On the application of simple explicit water models to the simulations of biomolecules

Abstract

Computer simulations of biomolecular systems have achieved a significant importance in science as they provide information regarding structure, dynamics, and energetics of biomolecules that are inaccessible to experimental measuring techniques. In this work, some important aspects of the simulation of biomolecular systems are described. An overview of the most popular protein force fields, simple explicit water models for the simulation of liquid water, and different approaches to treat the boundaries of the system is presented. Also, studies conducted in our group illustrating successful simulations of three biomolecules (thrombin, L-type calcium channel and human Cytomegalovirus protease) through the application of simple explicit water models combined with protein force fields are discussed.

On the Application of Accelerated Molecular Dynamics to Liquid Water Simulations

“…Thus, (6) which corresponds to the Boltzmann factor of the bias energy. Substituting equation 6 into equation 5, we get (7) Therefore, correct canonical ensemble averages on the unmodified potential V(r) can be obtained in the accelerated MD simulation by reweighting each configuration sampled on the modified potential V*(r) by the factor e βΔV(r) . This procedure guarantees that the ensemble average obtained as time average over the trajectory generated from the modified potential is Boltzmann weighted.…”

Molecular models of alginic acid: Interactions with calcium ions and calcite surfaces

“…A detailed molecular level understanding of the complex chemical contributions to cation binding is essential to fully comprehend these phenomena. The use of molecular modeling methods such as energy optimization and molecular dynamics in this study allows access to additional insights that may be difficult, if nearly impossible, to obtain experimentally (Guimarães et al, 2004) and ultimately broadens the understanding of these chemical interactions. Also, a fundamental understanding of the atomistic interactions of organic species with mineral surfaces during dissolution and precipitation needs to be developed Welch and Vandevivere, 1994).…”

“…Previous modeling efforts have been limited by the availability of an energy force field that can simultaneously simulate these complicated systems, especially those involving a hydrated organic-inorganic interface (de Leeuw et al, 1998(de Leeuw et al, , 2004Hwang et al, 2001;Cormack et al, 2004;Duffy and Harding, 2004). Attempts to model different aspects of these systems have been performed using static calculations (de Leeuw and Cooper, 2004), in vacuo (Duckworth et al, 2003), by focusing on the interaction of organics with cations (Braccini et al, 1999) and water (Guimarães et al, 2004), by modeling mineral surfaces with monolayers of water (Kerisit and Parker, 2004a), or by combination of force field models (de Leeuw and Cooper, 2004).…”

Structure and dynamics of microbe-exuded polymers and their interactions with calcite surfaces.

“…A detailed molecular level understanding of the complex chemical contributions to cation binding is essential to understand fully this phenomenon. The use of molecular modeling methods such as energy optimization and molecular dynamics in this study allows access to additional insights that may be difficult, if not impossible, to obtain experimentally (Guimarães et al, 2004) and ultimately broadens the understanding of these chemical interactions. Also, a fundamental understanding of the atomistic interactions of organic species with mineral surfaces during dissolution and precipitation needs to be developed Welch and Vandevivere, 1994).…”

“…Previous modeling efforts have been limited by the availability of an energy force field that can simultaneously simulate these complicated systems. Attempts to model different aspects of the systems have been performed using static calculations (de Leeuw and Cooper, 2004), in vacuo (Duckworth et al, 2003), by focusing on the interaction of organics with cations (Braccini et al, 1999) and water (Guimarães et al, 2004), by modeling minerals with monolayers of water (Kerisit and Parker, 2004), or by combination of potential models (de Leeuw and Cooper, 2004). To our knowledge, no previous study has developed a general and accurate set of force field parameters to model the interactions of organic species, with water, calcium ions, and the carbonate substrate.…”