Refinement of Protein NMR Structure under Membrane-like Environments with an Implicit Solvent Model

Systematic Assessment of the Effects of an All-Atom Force Field and the Implicit Solvent Model on the Refinement of NMR Structures with Subsets of Distance Restraints

Employment of a time consuming, sophisticated calculation using the all-atom force field and generalizedBorn implicit solvent model (GBIS) for refinement of NMR structures has become practical through advances in computational methods and capacities. GBIS refinement improves the qualities of the resulting NMR structures with reduced computational times. However, the contribution of GBIS to NMR ...

Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling.

Determining an accurate initial native-like protein fold is one of the most important and time-consuming steps of de novo NMR structure determination. Here we demonstrate that high-quality native-like models can be rapidly generated from initial structures obtained using limited NOE assignments, through replica exchange molecular dynamics refinement with a generalized Born implicit solvent (REX...

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models.

Since biomolecules exist in aqueous and membrane environments, the accurate modeling of solvation, and hydrogen bonding interactions in particular, is essential for the exploration of structure and function in theoretical and computational studies. In this chapter, we focus on alternatives to explicit solvent models and discuss recent advances in generalized Born (GB) implicit solvent theories....

Nano-SbCl5/SiO2 as an Efficient Catalyst for One-Pot Synthesis of 2, 4, 5-Trisubstituted Imidazoles Under Solvent- Free Condition

A general synthetic route to the synthesis of imidazoles has been developed using nano SbCl5/SiO2 under solvent-free conditions. The multi-component reactions of aldehydes, benzil and ammonium acetate were carried out to afford some trisubstituted imidazole derivatives. This method provides several advantages like simple work-up, environmentally benign, and shorter reaction times along wi...