Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function

Overview

Journal J Chem Inf Model

Publisher American Chemical Society

Specialties Chemistry
Medical Informatics

Date 2021 Aug 10

PMID 34375103

Citations 7

Authors

Himansu S Biswal

Akshay Kumar Sahu

Antonio Frontera

Antonio Bauza

Affiliations

Soon will be listed here.

Abstract

Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB's, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational ( calculations) study, we demonstrate that Zn SpB's are abundant and might be involved in protein structure and enzyme inhibition.

Citing Articles

Solvent and additive-controlled supramolecular isomerism in zinc coordination polymers.

Khorshidi G, Notash B Sci Rep. 2024; 14(1):27586.

PMID: 39528602 PMC: 11554826. DOI: 10.1038/s41598-024-77298-6.

Synthesis, Structural Characterization, and Theoretical Analysis of Nonconventional Bonding in Dinuclear Zinc(II) Complexes with Tridentate Schiff Bases.

Halder B, Middya P, Gomila R, Frontera A, Chattopadhyay S ACS Omega. 2024; 9(40):41787-41796.

PMID: 39398134 PMC: 11465551. DOI: 10.1021/acsomega.4c06136.

Spodium Bonds Involving Methylmercury and Ethylmercury in Proteins: Insights from X-ray Analysis and Computations.

Burguera S, Sahu A, Frontera A, Biswal H, Bauza A Inorg Chem. 2023; 62(45):18524-18532.

PMID: 37902775 PMC: 10647129. DOI: 10.1021/acs.inorgchem.3c02716.

Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications.

Burguera S, Frontera A, Bauza A Inorg Chem. 2023; 62(17):6740-6750.

PMID: 37083254 PMC: 10155183. DOI: 10.1021/acs.inorgchem.3c00369.

Matere Bonds vs. Multivalent Halogen and Chalcogen Bonds: Three Case Studies.

Gomila R, Frontera A Molecules. 2022; 27(19).

PMID: 36235133 PMC: 9571139. DOI: 10.3390/molecules27196597.

References

Bai Y, Sosnick T, Mayne L, Englander S . Protein folding intermediates: native-state hydrogen exchange. Science. 1995; 269(5221):192-7. PMC: 3432310. DOI: 10.1126/science.7618079. View

Bauza A, Frontera A . Aerogen Bonding Interaction: A New Supramolecular Force?. Angew Chem Int Ed Engl. 2015; 54(25):7340-3. DOI: 10.1002/anie.201502571. View

Scheiner S . The pnicogen bond: its relation to hydrogen, halogen, and other noncovalent bonds. Acc Chem Res. 2012; 46(2):280-8. DOI: 10.1021/ar3001316. View

Dudev T, Lim C . Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem Rev. 2003; 103(3):773-88. DOI: 10.1021/cr020467n. View

Cordero B, Gomez V, Platero-Prats A, Reves M, Echeverria J, Cremades E . Covalent radii revisited. Dalton Trans. 2008; (21):2832-8. DOI: 10.1039/b801115j. View

Heinig M, Frishman D . STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res. 2004; 32(Web Server issue):W500-2. PMC: 441567. DOI: 10.1093/nar/gkh429. View

Karmakar M, Frontera A, Chattopadhyay S, Mooibroek T, Bauza A . Intramolecular Spodium Bonds in Zn(II) Complexes: Insights from Theory and Experiment. Int J Mol Sci. 2020; 21(19). PMC: 7582961. DOI: 10.3390/ijms21197091. View

Becke . Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A Gen Phys. 1988; 38(6):3098-3100. DOI: 10.1103/physreva.38.3098. View

Christianson D . Structural biology of zinc. Adv Protein Chem. 1991; 42:281-355. DOI: 10.1016/s0065-3233(08)60538-0. View

10.

Weigend F, Ahlrichs R . Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys Chem Chem Phys. 2005; 7(18):3297-305. DOI: 10.1039/b508541a. View

11.

Margiotta E, van der Lubbe S, de Azevedo Santos L, Paragi G, Moro S, Bickelhaupt F . Halogen Bonds in Ligand-Protein Systems: Molecular Orbital Theory for Drug Design. J Chem Inf Model. 2020; 60(3):1317-1328. PMC: 7093837. DOI: 10.1021/acs.jcim.9b00946. View

12.

Schneider H . Binding mechanisms in supramolecular complexes. Angew Chem Int Ed Engl. 2009; 48(22):3924-77. DOI: 10.1002/anie.200802947. View

13.

Vickaryous W, Herges R, Johnson D . Arsenic-pi interactions stabilize a self-assembled As2L3 supramolecular complex. Angew Chem Int Ed Engl. 2004; 43(43):5831-3. DOI: 10.1002/anie.200461011. View

14.

Zeng R, Gong Z, Yan Q . Chalcogen-Bonding Supramolecular Polymers. J Org Chem. 2020; 85(13):8397-8404. DOI: 10.1021/acs.joc.0c00723. View

15.

Alvarez S . A cartography of the van der Waals territories. Dalton Trans. 2013; 42(24):8617-36. DOI: 10.1039/c3dt50599e. View

16.

Bauza A, Quinonero D, Deya P, Frontera A . Pnicogen-π complexes: theoretical study and biological implications. Phys Chem Chem Phys. 2012; 14(40):14061-6. DOI: 10.1039/c2cp42672b. View

17.

Mahmoudi G, Masoudiasl A, Babashkina M, Frontera A, Doert T, White J . On the importance of π-hole spodium bonding in tricoordinated Hg complexes. Dalton Trans. 2020; 49(48):17547-17551. DOI: 10.1039/d0dt03938a. View

18.

Christianson D, Cox J . Catalysis by metal-activated hydroxide in zinc and manganese metalloenzymes. Annu Rev Biochem. 2000; 68:33-57. DOI: 10.1146/annurev.biochem.68.1.33. View

19.

Contreras-Garcia J, Johnson E, Keinan S, Chaudret R, Piquemal J, Beratan D . NCIPLOT: a program for plotting non-covalent interaction regions. J Chem Theory Comput. 2011; 7(3):625-632. PMC: 3080048. DOI: 10.1021/ct100641a. View

20.

Xu Z, Liu Z, Chen T, Chen T, Wang Z, Tian G . Utilization of halogen bond in lead optimization: a case study of rational design of potent phosphodiesterase type 5 (PDE5) inhibitors. J Med Chem. 2011; 54(15):5607-11. DOI: 10.1021/jm200644r. View