scholarly journals Structural studies of MMP-3 interaction with triple-helical collagen introduce the enzyme’s new roles in tissue remodelling

2019 ◽  
Author(s):  
Szymon W. Manka ◽  
Dominique Bihan ◽  
Richard W. Farndale
Keyword(s):  
Triple Helix ◽  
Binding Mode ◽  
Dependent Manner ◽  
Tissue Remodelling ◽  
Collagen Binding ◽  
Matrix Metalloproteinase 3 ◽  
Interaction Sites ◽  
Binding Data ◽  
Collagen Iii ◽  
The Individual

AbstractMatrix metalloproteinase-3 (MMP-3 or stromelysin 1) participates in normal extracellular matrix (ECM) turnover during embryonic development, organ morphogenesis and wound healing, and in tissue-destructive diseases, such as aneurysm, cancer, arthritis and heart failure. Despite its ability to hydrolyse numerous proteins in the ECM, MMP-3 fails to cleave the triple helix of interstitial fibrillar collagens. Nonetheless, it can still bind to these collagens although the mechanism, location and role of binding are not known. We used the Collagen Toolkits, libraries of triple-helical peptides that embrace the entire helical domains of collagens II and III, to map MMP-3 interaction sites. The enzyme recognises five sites on collagen II and three sites on collagen III. They share a glycine-phenylalanine-hydroxyproline/alanine (GFO/A) motif that is recognised by the enzyme in a context-dependent manner. Neither MMP-3 zymogen (proMMP-3) nor the individual catalytic (Cat) and hemopexin (Hpx) domains of MMP-3 interact with the peptides, revealing cooperative binding of both domains to the triple helix. The Toolkit binding data combined with molecular modelling enabled us to deduce the putative collagen-binding mode of MMP-3, where all three collagen chains make contacts with the enzyme in the valley running across both Cat and Hpx domains. The observed binding pattern casts light on how MMP-3 could regulate collagen turnover and compete with various collagen-binding proteins regulating cell adhesion and proliferation.

scholarly journals Structural studies of the MMP-3 interaction with triple-helical collagen introduce new roles for the enzyme in tissue remodelling

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Szymon W. Manka ◽  
Dominique Bihan ◽  
Richard W. Farndale
Keyword(s):  
Binding Mode ◽  
Dependent Manner ◽  
Tissue Destruction ◽  
Tissue Remodelling ◽  
Collagen Binding ◽  
Matrix Metalloproteinase 3 ◽  
Interaction Sites ◽  
Binding Data ◽  
Collagen Iii ◽  
The Individual

AbstractMatrix metalloproteinase-3 (MMP-3) participates in normal extracellular matrix turnover during embryonic development, organ morphogenesis and wound healing, and in tissue-destruction associated with aneurysm, cancer, arthritis and heart failure. Despite its inability to cleave triple-helical collagens, MMP-3 can still bind to them, but the mechanism, location and role of binding are not known. We used the Collagen Toolkits, libraries of triple-helical peptides that embrace the entire helical domains of collagens II and III, to map MMP-3 interaction sites. The enzyme recognises five sites on collagen II and three sites on collagen III. They share a glycine-phenylalanine-hydroxyproline/alanine (GFO/A) motif that is recognised by the enzyme in a context-dependent manner. Neither MMP-3 zymogen (proMMP-3) nor the individual catalytic (Cat) and hemopexin (Hpx) domains of MMP-3 interact with the peptides, revealing cooperative binding of both domains to the triple helix. The Toolkit binding data combined with molecular modelling enabled us to deduce the putative collagen-binding mode of MMP-3, where all three collagen chains make contacts with the enzyme in the valley running across both Cat and Hpx domains. The observed binding pattern casts light on how MMP-3 could regulate collagen turnover and compete with various collagen-binding proteins regulating cell adhesion and proliferation.

scholarly journals In VitroAnalyses of the Effects of Heparin and Parabens on Candida albicans Biofilms and Planktonic Cells

2011 ◽  
Vol 56 (1) ◽  
pp. 148-153 ◽  
Author(s):  
Marisa H. Miceli ◽  
Stella M. Bernardo ◽  
T. S. Neil Ku ◽  
Carla Walraven ◽  
Samuel A. Lee
Keyword(s):  
Candida Albicans ◽  
Metabolic Activity ◽  
Biofilm Formation ◽  
High Dose ◽  
Dependent Manner ◽  
Planktonic Cells ◽  
Content Type ◽  
Heparin Sodium ◽  
The Individual

ABSTRACTInfections and thromboses are the most common complications associated with central venous catheters. Suggested strategies for prevention and management of these complications include the use of heparin-coated catheters, heparin locks, and antimicrobial lock therapy. However, the effects of heparin onCandida albicansbiofilms and planktonic cells have not been previously studied. Therefore, we sought to determine thein vitroeffect of a heparin sodium preparation (HP) on biofilms and planktonic cells ofC. albicans. Because HP contains two preservatives, methyl paraben (MP) and propyl paraben (PP), these compounds and heparin sodium without preservatives (Pure-H) were also tested individually. The metabolic activity of the mature biofilm after treatment was assessed using XTT [2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] reduction and microscopy. Pure-H, MP, and PP caused up to 75, 85, and 60% reductions of metabolic activity of the mature preformedC. albicansbiofilms, respectively. Maximal efficacy against the mature biofilm was observed with HP (up to 90%) compared to the individual compounds (P< 0.0001). Pure-H, MP, and PP each inhibitedC. albicansbiofilm formation up to 90%. A complete inhibition of biofilm formation was observed with HP at 5,000 U/ml and higher. When tested against planktonic cells, each compound inhibited growth in a dose-dependent manner. These data indicated that HP, MP, PP, and Pure-H havein vitroantifungal activity againstC. albicansmature biofilms, formation of biofilms, and planktonic cells. Investigation of high-dose heparin-based strategies (e.g., heparin locks) in combination with traditional antifungal agents for the treatment and/or prevention ofC. albicansbiofilms is warranted.

scholarly journals Antiviral Activity of the PropylamylatinTM Formula against the Novel Coronavirus SARS-CoV-2 In Vitro Using Direct Injection and Gas Assays in Virus Suspensions

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 415
Author(s):  
Ashley N. Brown ◽  
Gary Strobel ◽  
Kaley C. Hanrahan ◽  
Joe Sears
Keyword(s):  
Propionic Acid ◽  
Infectious Virus ◽  
Direct Injection ◽  
Plaque Assay ◽  
Antiviral Effect ◽  
Dependent Manner ◽  
Global Public Health ◽  
Novel Coronavirus ◽  
The Individual

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of novel coronavirus disease 2019 (COVID-19), has become a severe threat to global public health. There are currently no antiviral therapies approved for the treatment or prevention of mild to moderate COVID-19 as remdesivir is only approved for severe COVID-19 cases. Here, we evaluated the antiviral potential of a Propylamylatin formula, which is a mixture of propionic acid and isoamyl hexanoates. The Propylamylatin formula was investigated in gaseous and liquid phases against 1 mL viral suspensions containing 105 PFU of SARS-CoV-2. Viral suspensions were sampled at various times post-exposure and infectious virus was quantified by plaque assay on Vero E6 cells. Propylamylatin formula vapors were effective at inactivating infectious SARS-CoV-2 to undetectable levels at room temperature and body temperature, but the decline in virus was substantially faster at the higher temperature (15 min versus 24 h). The direct injection of liquid Propylamylatin formula into viral suspensions also completely inactivated SARS-CoV-2 and the rapidity of inactivation occurred in an exposure dependent manner. The overall volume that resulted in 90% viral inactivation over the course of the direct injection experiment (EC90) was 4.28 µls. Further investigation revealed that the majority of the antiviral effect was attributed to the propionic acid which yielded an overall EC90 value of 11.50 µls whereas the isoamyl hexanoates provided at most a 10-fold reduction in infectious virus. The combination of propionic acid and isoamyl hexanoates was much more potent than the individual components alone, suggesting synergy between these components. These findings illustrate the therapeutic promise of the Propylamylatin formula as a potential treatment strategy for COVID-19 and future studies are warranted.

scholarly journals Solvents to Fragments to Drugs: MD Applications in Drug Design

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3269 ◽  
Author(s):  
Lucas Defelipe ◽  
Juan Arcon ◽  
Carlos Modenutti ◽  
Marcelo Marti ◽  
Adrián Turjanski ◽  
...  
Keyword(s):  
Binding Free Energy ◽  
Mixed Solvents ◽  
Md Simulations ◽  
Binding Mode ◽  
Condensed State ◽  
Protein Targets ◽  
Drug Candidates ◽  
Interaction Sites ◽  
Aqueous Solvation ◽  
The Common

Simulations of molecular dynamics (MD) are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: Binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals solvent structures and preferential interaction sites (hot spots) on the protein surface. The information provided by water and its cosolvents can be used very effectively to understand protein ligand recognition and to improve the predictive capability of well-established methods such as molecular docking. The application of MD simulations to the study of the association of proteins with drug-like compounds is currently only possible for specific cases, as it remains computationally very expensive and labor intensive. MDmix simulations on the other hand, can be used systematically to address some of the common tasks in SBDD. With the advent of new tools and faster computers we expect to see an increase in the application of mixed solvent MD simulations to a plethora of protein targets to identify new drug candidates.

Monoclonal antibodies reveal the alteration of the rhodocetin structure upon α2β1 integrin binding

2011 ◽  
Vol 440 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Thilo Bracht ◽  
Flávia Figueiredo de Rezende ◽  
Jörg Stetefeld ◽  
Lydia M. Sorokin ◽  
Johannes A. Eble
Keyword(s):  
Monoclonal Antibodies ◽  
Dependent Manner ◽  
Hydrophilic Surfaces ◽  
Sequence Homologies ◽  
Molecular Masses ◽  
The Individual ◽  
Β Chain ◽  
Α2β1 Integrin ◽  
Characteristic Domain ◽  
Integrin Α2

The α2β1 antagonist rhodocetin from Calloselasma rhodostoma is a heterotetrameric CLRP (C-type lectin-related protein) consisting of four distinct chains, α, β, γ and δ. Via their characteristic domain-swapping loops, the individual chains form two subunits, αβ and γδ. To distinguish the four chains which share similar molecular masses and high sequence homologies, we generated 11 mAbs (monoclonal antibodies) with different epitope specificities. Four groups of distinct mAbs were generated: the first targeted the rhodocetin β chain, the second group bound to the αβ subunit mostly in a conformation-dependent manner, the third group recognized the γδ subunit only when separated from the αβ subunit, whereas a fourth group interacted with the γδ subunit both in the heterotetrameric molecule and complexed with the integrin α2 A-domain. Using the specific mAbs, we have shown that the rhodocetin heterotetramer dissociates into the αβ and γδ subunit upon binding to the integrin α2 A-domain at both the molecular and cellular levels. After dissociation, the γδ subunit firmly interacts with the α2β1 integrin, thereby blocking it, whereas the rhodocetin αβ subunit is released from the complex. The small molecular interface between the αβ and γδ subunits within rhodocetin is mostly mediated by charged residues, which causes the two dissociated subunits to have hydrophilic surfaces.

scholarly journals Characteristics of Sustainable Bioeconomy in the CEE Macro-region

2018 ◽  
Vol 27 (5) ◽  
pp. 5-26 ◽  
Author(s):  
Viktória Vásáry ◽  
Dorottya Szabó
Keyword(s):  
Triple Helix ◽  
Food Industry ◽  
Research Area ◽  
Sustainable Growth ◽  
Eastern European ◽  
Strategic Research ◽  
Knowledge Based ◽  
Research And Innovation ◽  
Transnational Cooperation ◽  
The Individual

In the coming decades to achieve further progress in sustainable growth of agriculture, aquaculture, forestry and food industry in the CEE countries there is a need to face specific challenges through the lens of bioeconomy, thus by shifting the emphasis to research, innovation and transnational cooperation for knowledge-based development. A shared strategic research and innovation framework that has already been offered by the Central-Eastern European Initiative for Knowledge-based Agriculture, Aquaculture and Forestry in the Bioeconomy, i.e. by the BIOEAST Initiative might enable these countries to work towards the development of a sustainable bioeconomy while effectively joining the European Research Area. The study is aimed at conceptualizing bioeconomy, analysing key socio-economic indicators of the ‘BIOEAST countries’ bioeconomy and describing the implications for policymakers based on the results of the ‘BIOEAST Bioeconomy Capacity Building Survey’. Based on the results of the survey the major findings of the research verify and strengthen the objectives of the BIOEAST Initiative. The individual results of the survey in terms of major bottlenecks in the supply chain, missing elements hindering competitiveness, the opportunities to raise competitiveness and functions of the intervention system led to the conclusion that the creation of sustainable bioeconomy explicitly requires triple-helix stakeholders to find efficient collaboration mechanisms and build synergies.

scholarly journals Personality and social foraging tactic use in free-living Eurasian tree sparrows (Passer montanus)

2019 ◽  
Vol 30 (4) ◽  
pp. 894-903 ◽  
Author(s):  
Attila Fülöp ◽  
Zoltán Németh ◽  
Bianka Kocsis ◽  
Bettina Deák-Molnár ◽  
Tímea Bozsoky ◽  
...  
Keyword(s):  
Social Evolution ◽  
Social Foraging ◽  
Dependent Manner ◽  
Behavioral Differences ◽  
Free Living ◽  
Living Tree ◽  
Passer Montanus ◽  
The Individual ◽  
Time Of Feeding ◽  
Foraging Tactic

AbstractGroup-foraging individuals often use alternative behavioral tactics to acquire food: some individuals, the producers, actively search for food, whereas others, the scroungers, look for opportunities to exploit the finders’ discoveries. Although the use of social foraging tactics is partly flexible, yet some individuals tend to produce more, whereas others largely prefer to scrounge. This between-individual variation in tactic use closely resembles the phenomenon of animal personality; however, the connection between personality and social foraging tactic use has rarely been investigated in wild animals. Here, we studied this relationship in free-living Eurasian tree sparrows (Passer montanus) during 2 winters. We found that in females, but not in males, social foraging tactic use was predicted by personality: more exploratory (i.e., more active in a novel environment) females scrounged more. Regardless of sex, the probability of scrounging increased with the density of individuals foraging on feeders and the time of feeding within a foraging bout, that is, the later the individual foraged within a foraging bout the higher the probability of scrounging was. Our results demonstrate that consistent individual behavioral differences are linked, in a sex-dependent manner, to group-level processes in the context of social foraging in free-living tree sparrows, suggesting that individual behavioral traits have implications for social evolution.

scholarly journals Beyond non-integer Hill coefficients: A novel approach to analyzing binding data, applied to Na+-driven transporters

2015 ◽  
Vol 145 (6) ◽  
pp. 555-563 ◽  
Author(s):  
Silvia Ravera ◽  
Matthias Quick ◽  
Juan P. Nicola ◽  
Nancy Carrasco ◽  
L. Mario Amzel
Keyword(s):  
Hill Equation ◽  
Integer Coefficient ◽  
Novel Approach ◽  
Binding Data ◽  
Na Ions ◽  
Hill Coefficients ◽  
Integer Exponent ◽  
The Individual ◽  
The Hill ◽  
Analyze Data

Prokaryotic and eukaryotic Na+-driven transporters couple the movement of one or more Na+ ions down their electrochemical gradient to the active transport of a variety of solutes. When more than one Na+ is involved, Na+-binding data are usually analyzed using the Hill equation with a non-integer exponent n. The results of this analysis are an overall Kd-like constant equal to the concentration of ligand that produces half saturation and n, a measure of cooperativity. This information is usually insufficient to provide the basis for mechanistic models. In the case of transport using two Na+ ions, an n &lt; 2 indicates that molecules with only one of the two sites occupied are present at low saturation. Here, we propose a new way of analyzing Na+-binding data for the case of two Na+ ions that, by taking into account binding to individual sites, provides far more information than can be obtained by using the Hill equation with a non-integer coefficient: it yields pairs of possible values for the Na+ affinities of the individual sites that can only vary within narrowly bounded ranges. To illustrate the advantages of the method, we present experimental scintillation proximity assay (SPA) data on binding of Na+ to the Na+/I− symporter (NIS). SPA is a method widely used to study the binding of Na+ to Na+-driven transporters. NIS is the key plasma membrane protein that mediates active I− transport in the thyroid gland, the first step in the biosynthesis of the thyroid hormones, of which iodine is an essential constituent. NIS activity is electrogenic, with a 2:1 Na+/I− transport stoichiometry. The formalism proposed here is general and can be used to analyze data on other proteins with two binding sites for the same substrate.

scholarly journals Terminal short arm domains of basement membrane laminin are critical for its self-assembly.

1990 ◽  
Vol 110 (3) ◽  
pp. 825-832 ◽  
Author(s):  
J C Schittny ◽  
P D Yurchenco
Keyword(s):  
Self Assembly ◽  
Affinity Column ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Calcium Dependent ◽  
Domain Specific ◽  
Binding Domains ◽  
Individual Domain ◽  
The Individual

Laminin self-assembles into large polymers by a cooperative two-step calcium-dependent mechanism (Yurchenco, P. D., E. C. Tsilibary, A. S. Charonis, and H. Furthmayr. 1985. J. Biol. Chem. 260:7636-7644). The domain specificity of this process was investigated using defined proteolytically generated fragments corresponding to the NH2-terminal globule and adjacent stem of the short arm of the B1 chain (E4), a complex of the two short arms of the A and B2 chains attached to the proximal stem of a third short arm (E1'), a similar complex lacking the globular domains (P1'), and the distal half of the long arm attached to the adjacent portion of the large globule (E8). Polymerization, followed by an increase of turbidity at 360 nm in neutral isotonic TBS containing CaCl2 at 35 degrees C, was quantitatively inhibited in a concentration-dependent manner with laminin fragments E4 and E1' but not with fragments E8 and P1'. Affinity retardation chromatography was used for further characterization of the binding of laminin domains. The migration of fragment E4, but not of fragments E8 and P1', was retarded in a temperature- and calcium-dependent fashion on a laminin affinity column but not on a similar BSA column. These data are evidence that laminin fragments E4 and E1' possess essential terminal binding domains for the self-aggregation of laminin, while fragments E8 and P1' do not. Furthermore, the individual domain-specific interactions that contribute to assembly are calcium dependent and of low affinity.

scholarly journals Chloroquine augments the binding of insulin to its receptor

1995 ◽  
Vol 311 (3) ◽  
pp. 787-795 ◽  
Author(s):  
A P Bevan ◽  
J R Christensen ◽  
J Tikerpae ◽  
G D Smith
Keyword(s):  
Binding Sites ◽  
Slow Component ◽  
Insulin Binding ◽  
Dissociation Rate ◽  
Receptor Interaction ◽  
Dependent Manner ◽  
Binding Model ◽  
Binding Data ◽  
Plasma Membrane Receptor ◽  
Dissociation Rate Constants

The effect of chloroquine on the interaction of insulin with its receptor has been investigated under both equilibrium and non-equilibrium conditions. Chloroquine was found to augment insulin binding in a pH-dependent manner between pH 6.0 and pH 8.5, with the maximum occurring at approximately pH 7.0. Analysis of the equilibrium binding data in terms of independent binding sites gave equivocal results but suggested an increase in the high-affinity component. Analysis using the negative co-operativity binding model of De Meyts, Bianco and Roth [J. Biol. Chem. (1976) 251, 1877-1888] suggested that the affinity at both high and low occupancy was increased equally. The kinetics of association of insulin with the plasma-membrane receptor indicated that, although the net rate of association increased in the presence of chloroquine, this was due to a reduction in the dissociation rate rather than an increase in the association rate. This was confirmed by direct measurement of the rates of dissociation. Dissociation was found to be distinctly biphasic, with fast and slow components. Curve fitting suggested that the decrease in dissociation rate in the presence of chloroquine was not due to a decrease in either of the two dissociation rate constants, but rather to an increase in the amount of insulin dissociating by the slow component. It was also found that the increase in dissociation rate in the presence of excess insulin, ascribed to negative co-operativity, could be accounted for by an increase in the amount of insulin dissociating by the faster pathway, rather than by an increase in the dissociation rate constant. Thus chloroquine appears to have the opposite effect to excess insulin, and evidence was found for the induction of positive co-operativity in the insulin-receptor interaction at high chloroquine concentrations. Evidence was also found for the presence of low-affinity chloroquine binding sites with binding parameters similar to the concentration dependence of the chloroquine-induced augmentation of insulin binding.

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