Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions

Science Communicator Platform

Stay connected! Follow us on X network (Twitter):

Share By

Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions

Mahnam K¹ ; Saffar B^{2, 3} ; Mobinidehkordi M^{2, 3} ; Fassihi A⁴ ; Mohammadi A²

Source: Research in Pharmaceutical Sciences Published:2014

Abstract

Heavy metal toxicity has serious adverse effects on the environment. The metal sequestering characteristics of a novel metal binding peptide (Glu-Cys)11 Gly+linker+hexahistidine (EC11:His 6) was investigated to determine if it can absorb Cu2+ or Zn2+ cations. Molecular dynamics simulations were carried out using a model of 6 Cu2+ or Zn2+ and other ions enclosed in a fully hydrated simulation box with the designed peptide. Totally, 240 nano second (ns) simulations were done in three phases. Results showed that the selected linker is able to separate two domains of this peptide and that the carboxyl oxygens of Glu residues of EC11 in the designed peptide can absorb these ions. Sequestration of Cu2+ or Zn2+ ions by the designed peptide does not change overall tertiary and secondary structures of peptide.

Related Docs

View other Related Docs

1. Insights Into the Human A1 Adenosine Receptor From Molecular Dynamics Simulation: Structural Study in the Presence of Lipid Membrane, Medicinal Chemistry Research (2015)

2. Homology Modeling of Human Ccr5 and Analysis of Its Binding Properties Through Molecular Docking and Molecular Dynamics Simulation, Biochimica et Biophysica Acta - Biomembranes (2011)

3. Exploring a Model of a Chemokine Receptor/Ligand Complex in an Explicit Membrane Environment by Molecular Dynamics Simulation: The Human Ccr1 Receptor, Journal of Chemical Information and Modeling (2011)

Experts (# of related papers)

View all Related Experts

Afshin Fassihi (9)

Lotfollah Saghaie Dehkordi (5)

Other Related Docs

4. Molecular Dynamics Simulation of Chemokine Receptors in Lipid Bilayer: A Case Study on C-C Chemokine Receptor Type 2, Chemical Biology and Drug Design (2013)

5. Characterization of Adenosine Receptor in Its Native Environment: Insights From Molecular Dynamics Simulations of Palmitoylated/Glycosylated, Membrane-Integrated Human A2b Adenosine Receptor, Journal of Molecular Modeling (2012)

6. Exploring the Interaction Between Epidermal Growth Factor Receptor Tyrosine Kinase and Some of the Synthesized Inhibitors Using Combination of In-Silico and In-Vitro Cytotoxicity Methods, Research in Pharmaceutical Sciences (2018)

7. Theoretical Design of a New Chimeric Protein for the Treatment of Breast Cancer, Research in Pharmaceutical Sciences (2016)

8. The Interaction of a New Schiff Base Ligand With Human Serum Albumin: Molecular Docking and Molecular Dynamics Simulation Studies, Journal of Macromolecular Science, Part B: Physics (2017)

9. Rational Design of a New Variant of Reteplase With Optimized Physicochemical Profile and Large-Scale Production in Escherichia Coli, World Journal of Microbiology and Biotechnology (2022)

10. In Silico Analysis of Transmembrane Protein 31 (Tmem31)Antigen to Design Novel Multiepitope Peptide and Dna Cancer Vaccines Against Melanoma, Molecular Immunology (2019)

11. Design and Production of New Chimeric Reteplase With Enhanced Fibrin Affinity: A Theoretical and Experimental Study, Journal of Biomolecular Structure and Dynamics (2021)

12. In Silico Design of Novel Fak Inhibitors Using Integrated Molecular Docking, 3D-Qsar and Molecular Dynamics Simulation Studies, Journal of Biomolecular Structure and Dynamics (2022)

13. Damage Intensity of Carvacrol on Prostatic Cancer Cells Linedu145 and Molecular Dynamic Simulation of It Effect on Apoptotic Factors, International Journal of PharmTech Research (2016)

14. Molecular Modelling Study on Pyrrolo[2,3-B]Pyridine Derivatives As C-Met Kinase Inhibitors: A Combined Approach Using Molecular Docking, 3D-Qsar Modelling and Molecular Dynamics Simulation, Molecular Simulation (2020)

15. Gp41 Inhibitory Activity Prediction of Theaflavin Derivatives Using Ligand/Structure-Based Virtual Screening Approaches, Computational Biology and Chemistry (2019)

16. Preparing a Database of Corrected Protein Structures Important in Cell Signaling Pathways, Research in Pharmaceutical Sciences (2023)

17. Rational Design of a New Mutant of Tobacco Etch Virus Protease in Order to Increase the in Vitro Solubility, Research in Pharmaceutical Sciences (2020)

18. Identification and Characterization of a Novel Nanobody Against Human Placental Growth Factor to Modulate Angiogenesis, Molecular Immunology (2016)

Style	Citing Format
MLA	Mahnam K, et al.. "Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions." Research in Pharmaceutical Sciences, vol. 9, no. 1, 2014, pp. 69-82.
APA	Mahnam K, Saffar B, Mobinidehkordi M, Fassihi A, Mohammadi A (2014). Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions. Research in Pharmaceutical Sciences, 9(1), 69-82.
Chicago	Mahnam K, Saffar B, Mobinidehkordi M, Fassihi A, Mohammadi A. "Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions." Research in Pharmaceutical Sciences 9, no. 1 (2014): 69-82.
Harvard	Mahnam K et al. (2014) 'Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions', Research in Pharmaceutical Sciences, 9(1), pp. 69-82.
Vancouver	Mahnam K, Saffar B, Mobinidehkordi M, Fassihi A, Mohammadi A. Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions. Research in Pharmaceutical Sciences. 2014;9(1):69-82.
BibTex	@article{ author = {Mahnam K and Saffar B and Mobinidehkordi M and Fassihi A and Mohammadi A}, title = {Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions}, journal = {Research in Pharmaceutical Sciences}, volume = {9}, number = {1}, pages = {69-82}, year = {2014} }
RIS	TY - JOUR AU - Mahnam K AU - Saffar B AU - Mobinidehkordi M AU - Fassihi A AU - Mohammadi A TI - Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions JO - Research in Pharmaceutical Sciences VL - 9 IS - 1 SP - 69 EP - 82 PY - 2014 ER -

Science Communicator Platform

Authors

Abstract