scholarly journals Biomolecular electrostatics and solvation: a computational perspective

2012 ◽  
Vol 45 (4) ◽  
pp. 427-491 ◽  
Author(s):  
Pengyu Ren ◽  
Jaehun Chun ◽  
Dennis G. Thomas ◽  
Michael J. Schnieders ◽  
Marcelo Marucho ◽  
...  
Keyword(s):  
Molecular Interactions ◽  
Electrostatic Interactions ◽  
Membrane Lipids ◽  
Biological Molecules ◽  
Computational Aspect ◽  
Special Importance ◽  
Computational Biophysics ◽  
Aqueous Ions ◽  
Solvation Models ◽  
Insight Into

AbstractAn understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

scholarly journals Electrostatic interactions in soft particle systems: mesoscale simulations of ionic liquids

Soft Matter ◽  
2018 ◽  
Vol 14 (21) ◽  
pp. 4252-4267 ◽  
Author(s):  
Yong-Lei Wang ◽  
You-Liang Zhu ◽  
Zhong-Yuan Lu ◽  
Aatto Laaksonen
Keyword(s):  
Ionic Liquids ◽  
Physicochemical Properties ◽  
Dynamic Behavior ◽  
Computer Simulations ◽  
Molecular Interactions ◽  
Electrostatic Interactions ◽  
Particle Systems ◽  
Soft Particle ◽  
Mesoscale Simulations ◽  
Insight Into

Computer simulations provide a unique insight into the microscopic details, molecular interactions and dynamic behavior responsible for many distinct physicochemical properties of ionic liquids.

scholarly journals Lipidomics Provides New Insight into Pathogenesis and Therapeutic Targets of the Ischemia—Reperfusion Injury

2021 ◽  
Vol 22 (6) ◽  
pp. 2798
Author(s):  
Zoran Todorović ◽  
Siniša Đurašević ◽  
Maja Stojković ◽  
Ilijana Grigorov ◽  
Slađan Pavlović ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Time Course ◽  
Membrane Lipids ◽  
Lipid Analysis ◽  
Cell Damage ◽  
Ischemia Reperfusion ◽  
Enzyme Inactivation ◽  
Critical Event ◽  
Tissue Ischemia ◽  
Insight Into

Lipids play an essential role in both tissue protection and damage. Tissue ischemia creates anaerobic conditions in which enzyme inactivation occurs, and reperfusion can initiate oxidative stress that leads to harmful changes in membrane lipids, the formation of aldehydes, and chain damage until cell death. The critical event in such a series of harmful events in the cell is the unwanted accumulation of fatty acids that leads to lipotoxicity. Lipid analysis provides additional insight into the pathogenesis of ischemia/reperfusion (I/R) disorders and reveals new targets for drug action. The profile of changes in the composition of fatty acids in the cell, as well as the time course of these changes, indicate both the mechanism of damage and new therapeutic possibilities. A therapeutic approach to reperfusion lipotoxicity involves attenuation of fatty acids overload, i.e., their transport to adipose tissue and/or inhibition of the adverse effects of fatty acids on cell damage and death. The latter option involves using PPAR agonists and drugs that modulate the transport of fatty acids via carnitine into the interior of the mitochondria or the redirection of long-chain fatty acids to peroxisomes.

scholarly journals Current Research on Polyelectrolyte Nanostructures: From Molecular Interactions to Biomedical Applications

Macromol ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 155-172
Author(s):  
Aristeidis Papagiannopoulos
Keyword(s):  
Physical Properties ◽  
Molecular Interactions ◽  
Interdisciplinary Research ◽  
Biomedical Applications ◽  
Electrostatic Interactions ◽  
Soft Matter ◽  
Extracellular Polysaccharides ◽  
Polymer Science ◽  
Biological Matter ◽  
Biomedical Field

Polyelectrolytes have been at the center of interdisciplinary research for many decades. In the field of polymer science and soft matter, they have provided the dimensions of electrostatic interactions, which opens a vast variety of opportunities for new physical properties and applications. In biological matter, polyelectrolytes are present in many forms, from extracellular polysaccharides to complex DNA molecules and proteins. This review discusses the recent research on polyelectrolytes covering the fundamental level of their conformations and nanostructures, their molecular interactions with materials that have close relevance to bioapplications and their applications in the biomedical field. This approach is motivated by the fact that the polyelectrolyte research is constantly active in all the aforementioned levels and continually affects many critical scientific areas.

scholarly journals Role of Dispersion Attraction in Differential Geometry Based Nonpolar Solvation Models

2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Zhan Chen
Keyword(s):  
Differential Geometry ◽  
Electrostatic Interactions ◽  
Polar Component ◽  
Great Success ◽  
Free Energies ◽  
Dispersion Interactions ◽  
Solvation Models ◽  
Nonpolar Solvation ◽  
Solvation Analysis

AbstractDifferential geometry (DG) based solvation models have shown their great success in solvation analysis by avoiding the use of ad hoc surface definitions, coupling the polar and nonpolar free energies, and generating solvent-solute boundary in a physically self-consistent fashion. Parameter optimization is a key factor for their accuracy, predictive ability of solvation free energies, and other applications. Recently, a series of efforts have been made to improve the parameterization of these new implicit solvent models. In thiswork, we aim at studying the role of dispersion attraction in the parameterization of our DG based solvation models. To this end, we first investigate the necessity of van derWaals (vdW) dispersion interactions in the model and then carry out systematic parameterization for the model in the absence of electrostatic interactions. In particular, we explore how the changes in Lennard-Jones (L-J) potential expression, its decomposition scheme, and choices of some fixed parameter values affect the optimal values of other parameters as well as the overall modeling error. Our study on nonpolar solvation analysis offers insights into the parameterization of nonpolar components for the full DG based models by eliminating uncertainties from the electrostatic polar component. Therefore, it can be regarded as a step towards better parameterization for the full DG based model.

scholarly journals Insight into Inhibitor Binding in the Eukaryotic Proteasome: Computations of the 20S CP

2018 ◽  
Vol 19 (12) ◽  
pp. 3858
Author(s):  
Milan Hodošček ◽  
Nadia Elghobashi-Meinhardt
Keyword(s):  
Electrostatic Interactions ◽  
Active Sites ◽  
Sampling Period ◽  
Md Simulations ◽  
Structural Features ◽  
Relaxation Dynamics ◽  
Inhibitor Binding ◽  
Computational Analyses ◽  
Insight Into ◽  
Proteolytic Chamber

A combination of molecular dynamics (MD) simulations and computational analyses uncovers structural features that may influence substrate passage and exposure to the active sites within the proteolytic chamber of the 20S proteasome core particle (CP). MD simulations of the CP reveal relaxation dynamics in which the CP slowly contracts over the 54 ns sampling period. MD simulations of the SyringolinA (SylA) inhibitor within the proteolytic B 1 ring chamber of the CP indicate that favorable van der Waals and electrostatic interactions account for the predominant association of the inhibitor with the walls of the proteolytic chamber. The time scale required for the inhibitor to travel from the center of the proteolytic chamber to the chamber wall is on the order of 4 ns, accompanied by an average energetic stabilization of approximately −20 kcal/mol.

Analysis of the Evolution and Structure of Systems Biology

2012 ◽  
Vol 488-489 ◽  
pp. 1006-1010
Author(s):  
Chao Liu ◽  
Lian Fen Liu ◽  
Fu Guo Li ◽  
Nai Hua Jiang ◽  
Wen Juan Guo ◽  
...  
Keyword(s):  
Systems Biology ◽  
Molecular Interactions ◽  
Close Association ◽  
Physiological Responses ◽  
Biological Molecules ◽  
System Level ◽  
Biological Research ◽  
Research Practice ◽  
Research Model ◽  
Fundamental Challenge

Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Systems biology aims to understand the biology from the system level. The fundamental challenge of systems biology is to establish a complete, detailed description of the link between biological molecules and to study molecular interactions and the close association between the physiological responses. Systems biology methods in the system under the guidance will enable us to break the shackles of the old research model to study life from the grasp of the whole phenomenon. We must effectively grasp and follow the systems biology approach to guide our biological research practice.

Molecular interactions shaping the tetraspanin web

2017 ◽  
Vol 45 (3) ◽  
pp. 741-750 ◽  
Author(s):  
Sjoerd J. van Deventer ◽  
Vera-Marie E. Dunlock ◽  
Annemiek B. van Spriel
Keyword(s):  
Molecular Interactions ◽  
Intracellular Signaling ◽  
Spatial Organization ◽  
Complex Mixture ◽  
Point Of View ◽  
Intramolecular Interactions ◽  
Fundamental Understanding ◽  
High Degree ◽  
Partner Proteins ◽  
Insight Into

To facilitate the myriad of different (signaling) processes that take place at the plasma membrane, cells depend on a high degree of membrane protein organization. Important mediators of this organization are tetraspanin proteins. Tetraspanins interact laterally among themselves and with partner proteins to control the spatial organization of membrane proteins in large networks called the tetraspanin web. The molecular interactions underlying the formation of the tetraspanin web were hitherto mainly described based on their resistance to different detergents, a classification which does not necessarily correlate with functionality in the living cell. To look at these interactions from a more physiological point of view, this review discusses tetraspanin interactions based on their function in the tetraspanin web: (1) intramolecular interactions supporting tetraspanin structure, (2) tetraspanin–tetraspanin interactions supporting web formation, (3) tetraspanin–partner interactions adding functional partners to the web and (4) cytosolic tetraspanin interactions regulating intracellular signaling. The recent publication of the first full-length tetraspanin crystal structure sheds new light on both the intra- and intermolecular tetraspanin interactions that shape the tetraspanin web. Furthermore, recent molecular dynamic modeling studies indicate that the binding strength between tetraspanins and between tetraspanins and their partners is the complex sum of both promiscuous and specific interactions. A deeper insight into this complex mixture of interactions is essential to our fundamental understanding of the tetraspanin web and its dynamics which constitute a basic building block of the cell surface.

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