Investigation on the interaction of acid phosphatase with putrescine using docking, simulations methods and multispectroscopic techniques
Authors: Sadegh Farhadian
Ali Akbar Saboury
Sima Moradi
Behzad Shareghi
Journal: International Journal of Biological Macromolecules (2020)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Circular dichroism (CD); Kinetic techniques; Molecular dynamics (MD) simulations; Thermal stability.
Affiliations: Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord 88186/34141, Iran., Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran., Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord 88186/34141, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran. Electronic address: .

Abstract:  The effect of putrescine on the dynamics, conformation, and kinetics of acid phosphatase investigated via different experimental and theoretical methods. The Stern-Volmer constants (Ksv) for the acid phosphatase- putrescine compound was obtained at different temperatures. Therefore, putrescine quenched the intensity of the enzyme via the static method. Gibbs free energy displayed which binding process was spontaneous. MD simulation, docking method, and thermodynamic parameters revealed the van der Waals forces and hydrogen bonding that had the specific interaction in unfolding the compound. After putrescine binding, the Vmax amounts of acid phosphatase without changed, and the value of kcat/Km increased. The Tm the acid phosphatase-putrescine compound was decreased. Presumably because of more surface hydrophilicity and further H-bond formation underlying the putrescine modification. As confirmed by fluorescence spectra and UV-Visible spectroscopy. Circular dichroism (CD) and UV absorption investigations also demonstrated which binding of putrescine to acid phosphatase led to microenvironmental variations around the protein. Therefore, putrescine cause changes in its structure and function. The results, therefore, showed the effect of putrescine was because of its kosmotropic specifications. Molecular dynamics simulation and Molecular docking results further confirmed the results obtained by CD and spectroscopy experiments. 

Retracted: No

PubPeer comments:
 I am confused about this article, and hope the authors can explain. The paper cites one of my own publications on the rather generic statement that  Fluorescence measurements could provide information about the binding between the enzyme and small ligand molecules [41,42] . Now, the article I wrote together with Prof. Lorenzo Stella is entitled  Fluorescence quenching and ligand binding: A critical discussion of a popular methodology . In this article we heavily criticize the commonly used, or rather abused, methodology of fluorescence quenching to study protein-ligand binding. Considering the fact that the authors *cite* my article, one would expect them to also have *read* the article. And yet the authors have decided to use an equation (eq. 4) that we not only argue is inappropriate, but also *show* to be inappropriate. The authors also have an, in my opinion, incorrect discussion on static vs dynamic quenching, as we explain in our article. So, the question to ask is why the authors considered our article relevant enough to cite, and at the same time irrelevant regarding its actual main content? This would suggest the authors have evidence that our criticism in the article is not correct, and I would be very interested to learn what we got wrong. Thank you for your consideration. ,