Topics

Capturing the effects of explicit waters in implicit electrostatics modeling: Qualitative justification of Gaussian-based dielectric models in DelPhi.

08:00 EDT 10th March 2020 | BioPortfolio

Summary of "Capturing the effects of explicit waters in implicit electrostatics modeling: Qualitative justification of Gaussian-based dielectric models in DelPhi."

Recently we have implemented a smooth Gaussian-based dielectric function in DelPhi (J. Chem. Theory Comput. 2013, 9, 4, 2126-2136) that models the solute as an object with inhomogeneous dielectric permittivity and provides a smooth transition of dielectric permittivity from surface bound water to bulk solvent. While intuitively it is well understood that protein hydrophobic core is less polarizable than the hydrophilic protein surface, less attention is paid on the polarizability of water molecules inside and on the surface of the solute. Here we apply explicit water simulations to study the behavior of water molecules buried inside a protein and waters at the surface of the same protein, and contrast it with the behavior of the bulk water. We selected a protein that is experimentally shown to have five cavities, most of which are occupied by water molecules. We demonstrate through molecular dynamics (MD) simulations that the behavior of water in the cavity is drastically different from that in the bulk. These observations were made by comparing their mean residence times, dipole orientation relaxation times and average dipole moment fluctuations. We also show that the bulk region has a non-uniform distribution of these tempo-spatial properties. From the point of view of continuum electrostatics, we argue that dielectric "constant" in water filled cavities in proteins and space close to molecular surface should differ from that assigned to the bulk water. This provides support for Gaussian-based smooth dielectric model for solving electrostatics in the Poisson-Boltzmann Equation (PBE) framework. Furthermore, we demonstrate that using a single energy minimized structure Gaussian-based model is capable of reproducing averaged over MD trajectories polar solvation energy. Thus, we argue that Gaussian-based smooth dielectric function not only captures correct physics but also provides efficient way of computing ensemble averaged quantities.

Affiliation

Journal Details

This article was published in the following journal.

Name: Journal of chemical information and modeling
ISSN: 1549-960X
Pages:

Links

DeepDyve research library

PubMed Articles [16809 Associated PubMed Articles listed on BioPortfolio]

Lack of generalization between explicit and implicit visuomotor learning.

Visuomotor adaptation has been thought to occur implicitly, although recent findings suggest that it involves both explicit and implicit processes. Here, we investigated generalization between an expl...

Implicit and explicit spatial-numerical representations diverge in number-form synesthetes.

In number-form (NF) synesthesia-a condition in which people report vivid, automatic and consistent mental layouts for numerical sequences-numbers and space are closely linked. These explicit associati...

Forgotten but not gone: FMRI evidence of implicit memory for negative stimuli 24 hours after the initial study episode.

Endel Tulving conducted pioneering work on the explicit and implicit memory systems and demonstrated that priming effects can be long-lasting. It is also well-established that emotion can amplify expl...

The Value of Interracial Contact for Reducing Anti-Black Bias Among Non-Black Physicians: A Cognitive Habits and Growth Evaluation (CHANGE) Study Report.

Although scholars have long studied circumstances that shape prejudice, inquiry into factors associated with long-term prejudice reduction has been more limited. Using a 6-year longitudinal study of n...

Effect of metabolic state on implicit and explicit responses to food in young healthy females.

Recent neuroscience research has delineated key psychological components of reward: wanting, liking and learning. Each component is further divided into explicit and implicit processes. While explicit...

Clinical Trials [2572 Associated Clinical Trials listed on BioPortfolio]

Comparison of Explicit, Implicit and no Values Clarification Decision Aids for Men Considering Prostate Cancer Screening

The investigators aim at comparing the perceived clarity of personal values in men considering PSA screening using decision aids with no VCM versus an implicit VCM versus an explicit VCM. ...

Literacy and Smoking Risk Communications

Objectives: Smokers with varying levels of health literacy as assessed by the S-TOFHLA (i.e., inadequate, marginal, adequate) recruited from the community will listen to one of 4 di...

Implicit Learning in Stroke Study

This trial will compare an Implicit Learning Approach (ILA) to usual care, during the rehabilitation of mobility post stroke. It is a multicentre, assessor blind, cluster randomised contr...

Evaluation of Methods for Measuring Food Reward and Food-related Behavior in Healthy Individuals

Most of the decisions and actions affecting energy balance are driven by implicit and explicit motivational processes. In modern obesogenic environment where highly palatable and energy-de...

Exploring the Effects of Diazepam and Lorazepam

Aims : - exploring lorazepam (0.038 mg/kg) effects, after a single oral intake, in healthy volunteers, on the neural correlates of encoding and retrieval of information during a ...

Medical and Biotech [MESH] Definitions

The qualitative or quantitative estimation of the likelihood of adverse effects that may result from exposure to specified health hazards or from the absence of beneficial influences. (Last, Dictionary of Epidemiology, 1988)

Research that derives data from observation, interviews, or verbal interactions and focuses on the meanings and interpretations of the participants (From Holloway and Wheeler, "Ethical issues in qualitative nursing research," Nursing Ethics, 1995 Sep; 2(3): 223-232).

Therapy by various hot or warm baths in natural mineral waters, spas, or "cures". It includes not only bathing in, but also drinking the waters, but it does not include whirlpool baths (HYDROTHERAPY).

Process of capturing very reduced images for preservation and storage.

The process of discovering or asserting an objective or intrinsic relation between two objects or concepts; a faculty or power that enables a person to make judgments; the process of bringing to light and asserting the implicit meaning of a concept; a critical evaluation of a person or situation.

Quick Search


DeepDyve research library

Relevant Topic

Nutrition
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...


Searches Linking to this Article