binary complexes
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2021 ◽  
Author(s):  
Arne Elofsson ◽  
David Burke ◽  
Patrick Bryant ◽  
Inigo Barrio-Hernandez ◽  
Danish Memon ◽  
...  

Abstract All cellular functions are governed by complex molecular machines that assemble through protein-protein interactions. Their atomic details are critical to the study of their molecular mechanisms but fewer than 5% of hundreds of thousands of human interactions have been structurally characterized. Here, we test the potential and limitations of recent progress in deep-learning methods using AlphaFold2 to predict structures for 65,484 human interactions. We show that higher confidence models are enriched in interactions supported by affinity or structure based methods and can be orthogonally confirmed by spatial constraints defined by cross-link data. We identify 3,137 high confidence models, of which 1,371 have no homology to a known structure, from which we identify interface residues harbouring disease mutations, suggesting potential mechanisms for pathogenic variants. We find groups of interface phosphorylation sites that show patterns of co-regulation across conditions, suggestive of coordinated tuning of multiple interactions as signalling responses. Finally, we provide examples of how the predicted binary complexes can be used to build larger assemblies. Accurate prediction of protein complexes promises to greatly expand our understanding of the atomic details of human cell biology in health and disease.


PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260786
Author(s):  
Bhargavi Bhat ◽  
Shuhao Liu ◽  
Yu-Ting Lin ◽  
Martin L. Sentmanat ◽  
Joseph Kwon ◽  
...  

Hydraulic fracturing of unconventional reservoirs has seen a boom in the last century, as a means to fulfill the growing energy demand in the world. The fracturing fluid used in the process plays a substantial role in determining the results. Hence, several research and development efforts have been geared towards developing more sustainable, efficient, and improved fracturing fluids. Herein, we present a dynamic binary complex (DBC) solution, with potential to be useful in the hydraulic fracturing domain. It has a supramolecular structure formed by the self-assembly of low molecular weight viscosifiers (LMWVs) oleic acid and diethylenetriamine into an elongated entangled network under alkaline conditions. With less than 2 wt% constituents dispersed in aqueous solution, a viscous gel that exhibits high viscosities even under shear was formed. Key features include responsiveness to pH and salinity, and a zero-shear viscosity that could be tuned by a factor of ~280 by changing the pH. Furthermore, its viscous properties were more pronounced in the presence of salt. Sand settling tests revealed its potential to hold up sand particles for extended periods of time. In conclusion, this DBC solution system has potential to be utilized as a smart salt-responsive, pH-switchable hydraulic fracturing fluid.


Pharmaceutics ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 1997
Author(s):  
Ameeduzzafar Zafar ◽  
Nabil K. Alruwaili ◽  
Syed Sarim Imam ◽  
Omar Awad Alsaidan ◽  
Faisal K. Alkholifi ◽  
...  

The current study was designed to prepare the inclusion complex Genistein (GS) using Hydroxypropyl β cyclodextrin (HP β CD) and poloxamer 188 (PL 188). The binary inclusion complex (GS BC) and ternary inclusion complex (GS TC) were developed by microwave irradiation technique and evaluated for a comparative dissolution study. Further, the samples were assessed for FTIR, DSC, XRD, and NMR for the confirmation of complex formation. Finally, antioxidant and antimicrobial studies and cytotoxicity studies on a breast cancer (MCF-7) cell line were conducted. The dissolution study result showed a marked increment in GS dissolution/release after incorporation in binary (GS: HP β CD, 1:1) and ternary (GS: HP β CD: PL 188; 1:1:0.5) inclusion complexes. Moreover, the ternary complex exhibited a significant enhancement (p < 0.05) in dissolution than did the binary complexes. This might be due to the presence of PL 188, which helps in solubility enhancement of GS. DSC, XRD and SEM evaluation confirmed the modification in the structure of GS. FTIR and NMR results indicated the formation of an inclusion complex. The antioxidant and antimicrobial activity results revealed that GS TC has shown significant (p < 0.05) higher activity than pure GS. The cytotoxicity study results also depicted concentration-dependent cytotoxicity. GS TC exhibited significantly (p < 0.05) high cytotoxicity to cancer cells (IC50 = 225 µg/mL) than pure GS (IC50 = 480 µg/mL). Finally, it was concluded that a remarkable enhancement in the dissolution was observed after the inclusion of GS in the ternary complex and it therefore has significant potential for the treatment of breast cancer.


Author(s):  
Kattamanchi Gnananath ◽  
Kalakonda Sri Nataraj ◽  
Battu Ganga Rao ◽  
Kolli Prabhanjan Kumar ◽  
Kommavari Chandrasekhar ◽  
...  

Aim: The aim of this study was to simultaneously enhance the solubility and stability of bacogenins by a ternary system comprised of hydrogenated soy lecithin and a third auxiliary substance, fulvic acid. Method: Both ternary and binary complexes were prepared using the solvent evaporation method and prepared binary and ternary systems were characterized by Fourier transform infrared technique, differential scanning calorimeter and scanning electron microscope. The entrapment efficacy in both binary and ternary system was calculated and the effect on the solubility, dissolution and stability of bacogenins (hydrolyzed bacoside rich extract) in 40% ethanol was found out. Furthermore, the prepared formulations were subjected to behavioural pharmacological studies. Results : FTIR, DSC, and SEM studies in totality confirmed the formation of binary and ternary complexes. Enhancement in solubility was observed, and the order of releasecharacteristics was found to be BHFS> BHSL>BHF> BH when the dissolution studies were carried out in 40% aqueous solution of ethanol. A significant improvement in the memory and antioxidant capacity was noticed in both binary, ternary complexes and fulvic acid treatment groups. Conclusion: The results revealed that the ternary complex could be a promising drug delivery system to improve the oral bioavailability of the bacogenins.


2021 ◽  
Author(s):  
David F Burke ◽  
Patrick Bryant ◽  
Inigo Barrio-Hernandez ◽  
Danish Memon ◽  
Gabriele Pozzati ◽  
...  

All cellular functions are governed by complex molecular machines that assemble through protein-protein interactions. Their atomic details are critical to the study of their molecular mechanisms but fewer than 5% of hundreds of thousands of human interactions have been structurally characterized. Here, we test the potential and limitations of recent progress in deep-learning methods using AlphaFold2 to predict structures for 65,484 human interactions. We show that higher confidence models are enriched in interactions supported by affinity or structure based methods and can be orthogonally confirmed by spatial constraints defined by cross-link data. We identify 3,137 high confidence models, of which 1,371 have no homology to a known structure, from which we identify interface residues harbouring disease mutations, suggesting potential mechanisms for pathogenic variants. We find groups of interface phosphorylation sites that show patterns of co-regulation across conditions, suggestive of coordinated tuning of multiple interactions as signalling responses. Finally, we provide examples of how the predicted binary complexes can be used to build larger assemblies. Accurate prediction of protein complexes promises to greatly expand our understanding of the atomic details of human cell biology in health and disease.


Author(s):  
K. T. Ishola ◽  
O. T. Olanipekun ◽  
O. T. Bolarinwa ◽  
R. D. Oladeji ◽  
A. Abubakar

An understanding of the principles of complex equilibria and species distribution in different solutions is important in expounding and correlating the interaction of different ligands with different metal ions in complex formation. Therefore, acid-base equilibria involved in the formation of binary and ternary complexes of Co (II), Cu (II) and Pb (II) with methionine (Met) and uracil (Urc) have been determined by potentiometric titration technique. The stability constants of the complexes were evaluated at 35 ± 0.1°C and 0.02 M ionic strength (kept constant with NaNO3) in aqueous and organic-aqueous media. The species distribution in solutions as a function of pH was determined using the Hyss program. The stability of the ternary complexes relative to the corresponding binary complexes of the secondary ligand is measured in terms ΔlogK and % RS values. The ternary complexes are observed to be more stable than binary complexes in the media except for [CuMetUrc] ternary complex in organic-aqueous medium where the ternary complex is less stable than the binary complex of the uracil. The overall stability of the ternary complexes was higher in organic-aqueous system than aqueous system. The stability of the complexes was found to be correlated with the covalent index of the metal ions and Jahn Teller distortion. pH-studies of these systems revealed an increase in the concentrations of the ternary complexes with increase in pH. The formation of binary complexes was shown to be favoured in physiological pH range (3-7) while that of the ternary complexes is observed to be favoured in the pH range 5-10.


Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5290
Author(s):  
Michał Zabiszak ◽  
Justyna Frymark ◽  
Martyna Nowak ◽  
Jakub Grajewski ◽  
Klaudia Stachowiak ◽  
...  

Binary complexes of α-hydroxy acids (L-Tartaric acid and L-Malic acid) with d-electron metal ions (copper, cobalt, nickel) were investigated. Potentiometric measurements have been performed in aqueous solution with computer analysis of the data for determination of the stability constants of complexes formed in the studied systems. The coordination mode of the complexes was defined using spectroscopic methods: electron paramagnetic resonance (EPR), ultraviolet-visible (UV-Vis), circular dichroism (CD), and infrared (IR). Results of the equilibrium studies have provided evidence for the formation of dimers with copper(II) ions and monomers with cobalt(II) and nickel(II) ions.


2021 ◽  
Vol 17 (8) ◽  
pp. e1009808
Author(s):  
Edgar E. Llontop ◽  
William Cenens ◽  
Denize C. Favaro ◽  
Germán G. Sgro ◽  
Roberto K. Salinas ◽  
...  

Type IV pili (T4P) are thin and flexible filaments found on the surface of a wide range of Gram-negative bacteria that undergo cycles of extension and retraction and participate in a variety of important functions related to lifestyle, defense and pathogenesis. During pilus extensions, the PilB ATPase energizes the polymerization of pilin monomers from the inner membrane. In Xanthomonas citri, two cytosolic proteins, PilZ and the c-di-GMP receptor FimX, are involved in the regulation of T4P biogenesis through interactions with PilB. In vivo fluorescence microscopy studies show that PilB, PilZ and FimX all colocalize to the leading poles of X. citri cells during twitching motility and that this colocalization is dependent on the presence of all three proteins. We demonstrate that full-length PilB, PilZ and FimX can interact to form a stable complex as can PilB N-terminal, PilZ and FimX C-terminal fragments. We present the crystal structures of two binary complexes: i) that of the PilB N-terminal domain, encompassing sub-domains ND0 and ND1, bound to PilZ and ii) PilZ bound to the FimX EAL domain within a larger fragment containing both GGDEF and EAL domains. Evaluation of PilZ interactions with PilB and the FimX EAL domain in these and previously published structures, in conjunction with mutagenesis studies and functional assays, allow us to propose an internally consistent model for the PilB-PilZ-FimX complex and its interactions with the PilM-PilN complex in the context of the inner membrane platform of the X. citri Type IV pilus.


2021 ◽  
Author(s):  
Atnafu Guadie Assefa ◽  
Molla Tefera Negash ◽  
Mulugeta Legesse Akele ◽  
Bewketu Mehari Workneh ◽  
Ayal Adugna Mesfin ◽  
...  

Abstract Background Despite the availability of information about the effect of aqua-surfactants media on the stability of binary complexes, data related to mixed ligand complexes of Phen and Orn with essential metals in aqua-surfactant medium is scarce. The aim of this study was, to determine the stabilities of the mixed ligand complexes of essential metal ions (Co2+, Ni2+, Cu2+) with Phen and Orn in aqua-TBAB and PEG-400 surfactants with an eye on the prediction of the bioavailability of the metal complexes. Results Complexes of some essential metal (M) ions (Co2+, Ni2+, Cu2+) of L-ornithine (L) and 1,10-phenanthroline (X) ligands in various concentrations (0.0–2.5% v/v) of aqueous tetrabutylammonium bromide (TBAB) or polyethylene glycol-400 (PEG-400) surfactant were synthesized pH-metrically at 298 K and 0.16 mol L− 1 ionic strength. The relative amounts of L:M:X were 2.5:1.0:2.5; 5.0:1.0:2.5; 2.5:1.0:5.0. The data acquisition of acid-base equilibria and determination of stability constants were performed using MINIQUAD75 algorithm. The distribution patterns of the complexes with varying pH and compositions of surfactants were presented from the plots of SIM run data. Conclusions The best fit chemical models were found to be MLXH, MLX2H in the lower pH, and MLX, ML2X in the higher pH ranges for all the metals. The logged values of stability constants decreased linearly with increasing concentrations of surfactants, indicating the dominance of electrostatic factors. The log of the disproportionation constant and the change in log values of the mixed ligand constant indicated additional stability of the mixed ligand complexes, compared to the parent binary complexes due to interactions outside the coordination sphere. This makes the mixed ligand complexes more amenable to metal ion storage and transport and threw light to have information on the less stable binary complexes easily bioavailability while the mixed ligand complexes could be stored and transported in the bio-fluids. Significant change on the magnitudes of the stability constants, high values of standard deviation and rejection of some of the proposed chemical models were observed due to pessimistic error, indicating the sufficiency of the models to represent the data and accuracy of the method employed.


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