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Molecular mechanics force field calculations have historically shown significant limitations in modeling the energetic and conformational interconversions of highly substituted furanose rings. This is primarily due to the gauche effect that is not easily captured using pairwise energy potentials. In this study, we present a refinement to the set of torsional parameters in the General Amber Force Field (gaff) used to calculate the potential energy of mono, di-, and gem-fluorinated nucleosides. The parameters were optimized to reproduce the pseudorotation phase angle and relative energies of a diverse set of mono- and difluoro substituted furanose ring systems using quantum mechanics umbrella sampling techniques available in the IpolQ engine in the Amber suite of programs. The parameters were developed to be internally consistent with the gaff force field and the TIP3P water model. The new set of angle and dihedral parameters and partial charges were validated by comparing the calculated phase angle probability to those obtained from experimental nuclear magnetic resonance experiments. [ABSTRACT FROM AUTHOR]

To study the microscopic thermal aging mechanism of insulating paper cellulose through molecular dynamics simulation, it is important to select suitable DP (Degree of Polymerization) and force field for the cellulose model to shorten the simulation time and obtain correct and objective simulation results. Here, the variation of the mechanical properties and solubility parameters of models with different polymerization degrees and force fields were analyzed. Numerous cellulose models with different polymerization degrees were constructed to determine the relative optimal force field from the perspectives of the similarity of the density of cellulose models in equilibrium to the actual cellulose density, and the volatility and repeatability of the mechanical properties of the models through the selection of a stable polymerization degree using the two force fields. The results showed that when the polymerization degree was more than or equal to 10, the mechanical properties and solubility of cellulose models with the COMPASS (Condensed-phase Optimized Molecular Potential for Atomistic Simulation Studies) and PCFF (Polymer Consistent Force Field) force fields were in steady states. The steady-state density of the cellulose model using the COMPASS force field was closer to the actual density of cellulose. Thus, the COMPASS force field is favorable for molecular dynamics simulation of amorphous cellulose. [ABSTRACT FROM AUTHOR]

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations. [ABSTRACT FROM AUTHOR]

G-quadruplexes have drawn widespread attention for serving as a potential anti-cancer target and their application in material science. Molecular dynamics (MD) simulation is the key theoretical tool in the study of GQ's structure-function relationship. In this article, we systematically benchmarked the five force fields of parmbsc0, parmbsc1, OL15, AMOEBA, and Drude2017 on the MD simulation of G-quadruplex from four aspects: structural stability, central ion channel stability, description of Hoogsteen hydrogen bond network, and description of the main chain dihedral angle. The results show that the overall performance of the Drude force field is the best. Although there may be a certain over-polarization effect, it is still the best choice for the MD simulation of G-quadruplexes. [ABSTRACT FROM AUTHOR]