366
Views
15
CrossRef citations to date
0
Altmetric
Articles

Landscape of ππ and sugar–π contacts in DNA–protein interactions

, , , , &
Pages 184-200 | Received 03 Dec 2014, Accepted 26 Jan 2015, Published online: 27 Feb 2015

References

  • Ahvazi, B., Coulombe, R., Delarge, M., Vedadi, M., Zhang, L., Meighen, E., & Vrielink, A. (2000). Crystal structure of the NADP+ -dependent aldehyde dehydrogenase from Vibrio harveyi: Structural implications for cofactor specificity and affinity. Biochemical Journal, 349, 853–861.
  • Asensio, J. L., Ardá, A., Cañada, F. J., & Jiménez-Barbero, J. (2012). Carbohydrate–aromatic interactions. Accounts of Chemical Research, 46, 946–954.
  • Auffinger, P., Bielecki, L., & Westhof, E. (2004). Anion binding to nucleic acids. Structure, 12, 379–388.10.1016/j.str.2004.02.015
  • Baker, C. M., & Grant, G. H. (2007). Role of aromatic amino acids in protein–nucleic acid recognition. Biopolymers, 85, 456–470.10.1002/bip.v85:5/6
  • Biot, C., Buisine, E., Kwasigroch, J. M., Wintjens, R., & Rooman, M. (2002). Probing the energetic and structural role of amino acid/nucleobase cation–π interactions in protein–ligand complexes. Journal of Biological Chemistry, 277, 40816–40822.10.1074/jbc.M205719200
  • Biot, C., Buisine, E., & Rooman, M. (2003). Free-energy calculations of protein−ligand cation–π and amino−π interactions: From vacuum to proteinlike environments. Journal of the American Chemical Society, 125, 13988–13994.10.1021/ja035223e
  • Brooks, S. C., Adhikary, S., Rubinson, E. H., & Eichman, B. F. (2013). Recent advances in the structural mechanisms of DNA glycosylases. Biochimica et Biophysica Acta, Proteins and Proteomics, 1834, 247–271.10.1016/j.bbapap.2012.10.005
  • Brown, J. A., & Suo, Z. (2011). Unlocking the sugar “Steric Gate” of DNA polymerases. Biochemistry, 50, 1135–1142.10.1021/bi101915z
  • Cauet, E., Rooman, M., Wintjens, R., Lievin, J., & Biot, C. (2005). Histidine–aromatic interactions in proteins and protein–ligand complexes: Quantum chemical study of X-ray and model structures. Journal of Chemical Theory and Computation, 1, 472–483.10.1021/ct049875k
  • Cerny, J., & Hobza, P. (2007). Non-covalent interactions in biomacromolecules. Physical Chemistry Chemical Physics, 9, 5291–5303.10.1039/b704781a
  • Chourasia, M., Sastry, G. M., & Sastry, G. N. (2011). Aromatic–aromatic interactions database, A2ID: An analysis of aromatic π-networks in proteins. International Journal of Biological Macromolecules, 48, 540–552.10.1016/j.ijbiomac.2011.01.008
  • Churchill, C. D. M., Rutledge, L. R., & Wetmore, S. D. (2010). Effects of the biological backbone on stacking interactions at DNA–protein interfaces: The interplay between the backbone-pi and pi–pi components. Physical Chemistry Chemical Physics, 12, 14515–14526.10.1039/c0cp00550a
  • Copeland, K. L., Anderson, J. A., Farley, A. R., Cox, J. R., & Tschumper, G. S. (2008). Probing phenylalanine/adenine π-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations. Journal of Physical Chemistry B, 112, 14291–14295.10.1021/jp805528v
  • Copeland, K. L., Pellock, S. J., Cox, J. R., Cafiero, M. L., & Tschumper, G. S. (2013). Examination of tyrosine/adenine stacking interactions in protein complexes. Journal of Physical Chemistry B, 117, 14001–14008.10.1021/jp408027j
  • Crowley, P. B., & Golovin, A. (2005). Cation–π interactions in protein–protein interfaces. Proteins: Structure, Function, and Bioinformatics, 59, 231–239.10.1002/prot.20417
  • Dougherty, D. A. (2013). The cation–pi interaction. Accounts of Chemical Research, 46, 885–893.10.1021/ar300265y
  • Egli, M., & Sarkhel, S. (2007). Lone pair–aromatic interactions: To stabilize or not to stabilize. Accounts of Chemical Research, 40, 197–205.10.1021/ar068174u
  • Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2009). Gaussian 09. Wallingford CT: Gaussian.
  • Gallivan, J. P., & Dougherty, D. A. (1999). Cation–π interactions in structural biology. Proceedings of the National Academy of Sciences of the United States of America, 96, 9459–9464.10.1073/pnas.96.17.9459
  • Gromiha, M. M., Santhosh, C., & Ahmad, S. (2004). Structural analysis of cation–π interactions in DNA binding proteins. International Journal of Biological Macromolecules, 34, 203–211.10.1016/j.ijbiomac.2004.04.003
  • Gromiha, M. M., Santhosh, C., & Suwa, M. (2004). Influence of cation–π interactions in protein–DNA complexes. Polymer, 45, 633–639.10.1016/j.polymer.2003.10.069
  • Gromiha, M. M., Slebcrs, J. G., Selvaraj, S., Kono, H., & Sarai, A. (2005). Role of inter and intramolecular interactions in protein–DNA recognition. Gene, 364, 108–113.10.1016/j.gene.2005.07.022
  • HyperChem. Professional 7.5 ed. Gainesville, FL: Hypercube.
  • Jenkins, D. D., Harris, J. B., Howell, E. E., Hinde, R. J., & Baudry, J. (2013). STAAR: Statistical analysis of aromatic rings. Journal of Computational Chemistry, 34, 518–522.10.1002/jcc.23164
  • Joyce, C. M. (1997). Choosing the right sugar: How polymerases select a nucleotide substrate. Proceedings of the National Academy of Sciences of the United States of America, 94, 1619–1622.10.1073/pnas.94.5.1619
  • Jurecka, P., Sponer, J., Cerny, J., & Hobza, P. (2006). Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Physical Chemistry Chemical Physics, 8, 1985–1993.10.1039/b600027d
  • Lau, A. Y., Wyatt, M. D., Glassner, B. J., Samson, L. D., & Ellenberger, T. (2000). Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG. Proceedings of the National Academy of Sciences of the United States of America, 97, 13573–13578.10.1073/pnas.97.25.13573
  • Lejeune, D., Delsaux, N., Charloteaux, B., Thomas, A., & Brasseur, R. (2005). Protein–nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure. Proteins: Structure, Function, and Bioinformatics, 61, 258–271.10.1002/prot.20607
  • Luscombe, N. M., Laskowski, R. A., & Thornton, J. M. (2001). Amino acid–base interactions: A three-dimensional analysis of protein–DNA interactions at an atomic level. Nucleic Acids Research, 29, 2860–2874.10.1093/nar/29.13.2860
  • Luscombe, N. M., & Thornton, J. M. (2002). Protein–DNA interactions: Amino acid conservation and the effects of mutations on binding specificity. Journal of Molecular Biology, 320, 991–1009.10.1016/S0022-2836(02)00571-5
  • Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., … Wood, P. A. (2008). Mercury CSD 2.0–New features for the visualization and investigation of crystal structures. Journal of Applied Crystallography, 41, 466–470.10.1107/S0021889807067908
  • Mahadevi, A. S. & Sastry, G. N. (2012). Cation–π interaction: Its role and relevance in chemistry, biology, and material science. Chemical Reviews. 113: 2100–2138).
  • Mandel-Gutfreund, Y., Schueler, O., & Margalit, H. (1995). Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles. Journal of Molecular Biology, 253, 370–382.10.1006/jmbi.1995.0559
  • Mao, L., Wang, Y., Liu, Y., & Hu, X. (2004). Molecular determinants for ATP-binding in proteins: A data mining and quantum chemical analysis. Journal of Molecular Biology, 336, 787–807.10.1016/j.jmb.2003.12.056
  • Marsili, S., Chelli, R., Schettino, V., & Procacci, P. (2008). Thermodynamics of stacking interactions in proteins. Physical Chemistry Chemical Physics, 10, 2673–2685.10.1039/b718519g
  • Matthews, B. W. (1988). No code for recognition. Nature, 335, 294–295.
  • Nakajima, K., Yamashita, A., Akama, H., Nakatsu, T., Kato, H., Hashimoto, T., … Yamada, Y. (1998). Crystal structures of two tropinone reductases: Different reaction stereospecificities in the same protein fold. Proceedings of the National Academy of Sciences of the United States of America, 95, 4876–4881.10.1073/pnas.95.9.4876
  • Pabo, C. O., & Sauer, R. T. (1992). Transcription factors: Structural families and principles of DNA recognition. Annual Review of Biochemistry, 61, 1053–1095.10.1146/annurev.bi.61.070192.005201
  • Pellequer, J. L., Zhao, B. T., Kao, H. I., Bell, C. W., Li, K., Li, Q. X., … Roberts, V. A. (2000). Stabilization of bound polycyclic aromatic hydrocarbons by a π-cation interaction. Journal of Molecular Biology, 302, 691–699.10.1006/jmbi.2000.4033
  • Philip, V., Harris, J., Adams, R., Nguyen, D., Spiers, J., Baudry, J., … Hinde, R. J. (2011). A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: Searching for anion–π pairs. Biochemistry, 50, 2939–2950.10.1021/bi200066k
  • Prabakaran, P., Siebers, J. G., Ahmad, S., Gromiha, M. M., Singarayan, M. G., & Sarai, A. (2006). Classification of protein–DNA complexes based on structural descriptors. Structure 14, 1355–1367).
  • Raju, R. K., Ramraj, A., Hillier, I. H., Vincent, M. A., & Burton, N. A. (2009). Carbohydrate–aromatic [small π] interactions: A test of density functionals and the DFT-D method. Physical Chemistry Chemical Physics, 11, 3411–3416.10.1039/b822877a
  • Rooman, M., Lievin, J., Buisine, E., & Wintjens, R. (2002). Cation–π/H-bond stair motifs at protein–DNA interfaces. Journal of Molecular Biology, 319, 67–76.10.1016/S0022-2836(02)00263-2
  • Rutledge, L. R., Durst, H. F., & Wetmore, S. D. (2009). Evidence for stabilization of DNA/RNA–protein complexes arising from nucleobase-amino acid stacking and T-shaped interactions. Journal of Chemical Theory and Computation, 5, 1400–1410.10.1021/ct800567q
  • Rutledge, L. R., & Wetmore, S. D. (2011). Modeling the chemical step utilized by human alkyladenine DNA glycosylase: A concerted mechanism AIDS in selectively excising damaged purines. Journal of the American Chemical Society, 133, 16258–16269.10.1021/ja207181c
  • Sathyapriya, R., Vijayabaskar, M., & Vishveshwara, S. (2008). Insights into protein–DNA interactions through structure network analysis. PLoS Computational Biology, 4, e1000170.10.1371/journal.pcbi.1000170
  • Schermerhorn, K. M., & Delaney, S. (2014). A chemical and kinetic perspective on base excision repair of DNA. Accounts of Chemical Research, 47, 1238–1246.10.1021/ar400275a
  • Schottel, B. L., Chifotides, H. T., & Dunbar, K. R. (2008). Anion–π interactions. Chemical Society Reviews, 37, 68–83.10.1039/b614208g
  • Schrodinger, LLC (2010). The PyMOL molecular graphics system (version 1.3r1).
  • Schwans, J. P., Sunden, F., Lassila, J. K., Gonzalez, A., Tsai, Y., & Herschlag, D. (2013). Use of anion–aromatic interactions to position the general base in the ketosteroid isomerase active site. Proceedings of the National Academy of Sciences of the United States of America, 110, 11308–11313.10.1073/pnas.1206710110
  • Spiwok, V., Lipovová, P., Skálová, T., Buchtelová, E., Hašek, J., & Králová, B. (2004). Role of CH/π interactions in substrate binding by Escherichia coli β-galactosidase. Carbohydrate Research, 339, 2275–2280.10.1016/j.carres.2004.06.016
  • Spiwok, V., Lipovová, P., Skálová, T., Vondráčková, E., Dohnálek, J., Hašek, J., & Králová, B. (2006). Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance. Journal of Computer-Aided Molecular Design, 19, 887–901.10.1007/s10822-005-9033-z
  • Sujatha, M. S., Sasidhar, Y. U., & Balaji, P. V. (2004). Energetics of galactose– and glucose–aromatic amino acid interactions: Implications for binding in galactose-specific proteins. Protein Science, 13, 2502–2514.10.1110/(ISSN)1469-896X
  • Suzuki, M. (1994). A framework for the DNA–protein recognition code of the probe helix in transcription factors: The chemical and stereochemical rules. Structure, 2, 317–326.10.1016/S0969-2126(00)00033-2
  • Tatko, C. (2008). Sugars stack up. Nature Chemical Biology, 4, 586–587.10.1038/nchembio1008-586
  • Wang, W., Wu, E. Y., Hellinga, H. W., & Beese, L. S. (2012). Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. Journal of Biological Chemistry, 287, 28215–28226.10.1074/jbc.M112.366609
  • Wilson, K. A., Kellie, J. L., & Wetmore, S. D. (2014). DNA–protein π-interactions in nature: Abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar. Nucleic Acids Research, 42, 6726–6741.10.1093/nar/gku269
  • Wimmerová, M., Kozmon, S., Nečasová, I., Mishra, S. K., Komárek, J., & Koča, J. (2012). Stacking interactions between carbohydrate and protein quantified by combination of theoretical and experimental methods. PLoS One, 7, e46032.10.1371/journal.pone.0046032
  • Wintjens, R., Lievin, J., Rooman, M., & Buisine, E. (2000). Contribution of cation–π interactions to the stability of protein–DNA complexes. Journal of Molecular Biology, 302, 395–410.
  • Zacharias, N., & Dougherty, D. A. (2002). Cation–π interactions in ligand recognition and catalysis. Trends in Pharmacological Sciences, 23, 281–287.10.1016/S0165-6147(02)02027-8

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.