A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA
Abstract
:1. Introduction
2. Results
2.1. Gal4 Binding to Specific and Nonspecific DNA Sequences
2.2. Analysis of Equilibrium and Kinetics through a Nested–Well Binding Model
2.3. Entropy–Enthalpy Compensation
2.4. Structure and Interface of the DNA–Gal4 Complex: A Molecular Dynamics Study
2.5. Entropy–Enthalpy Compensation upon Binding from the Molecular Dynamics Study
3. Discussion and Conclusions
4. Materials and Methods
4.1. Biomolecules and Reagents
4.2. RPI Measurements
4.3. All-Atom Molecular Dynamics Simulations and Analysis
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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# | Name | Length | Sequence |
---|---|---|---|
1 | GAL4-HP | 106 | /5AmMC6/AAA AAA AAA ATG AAA TGT TGG AAG GGT CGG AGG ACA GTC CTC CGG GTG GTA TAG TCT CCT ACC TAT ACC ACC CGG AGG ACT GTC CTC CGA CCC TTC CAA CAT TTC A |
2 | NSP-HP | 106 | /5AmMC6/AAA AAA AAA ATG AAA TGT TGG TTG CGT CTC TCC TAT GTT GCG TCG GTG GTA TAG TCT CCT ACC TAT ACC ACC GAC GCA ACA TAG GAG AGA CGC AAC CAA CAT TTC A |
3 | GAL4-BE | 54 | /5AmMC6/AAA AAA AAA ATG AAA TGT TGG AAG GGT CGG AGG ACA GTC CTC CGG GTG GTA TAG |
4 | NSP-BE | 54 | /5AmMC6/AAA AAA AAA ATG AAA TGT TGG TTG CGT CTC TCC TAT GTT GCG TCG GTG GTA TAG |
5 | GAL4-BE-C | 44 | CTA TAC CAC CCG GAG GAC TGT CCT CCG ACC CTT CCA ACA TTT CA |
6 | NSP-BE-C | 44 | CTA TAC CAC CGA CGC AAC ATA GGA GAG ACG CAA CCA ACA TTT CA |
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Carzaniga, T.; Zanchetta, G.; Frezza, E.; Casiraghi, L.; Vanjur, L.; Nava, G.; Tagliabue, G.; Dieci, G.; Buscaglia, M.; Bellini, T. A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA. Int. J. Mol. Sci. 2021, 22, 3813. https://doi.org/10.3390/ijms22083813
Carzaniga T, Zanchetta G, Frezza E, Casiraghi L, Vanjur L, Nava G, Tagliabue G, Dieci G, Buscaglia M, Bellini T. A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA. International Journal of Molecular Sciences. 2021; 22(8):3813. https://doi.org/10.3390/ijms22083813
Chicago/Turabian StyleCarzaniga, Thomas, Giuliano Zanchetta, Elisa Frezza, Luca Casiraghi, Luka Vanjur, Giovanni Nava, Giovanni Tagliabue, Giorgio Dieci, Marco Buscaglia, and Tommaso Bellini. 2021. "A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA" International Journal of Molecular Sciences 22, no. 8: 3813. https://doi.org/10.3390/ijms22083813