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Journal articles 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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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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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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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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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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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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Grigore-Gurgu, Leontina, Oana Crăciunescu, Iuliana Aprodu, et al. "Tailoring the Health-Promoting Potential of Protein Hydrolysate Derived from Fish Wastes and Flavonoids from Yellow Onion Skins: From Binding Mechanisms to Microencapsulated Functional Ingredients." Biomolecules 10, no. 10 (2020): 1416. http://dx.doi.org/10.3390/biom10101416.

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This study focuses on combining different bioprocessing tools in order to develop an in-depth engineering approach for enhancing the biological properties of two valuable food by-products, namely fish waste and yellow onion skins, in a single new bioactive formulation. Bone tissue from phytophagous carp (Hypophthalmichthys molitrix) was used to obtain bioactive peptides through papain-assisted hydrolysis. The peptides with molecular weight lower than 3 kDa were characterized through MALDI-ToF/ToF mass spectrometry and bioinformatics tools. As a prerequisite for microencapsulation, the ability

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Shamsi, Anas, Taj Mohammad, Mohd Shahnawaz Khan, et al. "Unraveling Binding Mechanism of Alzheimer’s Drug Rivastigmine Tartrate with Human Transferrin: Molecular Docking and Multi-Spectroscopic Approach towards Neurodegenerative Diseases." Biomolecules 9, no. 9 (2019): 495. http://dx.doi.org/10.3390/biom9090495.

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Studying drug–protein interactions has gained significant attention lately, and this is because the majority of drugs interact with proteins, thereby altering their structure and, moreover, their functionality. Rivastigmine tartrate (RT) is a drug that is in use for mild to moderate Alzheimer therapy. This study was targeted to characterize the interaction between human transferrin (hTf) and RT by employing spectroscopy, isothermal titration calorimetry (ITC), and molecular docking studies. Experimental results of fluorescence quenching of hTf induced by RT implied the formation of a static co

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Rophi, Apriani Herni, Yohanes Bare, and Dewi Ratih Tirto Sari. "The Potential of Acetylfuran and Furfural from Tamarindus indica as Lipoxygenase Inhibitor: In Silico Study." JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA 8, no. 2 (2021): 139. http://dx.doi.org/10.20473/jfiki.v8i22021.139-142.

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Background: Tamarindus indica is a type of plant sub-family Caesalpinioideae, which is predicted to have anti-inflammatory properties. When inflammation occurs, arachidonic acid will undergo metabolism, the LOX pathway will release 5-lipoxygenase (5-LOX). Objective: This study aimed to analyze the potential of acetylfuran and furfural compounds on LOX action. Methods: The compound Acetylfuran (CID 14505), Furfural (CID 7362) were downloaded from the PubChem database. The 5-LOX protein was obtained from PDB (6N2W), preparation by removing ligands and molecules that bind to Discovery Studio V19.

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Tang, Chenyu, Bing Tan, and Xiangjun Sun. "Elucidation of Interaction between Whey Proteins and Proanthocyanidins and Its Protective Effects on Proanthocyanidins during In-Vitro Digestion and Storage." Molecules 26, no. 18 (2021): 5468. http://dx.doi.org/10.3390/molecules26185468.

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Whey proteins and oligomeric proanthocyanidins have nutritional value and are widely used in combination as food supplements. However, the effect of the interactions between proanthocyanidins and whey proteins on their stability has not been studied in depth. In this work, we aimed to characterize the interactions between β-Lactoglobulin (β-LG) and α-lactalbumin (α-LA) and oligomeric proanthocyanidins, including A1, A2, B1, B2, B3, and C1, using multi-spectroscopic and molecular docking methods. Fluorescence spectroscopic data revealed that all of the oligomeric proanthocyanidins quenched the

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Koirala, Rajendra Prasad, Shyam Prakash Khanal, Sudip Shiwakoti, and Narayan Prasad Adhikari. "Intermolecular Interaction of Hthyni Protein with Double Methylated DNA at 5m-Cytosine Nucleotide." Journal of Institute of Science and Technology 25, no. 1 (2020): 37–44. http://dx.doi.org/10.3126/jist.v25i1.29444.

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Human thymocyte nuclear protein 1 (hTHYN1) is one of the DNA binding proteins. It is essential for the regulation of Pax5 expression and the development of B cells in humans. Its thermodynamic and biological functions have been unclear yet. The study of the binding mechanism of hTHYN1 protein with DNA is essential to understand various biochemical functions in the human body. In this work, molecular dynamics (MD) simulations have been performed to understand the binding mechanisms of double methylated DNA (dmDNA) at cytosine nucleotide with hTHYN1 protein. Hydrogen bonding and other non-bonded

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Sun, Qifan, Xin Gao, Hongna Bi, Yingbo Xie, and Lin Tang. "Assessment of Binding Interaction between Bovine Lactoferrin and Tetracycline Hydrochloride: Multi-Spectroscopic Analyses and Molecular Modeling." Molecules 23, no. 8 (2018): 1900. http://dx.doi.org/10.3390/molecules23081900.

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In this paper, the interaction between bovine lactoferrin (bLf) and tetracycline hydrochloride (TCH) was researched by microscale thermophoresis (MST), multi-spectroscopic methods, and molecular docking techniques. Normal fluorescence results showed that TCH effectively quenched the intrinsic fluorescence of bLf via static quenching. Moreover, MST confirmed that the combination force between bLf and TCH was very strong. Thermodynamic parameters and molecular docking further revealed that electrostatic forces, van der Waals, and hydrogen bonding forces played vital roles in the interaction betw

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Makegowda, Manjushree, and Revanasiddappa Hosakere Doddarevanna. "Spectroscopic and molecular docking elucidation to binding characteristics of bovine serum albumin with bupropion an aminoketone-medication for nicotine addiction." European Journal of Chemistry 10, no. 2 (2019): 146–55. http://dx.doi.org/10.5155/eurjchem.10.2.146-155.1845.

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One of the highly soluble protein presents in circulatory system of bovine body is bovine serum albumin (BSA). Bupropion hydrochloride (BRN) served to treat prime smoking cessation and disorder due to depressive. BRN binding to BSA was studied by molecular docking and lots of spectroscopic (UV-vis, emission, synchronous, 3D fluorescence, CD and FT-IR) methods at pH = 7.40. Static quenching with strong binding was obtained for BSA-BRN system by forming complex. Secondary structures, conformations and microenvironments of BSA were altered after BRN interaction. Distance between BRN and BSA was a

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Igor Smirnov. "MRET treated water as a tool to mitigate mRNA jab side effects: A review." Open Access Research Journal of Biology and Pharmacy 2, no. 1 (2021): 029–36. http://dx.doi.org/10.53022/oarjbp.2021.2.1.0032.

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The viral RNA (ribonucleic acid) was found in virtually every organ in the body, which means the spike proteins as well. There are antibodies (like the “vaccine” is supposed to create) but they’re irrelevant because, based on a study from Japan, we now know that the spike S1 protein is what does the damage. That means the spike proteins created by the mRNA will be in every organ as well, and we now know it is the spike proteins that do the damage. Another significant mRNA jab side effect was found by Israeli researchers. They discovered a link between Pfizer’s COVID-19 vaccine and a rare blood

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Makegowda, Manjushree, and Revanasiddappa Hosakere Doddarevanna. "Molecular mechanistic vision on binding interaction of triptan drug, a serotonin (5-HT1) agonist with human serum albumin through multispectral and computational assessments." European Journal of Chemistry 11, no. 2 (2020): 145–55. http://dx.doi.org/10.5155/eurjchem.11.2.145-155.1971.

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The triptan drug such as eletriptan in combination with hydrochloride (ETP) is a 5-HT1 receptor agonist used to treat the migraine headache. Human serum albumin (HSA), the fundamental serum protein, executes various functions, that includes transporting and binding of many ligands. HSA binding interaction with ETP is elucidated from molecular docking in composite with fluorescence (emission, 3D and synchronous), UV-vis and FT-IR spectroscopy at 296, 304 and 312 K (pH = 7.40). ETP after interaction modified the HSA secondary structure and its micro-environments. Energy transfer and thermodynami

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Hall, Branwen M., Sue A. Roberts та Matthew H. J. Cordes. "Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the λ Cro complex". Nucleic Acids Research 47, № 13 (2019): 7118–29. http://dx.doi.org/10.1093/nar/gkz507.

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Abstract The gene cro promotes lytic growth of phages through binding of Cro protein dimers to regulatory DNA sites. Most Cro proteins are one-to-one orthologs, yet their sequence, structure and binding site sequences are quite divergent across lambdoid phages. We report the cocrystal structure of bacteriophage N15 Cro with a symmetric consensus site. We contrast this complex with an orthologous structure from phage λ, which has a dissimilar binding site sequence and a Cro protein that is highly divergent in sequence, dimerization interface and protein fold. The N15 Cro complex has less DNA be

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Stănciuc, Nicoleta, Gabriela Râpeanu, Gabriela Elena Bahrim та Iuliana Aprodu. "The Interaction of Bovine β-Lactoglobulin with Caffeic Acid: From Binding Mechanisms to Functional Complexes". Biomolecules 10, № 8 (2020): 1096. http://dx.doi.org/10.3390/biom10081096.

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In this study, the interaction of native and transglutaminase (Tgase) cross-linked β-lactoglobulin (β-LG) with caffeic acid (CA) was examined, aiming to obtain functional composites. Knowledge on the binding affinity and interaction mechanism was provided by performing fluorescence spectroscopy measurements, after heating the native and cross-linked protein at temperatures ranging from 25 to 95 °C. Regardless of the protein aggregation state, a static quenching mechanism of intrinsic fluorescence of β-LG by CA was established. The decrease of the Stern–Volmer constants with the temperature inc

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Chaves, Otavio Augusto, and Leonardo Vazquez. "Molecular docking analysis on the interaction between bovine serum albumin and three commercial fluoroquinolones: Ciprofloxacin, enrofloxacin and pefloxacin." European Journal of Chemistry 12, no. 2 (2021): 192–96. http://dx.doi.org/10.5155/eurjchem.12.2.192-196.2103.

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Fluoroquinolones are a family of broad spectrum, systemic antibacterial agents that have been used as therapy for infections in the respiratory and alimentary tract in animals. The pharmacodynamic of this class is widely described, predominantly to the commercial drugs ciprofloxacin (CIP), enrofloxacin (ENR), and pefloxacin (PEF). Bovine serum albumin (BSA) is the main endogenous carrier in the bovine bloodstream, being responsible for the biodistribution of different classes of molecules and drugs, including fluoroquinolones. The molecular features and interaction between BSA and fluoroquinol

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Zhou, Guangya, Manman Zhao, Ruirui Liang, et al. "A Study of the Mechanism of Binding between Neratinib and MAD2L1 Based on Molecular Simulation and Multi-spectroscopy Methods." Current Pharmaceutical Design 25, no. 40 (2020): 4287–95. http://dx.doi.org/10.2174/1381612825666191107102413.

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Background: Nilatinib is an irreversible tyrosine kinase inhibitor, which is used in the treatment of some kinds of cancer. To study the interaction between Neratinib and MAD2L1, a potential tumor target, is of guiding significance for enriching the medicinal value of Neratinib. Method: The binding mechanism between Mitotic arrest deficient 2-like protein 1 (MAD2L1) and Neratinib under simulative physiological conditions was investigated by molecule simulation and multi-spectroscopy approaches. Results: Molecular docking showed the most possible binding mode of Neratinib-MAD2L1 and the potenti

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Bochtler, Matthias. "Structural basis of the TAL effector–DNA interaction." Biological Chemistry 393, no. 10 (2012): 1055–66. http://dx.doi.org/10.1515/hsz-2012-0164.

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Abstract Phytopathogen transcription activator-like effectors (TALEs) bind DNA in a sequence specific manner in order to manipulate host transcription. TALE specificity correlates with repeat variable diresidues in otherwise highly stereotypical 34–35mer repeats. Recently, the crystal structures of two TALE DNA-binding domains have illustrated the molecular basis of the TALE cipher. The structures show that the TALE repeats form a right-handed superhelix that is wound around largely undistorted B-DNA to match its helical parameters. Surprisingly, repeat variable residue 1 is not in contact wit

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Mallappa, Mahanthappa, Mohammed Azharuddin Savanur, Babu Giriya Gowda, R. S. Vishwanth, and Bijesh Puthusseri. "Molecular Interaction of Hemorrheologic Agent, Pentoxifylline with Bovine Serum Albumin: An Approach to Investigate the Drug Protein Interaction Using multispectroscopic, Voltammetry and Molecular Modelling Techniques." Zeitschrift für Physikalische Chemie 233, no. 7 (2019): 973–94. http://dx.doi.org/10.1515/zpch-2018-0002.

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Abstract The interaction between pentoxifylline (PTX) and bovine serum albumin (BSA) was studied under physiological condition by spectroscopic, voltammetry and molecular modelling techniques. The results of fluorescence studies revealed that the quenching mechanism of BSA by PTX was a static procedure. Binding constant of PTX-BSA was calculated and its value found to be 8.895 × 104 M−1, which is in close agreement with the results obtained from UV-Visible and voltammetry approach. The negative values of thermodynamic parameters (ΔG, ΔH and ΔS) indicated that van der Waals force and hydrogen b

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FU, TING, XUE WU, ZHILONG XIU, JINGUANG WANG, LIU YIN, and GUOHUI LI. "UNDERSTANDING THE MOLECULAR MECHANISM OF BINDING MODES OF AURORA A INHIBITORS BY LONG TIME SCALE GPU DYNAMICS." Journal of Theoretical and Computational Chemistry 12, no. 08 (2013): 1341003. http://dx.doi.org/10.1142/s0219633613410034.

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Inhibition of Aurora A kinase interaction is considered to be a promising approach for the discovery of new molecularly targeted cancer therapeutics. In this study, the binding mechanisms of two different inhibitors with a contrasting binding affinity to Aurora A were investigated by long time scale GPU molecular dynamics (MD) simulations coupled with molecular mechanics-Poisson–Boltzmann/generalized Born surface area (MM-PB/GBSA) method. The results showed that the predicted binding free energies of these two complexes were consistent with the experimental data. Through analyzing the individu

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Shin, J. A. "Minimalist proteins: Design of new molecular recognition scaffolds." Pure and Applied Chemistry 76, no. 7-8 (2004): 1579–90. http://dx.doi.org/10.1351/pac200476071579.

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We hypothesize that we can exploit what Nature has already evolved by manipulating the alpha-helix molecular recognition scaffold. Therefore, minimalist proteins capable of sequence-specific, high-affinity binding of DNA were generated to probe how proteins are used and can be used to recognize DNA. The already minimal basic region/leucine zipper motif (bZIP) of GCN4 was reduced to an even more simplified structure by substitution with alanine residues —hence, a generic, Ala-based, helical scaffold. The proteins generated, wt bZIP, 4A,11A, and 18A, contain 0, 4, 11, and 18 alanine mutations in

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Bengali, Zain, and Lonnie D. Shea. "Gene Delivery by Immobilization to Cell-Adhesive Substrates." MRS Bulletin 30, no. 9 (2005): 659–62. http://dx.doi.org/10.1557/mrs2005.193.

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AbstractBiomaterials can potentially enhance the delivery of viral and nonviral vectors for both basic science and clinical applications.Vectors typically consist of nucleic acids (DNA, RNA) packaged with proteins, lipids, or cationic polymers, which facilitate cellular internalization and trafficking. These vectors can associate with biomaterials that support cell adhesion, a process we term substrate-mediated delivery. Substrate immobilization localizes the DNA and the delivery vector to the cellular microenvironment.The interaction between the vector and substrate must be appropriately bala

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Rodriguez, Jorge H., and Akshita Gupta. "Contact residue contributions to interaction energies between SARS-CoV-1 spike proteins and human ACE2 receptors." Scientific Reports 11, no. 1 (2021). http://dx.doi.org/10.1038/s41598-020-80942-6.

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AbstractSeveral viruses of the corona family interact, via their spike (S) proteins, with human cellular receptors. Spike proteins of SARS-CoV-1 and SARS-CoV-2 virions, being structurally related but not identical, mediate attachment to the human angiotensin-converting enzyme 2 (hACE2) receptor in similar but non-identical ways. Molecular-level understanding of interactions between spike proteins and hACE2 can aid strategies for blocking attachment of SARS-CoV-1, a potentially reemerging health threat, to human cells. We have identified dominant molecular-level interactions, some attractive an

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Rodriguez, Jorge H. "Attractive and repulsive residue fragments at the interface of SARS-CoV-2 and hACE2." Scientific Reports 11, no. 1 (2021). http://dx.doi.org/10.1038/s41598-021-91877-x.

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AbstractThe initial stages of SARS-CoV-2 coronavirus attachment to human cells are mediated by non-covalent interactions of viral spike (S) protein receptor binding domains (S-RBD) with human ACE2 receptors (hACE2). Structural characterization techniques, such as X-ray crystallography (XRC) and cryoelectron microscopy (cryo-EM), previously identified SARS-CoV-2 spike protein conformations and their surface residues in contact with hACE2. However, recent quantum-biochemical calculations on the structurally related S-RBD of SARS-CoV-1 identified some contact-residue fragments as intrinsically at

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"Spectroscopic and thermodynamic interaction studies of anti-diabetic drug with globular proteins." Biointerface Research in Applied Chemistry 9, no. 4 (2019): 4172–76. http://dx.doi.org/10.33263/briac94.172176.

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Drug-protein interaction is a fundamental problem in estimating the serious side effects of the drug. Hence, the main objective of this study was to study the interaction of acarbose with three different globular proteins i.e.; bovine serum albumin (BSA), human serum albumin (HSA), and hemoglobin (Hb) via UV-Visible absorption spectroscopic analysis. We were determined physicochemical parameters, binding constant, distribution constant and thermodynamic parameters activation energy, enthalpy, entropy, and Gibbs free energy by using UV-visible data. These both properties of acarbose-protein com

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Saipetch, Kornravee, Rajendra Khanal, Masaki Yamazaki, Qing-Long Fu, Chihiro Yoshimura, and Xin Kai Jin. "Exploring the fluorescence quenching interaction of amino acids and protein with natural organic matter by a multi-spectroscopic method." Water Supply, April 5, 2021. http://dx.doi.org/10.2166/ws.2021.103.

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Abstract The main objective of this research was to explore the fluorescence quenching mechanism of a humic substance (Suwannee River natural organic matter (SWNOM)) to amino acids (tryptophan, tyrosine) and protein (bovine serum albumin, (BSA)) by multi-spectroscopic methods. The locations of the peaks of tryptophan, tyrosine, and BSA from Parallel Factor Analysis were at Ex/Em 280/356 nm, 275/302 nm, and 280/344 nm, respectively. For SWNOM, two peaks appeared at Ex/Em of 240/448 nm, and 350/450 nm. Static quenching was the dominant quenching mechanism between BSA and SWNOM, whereas no quench

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Dragan, A. I., C. Crane-Robinson та P. L. Privalov. "Thermodynamic basis of the α-helix and DNA duplex". European Biophysics Journal, 24 квітня 2021. http://dx.doi.org/10.1007/s00249-021-01520-w.

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AbstractAnalysis of calorimetric and crystallographic information shows that the α-helix is maintained not only by the hydrogen bonds between its polar peptide groups, as originally supposed, but also by van der Waals interactions between tightly packed apolar groups in the interior of the helix. These apolar contacts are responsible for about 60% of the forces stabilizing the folded conformation of the α-helix and their exposure to water on unfolding results in the observed heat capacity increment, i.e. the temperature dependence of the melting enthalpy. The folding process is also favoured b

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"Biological Potency of New Benzimidazole Derived Imine Based Ligand and its Co(III), Ni(II), Cu(II) and Pt(II) Complexes: Synthesis, Structure, Antimicrobial, Antioxidant and BSA Interaction Studies." Biointerface Research in Applied Chemistry 11, no. 4 (2020): 11856–90. http://dx.doi.org/10.33263/briac114.1185611890.

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In this study, we report the synthesis and characterization of transition metal complexes (MC1, MC2, MC3, MC4) where M= Co(III), Ni(II), Cu(II) and Pt(II), respectively, using a new imine-based ligand, 2-{(E)-[(1H-benzimidazol-2-ylmethyl)imino]methyl}-4-bromophenol (HBMB). The molecular structure of the HBMB ligand and its complexes were confirmed by various analytical techniques such as UV-Vis, FT-IR, 1H, 13C-NMR, ESR, TGA/DTA, LC-MS, molar conductance, and magnetic moment measurements. The spectral data of complexes recommended tridentate binding modes of HBMB ligand and suggested an octahed

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Lawal, Bashir, Ching-Yu Lee, Ntlotlang Mokgautsi, et al. "mTOR/EGFR/iNOS/MAP2K1/FGFR/TGFB1 Are Druggable Candidates for N-(2,4-Difluorophenyl)-2′,4′-Difluoro-4-Hydroxybiphenyl-3-Carboxamide (NSC765598), With Consequent Anticancer Implications." Frontiers in Oncology 11 (March 26, 2021). http://dx.doi.org/10.3389/fonc.2021.656738.

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BackgroundThe application of computational and multi-omics approaches has aided our understanding of carcinogenesis and the development of therapeutic strategies. NSC765598 is a novel small molecule derivative of salicylanilide. This study aims to investigate the ligand-protein interactions of NSC765598 with its potential targets and to evaluate its anticancer activities in vitro.MethodsWe used multi-computational tools and clinical databases, respectively, to identify the potential drug target for NSC765598 and analyze the genetic profile and prognostic relevance of the targets in multiple ca

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Chan, Kun-Wei, Ruimin Pan, Matthew Costa, et al. "Structural Comparison of Human Anti-HIV-1 gp120 V3 Monoclonal Antibodies of the Same Gene Usage Induced by Vaccination and Chronic Infection." Journal of Virology 92, no. 18 (2018). http://dx.doi.org/10.1128/jvi.00641-18.

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ABSTRACTElucidating the structural basis of antibody (Ab) gene usage and affinity maturation of vaccine-induced Abs can inform the design of immunogens for inducing desired Ab responses in HIV vaccine development. Analyses of monoclonal Abs (MAbs) encoded by the same immunoglobulin genes at different stages of maturation can help to elucidate the maturation process. We have analyzed four human anti-V3 MAbs with the same VH1-3*01 and VL3-10*01 gene usage. Two MAbs, TA6 and TA7, were developed from a vaccinee in the HIV vaccine phase I trial DP6-001 with a polyvalent DNA prime/protein boost regi

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