽  
pp. 30-39 ◽  
Author(s):  
C. T. Bishop ◽  
M. B. Perry ◽  
F. Blank ◽  
F. P. Cooper
Keyword(s):  
Aqueous Solutions ◽  
Copper Complexes ◽  
Trichophyton Rubrum ◽  
Periodate Oxidation ◽  
Structural Features ◽  
Water Soluble ◽  
Major Constituent ◽  
Branch Points ◽  
Terminal Units ◽  
Hydrolysis Of

A group of polysaccharides, called galactomannans I, were precipitated as their insoluble copper complexes from aqueous solutions of the crude polysaccharides obtained from each of the organisms designated in the title. The five galactomannans I were homogeneous under conditions of electrophoresis and ultracentrifugation and had high positive specific rotations. The major constituent monosaccharide was D-mannose; amounts of D-galactose ranged from nil for the polysaccharide from T. rubrum to 13% for that from T. schönleinii. Methylation and hydrolysis of the five galactomannans I yielded varying amounts of the following: 2,3,5,6-tetra-O-methyl-D-galactose (not present in the products from T. rubrum), 2,3,4,6-tetra-O-methyl-D-mannose, 2,3,4-tri-O-methyl-D-mannose, 2,4,6-tri-O-methyl-D-mannose, 3,4-di-O-methyl-D-mannose, and 3,5-di-O-methyl-D-mannose. Periodate oxidation results agreed with the methylation studies. The gross structural features of each galactomannan I appear to be the same, namely, a basic chain of 1 → 6 linked α-D-mannopyranose units for approximately every 22 of which there is a 1 → 3 linked α-D-mannopyranose residue. Branch points occur along the 1 → 6 linked chain at the C2 positions of the D-mannopyranose units and once in every 45 units at the C2 position of a 1 → 6 linked D-mannofuranose residue. The D-galactose in the polysaccharides is present exclusively as non-reducing terminal furanose units; non-reducing terminal units of D-mannopyranose are also present. The variations in the identities and relative amounts of the non-reducing terminal units were the only apparent differences in the gross structural features within this group of polysaccharides.

Antioxidant Activity of Silk Fibroin Peptide Hydrolyzed by Pancreatin

2014 ◽  
Vol 1081 ◽  
pp. 110-114 ◽  
Author(s):  
Zhen Zhu ◽  
Hua Yin ◽  
Yan An
Keyword(s):  
Antioxidant Activity ◽  
Free Radical ◽  
Nitrogen Content ◽  
Silk Fibroin ◽  
Radical Scavenging ◽  
Amino Nitrogen ◽  
Free Radical Scavenging ◽  
Hydrolysis Process ◽  
Superoxide Free Radical ◽  
Hydrolysis Of

This research adopts the pancreatin hydrolysis of silk fibroin active peptide, evaluate the antioxidant activity of hydrolysates. In the process of hydrolysis of silk fibroin, by measuring the amino nitrogen content of neutral formaldehyde titration method. Find the amino nitrogen content gradually stabilized at around 0.37g/L, and superoxide free radical scavenging rate changing with time fluctuation trend, superoxide free radical scavenging rate to a maximum of 65.03% at 220min.The use of silk fibroin hydrolysis process optimization,reaction time 160min, enzyme concentration4% , substrate concentration 20mg/ml, pH 8, temperature 38°C. The hydrolysis process under the hydrolysate on superoxide radical scavenging rate of 72.73%. The scavenging rate of hydroxyl radical is 47.24%. Red blood cell hemolysis induced by H2O2 inhibition rate was 24.30%.

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