Design and Modeling of a Peptide Based NanoTweezer

2006 ◽  
Author(s):  
Gaurav Sharma ◽  
Kaushal Rege ◽  
Constantinos Mavroidis ◽  
Martin L. Yarmush
Keyword(s):  
Molecular Dynamics ◽  
Coiled Coil ◽  
Computational Results ◽  
Actuation Mechanism ◽  
Electrostatic Charges ◽  
Environmentally Responsive ◽  
Force Profile ◽  
Potential Applications ◽  
Polypeptide Chains ◽  
Molecular Dynamics Results

The design hypothesis, architectures, and preliminary computational results of a peptide based nanoTweezer are presented in this paper. We engineered the α-helical coiled coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally-responsive nanoTweezer. The dimeric coiled coil peptide consists of two identical ~4.5 nm long and ~3 nm wide polypeptide chains. The actuation mechanism depends on the modifying electrostatic charges along the peptide by varying the pH of the solution resulting in the reversible movement of helices and therefore, creating the motion of the tweezer. Preliminary molecular dynamics results indicated that pH changes led to a reversible deflection of 1–2 nm with the nanoTweezer. The force profile of the nanoTweezer motion and some potential applications are also discussed.

scholarly journals Development of a New Sr-O Parameterization to Describe the Influence of SrO on Iron-Phosphate Glass Structural Properties Using Molecular Dynamics Simulations

Materials ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4326
Author(s):  
Pawel Goj ◽  
Aleksandra Wajda ◽  
Pawel Stoch
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Interatomic Potential ◽  
Glass Structure ◽  
Ion Pairs ◽  
Glass Network ◽  
Iron Phosphate ◽  
Phosphate Glasses ◽  
Potential Applications ◽  
Dynamics Simulations

Iron-phosphate glasses, due to their properties, have many potential applications. One of the most promising seems to be nuclear waste immobilization. Radioactive 90Sr isotope is the main short-lived product of fission and, due to its high solubility, it can enter groundwater and pose a threat to the environment. On the other hand, Sr is an important element in hard tissue metabolic processes, and phosphate glasses containing Sr are considered bioactive. This study investigated the effect of SrO addition on a glass structure of nominal 30Fe2O3-70P2O5 chemical composition using classical molecular dynamics simulations. To describe the interaction between Sr-O ion pairs, new interatomic potential parameters of the Buckingham-type were developed and tested for crystalline compounds. The short-range structure of the simulated glasses is presented and is in agreement with previous experimental and theoretical studies. The simulations showed that an increase in SrO content in the glass led to phosphate network depolymerization. Analysis demonstrated that the non-network oxygen did not take part in the phosphate network depolymerization. Furthermore, strontium aggregation in the glass structure was observed to lead to the non-homogeneity of the glass network. It was demonstrated that Sr ions prefer to locate near to Fe(II), which may induce crystallization of strontium phosphates with divalent iron.

scholarly journals Effects of an Interchain Disulfide Bond on Tropomyosin Structure: A Molecular Dynamics Study

2018 ◽  
Vol 19 (11) ◽  
pp. 3376 ◽  
Author(s):  
Natalia A. Koubassova ◽  
Sergey Y. Bershitsky ◽  
Andrey K. Tsaturyan
Keyword(s):  
Heart Failure ◽  
Molecular Dynamics ◽  
Disulfide Bond ◽  
Coiled Coil ◽  
Middle Part ◽  
Actin Binding ◽  
Cross Linking ◽  
Interchain Disulfide Bond ◽  
Structural And Functional Properties ◽  
The Cross

Tropomyosin (Tpm) is a coiled-coil actin-binding dimer protein that participates in the regulation of muscle contraction. Both Tpm chains contain Cys190 residues which are normally in the reduced state, but form an interchain disulfide bond in failing heart. Changes in structural and functional properties of Tpm and its complexes with actin upon disulfide cross-linking were studied using various experimental methods. To understand the molecular mechanism underlying these changes and to reveal the possible mechanism of the involvement of the cross-linking in heart failure, molecular dynamics (MD) simulations of the middle part of Tpm were performed in cross-linked and reduced states. The cross-linking increased bending stiffness of Tpm assessed from MD trajectories at 27 °C in agreement with previous experimental observations. However, at 40 °C, the cross-linking caused a decrease in Tpm stiffness and a significant reduction in the number of main chain hydrogen bonds in the vicinity of residues 133 and 134. These data are in line with observations showing enhanced thermal unfolding of the least stable part of Tpm at 30–40 °C and accelerated trypsin cleavage at residue 133 at 40 °C (but not at 27 °C) upon cross-linking. These results allow us to speculate about the possible mechanism of involvement of Tpm cross-linking to heart failure pathogenesis.

Determination of the Stress Distribution at the Interface Metal-Oxide: Numerical and Theoretical Considerations

2005 ◽  
Vol 237-240 ◽  
pp. 145-150 ◽  
Author(s):  
Sébastien Garruchet ◽  
A. Hasnaoui ◽  
Olivier Politano ◽  
Tony Montesin ◽  
J. Marcos Salazar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Stress Distribution ◽  
Oxide Film ◽  
Metal Oxide ◽  
Reaction Kinetics ◽  
Analytical Model ◽  
Equilibrium Thermodynamics ◽  
Theoretical Considerations ◽  
Molecular Dynamics Results

In this paper we give a brief presentation of the approaches we have recently developed on the oxidation of metals. Firstly, we present an analytical model based on non-equilibrium thermodynamics to describe the reaction kinetics present during the oxidation of a metal. Secondly, we present the molecular dynamics results obtained with a code specially tailored to study the oxidation and growth of an oxide film of aluminium. Our simulations present an excellent agreement with experimental results.

Bio-inspired gene carriers with low cytotoxicity constructed via the assembly of dextran nanogels and nano-coacervates

Nanomedicine ◽  
2020 ◽  
Vol 15 (13) ◽  
pp. 1285-1296 ◽  
Author(s):  
Chenglong Wang ◽  
Jiayi You ◽  
Miaomiao Gao ◽  
Peipei Zhang ◽  
Guoxiong Xu ◽  
...  
Keyword(s):  
Positive Charge ◽  
Transfection Efficiency ◽  
Gene Carrier ◽  
Gene Carriers ◽  
Environmentally Responsive ◽  
Potential Applications ◽  
Internal Peptide ◽  
The Common ◽  
Low Cytotoxicity ◽  
Peptide Gene

Aim: To achieve safe and biocompatible gene carriers. Materials & methods: A core/shell-structured hierarchical carrier with an internal peptide/gene coacervate ‘core’ and a dextran nanogel ‘shell’ on the surface has been designed. Results: The dextran nanogels shield coacervate (DNSC) can effectively condense genes and release them in reducing environments. The dextran nanogel-based ‘shell’ can effectively shield the positive charge of the peptide/gene coacervate ‘core’, thus reducing the side effects of cationic gene carriers. In contrast with the common nonviral gene carriers that had high cytotoxicities, the DNSC showed a high transfection efficiency while maintaining a low cytotoxicity. Conclusion: The DNSC provides an effective environmentally responsive gene carrier with potential applications in the fields of gene therapy and gene carrier development.

Molecular Dynamics Simulation of Bi-Carboxyl Sidewall Functionalized Single-Wall Carbon Nanotubes in Water

2015 ◽  
Vol 1131 ◽  
pp. 106-109
Author(s):  
Shongpun Lokavee ◽  
Chatchawal Wongchoosuk ◽  
Teerakiat Kerdcharoen
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Single Wall Carbon Nanotubes ◽  
First Principles Calculations ◽  
Carboxylic Groups ◽  
Potential Applications ◽  
Walled Carbon Nanotubes ◽  
Defective Sites

Functionalized single-walled carbon nanotubes (f-SWNTs) have attracted great interest due to their enhancement of SWNT properties leading to an increase in potential applications beyond those of pristine SWNT. In this work, we have investigated the behavior of open-end (9,0) bi-carboxyl sidewall functionalized SWNTs in water using molecular dynamics (MD) technique within GROMACS software package based on the OPLS force fields with modified charges obtained from the first principles calculations. The model tubes including perfect and defective nanotubes covalently functionalized by bi-carboxylic groups on different sidewall surface orientation were fully optimized by B3LYP/6-31G(d,p). The simulations were performed at the constant volume and temperature in a rectangular box with periodic boundary conditions in which each system contains one model tube and ~1680 water molecules. The results form MD simulations showed that functionalization on the central carbon atom in the (C1,C ́1)SW-defective sites strongly affects on the dynamic behavior of CNT in water. Results showed that the hydrophilic behavior of the functionalized SWNT has been improved over the pristine and defective nanotubes.

Ab initio Computationally Generated Nanoporous Carbon and its Comparison to Experiment

2008 ◽  
Vol 1145 ◽  
Author(s):  
Cristina Romero ◽  
Ariel A. Valladares ◽  
R. M. Valladares ◽  
Alexander Valladares ◽  
Alipio G. Calles
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Nanoporous Carbon ◽  
Group Iv ◽  
Distribution Functions ◽  
Graphene Sheets ◽  
Radial Distribution Functions ◽  
Carbon Chains ◽  
Potential Applications ◽  
Dynamics Process

AbstractNanoporous carbon is a widely studied material due to its potential applications in hydrogen storage or for filtering undesirable products. Most of the developments have been experimental although some simulation work has been carried out based on the use of graphene sheets and/or carbon chains and classical molecular dynamics. Here we present an application of our recently developed ab initio method [1] for the generation of group IV porous materials. The method consists in constructing a crystalline diamond supercell with 216 atoms of carbon and a density of 3.546 g/cm3, then lengthening the supercell edge to obtain a density of 1.38 g/cm3, yielding a porosity of 61.1 % in order to be able to compare with experimental results reported in the literature [2]. We then subject the resulting supercell to an ab initio molecular dynamics process at 1000 K during 295 steps. The radial distribution functions obtained are compared to experiment to discern coincidences and discrepancies.

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