Role of Histidine-85 in the Catalytic Mechanism of Thymidine Phosphorylase As Assessed by Targeted Molecular Dynamics Simulations and Quantum Mechanical Calculations†

Biochemistry ◽  
2004 ◽  
Vol 43 (2) ◽  
pp. 405-414 ◽  
Author(s):  
Jesús Mendieta ◽  
Sonsoles Martín-Santamaría ◽  
Eva-María Priego ◽  
Jan Balzarini ◽  
María-José Camarasa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thymidine Phosphorylase ◽  
Catalytic Mechanism ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Targeted Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243429
Author(s):  
Dimitrios A. Mitsikas ◽  
Nicholas M. Glykos
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Type I ◽  
Quantum Mechanical Calculations ◽  
Water Solvent ◽  
Simulation Protocol ◽  
Dynamics Simulations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.

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