Manipulation of a DNA aptamer–protein binding site through arylation of internal guanine residues

2018 ◽  
Vol 16 (20) ◽  
pp. 3831-3840 ◽  
Author(s):  
Abigail J. Van Riesen ◽  
Kaila L. Fadock ◽  
Prashant S. Deore ◽  
Ahmed Desoky ◽  
Richard A. Manderville ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Binding Affinity ◽  
Target Recognition ◽  
Molecular Target ◽  
Dna Aptamer ◽  
Protein Binding Site ◽  
Chemically Modified ◽  
Structure Activity ◽  
Target Binding

Chemically modified aptamers have the opportunity to increase aptamer target binding affinity and provide structure–activity relationships to enhance our understanding of molecular target recognition by the aptamer fold.

scholarly journals Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2908 ◽  
Author(s):  
Preethi Seelam Prabhakar ◽  
Richard A. Manderville ◽  
Stacey D. Wetmore
Keyword(s):  
Binding Affinity ◽  
Structural Changes ◽  
Experimental Studies ◽  
Local Environment ◽  
Md Simulations ◽  
Fine Tuning ◽  
Dna Aptamer ◽  
Solvent Exposure ◽  
Chemically Modified ◽  
Target Binding

Aptamers are functional nucleic acids that bind to a range of targets (small molecules, proteins or cells) with a high affinity and specificity. Chemically-modified aptamers are of interest because the incorporation of novel nucleobase components can enhance aptamer binding to target proteins, while fluorescent base analogues permit the design of functional aptasensors that signal target binding. However, since optimally modified nucleoside designs have yet to be identified, information about how to fine tune aptamer stability and target binding affinity is required. The present work uses molecular dynamics (MD) simulations to investigate modifications to the prototypical thrombin-binding aptamer (TBA), which is a 15-mer DNA sequence that folds into a G-quadruplex structure connected by two TT loops and one TGT loop. Specifically, we modeled a previously synthesized thymine (T) analog, namely 5-furyl-2′-deoxyuridine (5FurU), into each of the six aptamer locations occupied by a thymine base in the TT or TGT loops of unbound and thrombin bound TBA. This modification and aptamer combination were chosen as a proof-of-principle because previous experimental studies have shown that TBA displays emissive sensitivity to target binding based on the local environment polarity at different 5FurU modification sites. Our simulations reveal that the chemically-modified base imparts noticeable structural changes to the aptamer without affecting the global conformation. Depending on the modification site, 5FurU performance is altered due to changes in the local environment, including the modification site structural dynamics, degree of solvent exposure, stacking with neighboring bases, and interactions with thrombin. Most importantly, these changes directly correlate with the experimentally-observed differences in the stability, binding affinity and emissive response of the modified aptamers. Therefore, the computational protocols implemented in the present work can be used in subsequent studies in a predictive way to aid the fine tuning of aptamer target recognition for use as biosensors (aptasensors) and/or therapeutics.

scholarly journals Functional homology between the yeast regulatory proteins GAL4 and LAC9: LAC9-mediated transcriptional activation in Kluyveromyces lactis involves protein binding to a regulatory sequence homologous to the GAL4 protein-binding site.

1987 ◽  
Vol 7 (12) ◽  
pp. 4400-4406 ◽  
Author(s):  
K D Breunig ◽  
P Kuger
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Transcriptional Activation ◽  
Kluyveromyces Lactis ◽  
Regulatory Protein ◽  
Binding Activity ◽  
Protein Binding Site ◽  
Regulatory Sequence ◽  
Functional Homology ◽  
Beta Galactosidase

As shown previously, the beta-galactosidase gene of Kluyveromyces lactis is transcriptionally regulated via an upstream activation site (UASL) which contains a sequence homologous to the GAL4 protein-binding site in Saccharomyces cerevisiae (M. Ruzzi, K.D. Breunig, A.G. Ficca, and C.P. Hollenberg, Mol. Cell. Biol. 7:991-997, 1987). Here we demonstrate that the region of homology specifically binds a K. lactis regulatory protein. The binding activity was detectable in protein extracts from wild-type cells enriched for DNA-binding proteins by heparin affinity chromatography. These extracts could be used directly for DNase I and exonuclease III protection experiments. A lac9 deletion strain, which fails to induce the beta-galactosidase gene, did not contain the binding factor. The homology of LAC9 protein with GAL4 (J.M. Salmeron and S. A. Johnston, Nucleic Acids Res. 14:7767-7781, 1986) strongly suggests that LAC9 protein binds directly to UASL and plays a role similar to that of GAL4 in regulating transcription.

scholarly journals Valine-279 Deletion–Mutation on Arginine Vasopressin Receptor 2 Causes Obstruction in G-Protein Binding Site: A Clinical Nephrogenic Diabetes Insipidus Case and Its Sub-Molecular Pathogenic Analysis

Biomedicines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 301
Author(s):  
Ming-Chun Chen ◽  
Yu-Chao Hsiao ◽  
Chun-Chun Chang ◽  
Sheng-Feng Pan ◽  
Chih-Wen Peng ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Protein Binding ◽  
Diabetes Insipidus ◽  
Binding Site ◽  
G Protein ◽  
Arginine Vasopressin ◽  
Nephrogenic Diabetes Insipidus ◽  
Md Simulations ◽  
Protein Binding Site ◽  
Vasopressin Receptor

Congenital nephrogenic diabetes insipidus (CNDI) is a genetic disorder caused by mutations in arginine vasopressin receptor 2 (AVPR2) or aquaporin 2 genes, rendering collecting duct cells insensitive to the peptide hormone arginine vasopressin stimulation for water reabsorption. This study reports a first identified AVPR2 mutation in Taiwan and demonstrates our effort to understand the pathogenesis caused by applying computational structural analysis tools. The CNDI condition of an 8-month-old male patient was confirmed according to symptoms, family history, and DNA sequence analysis. The patient was identified to have a valine 279 deletion–mutation in the AVPR2 gene. Cellular experiments using mutant protein transfected cells revealed that mutated AVPR2 is expressed successfully in cells and localized on cell surfaces. We further analyzed the pathogenesis of the mutation at sub-molecular levels via long-term molecular dynamics (MD) simulations and structural analysis. The MD simulations showed while the structure of the extracellular ligand-binding domain remains unchanged, the mutation alters the direction of dynamic motion of AVPR2 transmembrane helix 6 toward the center of the G-protein binding site, obstructing the binding of G-protein, thus likely disabling downstream signaling. This study demonstrated that the computational approaches can be powerful tools for obtaining valuable information on the pathogenesis induced by mutations in G-protein-coupled receptors. These methods can also be helpful in providing clues on potential therapeutic strategies for CNDI.

scholarly journals Antifungal Agents: Design, Synthesis, Antifungal Activity and Molecular Docking of Phloroglucinol Derivatives

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3116 ◽  
Author(s):  
Xingxing Teng ◽  
Yuanyuan Wang ◽  
Jinhua Gu ◽  
Peiqi Shi ◽  
Zhibin Shen ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Antifungal Activity ◽  
Protein Binding ◽  
Binding Site ◽  
Antifungal Agents ◽  
Trichophyton Rubrum ◽  
Trichophyton Mentagrophytes ◽  
Protein Binding Site ◽  
Antifungal Activities ◽  
Phloroglucinol Derivatives

Pseudoaspidinol is a phloroglucinol derivative with Antifungal activity and is a major active component of Dryopteris fragrans. In our previous work, we studied the total synthesis of pseudoaspidinol belonging to a phloroglucinol derivative and investigated its antifungal activity as well as its intermediates. However, the results showed these compounds have low antifungal activity. In this study, in order to increase antifungal activities of phloroglucinol derivatives, we introduced antifungal pharmacophore allylamine into the methylphloroglucinol. Meanwhile, we remained C1–C4 acyl group in C-6 position of methylphloroglucinol using pseudoaspidinol as the lead compound to obtain novel phloroglucinol derivatives, synthesized 17 compounds, and evaluated antifungal activities on Trichophyton rubrum and Trichophyton mentagrophytes in vitro. Molecular docking verified their ability to combine the protein binding site. The results indicated that most of the compounds had strong antifungal activity, in which compound 17 were found to be the most active on Trichophyton rubrum with Minimum Inhibitory Concentration (MIC) of 3.05 μg/mL and of Trichophyton mentagrophytes with MIC of 5.13 μg/mL. Docking results showed that compounds had a nice combination with the protein binding site. These researches could lay the foundation for developing antifungal agents of clinical value.

Replacement of Protein Binding-Site Waters Contributes to Favorable Halogen Bond Interactions

2019 ◽  
Vol 59 (7) ◽  
pp. 3136-3143
Author(s):  
Yuanxun Wang ◽  
Qiuyu Fu ◽  
Yu Zhou ◽  
Yunfei Du ◽  
Niu Huang
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Halogen Bond ◽  
Protein Binding Site
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