Solvent Site-Dipole Field Accompanying Protein-Ligand Approach Process

Abstract

We did a molecular dynamics simulation of a system consisting of a peptide and a protein in explicit solvent to study biomolecular approach process. In the initial structure of simulation, the minimum inter-biomolecular distance was 30 Å. During the simulation, the biomolecules approached and contacted to each other. In spite of diffusive motions of water molecules, the orientations of water molecules tended to order in the inter-biomolecular zone showing coherent spatial patterns (solvent site-dipole field) of the ordering. The degree of ordering was synchronized well with the inter-biomolecular distance. This result strongly suggests that the biomolecules distant to each other can interact via the solvent site-dipole field. The effective range for the coherent ordering (i.e., the interaction range via the solvent site-dipole field) was larger than 20 Å. A bridge-like structure of the solvent orientational ordering connected the two biomolecules. Biological and physicochemical significance of the ordering is discussed.

Density, Diffusion, and Site-Dipole Field of Solvent around Four Types of Flavonoid Studid by Molecular Dynamics

“…The MD simulations have an advantage in providing a quantity undetectable by experiments. Time-averaged orientations of water molecules at each spatial site showed coherent patterns (solvent site-dipole field) around proteins [1,[4][5][6][7][8][9][10][11]. These works indicate that the solvent site-dipole field is generated by contributions of many water molecules visiting at each site near protein: orientations of water molecules are restricted depending on the spatial sites.…”

“…This solvent site-dipoles field suggests that two biological molecules may interact via the field. In fact, MD simulations of systems consisting of two biological molecules demonstrated that the solvent site-dipoles field connected the two biological molecules even when the minimum distance between the biological molecules was about 14 Å [6,10] and 20 Å [11]. Contrarily, around spherical hydrophobic solutes, the solvent site-dipoles field computationally observed had a short (a few angstroms) effective range [12].…”

Functional understanding of solvent structure in GroEL cavity through dipole field analysis

“…This protocol is similar in spirit to that adopted by those using the "solvent-site" dipole field approach, in which individual water molecule dipoles are "reassigned" to grid points in a system. 12,13 The method we employ, however, is agnostic to the properties of individual water dipoles, and we calculate dipole moments from the general formula for point charges (Eq. (4)).…”

“…Previous methods, such as the "solvent-site" dipole field approach, have employed coarse-grained dipole fields to describe water in biophysical systems with some success. 12,13 Recent theoretical work has laid the groundwork for studying frustrated solvent properties through discrete vector field quantities. 14 In this paper, we use this theoretical FIG.…”

Solvent flow patterns fluctuating largely around a protein and correlation with solvent density fluctuations: A molecular dynamics study

“…[10][11][12][13][14][15][16] We have proposed two concepts related to the dynamics of water around solutes: the solvent site-dipole field [17][18][19][20][21] and solvent flow. 19 The sol-a͒ vent site-dipole field enhances the electrostatic interaction between biomolecules as with those involved in DNA-peptide, 17 protein-peptide, 19 and protein-substrate. 19 The sol-a͒ vent site-dipole field enhances the electrostatic interaction between biomolecules as with those involved in DNA-peptide, 17 protein-peptide, 19 and protein-substrate.…”