Designing electrostatic interactions in biological systems via charge optimization or combinatorial approaches: insights and challenges with a continuum electrostatic framework

Radhakrishnan, Mala L.

doi:10.1007/s00214-012-1252-5

Cited by 11 publications

(11 citation statements)

References 252 publications

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“…The penalty terms were obtained by multiplying one-half the potential differences due to charges on a given binding partner by its charges. Interaction terms were calculated multiplying bound-state potentials due to charges on a binding partner by charges on the other partner [34]. …”

Section: Methodsmentioning

confidence: 99%

Investigating the nucleic acid interactions of histone‐derived antimicrobial peptides

et al. 2017

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While many antimicrobial peptides (AMPs) disrupt bacterial membranes, some translocate into bacteria and interfere with intracellular processes. Buforin II and DesHDAP1 are thought to kill bacteria by interacting with nucleic acids. Here, molecular modeling and experimental measurements are used to show that neither nucleic acid binding peptide selectively binds DNA sequences. Simulations and experiments also show that changing lysines to arginines enhances DNA binding, suggesting that including additional guanidinium groups is a potential strategy to engineer more potent AMPs. Moreover, the lack of binding specificity may make it more difficult for bacteria to evolve resistance to these and other similar AMPs.

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Section: Methodsmentioning

confidence: 99%

Investigating the nucleic acid interactions of histone‐derived antimicrobial peptides

et al. 2017

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“…The strength of electrostatic interactions, much like that of hydrophobic interactions, are intimately dependent on the solvent environment. , Highly polar solvents interact directly with the charged components, and as a result partially mitigate the charge that is felt by the other system component, resulting in a lower “effective” charge . Aqueous solvents, for example, orient water around both cations and anions in a way that facilitates solvation of the anions but decreases the effective charges and the strength of the electrostatic interactions . Electrostatic interactions in nonpolar solvents, by contrast, are generally magnified, due to the inability of the solvent to solvate charged species effectively. , …”

Section: Underlying Principles Of Chemosensorsmentioning

confidence: 99%

Supramolecular Luminescent Sensors

2018

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There is great need for stand-alone luminescence-based chemosensors that exemplify selectivity, sensitivity, and applicability and that overcome the challenges that arise from complex, real-world media. Discussed herein are recent developments toward these goals in the field of supramolecular luminescent chemosensors, including macrocycles, polymers, and nanomaterials. Specific focus is placed on the development of new macrocycle hosts since 2010, coupled with considerations of the underlying principles of supramolecular chemistry as well as analytes of interest and common luminophores. State-of-the-art developments in the fields of polymer and nanomaterial sensors are also examined, and some remaining unsolved challenges in the area of chemosensors are discussed. CONTENTS 4.4. Explosives 4.5. Pharmaceutical Agents 4.6. Biologically Relevant 4.6.1. Adenosine Triphosphate (ATP)

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“…Continuum-theory models for the electrostatic effects, based on macroscopic dielectric theory and the Poisson equation, have been described as “unreasonably effective” (echoing Wigner's famous expression “the unreasonable effectiveness of mathematics in the natural sciences”). Indeed, considering the drastic simplifications involved in applying macroscopic concepts at the level of single atoms, it is shocking how successful Poisson-based theories have been [3, 4, 9, 10]. For example, standard Poisson theories provide a simple and intuitive means to consider the contributions of electrostatics to molecular binding [9, 11, 12], and to understand the basis for the fantastic selectivity of ion-channel proteins [13].…”

Section: Introductionmentioning

confidence: 99%

Gradient models in molecular biophysics: progress, challenges, opportunities

Bardhan

2013

Journal of the Mechanical Behavior of Materials

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In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

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Designing electrostatic interactions in biological systems via charge optimization or combinatorial approaches: insights and challenges with a continuum electrostatic framework

Cited by 11 publications

References 252 publications

Investigating the nucleic acid interactions of histone‐derived antimicrobial peptides

Investigating the nucleic acid interactions of histone‐derived antimicrobial peptides

Supramolecular Luminescent Sensors

Gradient models in molecular biophysics: progress, challenges, opportunities

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