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Relevant bibliographies by topics / Van der Waals forces. DNA-protein interactions. Protein binding

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Journal articles

Academic literature on the topic 'Van der Waals forces. DNA-protein interactions. Protein binding'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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Journal articles on the topic "Van der Waals forces. DNA-protein interactions. Protein binding"

1

Stöhr, Martin, and Alexandre Tkatchenko. "Quantum mechanics of proteins in explicit water: The role of plasmon-like solute-solvent interactions." Science Advances 5, no. 12 (2019): eaax0024. http://dx.doi.org/10.1126/sciadv.aax0024.

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Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions—the two main factors affecting the structure and dynamics of proteins in water. Typically, these interactions are only treated phenomenologically, via pairwise potential terms in classical force fields. Here, we use an explicit quantum-mechanical approach of density-functional tight-binding combined with the many-body dispersion formalism and demonstrate the relevance of many-body van der Waals forces both to protein energetics and to protein-water interactions. In con

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2

Wang, Tong, Jian Xin Xue, and Tian Xia. "A Learning Method for Predicting the Binding Strength in RNA-Protein Complexes." Applied Mechanics and Materials 644-650 (September 2014): 5291–94. http://dx.doi.org/10.4028/www.scientific.net/amm.644-650.5291.

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Hydrogen bond and van der Waals interactions between protein and RNA are important. We have developed a set of algorithms for predicting RNA-Protein binding strength by analyzing hydrogen bond and van der Waals interactions between protein and RNA. Firstly, we must identify the RNA-Protein binding sites. In this study, we use features including Pseudo Position-Specific Score Matrix (PsePSSM) computed by PSI-BLAST and Dipeptide Composition (DC) as feature vectors. Then, the classifier is employed to identify the residues that interact with RNA in RNA-binding protein. Then, take into account the

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3

Mackay, Simon P., and Patrick J. O’Malley. "Molecular Modelling of the Interaction of Cyanoacrylate Inhibitors with Photosystem II Part 1. The Effect of Hydrophobicity of Inhibitor Binding." Zeitschrift für Naturforschung C 48, no. 9-10 (1993): 773–81. http://dx.doi.org/10.1515/znc-1993-9-1015.

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Abstract Cyanoacrylate Inhibitors, Photosystem II, Hydrophobicity The secondary quinone binding site of photosystem II is also the binding site for many dif ferent herbicides. The 2-cyanoacrylate inhibitors are a potent class of electron transfer inhibitors which bind at this site and are extremely sensitive to minor structural variation. In order to understand their mode of binding, we have studied the interaction between the inhibitors and receptor in the D1 protein binding region (residues Leu 210 to Val 280) in terms of non bonded intermolecular forces. The intermolecular energy was cal

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4

Bare, Yohanes, Mansur S, Aprianus Pani Pili, and Maria Helvina. "Analysis of molecular interactions of 8-gingerol compounds in Ginger (Zingiber officinale) as ACE Inhibitor." BIOEDUSCIENCE 4, no. 2 (2020): 183–87. http://dx.doi.org/10.22236/j.bes/424944.

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Background: Hypertension is a disease with increasing characteristics of blood pressure. The ACE gene has a role in the conversion of ATI to ATII in hypertensive conditions. Healing is done by using the 8-gingerol content contained in ginger. The purpose of this study is to analyze the molecular interaction that occurs between 8-gingerol and ACE. Method: ACE model proteins (ID: 3bkk) were obtained from the Bank Data Protein database (PDB) through 8-gingerol ligands (CID: 168114) obtained from the PubChem database. ACE and 8-gingerol were docked by Discovery Study Client 4.1 software. Analysis

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5

Song, Yongbo, Yulan Niu, Hongyan Zheng, and Ying Yao. "Interaction of Bis-Guanidinium Acetates Surfactants with Bovine Serum Albumin Evaluated by Spectroscopy." Tenside Surfactants Detergents 58, no. 3 (2021): 187–94. http://dx.doi.org/10.1515/tsd-2020-2283.

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Abstract The interactions between cocopropane bis-guanidinium acetates, tallowpropane bis-guanidinium acetates with bovine serum albumin (BSA) in an aqueous solution were studied by fluorescence and circular dichroic spectroscopy measurements. The aim of the study was to elucidate the influence of the hydrophilic group and the length of the hydrophobic chain of these surfactants on the mechanism of binding to BSA. The results revealed that for both surfactants, at low concentrations, the Stern–Volmer plots had an upward curvature and at high concentrations, the quenching efficiency was decreas

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Janek, Tomasz, Lígia R. Rodrigues, Eduardo J. Gudiña, and Żaneta Czyżnikowska. "Metal-Biosurfactant Complexes Characterization: Binding, Self-Assembly and Interaction with Bovine Serum Albumin." International Journal of Molecular Sciences 20, no. 12 (2019): 2864. http://dx.doi.org/10.3390/ijms20122864.

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Studies on the specific and nonspecific interactions of biosurfactants with proteins are broadly relevant given the potential applications of biosurfactant/protein systems in pharmaceutics and cosmetics. The aim of this study was to evaluate the interactions of divalent counterions with the biomolecular anionic biosurfactant surfactin-C15 through molecular modeling, surface tension and dynamic light scattering (DLS), with a specific focus on its effects on biotherapeutic formulations. The conformational analysis based on a semi-empirical approach revealed that Cu2+ ions can be coordinated by t

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7

da Silva, Edinaldo N., Paulo A. B. da Silva, Angélica E. Graminha, et al. "Synthesis, Characterization, Cytotoxic Activity, and Interactions with CT-DNA and BSA of Cationic Ruthenium(II) Complexes Containing Dppm and Quinoline Carboxylates." Bioinorganic Chemistry and Applications 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/2562780.

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The complexes cis-[Ru(quin)(dppm)2]PF6 and cis-[Ru(kynu)(dppm)2]PF6 (quin = quinaldate; kynu = kynurenate; dppm = bis(diphenylphosphino)methane) were prepared and characterized by elemental analysis, electronic, FTIR, 1H, and 31P{H1} NMR spectroscopies. Characterization data were consistent with a cis arrangement for the dppm ligands and a bidentate coordination through carboxylate oxygens of the quin and kynu anions. These complexes were not able to intercalate CT-DNA as shown by circular dichroism spectroscopy. On the other hand, bovine serum albumin (BSA) binding constants and thermodynamic

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8

Krzyżak, Edward, Dominika Szkatuła, Benita Wiatrak, Tomasz Gębarowski, and Aleksandra Marciniak. "Synthesis, Cyclooxygenases Inhibition Activities and Interactions with BSA of N-substituted 1H-pyrrolo[3,4-c]pyridine-1,3(2H)-diones Derivatives." Molecules 25, no. 12 (2020): 2934. http://dx.doi.org/10.3390/molecules25122934.

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Inhibition of cyclooxygenase is the way of therapeutic activities for anti-inflammatory pharmaceuticals. Serum albumins are the major soluble protein able to bind and transport a variety of exogenous and endogenous ligands, including hydrophobic pharmaceuticals. In this study, a novel N-substituted 1H-pyrrolo[3–c]pyridine-1,3(2H)-diones derivatives were synthesized and biologically evaluated for their inhibitory activity against cyclooxygenases and interactions with BSA. In vitro, COX-1 and COX-2 inhibition assays were performed. Interaction with BSA was studied by fluorescence spectroscopy an

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De Luca, Sergio, Fan Chen, Prasenjit Seal, Martina H. Stenzel, and Sean C. Smith. "Binding and Release between Polymeric Carrier and Protein Drug: pH-Mediated Interplay of Coulomb Forces, Hydrogen Bonding, van der Waals Interactions, and Entropy." Biomacromolecules 18, no. 11 (2017): 3665–77. http://dx.doi.org/10.1021/acs.biomac.7b00657.

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Moldogazieva, Nurbubu T., Daria S. Ostroverkhova, Nikolai N. Kuzmich, Vladimir V. Kadochnikov, Alexander A. Terentiev та Yuri B. Porozov. "Elucidating Binding Sites and Affinities of ERα Agonists and Antagonists to Human Alpha-Fetoprotein by In Silico Modeling and Point Mutagenesis". International Journal of Molecular Sciences 21, № 3 (2020): 893. http://dx.doi.org/10.3390/ijms21030893.

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Alpha-fetoprotein (AFP) is a major embryo- and tumor-associated protein capable of binding and transporting a variety of hydrophobic ligands, including estrogens. AFP has been shown to inhibit estrogen receptor (ER)-positive tumor growth, which can be attributed to its estrogen-binding ability. Despite AFP having long been investigated, its three-dimensional (3D) structure has not been experimentally resolved and molecular mechanisms underlying AFP–ligand interaction remains obscure. In our study, we constructed a homology-based 3D model of human AFP (HAFP) with the purpose of molecular dockin

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