scholarly journals Heterogeneous Impacts of Protein-Stabilizing Osmolytes on Hydrophobic Interaction

2018 ◽  
Author(s):  
Mrinmoy Mukherjee ◽  
Jagannath Mondal
Keyword(s):  
Hydrophobic Interaction ◽  
Driving Force ◽  
Hydrophobic Interactions ◽  
Interaction Analysis ◽  
Protein Sequences ◽  
Methyl Groups ◽  
Complex Interplay ◽  
Diverse Range ◽  
Hydrophobic Collapse ◽  
Preferential Binding

AbstractOsmolytes’ mechanism of protecting proteins against denaturation is a longstanding puzzle, further complicated by the complex diversities inherent in protein sequences. An emergent approach in understanding osmolytes’ mechanism of action towards biopolymer has been to investigate osmolytes’ interplay with hydrophobic interaction, the major driving force of protein folding. However, the crucial question is whether all these protein-stabilizing osmolytes display a single unified mechanism towards hydrophobic interactions. By simulating the hydrophobic collapse of a macromolecule in aqueous solutions of two such osmoprotectants, Glycine and Trimethyl N-oxide (TMAO), both of which are known to stabilize protein’s folded conformation, we here demonstrate that these two osmolytes can impart mutually contrasting effects towards hydrophobic interaction. While TMAO preserves its protectant nature across diverse range of polymer-osmolyte interactions, glycine is found to display an interesting cross-over from being a protectant at weaker polymer-osmolyte interaction to a denaturant of hydrophobicity at stronger polymer-osmolyte interactions. A preferential-interaction analysis reveals that a subtle balance of conformation-dependent exclusion/binding of osmolyte molecules from/to the macromolecule holds the key to overall heterogenous behavior. Specifically, TMAO’s consistent stabilization of collapsed configuration of macromolecule is found to be a result of TMAO’s preferential binding to polymer via hydrophobic methyl groups. However, polar Glycine’s cross-over from being a protectant to denaturant across polymer-osmolyte interaction is rooted in its switch from preferential exclusion to preferential binding to the polymer with increasing interaction. Overall, by highlighting the complex interplay of osmolytes with hydrophobic interaction, this work puts forward the necessity of quantitative categorization of osmolytes’ action in protein.

scholarly journals Mitigating the Adverse Effects of Polychlorinated Biphenyl Derivatives on Estrogenic Activity via Molecular Modification Techniques

2021 ◽  
Vol 18 (9) ◽  
pp. 4999
Author(s):  
Wei He ◽  
Wenhui Zhang ◽  
Zhenhua Chu ◽  
Yu Li
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Hydrophobic Interaction ◽  
Oestrogen Receptor ◽  
Polychlorinated Biphenyl ◽  
Hydrophobic Interactions ◽  
Estrogenic Activity ◽  
Average Distance ◽  
Amino Acid Residues ◽  
Hydrophobic Amino Acid

The aim of this paper is to explore the mechanism of the change in oestrogenic activity of PCBs molecules before and after modification by designing new PCBs derivatives in combination with molecular docking techniques through the constructed model of oestrogenic activity of PCBs molecules. We found that the weakened hydrophobic interaction between the hydrophobic amino acid residues and hydrophobic substituents at the binding site of PCB derivatives and human oestrogen receptor alpha (hERα) was the main reason for the weakened binding force and reduced anti-oestrogenic activity. It was consistent with the information that the hydrophobic field displayed by the 3D contour maps in the constructed oestrogen activity CoMSIA model was one of the main influencing force fields. The hydrophobic interaction between PCB derivatives and oestrogen-active receptors was negatively correlated with the average distance between hydrophobic substituents and hydrophobic amino acid residues at the hERα-binding site, and positively correlated with the number of hydrophobic amino acid residues. In other words, the smaller the average distance between the hydrophobic amino acid residues at the binding sites between the two and the more the number of them, and the stronger the oestrogen activity expression degree of PCBS derivative molecules. Therefore, hydrophobic interactions between PCB derivatives and the oestrogen receptor can be reduced by altering the microenvironmental conditions in humans. This reduces the ability of PCB derivatives to bind to the oestrogen receptor and can effectively modulate the risk of residual PCB derivatives to produce oestrogenic activity in humans.

scholarly journals Energetic driving force for preferential binding of self-interstitial atoms to Fe grain boundaries over vacancies

2011 ◽  
Vol 64 (9) ◽  
pp. 908-911 ◽  
Author(s):  
M.A. Tschopp ◽  
M.F. Horstemeyer ◽  
F. Gao ◽  
X. Sun ◽  
M. Khaleel
Keyword(s):  
Grain Boundaries ◽  
Driving Force ◽  
Interstitial Atoms ◽  
Preferential Binding

scholarly journals Hydrophobic Interaction: A Promising Driving Force for the Biomedical Applications of Nucleic Acids

2020 ◽  
Vol 7 (16) ◽  
pp. 2001048 ◽  
Author(s):  
Fan Xiao ◽  
Zhe Chen ◽  
Zixiang Wei ◽  
Leilei Tian
Keyword(s):  
Nucleic Acids ◽  
Hydrophobic Interaction ◽  
Driving Force ◽  
Biomedical Applications

The Adsorption Mechanism of Sodium Lignosulfonate on Al2O3 Particle in the Aqueous Solution

2012 ◽  
Vol 550-553 ◽  
pp. 1120-1123
Author(s):  
Rong Li ◽  
Dong Jie Yang ◽  
Wen Yuan Guo ◽  
Xue Qing Qiu
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bond ◽  
Driving Force ◽  
Adsorption Mechanism ◽  
Hydrophobic Interactions ◽  
Adsorption Properties ◽  
Sodium Lignosulfonate ◽  
Ph Values ◽  
Electrostatic And Hydrophobic Interactions ◽  
Monolayer Coverage

The adsorption properties of sodium lignosulfonate (SL) on Al2O3 particles under different pH values have been investigated. Results show that at low pHs, SL adsorbs on the Al2O3 particles in the form of aggregate as dosage of SL increases; at high pHs, the adsorption is approximately monolayer coverage. With pH values ranging from 3 to 11, the adsorption results are found to be not significantly affected by the addition of urea, ruling out the hydrogen bond as the controlling factor. The paper demonstrates that the main driving force of adsorption is considered as the synergistic effect of electrostatic and hydrophobic interactions when pH pHIEP with additives of Na2SO4 and NaCl.

Desorptive behavior of chlorophenols in contaminated soils

1996 ◽  
Vol 33 (6) ◽  
pp. 263-270 ◽  
Author(s):  
C. N. You ◽  
J. C. Liu
Keyword(s):  
Soil Properties ◽  
Soil Water ◽  
Anionic Surfactant ◽  
Hydrophobic Interaction ◽  
Contaminated Soils ◽  
Driving Force ◽  
Water System ◽  
Ionic Surfactant ◽  
Effects Of Ph

A study was conducted to assess the desorptive behavior of chlorophenols in contaminated soils. Two soils spiked with three types of chlorophenols, i.e., 2,6-dichlorophenol (DCP), 2,4,6-trichlorophenol (TCP), and pentachlorophenol (PCP), respectively, were examined. The effects of pH, methanol, surfactants, and soil properties were investigated. Amount of three chlorophenols desorbed from soils increased with increasing pH. Deprotonated chlorophenols were more mobile than their conjugate acids. When methanol was added to the soil-water system, the amount of chlorophenols desorbed increased. The desorption of PCP was enhanced in the presence of anionic surfactant, SDS. However, when non-ionic surfactant, TX-100, was present, the desorption of PCP decreased. The effects of pH and surfactants on desorptive behavior of chlorophenols were most significant on PCP. Generally, the amount of chlorophenol adsorption deceased in the order PCP > TCP > DCP. Hydrophobic interaction was found to be the major driving force of adsorption reactions. It was therefore proposed that hydrophobicity of chlorophenols is an important factor controlling their desorptive behavior.

Hydrophobic interactions leading to a complex interplay between bioelectrocatalytic properties and multilayer meso-organization in layer-by-layer assemblies

2014 ◽  
Vol 16 (38) ◽  
pp. 20844-20855 ◽  
Author(s):  
M. Lorena Cortez ◽  
Nicolás De Matteis ◽  
Marcelo Ceolín ◽  
Wolfgang Knoll ◽  
Fernando Battaglini ◽  
...  
Keyword(s):  
Hydrophobic Interactions ◽  
Layer By Layer ◽  
Complex Interplay

scholarly journals Structural analysis of COVID-19 spike protein in recognizing the ACE2 receptor of different mammalian species and its susceptibility to viral infection.

2020 ◽  
Author(s):  
Tirthankar Koley ◽  
Shivani Madaan ◽  
Sanghati Roy Chowdhury ◽  
Manoj Kumar ◽  
Punit Kaur ◽  
...  
Keyword(s):  
Hydrophobic Interactions ◽  
Interaction Analysis ◽  
Mammalian Species ◽  
Protein Docking ◽  
Glycosylation Site ◽  
Spike Protein ◽  
Amino Acid Residues ◽  
New Public Health ◽  
Potential Mode ◽  
Novel Coronavirus

Abstract The pandemic COVID-19 caused by a novel coronavirus SARS-CoV-2 spread worldwide as a new public health emergency. The SARS-CoV-2 infects humans by binding to glycosylated ACE2 receptor present in the inner lining of the lungs, heart, intestine and kidney. The COVID spike 2 protein recognizes the ACE2 receptor at the N-terminal helices of the metalloprotease domain. The residues Gln24, Thr27, Lys31, His34, Glu37, Asp38, Tyr41, Gln42 from helix α1; Leu79, Met82, Tyr83 from helix α2 and Gln325, Glu329, Asn330, Lys353 from loop connecting β4 and β5 strands form a concave surface surrounded by four glycosylation sites Asn53, Asn90, Asn103 and Asn322 form interactions with the spike protein. However, no significant data on the susceptibility of animals for infection or transmission. Therefore, we performed the comparative protein-protein docking analysis using the crystal structure of spike protein and homology models of the ACE2 receptor from 16 commonly found mammalian species to understand the potential mode of spike binding. Our comprehensive sequence and structure-based interaction analysis revealed the natural substitution of amino acid residues Gln24, His34, Phe40 and Met82 in the N-terminal α1 and α2 helices results in loss of crucial network of hydrogen-bonded and hydrophobic interactions with spike 2 RBD domain. Besides, the absence of N-linked glycosylation site Asn103 in other mammals further reduces the binding affinity between spike and ACE2 receptor. Hence, these changes explain the differences in the susceptibility and host pathogenesis in other mammalian species.

scholarly journals Heat and SDS insensitive NDK dimers are largely stabilised by hydrophobic interaction to form functional hexamer in Mycobacterium smegmatis.

2013 ◽  
Vol 60 (2) ◽  
Author(s):  
Muthu Arumugam ◽  
Parthasarathi Ajitkumar
Keyword(s):  
Hydrophobic Interaction ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Nucleoside Diphosphate Kinase ◽  
Dimensional Structure ◽  
Recombinant Enzymes ◽  
Basic Subunit ◽  
Oligomeric Form ◽  
The Stability ◽  
And Function

The primary structure and function of nucleoside diphosphate kinase (NDK), a substrate non-specific enzyme involved in the maintenance of nucleotide pools is also implicated to play pivotal roles in many other cellular processes. NDK is conserved from bacteria to human and forms a homotetramer or hexamer to exhibit its biological activity. However, the nature of the functional oligomeric form of the enzyme differs among different organisms. The functional form of NDKs from many bacterial systems, including that of the human pathogen, Mycobacterium tuberculosis (MtuNDK), is a hexamer, although some bacterial NDKs are tetrameric in nature. The present study addresses the oligomeric property of MsmNDK and how a dimer, the basic subunit of a functional hexamer, is stabilized by hydrogen bonds and hydrophobic interactions. Homology modeling was generated using the three-dimensional structure of MtuNDK as a template; the residues interacting at the monomer-monomer interface of MsmNDK were mapped. Using recombinant enzymes of wild type, catalytically inactive mutant, and monomer-monomer interactive mutants of MsmNDK, the stability of the dimer was verified under heat, SDS, low pH, and methanol. The predicted residues (Gln17, Ser24 and Glu27) were engaged in dimer formation, however the mutated proteins retained the ATPase and GTPase activity even after introducing single (MsmNDK- Q17A, MsmNDK-E27A, and MsmNDK-E27Q) and double (MsmNDK-E27A/Q17A) mutation. However, the monomer-monomer interaction could be abolished using methanol, indicating the stabilization of the monomer-monomer interaction by hydrophobic interaction.

scholarly journals Virtual Screening of Phytochemical Compounds as Potential Inhibitors against SARS-CoV-2 Infection

2020 ◽  
Author(s):  
Ram Kothandan ◽  
Cashlin Anna Suveetha Gnana Rajan ◽  
Janamitra Arjun ◽  
Rejoe Raymond Michael Raj ◽  
Sowfia Syed
Keyword(s):  
Hydrophobic Interaction ◽  
Interaction Analysis ◽  
Respiratory Illness ◽  
Docking Studies ◽  
Cell Surface Receptor ◽  
Retroviral Infection ◽  
S Protein ◽  
Surface Receptor ◽  
Phytochemical Compounds ◽  
Potential Inhibitors

Abstract Background: The present pandemic situation due to coronavirus has led to the search for newer prevention, diagnostic and treatment methods. The onset of the corona infection in a human results in acute respiratory illness followed by death if not diagnosed and treated with suitable anti-retroviral drugs. With the unavailability of the targeted drug treatment, several repurposed drugs are being used for treatment, However, the side-effects of the drugs urges us to move to a search for newer synthetic or phytochemical based drugs. The present study investigates the use of various phytochemicals virtually screened from various plant sources in Western Ghats, India and subsequently molecular docking studies were performed to identify the efficacy of the drug in retroviral infection particularly coronavirus infection.Results: Out of 57 phytochemical screened initially based on the structural and physicochemical properties, 39 were effectively used for the docking analysis. Finally 5 lead compound with highest hydrophobic interaction and number of H-bonds were screened. Results from the interaction analysis suggests, Piperolactam A to be pocketed well with good hydrophobic interaction with the residues in the binding region R1. ADME and toxicity profiling also reveals Piperolactam A with higher LogS vlaues indicating higher permeation and hydrophilicity. Toxicity profiling suggests that the 5 screened compounds to be relatively safe.Conclusion: The insilico methods used in this study suggests that the compound Piperolactum A to be the most effective inhibitor of S-protein from binding to the GRP78 receptor. By blocking the binding of the S-protein to the CS-GRP78 cell surface receptor, they can inhibit the binding of the virus to the host.

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