Educational guide
Predictive Analytics for Biomineralization Peptide Binding Affinity
References Janairo, J. I. B. (2016). Peptide-mediated biomineralization . Singapore: Springer. https://doi.org/10.1007/978-981-10-0858-0 . Book Google Scholar Coppage, R., Slocik, J. M., Briggs, B. D., Frenkel, A. I., Heinz, H., Naik, R. R., & Knecht, M. R. (2
This guide cannot diagnose a condition or recommend a personal treatment plan. Discuss medical questions with a qualified professional.
References
Janairo, J. I. B. (2016). Peptide-mediated biomineralization. Singapore: Springer. https://doi.org/10.1007/978-981-10-0858-0.
Coppage, R., Slocik, J. M., Briggs, B. D., Frenkel, A. I., Heinz, H., Naik, R. R., & Knecht, M. R. (2011). Crystallographic recognition controls peptide binding for bio-based nanomaterials. Journal of the American Chemical Society, 133(32), 12346–12349. https://doi.org/10.1021/ja203726n.
Bedford, N. M., Ramezani-dakhel, X. H., Slocik, J. M., Briggs, B. D., Ren, Y., Frenkel, A. I., et al. (2015). Elucidation of peptide-directed palladium surface structure for biologically tunable nanocatalysts. ACS Nano, 9(5), 5082–5092.
Palafox-Hernandez, J. P., Tang, Z., Hughes, Z. E., Li, Y., Swihart, M. T., Prasad, P. N., et al. (2014). Comparative study of materials-binding peptide interactions with gold and silver surfaces and nanostructures: A thermodynamic basis for biological selectivity of inorganic materials. Chemistry of Materials, 26(17), 4960–4969. https://doi.org/10.1021/cm501529u.
Wright, L. B., Palafox-Hernandez, J. P., Rodger, P. M., Corni, S., & Walsh, T. R. (2015). Facet selectivity in gold binding peptides: Exploiting interfacial water structure. Chemical Science, 6(9), 5204–5214. https://doi.org/10.1039/C5SC00399G.
Coppage, R., Slocik, J. M., Sethi, M., Pacardo, D. B., Naik, R. R., & Knecht, M. R. (2010). Elucidation of peptide effects that control the activity of nanoparticles. Angewandte Chemie - International Edition, 49(22), 3767–3770. https://doi.org/10.1002/anie.200906949.
Coppage, R., Slocik, J. M., Briggs, B. D., Frenkel, A. I., Naik, R. R., & Knecht, M. R. (2012). Determining peptide sequence effects that control the size, structure, and function of nanoparticles. ACS Nano. https://doi.org/10.1021/nn204600d.
Choi, N., Tan, L., Jang, J., Um, Y. M., Yoo, P. J., & Choe, W.-S. (2012). The interplay of peptide sequence and local structure in TiO2 biomineralization. Journal of Inorganic Biochemistry, 115, 20–27. https://doi.org/10.1016/j.jinorgbio.2012.05.011.
Hnilova, M., Oren, E. E., Seker, U. O. S., Wilson, B. R., Collino, S., Evans, J. S., et al. (2008). Effect of molecular conformations on the adsorption behavior of gold-binding peptides. Langmuir, 24(8), 12440–12445. https://doi.org/10.1021/la801468c.
Sakaguchi, T., Janairo, J. I. B., Lussier-Price, M., Wada, J., Omichinski, J. G., & Sakaguchi, K. (2017). Oligomerization enhances the binding affinity of a silver biomineralization peptide and catalyzes nanostructure formation. Scientific Reports. https://doi.org/10.1038/s41598-017-01442-8.
Yu, J., Becker, M. L., & Carri, G. A. (2012). The influence of amino acid sequence and functionality on the binding process of peptides onto gold surfaces. Langmuir, 28(2), 1408–1417. https://doi.org/10.1021/la204109r.
Coppage, R., Slocik, J. M., Ramezani-Dakhel, H., Bedford, N. M., Heinz, H., Naik, R. R., & Knecht, M. R. (2013). Exploiting localized surface binding effects to enhance the catalytic reactivity of peptide-capped nanoparticles. Journal of the American Chemical Society, 135(30), 11048–11054. https://doi.org/10.1021/ja402215t.
Heinz, H., Farmer, B. L., Pandey, R. B., Slocik, J. M., Patnaik, S. S., Pachter, R., & Naik, R. R. (2009). Nature of molecular interactions of peptides with gold , palladium , and Pd - Au bimetal surfaces in aqueous solution. Journal of the American Chemical Society, 131(16), 9704–9714.
Verde, A. V., Acres, J. M., & Maranas, J. K. (2009). Investigating the specificity of peptide adsorption on gold using molecular dynamics simulations. Biomacromolecules, 10(8), 2118–2128. https://doi.org/10.1021/bm9002464.
Hughes, Z. E., Nguyen, M. A., Li, Y., Swihart, M. T., Walsh, T. R., & Knecht, M. R. (2017). Elucidating the influence of materials-binding peptide sequence on Au surface interactions and colloidal stability of Au nanoparticles. Nanoscale, 9(1), 421–432. https://doi.org/10.1039/C6NR07890G.
Du, N., Knecht, M. R., Swihart, M. T., Tang, Z., Walsh, T. R., & Zhang, A. (2015). Identifying affinity classes of inorganic materials binding sequences via a graph-based model. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(1), 193–204. https://doi.org/10.1109/TCBB.2014.2321158.
Liang, G., & Li, Z. (2007). Factor analysis scale of generalized amino acid information as the source of a new set of descriptors for elucidating the structure and activity relationships of cationic antimicrobial peptides. QSAR & Combinatorial Science, 26(6), 754–763. https://doi.org/10.1002/qsar.200630145.
Kidera, A., Konish, Y., Oka, M., Ooi, T., & Scheraga, H. A. (1985). Statistical analysis of the physical properties of the 20 naturally occurring amino acids. Journal of Protein Chemistry, 4. https://doi.org/10.1007/BF01025492.
Cruciani, G., Baroni, M., Carosati, E., Clementi, M., Valigi, R., & Clementi, S. (2004). Peptide studies by means of principal properties of amino acids derived from MIF descriptors. Journal of Chemometrics, 18(3–4), 146–155. https://doi.org/10.1002/cem.856.
Osorio, D., Rondon-Villarreal, P., & Torres, R. (2015). Peptides: a package for data mining of antimicrobial peptides. The R Journal, 7(1), 4–14.
R Core Team. (2017). R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
Liu, Y., Zhao, T., Ju, W., Shi, S., Shi, S., & Shi, S. (2017). Materials discovery and design using machine learning. Journal of Materiomics, 3(3), 159–177. https://doi.org/10.1016/j.jmat.2017.08.002.
Murphy, L. R., Matubayasi, N., Payne, V. A., & Levy, R. M. (1998). Protein hydration and unfolding--insights from experimental partial specific volumes and unfolded protein models. Folding & Design, 3(2), 105–118. https://doi.org/10.1016/S1359-0278(98)00016-9.
Skelton, A. A., Liang, T., & Walsh, T. R. (2009). Interplay of sequence, conformation, and binding at the peptide - titania interface as mediated by water. ACS Applied Materials and Interfaces, 1(7), 1482–1491. https://doi.org/10.1021/am9001666.
Božič Abram, S., Aupič, J., Dražić, G., Gradišar, H., & Jerala, R. (2016). Coiled-coil forming peptides for the induction of silver nanoparticles. Biochemical and Biophysical Research Communications, 472(3), 566–571. https://doi.org/10.1016/j.bbrc.2016.03.042.
Okochi, M., Ogawa, M., Kaga, C., Sugita, T., Tomita, Y., Kato, R., & Honda, H. (2010). Screening of peptides with a high affinity for ZnO using spot-synthesized peptide arrays and computational analysis. Acta Biomaterialia, 6(6), 2301–2306. https://doi.org/10.1016/j.actbio.2009.12.025.