Prediction of Protein Binding to DNA in the Presence of Water-Mediated Hydrogen Bonds

Deng, Yuefan; Glimm, James; Wang, Yuan; Korobka, Alex; Eisenberg, Moshe; Grollman, Arthur P.

doi:10.1007/s008940050121

Cited by 7 publications

(2 citation statements)

References 5 publications

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“…these structures and human DNA. 9 It is believed that negative biological outcomes such as abnormal functionalities, replication errors and self-repair mismatches can occur when molecules bind to DNA and impact its shape. These outcomes have the potential of leading to diseased conditions, including cancer.…”

Section: Introductionmentioning

confidence: 99%

Molecular Simulation of Nicotine-Related Alkaloids Interaction with Human DNA

Neto¹,

Sena²,

Neto³

et al. 2014

Jnl of Comp & Theo Nano

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In this work molecular dynamics theory was applied to simulate the interaction of nicotine-related alkaloids with a human segment of deoxyribonucleic acid (DNA). The left molecular docking technique, we observe which of the studied molecules have higher toxicological potential and DNA bases which are more sensitive to the presence of these molecules. The molecules interacting with DNA were nicotine, nornicotine, anabasine, nicotinic acid, nicotinamide and trigonelline. The interaction of DNA with water was simulated and the results were used as a reference to analyze the toxic potential of alkaloids. Variations on kinetic, potential and total energy were calculated during simulation. The results show nicotine and nornicotine docks to DNA, causing deformation which can lead to mutations on DNA structure. We found that compared to other bases, which form the DNA base adenine is more stable in the presence of the molecules studied.

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Section: Introductionmentioning

confidence: 99%

Molecular Simulation of Nicotine-Related Alkaloids Interaction with Human DNA

Neto¹,

Sena²,

Neto³

et al. 2014

Jnl of Comp & Theo Nano

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“…Over the past years a variety of problems concerned with protein-DNA complexes have been investigated (Deng et al, 1999;Luscombe et al, 2001), but protein-RNA complexes have received much less attention despite their importance. In contrast to the regular helical structure of DNA, RNA molecules form complex secondary and tertiary structures consisting of stems, loops, and pseudoknots.…”

Section: Introductionmentioning

confidence: 99%

Mining Molecular Structure Data for the Patterns of Interactions Between Protein and RNA

Han

Nepal

2007

Computational Science – ICCS 2007

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Abstract. Mining useful information from a large amount of biological data is becoming important, but most data mining research in bioinformatics is limited to molecular sequence data. We have developed a set of algorithms for analyzing hydrogen bond and van der Waals interactions between protein and RNA. Analysis of the most representative set of protein-RNA complexes revealed several interesting observations: (1) in both hydrogen bond and van der Waals interactions, arginine has the highest interaction propensity, whereas cytosine has the lowest interaction propensity; (2) side chain contacts are more frequent than main chain contacts in amino acids, whereas backbone contacts are more frequent than base contacts in nucleotides; (3) amino acids, in which side chain contacts are dominant, reveal more diverse interaction propensities than nucleotides; and (4) valine rarely binds to any nucleotide. The interaction patterns found in this study should prove useful for determining binding sites in protein-RNA complexes.

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