Deciphering the Molecular Details of Interactions Between Heavy Metals and Proteins: Molecular Docking Study
Abstract
Understanding the interaction of heavy metals with proteins is pivotal for unraveling their roles in biochemical processes and metal-induced diseases, with wide-ranging implications spanning medicine, environmental science, and biotechnology, thereby driving progress in therapeutics, pollution mitigation, and biomaterial innovation. In the present study the molecular docking technique was employed to identify and characterize the binding sites of the set of heavy metals (Cu2+, Fe3+, Mg2+, Mn2+, Zn2+, Cd2+, Fe2+, Ni2+, Hg2+, Co2+, Cu+, Au+, Ba2+, Pb2+, Pt2+, Sm3+, and Sr2+) and proteins ((β-lactoglobulin, 7S globulin and glycinin from soybeans) to evaluate the impact of protein structure on their ion-binding abilities and selectivity. Our docking results indicate that essential and toxic heavy metals interact with multiple binding sites of proteins, presumably by electrostatic interactions and metal chelation with cysteine, aspartic acid, glutamic acid, and histidine amino acid residues. The comparison of binding residues favorable for heavy metal complexation among different proteins indicates that metals exhibit distinct preferences for various amino acid residues highlighting the importance of both the metal and the protein properties for stabilizing protein-metal complexation.
Downloads
References
J.H. Duffus, Pure Appl. Chem. 74(5), 793 (2002). https://doi.org/10.1351/pac200274050793.
P.B. Tchounwou, C.G. Yedjou, A.K. Patlolla, and D.J. Sutton. Exp. Suppl. 101, 133 (2012). https://doi.org/10.1007/978-3-7643-8340-4_6
M.A. Zoroddu, J. Aaseth, G. Crisponi, S. Medici, M. Peana, and V.M. Nurchi, J. Bioorg Chem. 195, 120 (2019). https://doi.org/10.1016/j.jinorgbio.2019.03.013
M. Balali-Mood, K. Naseri, Z. Tahergorabi, M. Reza Khazdair, and M. Sadeghi, Front Pharmacol. 12, 643972 (2021). https://doi.org/10.3389/fphar.2021.643972
R. Singh, N. Gautam, A. Mishra, and R. Gupta, Indian J. Pharmacol. 43, 246 (2011). https://doi.org/10.4103/253-7613.81505
J.-J. Kim, Y.-S. Kim, V. Kumar. And J. Trace Elem. Med Biol. 54, 226 (2019). https://doi.org/10.1016/j.jtemb.2019.05.003
M. Jaishankar, T. Tseten, N. Anbalagan, B. Mathew, and K. Beeregowda, Interdiscip Toxicol. 7, 60 (2014). https://doi.org/10.2478/intox-2014-0009
M. Valko, H. Morris, and M.T.D. Cronin, Curr Med. Chem. 12, 1161 (2005). https://doi.org/10.2174/09298670537646635
J.G. Paithankar, S. Saini, S. Dwidevi, A. Sharma, and D.K. Chowdhuri, Chemosphere, 262, 128350 (2021). https://doi.org/10.1016/j.chemosphere.2020.128350
Q. Sun, Y. Li, L. Shi, R. Hussain, K. Mehmood, Z. Tang, and H. Zhang, Toxicology, 469, 153136 (2022). https://doi.org/10.1016/j.tox.2022.153136
Z. Fu, and S. Xi. Toxicol. Mech. Methods. 30, 167 (2020). https://doi.org/10.1080/15376516.2019.1701594
C. Giaginis, E. GAtzidou, S. Theocharis, Toxicol. Appl. Pharmacol, 213, 282 (2006). https://doi.org/10.1016/j.taap.2006.03.008
M.E. Morales, RS. Derbes, C.M. Ade, et al., PloS One, 11, e0151367 (2016). https://doi.org/ journal.pone.0151367
D. Witkowska, J. Słowik, and K. Chilicka, Molecules, 26, 6060 (2021). https://doi.org/10.3390/molecules26196060
J.L. Reyes, E. Molina-Jijon, R. Rodriguez-Munoz, et al. Biomed Res. Int. 2013, 730789 (2013). https://doi.org/10.1155/2013/730789
S. Nahar, and H.A. Tajmir-Riahi, J. Coll. Int. Sci. 178, 648 (1996). https://doi.org/10.1006/jcis.1996.0162
B. Saif, and P. Yang, ACS Appl/ Bio Mater. 4, 1156 (2021). https://doi.org/10.1121/acsabm.0c01375
A. Beloqui, and A.L. Cortajarena, Curr. Opin. Struct. Biol. 63, 74 (2020). https://doi.org/10.1116/j.sbi.2020.04.005
A. Aires, D. Maestro, J. Ruiz del Ro, et al. Chem. Sci, 12, 2480 (2021). https://doi.org/10.1039/DOSC05215A
W.L. Soon, M. Peydayesh, R. Mezzenga, and A. Mizerez, Chem Eng. J. 445, 136513 (2022), https://doi.org/10.1016/j.cej.2022.136513
D. Liu, Z. Li, W. Li, Z. Zhong, J. Xu, J. Ren, and Z. Ma, Ind. Eng. Chem. Res. 52(32), 11036 (2013). https://doi.org/10.1021/ie401092f
M. Peydayesh, S. Bolisetty, T. Mohammadi, and R. Mezzenga, Langmuir, 35, 4161 (2019) https://doi.org/10.1021/acs.langmuir.8b04234.
A. Gao, K. Xie, X. Song, K. Zhang, and A. Hou, Ecol. Eng. 99, 343 (2017). https://doi.org/10.1016/j.ecoleng.2016.11.008
A. de Almeida, B.L. Oliveira, J.D.G. Correia, G. Soveral, and A. Casini. Coord. Chem. Rev. 257, 2689 (2013). https://doi.org/10.1016/j.ccr.2013.01.031
T.A. Sales, I.G. Prandi, et al. Int. J. Mol. Sci. 20, 1829 (2019). https://doi.org/10.3390/ijms20081829
P. Sharma, A.K. Pandey, A. Udayan, and S. Kumar. Bioresource Technology, 326, 1124750 (2021). https://doi.org/10.1016/j.biortech.2021.124750
Z. Yang, F, Yang, J.L. Liu, H.T. Wum H. Yang, et al. Sci Total Environ. 809, 151099 (2022). https://doi.org/10.1016/j.scitotenv.2021.151099
K.B. Handing, E.Niedzialkowska, I.G. Shabalin, M.L. Kuhn, H. Zheng, and W. Minor. Nat Protoc. 13, 1062 (2018). https://doi.org/10.1038/nprot.2018.018
D. Shalev. Int. J. Mol. Sci. 23, 15957 (2022). https://doi.org/10.3390/ijms232415957.
M.P. Chantada-Varquez, A. Moreda-Pineiro, M.C. Barciels-Alonso, and P. Bermejo-Barrera, Appl. Spectr. Rev. 52, 145 (2017). https://doi.org/10.1080/05704928.2016.1213736
Y.F. Lin, C.W. Cheng, C.S. Shin, J.K. Hwang, C.S. Yu, and C.H. Lu, J. Chem. Inf. Model, 56, 2287 (2016). https://doi.org/10.1021/acs.jcim.6b00407
J. Zang, C. Li, K. Zhou, H. Dong, B. Chen, F. Wang, and G. Zhao, Anal. Chem. 88, 10275 (2016). https://doi.org/10.1021/acs.analchem.6b03011
K.M.G. Olibeira, V.L. Valente-Mesquita, M.M. Botelho, L. Sawyer, S.T. Ferreir, and I. Polikarpov, Europ. J. Biochem. 268, 477 (2003). https://doi.org/10.1046/j.1432-1033.2001.01918.x
A. Rodzik, P. Pomastowski, G.N. Sagandykova, and B. Buszewski, Int. J. Mol. Sci, 21, 2156 (2020). https://doi.org/10.3390/ijms21062156
R. Pearson, J. Chem. Educ. 45, 981 (1968). https://doi.org/10.1021/ed045p581
T. Hashimoto, T. Shimuzu, M. Yamabe, M. Taichi, et al. FEBS Journal, 278, 1944 (2011). https://doi.org/10.1111/j.1742-4658.2011.08111.x
D. Hwang. And S. Damodaran, Int. J. Appl. Polymer Sci. 64, 891 (1997). https://doi.org/10.1002/(SICI)1097-4628(19970502)64:5<891::AID-APP9>3.0.CO;2-K
J. Liu, D. Su, J. Yao, Y. Huang, Z. Shao, and X. Chen, J. Mat. Chem. A, 5, 4163 (2017). https://doi.org/10.1039/C6TA10814H
M. Adachi, J. Kanamori, T. Masuda, K. Yagasaki, K. Kitamura, B. Mikami, and S. Utsumi. PNAS, 100, 7395 (2003). https://doi.org/10.1073/pnas.0832158100
Copyright (c) 2024 O. Zhytniakivska
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgment of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgment of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
