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Gou D, Huang K, Liu Y, Shi H, Wu Z. Molecular Dynamics Research of Spatial Orientation and Kinetic Energy of Active Site Collision of Carnosine under Weak Microwave Irradiation. J Phys Chem B 2022; 126:7686-7700. [PMID: 36134752 DOI: 10.1021/acs.jpcb.2c03930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular mechanism of the microwave nonthermal effect is still not clear. This work investigated the spatial orientation and kinetic energy of active site collision of carnosine, a natural bioactive dipeptide, under the weak microwave irradiation using the molecular dynamics simulation. Our results showed the influences of the temperature, microwave intensity, microwave frequency, and microwave polarization mode (linear polarization and circular polarization) on the spatial orientation and kinetic energy of active site collision of carnosine. First, under the constant intensity and frequency of linear polarization microwave irradiation, the increment of the collision probability between the 6N atom of carnosine and the 28H atom of the other carnosine at effective space angle decreases from 85.0% to 3.5% with increasing temperature. Second, with the increase of microwave intensity, the change of spatial orientation and kinetic energy becomes more and more significant. However, the change of circular polarization microwaves on the spatial orientation and kinetic energy of collision is weaker than that of linear polarization. Third, under the constant intensity of linear polarization microwave irradiation, the collision probability between the 6N atom and the 28H atom at effective space angle decreases from 70.2% to 14.7% with increasing frequency. Finally, under the microwave polarization, the spatial orientation and kinetic energy of molecular collision are changed, which is summarized as the microwave postpolarization effect (MWPPE). The dependence of MWPPE on temperature, microwave intensity, microwave frequency, and polarization mode is very complicated. In the end, this effect can provide a new insight into the molecular mechanism of the microwave nonthermal effect.
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Affiliation(s)
- Dezhi Gou
- College of Electronics and Information Engineering, Sichuan University, Chengdu 610065, China
| | - Kama Huang
- College of Electronics and Information Engineering, Sichuan University, Chengdu 610065, China
| | - Ying Liu
- College of Electronics and Information Engineering, Sichuan University, Chengdu 610065, China
| | - Hongxiao Shi
- College of Electronics and Information Engineering, Sichuan University, Chengdu 610065, China
| | - Zhiyan Wu
- College of Electronic and Electrical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
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Pavlin M, Rossetti G, De Vivo M, Carloni P. Carnosine and Homocarnosine Degradation Mechanisms by the Human Carnosinase Enzyme CN1: Insights from Multiscale Simulations. Biochemistry 2016; 55:2772-84. [PMID: 27105448 DOI: 10.1021/acs.biochem.5b01263] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The endogenous dipeptide l-carnosine, and its derivative homocarnosine, prevent and reduce several pathologies like amytrophic lateral sclerosis (ALS), Alzheimer's disease, and Parkinson's disease. Their beneficial action is severely hampered because of the hydrolysis by carnosinase enzymes, in particular the human carnosinase, hCN1. This belongs to the metallopeptidase M20 family, where a cocatalytic active site is formed by two Zn(2+) ions, bridged by a hydroxide anion. The protein may exist as a monomer and as a dimer in vivo. Here we used hybrid quantum mechanics/molecular mechanics simulations based on the dimeric apoenzyme's structural information to predict the Michaelis complexes with l-carnosine and its derivative homocarnosine. On the basis of our calculations, we suggest that (i) l-carnosine degradation occurs through a nucleophilic attack of a Zn(2+)-coordinated bridging moiety for both monomer and dimer. This mechanistic hypothesis for hCN1 catalysis differs from previous proposals, while it is in agreement with available experimental data. (ii) The experimentally measured higher affinity of homocarnosine for the enzyme relative to l-carnosine might be explained, at least in part, by more extensive interactions inside the monomeric and dimeric hCN1's active site. (iii) Hydrogen bonds at the binding site, present in the dimer but absent in the monomer, might play a role in the experimentally observed higher activity of the dimeric form. Investigations of the enzymatic reaction are required to establish or disprove this hypothesis. Our results may serve as a basis for the design of potent hCN1 inhibitors.
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Affiliation(s)
- Matic Pavlin
- Laboratory for Computational Biophysics, German Research School for Simulation Sciences (GRS), Forschungszentrum Jülich-RWTH Aachen , 52425 Jülich, Germany.,Computational Biomedicine Section (INM-9), Institute for Neuroscience and Medicine (INM), and Institute of Advanced Simulation (IAS), Forschungszentrum Jülich , 52425 Jülich, Germany
| | - Giulia Rossetti
- Computational Biomedicine Section (INM-9), Institute for Neuroscience and Medicine (INM), and Institute of Advanced Simulation (IAS), Forschungszentrum Jülich , 52425 Jülich, Germany.,Jülich Supercomputing Center (JSC), Forschungszentrum Jülich , 52425 Jülich, Germany.,Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University , Pauwelsstraße 30, 52074 Aachen, Germany
| | - Marco De Vivo
- Computational Biomedicine Section (INM-9), Institute for Neuroscience and Medicine (INM), and Institute of Advanced Simulation (IAS), Forschungszentrum Jülich , 52425 Jülich, Germany.,Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia , Via Morego 30, 16163 Genoa, Italy
| | - Paolo Carloni
- Laboratory for Computational Biophysics, German Research School for Simulation Sciences (GRS), Forschungszentrum Jülich-RWTH Aachen , 52425 Jülich, Germany.,Computational Biomedicine Section (INM-9), Institute for Neuroscience and Medicine (INM), and Institute of Advanced Simulation (IAS), Forschungszentrum Jülich , 52425 Jülich, Germany
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