On the interactions of peptides with gold nanoparticles: effects of sequence and size

References

• Ai, K., Liu, Y., & Lu, L. (2009). Hydrogen-bonding recognition-induced color change of gold nanoparticles for visual detection of melamine in raw milk and infant formula. Journal of the American Chemical Society, 131(27), 9496–9497. https://doi.org/10.1021/ja9037017
   PubMed Web of Science ®Google Scholar
• Bananezhad, A., Ganjali, M. R., Karimi-Maleh, H., & Norouzi, P. (2017). Fabrication of amplified nanostructure based sensor for analysis of N-Acetylcysteine in presence of high concentration folic acid. International Journal of Electrochemical Science, 12, 8045–8058. https://doi.org/10.20964/2017.09.34
   Web of Science ®Google Scholar
• Bedford, N. M., Hughes, Z. E., Tang, Z., Li, Y., Briggs, B. D., Ren, Y., Swihart, M. T., Petkov, V. G., Naik, R. R., Knecht, M. R., & Walsh, T. R. (2016). Sequence-dependent structure/function relationships of catalytic peptide-enabled gold nanoparticles generated under ambient synthetic conditions. Journal of the American Chemical Society, 138(2), 540–548. https://doi.org/10.1021/jacs.5b09529
   PubMed Web of Science ®Google Scholar
• Botteon, C., Silva, L., Ccana-Ccapatinta, G., Silva, T., Ambrosio, S., Veneziani, R., Bastos, J., & Marcato, P. (2021). Biosynthesis and characterization of gold nanoparticles using Brazilian red propolis and evaluation of its antimicrobial and anticancer activities. Scientific Reports, 11(1), 16. https://doi.org/10.1038/s41598-021-81281-w
   PubMed Web of Science ®Google Scholar
• Brown, S., Sarikaya, M., & Johnson, E. (2000). A genetic analysis of crystal growth. Journal of Molecular Biology, 299(3), 725–735. https://doi.org/10.1006/jmbi.2000.3682
   PubMed Web of Science ®Google Scholar
• Cabaleiro-Lago, C., Quinlan-Pluck, F., Lynch, I., Lindman, S., Minogue, A. M., Thulin, E., Walsh, D. M., Dawson, K. A., & Linse, S. (2008). Inhibition of amyloid β protein fibrillation by polymeric nanoparticles. Journal of the American Chemical Society, 130(46), 15437–15443. https://doi.org/10.1021/ja8041806
   PubMed Web of Science ®Google Scholar
• Carlsson, J., Boukharta, L., & Åqvist, J. (2008). Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase. Journal of Medicinal Chemistry, 51(9), 2648–2656. https://doi.org/10.1021/jm7012198
   PubMed Web of Science ®Google Scholar
• Case, D. A., Babin, V., Berryman, J., Betz, R., Cai, Q., Cerutti, D., Cheatham, T., III, Darden, T., Duke., & R., Gohlke. (2020). H. Amber 20.
   Google Scholar
• 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 ed. in English), 49(22), 3767–3770. https://doi.org/10.1002/anie.200906949
   PubMed Web of Science ®Google Scholar
• Diallo, M. S., Fromer, N. A., & Jhon, M. S. (2013). Nanotechnology for sustainable development (pp. 1–16). Springer. https://doi.org/10.1007/978-3-319-05041-6_1
   Google Scholar
• Evans, E., Gabriel, E. F. M., Benavidez, T. E., Coltro, W. K. T., & Garcia, C. D. (2014). Modification of microfluidic paper-based devices with silica nanoparticles. The Analyst, 139(21), 5560–5567. https://doi.org/10.1039/C4AN01147C
   PubMed Web of Science ®Google Scholar
• Feng, J.-J., Guo, H., Li, Y.-F., Wang, Y.-H., Chen, W.-Y., & Wang, A.-J. (2013). Single molecular functionalized gold nanoparticles for hydrogen-bonding recognition and colorimetric detection of dopamine with high sensitivity and selectivity. ACS Applied Materials & Interfaces, 5(4), 1226–1231. https://doi.org/10.1021/am400402c
   PubMed Web of Science ®Google Scholar
• Hall Sedlak, R., Hnilova, M., Grosh, C., Fong, H., Baneyx, F., Schwartz, D., Sarikaya, M., Tamerler, C., & Traxler, B. (2012). Engineered Escherichia coli silver-binding periplasmic protein that promotes silver tolerance. Applied and Environmental Microbiology, 78(7), 2289–2296. https://doi.org/10.1128/AEM.06823-11
   PubMed Web of Science ®Google Scholar
• Heinz, H., Lin, T.-J., Kishore Mishra, R., & Emami, F. S. (2013). Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: The INTERFACE force field. Langmuir : The ACS Journal of Surfaces and Colloids, 29(6), 1754–1765. https://doi.org/10.1021/la3038846
   PubMed Web of Science ®Google Scholar
• Hnilova, M., Liu, X., Yuca, E., Jia, C., Wilson, B., Karatas, A. Y., Gresswell, C., Ohuchi, F., Kitamura, K., & Tamerler, C. (2012). Multifunctional protein-enabled patterning on arrayed ferroelectric materials. ACS Applied Materials & Interfaces, 4(4), 1865–1871. https://doi.org/10.1021/am300177t
   PubMed Web of Science ®Google Scholar
• Hnilova, M., Oren, E. E., Seker, U. O., Wilson, B. R., Collino, S., Evans, J. S., Tamerler, C., & Sarikaya, M. (2008). Effect of molecular conformations on the adsorption behavior of gold-binding peptides. Langmuir : The ACS Journal of Surfaces and Colloids, 24(21), 12440–12445. https://doi.org/10.1021/la801468c
   PubMed Web of Science ®Google Scholar
• Ho, B. K., & Dill, K. A. (2006). Folding very short peptides using molecular dynamics. PLoS Computational Biology, 2(4), e27. https://doi.org/10.1371/journal.pcbi.0020027
   PubMed Web of Science ®Google Scholar
• Huang, C. C., Yang, Z., Lee, K. H., & Chang, H. T. (2007). Synthesis of highly fluorescent gold nanoparticles for sensing mercury (II). Angewandte Chemie, 119(36), 6948–6952. https://doi.org/10.1002/ange.200700803
   Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• John, T., Gladytz, A., Kubeil, C., Martin, L. L., Risselada, H. J., & Abel, B. (2018). Impact of nanoparticles on amyloid peptide and protein aggregation: A review with a focus on gold nanoparticles. Nanoscale, 10(45), 20894–20913. https://doi.org/10.1039/C8NR04506B
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Joung, I. S., & Cheatham, T. E. III, (2008). Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. The Journal of Physical Chemistry. B, 112(30), 9020–9041. https://doi.org/10.1021/jp8001614
   PubMed Web of Science ®Google Scholar
• Keller, A., Fritzsche, M., Yu, Y.-P., Liu, Q., Li, Y.-M., Dong, M., & Besenbacher, F. (2011). Influence of hydrophobicity on the surface-catalyzed assembly of the islet amyloid polypeptide. ACS Nano, 5(4), 2770–2778. https://doi.org/10.1021/nn1031998
   PubMed Web of Science ®Google Scholar
• Khavani, M., Izadyar, M., & Housaindokht, M. R. (2019). RNA aptasensor based on gold nanoparticles for selective detection of neomycin B, molecular approach. Journal of the Iranian Chemical Society, 16(11), 2389–2400. https://doi.org/10.1007/s13738-019-01708-0
   Web of Science ®Google Scholar
• Khavani, M., Mehranfar, A., & Izadyar, M. (2021). A theoretical approach on the ability of functionalized gold nanoparticles for detection of Cd2+. Scientific Reports, 11(1), 13. https://doi.org/10.1038/s41598-021-02933-5
   PubMed Web of Science ®Google Scholar
• Khavani, M., Mehranfar, A., & Mofrad, M. R. (2022). Effects of ionic liquids on the stabilization process of gold nanoparticles. The Journal of Physical Chemistry. B, 126(46), 9617–9631. https://doi.org/10.1021/acs.jpcb.2c05878
   PubMed Web of Science ®Google Scholar
• Kim, J., Rheem, Y., Yoo, B., Chong, Y., Bozhilov, K. N., Kim, D., Sadowsky, M. J., Hur, H.-G., & Myung, N. V. (2010). Peptide-mediated shape-and size-tunable synthesis of gold nanostructures. Acta Biomaterialia, 6(7), 2681–2689. https://doi.org/10.1016/j.actbio.2010.01.019
   PubMed Web of Science ®Google Scholar
• Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157(1), 105–132. https://doi.org/10.1016/0022-2836(82)90515-0
   PubMed Web of Science ®Google Scholar
• Li, L., Xiang, H., Xiong, Y., Zhao, H., Bai, Y., Wang, S., Sun, F., Hao, M., Liu, L., Li, T., Peng, Z., Xu, J., & Zhang, T. (2018). Ultrastretchable fiber sensor with high sensitivity in whole workable range for wearable electronics and implantable medicine. Advanced Science (Weinheim, Baden-Wurttemberg, Germany), 5(9), 1800558. https://doi.org/10.1002/advs.201800558
   PubMedGoogle Scholar
• Li, Y., Tang, Z., Prasad, P. N., Knecht, M. R., & Swihart, M. T. (2014). Peptide-mediated synthesis of gold nanoparticles: Effects of peptide sequence and nature of binding on physicochemical properties. Nanoscale, 6(6), 3165–3172. https://doi.org/10.1039/c3nr06201e
   PubMed Web of Science ®Google Scholar
• Liao, Y. H., Chang, Y. J., Yoshiike, Y., Chang, Y. C., & Chen, Y. R. (2012). Negatively charged gold nanoparticles inhibit Alzheimer’s amyloid‐β fibrillization, induce fibril dissociation, and mitigate neurotoxicity. Small (Weinheim an Der Bergstrasse, Germany), 8(23), 3631–3639. https://doi.org/10.1002/smll.201201068
   PubMed Web of Science ®Google Scholar
• Lin, E., & Shell, S. (2009). Convergence and heterogeneity in peptide folding with replica exchange molecular dynamics. Journal of Chemical Theory and Computation, 5(8), 2062–2073. https://doi.org/10.1021/ct900119n
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Mehranfar, A., Khavani, M., & Izadyar, M. (2022). A molecular dynamic study on the ability of phosphorene for designing new sensor for SARS-CoV-2 detection. Journal of Molecular Liquids, 345, 117852. https://doi.org/10.1016/j.molliq.2021.117852
   PubMed Web of Science ®Google Scholar
• Miller, B. R., III, McGee, Jr, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA. py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Nguyen, M. A., Hughes, Z. E., Liu, Y., Li, Y., Swihart, M. T., Knecht, M. R., & Walsh, T. R. (2018). Peptide-mediated growth and dispersion of Au nanoparticles in water via sequence engineering. The Journal of Physical Chemistry C, 122(21), 11532–11542. https://doi.org/10.1021/acs.jpcc.8b02392
   Web of Science ®Google Scholar
• Niemeyer, C. M. (2001). Nanoparticles, proteins, and nucleic acids: Biotechnology meets materials science. Angewandte Chemie International Edition, 40(22), 4128–4158. https://doi.org/10.1002/1521-3773(20011119)40:22
   PubMed Web of Science ®Google Scholar
• Pacardo, D. B., Sethi, M., Jones, S. E., Naik, R. R., & Knecht, M. R. (2009). Biomimetic synthesis of Pd nanocatalysts for the Stille coupling reaction. ACS Nano, 3(5), 1288–1296. https://doi.org/10.1021/nn9002709
   PubMed Web of Science ®Google Scholar
• Palafox-Hernandez, J. P., Tang, Z., Hughes, Z. E., Li, Y., Swihart, M. T., Prasad, P. N., Walsh, T. R., & Knecht, M. R. (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
   Web of Science ®Google Scholar
• Peelle, B. R., Krauland, E. M., Wittrup, K. D., & Belcher, A. M. (2005). Design criteria for engineering inorganic material-specific peptides. Langmuir : The ACS Journal of Surfaces and Colloids, 21(15), 6929–6933. https://doi.org/10.1021/la050261s
   PubMed Web of Science ®Google Scholar
• Prusiner, S. B. (1998). Prions. Proceedings of the National Academy of Sciences of the United States of America, 95(23), 13363–13383. https://doi.org/10.1073/pnas.95.23.13363
   PubMed Web of Science ®Google Scholar
• Rifai, E. A., Dijk, M., Vermeulen, N. P. E., Yanuar, A., & Geerke, D. P. (2019). A comparative linear interaction energy and MM/PBSA Study on SIRT1 − ligand binding free energy calculation. Journal of Chemical Information and Modeling, 59(9), 4018–4033. https://doi.org/10.1021/acs.jcim.9b00609
   PubMed Web of Science ®Google Scholar
• Risør, M. W., Juhl, D. W., Bjerring, M., Mathiesen, J., Enghild, J. J., Nielsen, N. C., & Otzen, D. E. (2017). Critical influence of cosolutes and surfaces on the assembly of serpin-derived amyloid fibrils. Biophysical Journal, 113(3), 580–596. https://doi.org/10.1016/j.bpj.2017.06.030
   PubMed Web of Science ®Google Scholar
• Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Sindhikara, D. J., Kim, S., Voter, A. F., & Roitberg, A. E. (2009). Bad seeds sprout perilous dynamics: Stochastic thermostat induced trajectory synchronization in biomolecules. Journal of Chemical Theory and Computation, 5(6), 1624–1631. https://doi.org/10.1021/ct800573m
   PubMed Web of Science ®Google Scholar
• Slocik, J. M., Stone, M. O., & Naik, R. R. (2005). Synthesis of gold nanoparticles using multifunctional peptides. Small (Weinheim an Der Bergstrasse, Germany), 1(11), 1048–1052. https://doi.org/10.1002/smll.200500172
   PubMed Web of Science ®Google Scholar
• Smith, L. J., Daura, X., & Gunsteren, W. F. (2002). Assessing equilibration and convergence in biomolecular simulations. Proteins, 48(3), 487–496. https://doi.org/10.1002/prot.10144
   PubMed Web of Science ®Google Scholar
• Suyetin, M., Bag, S., Anand, P., Borkowska-Panek, M., Gußmann, F., Brieg, M., Fink, K., & Wenzel, W. (2022). Modelling peptide adsorption energies on gold surfaces with an effective implicit solvent and surface model. Journal of Colloid and Interface Science, 605, 493–499. https://doi.org/10.1016/j.jcis.2021.07.090
   PubMed Web of Science ®Google Scholar
• Tan, Y. N., Lee, J. Y., & Wang, D. I. (2010). Uncovering the design rules for peptide synthesis of metal nanoparticles. Journal of the American Chemical Society, 132(16), 5677–5686. https://doi.org/10.1021/ja907454f
   PubMed Web of Science ®Google Scholar
• Tang, M., Gandhi, N. S., Burrage, K., & Gu, Y. (2019). Interaction of gold nanosurfaces/nanoparticles with collagen-like peptides. Physical Chemistry Chemical Physics: PCCP, 21(7), 3701–3711. https://doi.org/10.1039/C8CP05191G
   PubMed Web of Science ®Google Scholar
• Tang, Z., Palafox-Hernandez, J. P., Law, W.-C., Hughes, Z. E., Swihart, M. T., Prasad, P. N., Knecht, M. R., & Walsh, T. R. (2013). Biomolecular recognition principles for bionanocombinatorics: An integrated approach to elucidate enthalpic and entropic factors. ACS Nano, 7(11), 9632–9646. https://doi.org/10.1021/nn404427y
   PubMed Web of Science ®Google Scholar
• Tobias, D. J., Tu, K., & Klein, M. L. (1997). Atomic-scale molecular dynamics simulations of lipid membranes. Current Opinion in Colloid & Interface Science, 2(1), 15–26. https://doi.org/10.1016/S1359-0294(97)80004-0
   Web of Science ®Google Scholar
• Uberuaga, B. P., Anghel, M., & Voter, A. F. (2004). Synchronization of trajectories in canonical molecular-dynamics simulations: Observation, explanation, and exploitation. The Journal of Chemical Physics, 120(14), 6363–6374. https://doi.org/10.1063/1.1667473
   PubMed Web of Science ®Google Scholar
• Walsh, T. R., & Knecht, M. R. (2017). Biointerface structural effects on the properties and applications of bioinspired peptide-based nanomaterials. Chemical Reviews, 117(20), 12641–12704. https://doi.org/10.1021/acs.chemrev.7b00139
   PubMed Web of Science ®Google Scholar
• Walters, E. T., Mohebifar, M., Johnson, E. R., & Rowley, C. N. (2018). Evaluating the London dispersion coefficients of protein force fields using the exchange-hole dipole moment model. The Journal of Physical Chemistry. B, 122(26), 6690–6701. https://doi.org/10.1021/acs.jpcb.8b02814
   PubMed Web of Science ®Google Scholar
• Wang, S.-T., Lin, Y., Todorova, N., Xu, Y., Mazo, M., Rana, S., Leonardo, V., Amdursky, N., Spicer, C. D., Alexander, B. D., Edwards, A. A., Matthews, S. J., Yarovsky, I., & Stevens, M. M. (2017). Facet-dependent interactions of islet amyloid polypeptide with gold nanoparticles: Implications for fibril formation and peptide-induced lipid membrane disruption. Chemistry of Materials: a Publication of the American Chemical Society, 29(4), 1550–1560. https://doi.org/10.1021/acs.chemmater.6b04144
   PubMed Web of Science ®Google Scholar
• Wang, Z., Xu, Z., Zhao, W., & Sahai, N. (2015). A potential mechanism for amino acid-controlled crystal growth of hydroxyapatite. Journal of Materials Chemistry. B, 3(47), 9157–9167. https://doi.org/10.1039/C5TB01036E
   PubMed Web of Science ®Google Scholar
• Wang, Z., Xu, Z., Zhao, W., Chen, W., Miyoshi, T., & Sahai, N. (2016). Isoexergonic conformations of surface-bound citrate regulated bioinspired apatite nanocrystal growth. ACS Applied Materials & Interfaces, 8(41), 28116–28123. https://doi.org/10.1021/acsami.6b04822
   PubMed Web of Science ®Google Scholar
• Weiger, M. C., Park, J. J., Roy, M. D., Stafford, C. M., Karim, A., & Becker, M. L. (2010). Quantification of the binding affinity of a specific hydroxyapatite binding peptide. Biomaterials, 31(11), 2955–2963. https://doi.org/10.1016/j.biomaterials.2010.01.012
   PubMed Web of Science ®Google Scholar
• Xue, Y., Zhao, H., Wu, Z., Li, X., He, Y., & Yuan, Z. (2011). Colorimetric detection of Cd 2+ using gold nanoparticles cofunctionalized with 6-mercaptonicotinic acid and l-cysteine. The Analyst, 136(18), 3725–3730. https://doi.org/10.1039/C1AN15238F
   PubMed Web of Science ®Google Scholar
• Zhang, D., Neumann, O., Wang, H., Yuwono, V. M., Barhoumi, A., Perham, M., Hartgerink, J. D., Wittung-Stafshede, P., & Halas, N. J. (2009). Gold nanoparticles can induce the formation of protein-based aggregates at physiological pH. Nano Letters, 9(2), 666–671. https://doi.org/10.1021/nl803054
   PubMed Web of Science ®Google Scholar