Calculations of electrostatic interactions in biological systems and in solutions

1984 ◽  
Vol 17 (3) ◽  
pp. 283-422 ◽  
Author(s):  
Arieh Warshel ◽  
Stephen T. Russell
Keyword(s):  
Electrostatic Interactions ◽  
Structural Information ◽  
Van Der Waals ◽  
Effective Radius ◽  
Biological Molecules ◽  
Electrostatic Energy ◽  
Energy Correlation ◽  
Polar Solvents ◽  
Charged Amino Acids ◽  
The Given

Correlating the structure and action of biological molecules requires knowledge of the corresponding relation between structure and energy. Probably the most important factors in such a structure– energy correlation are associated with electrostatic interactions. Thus the key requirement for quantative understanding of the action of biological molecules is the ability to correlate electrostatic interactions with structural information. To appreciate this point it is useful to compare the electrostatic energy of a charged amino acid in a polar solvent to the corresponding van der Waals energy. The electrostatic free energy, ΔGel, can be approximated (as will be shown in Section II) by the Born formula (ΔGel = –(166Q2/ā) (I – I/E)). Where ΔGel is given in kcal/mol, Qis the charge of the given group, in units of electron charge, āis the effective radius of the group, and E is the dielectric constant of the solvent. With an effective radius of charged amino acids of approximately 2 Å, Born's formula gives about – 80 kcal/mol for their energy in polar solvents where E is larger than 10. This energy is two orders of magnitude larger than the van der Waals interaction of such groups and their surroundings.

scholarly journals Some Energy Issues for a Nanoscale Electrostatic Potential Well in Saline Solutions

Chemosensors ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 50
Author(s):  
Jingkun Guo ◽  
Zijin Lei ◽  
Fan Wang ◽  
Jingjing Xu ◽  
Shengyong Xu
Keyword(s):  
Electrostatic Potential ◽  
Electrostatic Interactions ◽  
Saline Solution ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Electrostatic Energy ◽  
Potential Well ◽  
Ionic Solution ◽  
Trapping Performance ◽  
Saline Solutions

An electrostatic potential well may be applied to trap and manipulate charged micro- and nanoparticles. An electrostatic potential well obtained from a certain charge distribution may be used to mimic the electrostatic interactions among biomolecules in live biosystems. In this study, we present a simulation study on the trapping performance of dipole clusters, which are arranged in 10 nm-sized, pentagon-shaped structures in a saline solution. The influence of electrostatic energy, entropy, and van der Waals interaction on the trapping performance of these nanostructures is then systematically calculated. The results show that the electrostatic potential well system demonstrated a moderate trapping capability, which could be enhanced using van der Waals interactions. The entropy significantly contributes to the trapping capability. This study offers some ideas for developing practical biomimetic electrostatic tweezers and nanorobots working in an ionic solution.

Direct visualization of phase-separated domains in lipid membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 290-291
Author(s):  
S. W. Hui ◽  
T. P. Stewart
Keyword(s):  
Lipid Membranes ◽  
Structural Information ◽  
Freeze Fracture ◽  
Biological Molecules ◽  
Vacuum Drying ◽  
Direct Visualization ◽  
X Ray Diffraction ◽  
Electron Microscopic ◽  
X Ray ◽  
Hydrocarbon Chains

Direct electron microscopic study of biological molecules has been hampered by such factors as radiation damage, lack of contrast and vacuum drying. In certain cases, however, the difficulties may be overcome by using redundent structural information from repeating units and by various specimen preservation methods. With bilayers of phospholipids in which both the solid and fluid phases co-exist, the ordering of the hydrocarbon chains may be utilized to form diffraction contrast images. Domains of different molecular packings may be recgnizable by placing properly chosen filters in the diffraction plane. These domains would correspond to those observed by freeze fracture, if certain distinctive undulating patterns are associated with certain molecular packing, as suggested by X-ray diffraction studies. By using an environmental stage, we were able to directly observe these domains in bilayers of mixed phospholipids at various temperatures at which their phases change from misible to inmissible states.

scholarly journals Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

2009 ◽  
Vol 62 (9) ◽  
pp. 1054 ◽  
Author(s):  
Defang Ouyang ◽  
Hong Zhang ◽  
Dirk-Peter Herten ◽  
Harendra S. Parekh ◽  
Sean C. Smith
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Structural Information ◽  
Structural Parameters ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Viral Gene ◽  
Conformational Structure ◽  
Crystal Forms ◽  
Gene Delivery Vectors

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A′-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA – namely major groove width, inclination and the number of base pairs in a helical twist – over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A′-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).

scholarly journals Phase Behavior of Melts of Diblock-Copolymers with One Charged Block

Polymers ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1027 ◽  
Author(s):  
Alexey A. Gavrilov ◽  
Alexander V. Chertovich ◽  
Igor I. Potemkin
Keyword(s):  
Phase Diagram ◽  
Phase Behavior ◽  
Electrostatic Interactions ◽  
Diblock Copolymers ◽  
Volume Fraction ◽  
Microphase Separation ◽  
Dissipative Particle Dynamics ◽  
Homogeneous Structure ◽  
Electrostatic Energy ◽  
Ordered Structures

In this work, we investigated the phase behavior of melts of block-copolymers with one charged block by means of dissipative particle dynamics with explicit electrostatic interactions. We assumed that all the Flory–Huggins χ parameters were equal to 0. We showed that the charge- correlation attraction solely can cause microphase separation with a long-range order; a phase diagram was constructed by varying the volume fraction of the uncharged block and the electrostatic interaction parameter λ (dimensionless Bjerrum length). The obtained phase diagram was compared to the phase diagram of “equivalent” neutral diblock-copolymers with the non-zero χ-parameter between the beads of different blocks. The neutral copolymers were constructed by grafting the counterions to the corresponding co-ions of the charged block with further switching off the electrostatic interactions. Surprisingly, the differences between these phase diagrams are rather subtle; the same phases in the same order are observed, and the positions of the order-disorder transition ODT points are similar if the λ-parameter is considered as an “effective” χ-parameter. Next, we studied the position of the ODT for lamellar structure depending on the chain length N. It turned out that while for the uncharged diblock copolymer the product χcrN was almost independent of N, for the diblock copolymers with one charged block we observed a significant increase in λcrN upon increasing N. This can be attributed to the fact that the counterion entropy prevents the formation of ordered structures, and its influence is more pronounced for longer chains since they undergo the transition to ordered structures at smaller values of λ, when the electrostatic energy becomes comparable to kbT. This was supported by studying the ODT in diblock-copolymers with charged blocks and counterions cross-linked to the charged monomer units. The ODT for such systems was observed at significantly lower values of λ, with the difference being more pronounced at longer chain lengths N. The fact that the microphase separation is observed even at zero Flory–Huggins parameter can be used for the creation of “high-χ” copolymers: The incorporation of charged groups (for example, ionic liquids) can significantly increase the segregation strength. The diffusion of counterions in the obtained ordered structures was studied and compared to the case of a system with the same number of charged groups but a homogeneous structure; the diffusion coefficient along the lamellar plane was found to be higher than in any direction in the homogeneous structure.

scholarly journals An accurate single descriptor for ion–π interactions

2020 ◽  
Vol 7 (6) ◽  
pp. 1036-1045 ◽  
Author(s):  
Zhangyun Liu ◽  
Zheng Chen ◽  
Jinyang Xi ◽  
Xin Xu
Keyword(s):  
Electrostatic Interactions ◽  
Quantitative Description ◽  
Physical Nature ◽  
Binding Energies ◽  
Electrostatic Energy ◽  
Π Interactions ◽  
Practical Strategy ◽  
Leading Term ◽  
Level Method ◽  
High Level

Abstract Non-covalent interactions between ions and π systems play an important role in molecular recognition, catalysis and biology. To guide the screen and design for artificial hosts, catalysts and drug delivery, understanding the physical nature of ion–π complexes via descriptors is indispensable. However, even with multiple descriptors that contain the leading term of electrostatic and polarized interactions, the quantitative description for the binding energies (BEs) of ion–π complexes is still lacking because of the intrinsic shortcomings of the commonly used descriptors. Here, we have shown that the impartment of orbital details into the electrostatic energy (coined as OEE) makes an excellent single descriptor for BEs of not only spherical, but also multiply-shaped, ion–π systems, highlighting the importance of an accurate description of the electrostatic interactions. Our results have further demonstrated that OEEs from a low-level method could be calibrated to BEs from a high-level method, offering a powerful practical strategy for an accurate prediction of a set of ion–π interactions.

Insights into the binding specificity and catalytic mechanism ofN-acetylhexosamine 1-phosphate kinases through multiple reaction complexes

2014 ◽  
Vol 70 (5) ◽  
pp. 1401-1410 ◽  
Author(s):  
Kuei-Chen Wang ◽  
Syue-Yi Lyu ◽  
Yu-Chen Liu ◽  
Chin-Yuan Chang ◽  
Chang-Jer Wu ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Catalytic Mechanism ◽  
Structural Information ◽  
Bifidobacterium Longum ◽  
Three Dimensional ◽  
Binding Specificity ◽  
Chemoenzymatic Synthesis ◽  
Leloir Pathway ◽  
The Given

Utilization ofN-acetylhexosamine in bifidobacteria requires the specific lacto-N-biose/galacto-N-biose pathway, a pathway differing from the Leloir pathway while establishing symbiosis between humans and bifidobacteria. The genelnpBin the pathway encodes a novel hexosamine kinase NahK, which catalyzes the formation ofN-acetylhexosamine 1-phosphate (GlcNAc-1P/GalNAc-1P). In this report, seven three-dimensional structures of NahK in complex with GlcNAc, GalNAc, GlcNAc-1P, GlcNAc/AMPPNP and GlcNAc-1P/ADP from bothBifidobacterium longum(JCM1217) andB. infantis(ATCC15697) were solved at resolutions of 1.5–2.2 Å. NahK is a monomer in solution, and its polypeptide folds in a crescent-like architecture subdivided into two domains by a deep cleft. The NahK structures presented here represent the first multiple reaction complexes of the enzyme. This structural information reveals the molecular basis for the recognition of the given substrates and products, GlcNAc/GalNAc, GlcNAc-1P/GalNAc-1P, ATP/ADP and Mg2+, and provides insights into the catalytic mechanism, enabling NahK and mutants thereof to form a choice of biocatalysts for enzymatic and chemoenzymatic synthesis of carbohydrates.

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