First-Principles Simulation of Dielectric Function in Biomolecules

The protein dielectric constant reflects the molecular heterogeneity of the proteins and can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. The long history of its computation and measurement attest to the vital importance of electrostatic interactions in protein physics that engendered diverse theoretical approaches based often on scattered methodologies with various adjustable parameters. We present a new robust computational method anchored in rigorous ab initio quantum mechanical calculation of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the electronic component of the static dielectric constants of small proteins under different conditions. We implement the new methodology to the 20 canonical amino acids individually, a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the Spike protein of SARS-COV-2. The calculated electronic dielectric constants for 1FUV and SD1 in vacuum are 28.06 and 50.02 respectively. They decrease in the presence of aqueous bathing solution.

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Ab Initio Electronic Dielectric “Constant” of Proteins: A Baseline for Electrostatic Interaction in Biomolecular Systems

10.26434/chemrxiv.14403188.v1 ◽

2021 ◽

Author(s):

Puja Adhikari ◽

Rudolf Podgornik ◽

Bahaa Jawad ◽

Wai-Yim Ching

Keyword(s):

Dielectric Constant ◽

Ab Initio ◽

Electrostatic Interactions ◽

Size Structure ◽

Dielectric Constants ◽

Computational Method ◽

Molecular Heterogeneity ◽

Bathing Solution ◽

Theoretical Approaches ◽

Small Proteins

The protein dielectric constant reflects the molecular heterogeneity of the proteins and can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. The long history of its computation and measurement attest to the vital importance of electrostatic interactions in protein physics that engendered diverse theoretical approaches based often on scattered methodologies with various adjustable parameters. We present a new robust computational method anchored in rigorous ab initio quantum mechanical calculation of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the electronic component of the static dielectric constants of small proteins under different conditions. We implement the new methodology to the 20 canonical amino acids individually, a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the Spike protein of SARS-COV-2. The calculated electronic dielectric constants for 1FUV and SD1 in vacuum are 28.06 and 50.02 respectively. They decrease in the presence of aqueous bathing solution.

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A Molecular Dynamics Simulation of the Tensile Behavior of Y-Branched-CNT/SiC Nanocomposite

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.804.7 ◽

2019 ◽

Vol 804 ◽

pp. 7-10

Author(s):

Guo Bin Zheng ◽

Hideaki Sano ◽

Osamu Nakagoe ◽

Shuji Tanabe

Keyword(s):

Molecular Dynamics ◽

Simulation Method ◽

Ceramic Materials ◽

Nanocomposite Materials ◽

Dynamics Simulation ◽

Uniaxial Tensile ◽

Direct Knowledge ◽

Uniaxial Tensile Stress ◽

Dynamics Method ◽

Insight Into

The purpose of incorporating CNTs into ceramic materials is to enhance the toughness of ceramic materials, in which the interface plays a key role. Due to the nanoscale of nanocomposites, however, it is not easy to acquire a direct knowledge of the interface behavior. In this research, we simulated the dynamics of CNT/SiC and branched CNT/SiC under uniaxial tensile stress using molecular dynamics method (LAMMPS). The simulation method using molecular dynamics provide an insight into designing an effectively toughened ceramic nanocomposite materials.

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Using a Simple Cellular Assay to Map NES Motifs in Cancer-Related Proteins, Gain Insight into CRM1-Mediated NES Export, and Search for NES-Harboring Micropeptides

International Journal of Molecular Sciences ◽

10.3390/ijms21176341 ◽

2020 ◽

Vol 21 (17) ◽

pp. 6341

Author(s):

Maria Sendino ◽

Miren Josu Omaetxebarria ◽

Gorka Prieto ◽

Jose Antonio Rodriguez

Keyword(s):

Nuclear Export ◽

Relevant Information ◽

Sequence Motifs ◽

Specific Sequence ◽

Cellular Assay ◽

Small Proteins ◽

Binding Groove ◽

Related Proteins ◽

Insight Into

The nuclear export receptor CRM1 (XPO1) recognizes and binds specific sequence motifs termed nuclear export signals (NESs) in cargo proteins. About 200 NES motifs have been identified, but over a thousand human proteins are potential CRM1 cargos, and most of their NESs remain to be identified. On the other hand, the interaction of NES peptides with the “NES-binding groove” of CRM1 was studied in detail using structural and biochemical analyses, but a better understanding of CRM1 function requires further investigation of how the results from these in vitro studies translate into actual NES export in a cellular context. Here we show that a simple cellular assay, based on a recently described reporter (SRVB/A), can be applied to identify novel potential NESs motifs, and to obtain relevant information on different aspects of CRM1-mediated NES export. Using cellular assays, we first map 19 new sequence motifs with nuclear export activity in 14 cancer-related proteins that are potential CRM1 cargos. Next, we investigate the effect of mutations in individual NES-binding groove residues, providing further insight into CRM1-mediated NES export. Finally, we extend the search for CRM1-dependent NESs to a recently uncovered, but potentially vast, set of small proteins called micropeptides. By doing so, we report the first NES-harboring human micropeptides.

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Insight into the effect of methylated urea on the phase transition of aqueous solutions of poly(N -isopropylacrylamide) by microcalorimetry: Hydrogen bonding and van der Waals interactions

Journal of Polymer Science Part B Polymer Physics ◽

10.1002/polb.24018 ◽

2016 ◽

Vol 54 (12) ◽

pp. 1145-1151 ◽

Cited By ~ 3

Author(s):

Yating Gao ◽

Jinxian Yang ◽

Haiyan Fan ◽

Yanwei Ding ◽

Xiaodong Ye

Keyword(s):

Phase Transition ◽

Hydrogen Bonding ◽

Aqueous Solutions ◽

Van Der Waals ◽

Van Der Waals Interactions ◽

Insight Into

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Computer Simulation of Vesicle Fusion

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.474-476.943 ◽

2011 ◽

Vol 474-476 ◽

pp. 943-948

Author(s):

Shao Gui Wu ◽

Hong Xia Guo

Keyword(s):

Computer Simulation ◽

Molecular Level ◽

Dissipative Particle Dynamics ◽

Simulation Method ◽

Particle Dynamics ◽

Vesicle Fusion ◽

Simulation System ◽

Dynamics Simulation ◽

Dissipative Particle Dynamics Simulation ◽

Insight Into

A dissipative particle dynamics simulation method is used to get insight into molecular-level details of vesicle fusion in this study. For simplicity, the simulation system contains water and amphiphiles. The fusion mechanism is investigated in detail. It is found that the whole fusion process is in well agreement with the “stalk-pore” hypothesis. The dynamics of vesicle fusion is analyzed by monitoring the time evolutions of morphologies.

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Mass Transport in Nanoalloys Studied by Atomistic Models

Diffusion Foundations ◽

10.4028/www.scientific.net/df.12.23 ◽

2017 ◽

Vol 12 ◽

pp. 23-37 ◽

Cited By ~ 1

Author(s):

Riccardo Ferrando

Keyword(s):

Molecular Dynamics ◽

Mass Transport ◽

Molecular Dynamics Simulations ◽

Gas Phase ◽

Metallic Nanoparticles ◽

Simulation Method ◽

Impurity Atoms ◽

Atomistic Models ◽

Dynamics Simulations ◽

Small Nanoparticles

The diffusion of atoms in nanoparticles can be studied computationally by Molecular Dynamics simulations, a simulation method which allow to follow the actual trajectories of the diffusing atoms. Here we focus on the simulation of diffusion in metallic nanoparticles, first considering the case of single impurity atoms in matrix clusters, and then on the simulation of the growth in gas phase. We show that diffusion of atoms in nanoparticles can take place by a variety of different mechanisms, which very often involve collective displacements. These collective displacements are facilitated in the vicinity of the cluster surface, which, in small nanoparticles, includes a large portion of the nanoparticle itself.

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Insight into the influence of liquid paraffin for methanol synthesis on Cu(110) surface using continuum and atomistic models

Applied Surface Science ◽

10.1016/j.apsusc.2016.06.074 ◽

2016 ◽

Vol 387 ◽

pp. 58-65 ◽

Cited By ~ 4

Author(s):

Wei-Hong Jiao ◽

Shi-Zhong Liu ◽

Zhi-Jun Zuo ◽

Rui-Peng Ren ◽

Zhi-Hua Gao ◽

...

Keyword(s):

Methanol Synthesis ◽

Liquid Paraffin ◽

Atomistic Models ◽

Insight Into

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Three-dimensional numerical investigation on micro-meter droplet impact and penetration into the porous media with different velocities

MATEC Web of Conferences ◽

10.1051/matecconf/202235501009 ◽

2022 ◽

Vol 355 ◽

pp. 01009

Author(s):

Hongxin Deng ◽

Yanlu Huang ◽

Yongqiang Yang ◽

Shibiao Wu ◽

Zhiyi Chen

Keyword(s):

Porous Media ◽

Three Dimensional ◽

Simulation Method ◽

Lateral Spreading ◽

Droplet Impact ◽

Lateral Spread ◽

Powder System ◽

Direct Numerical Method ◽

Insight Into ◽

Penetration Time

Droplets impacting and penetration into porous media is commonly seen in natural and engineering processes, in which the kinetics and capillary effect are of great importance to the lateral spreading and vertical penetration. In this study, a three-dimensional numerical simulation method was proposed to study the micro-meter droplet impact and penetration into the porous media. It is found that both the lateral spread and vertical penetration occur on the millisecond timescale and larger velocity will enhance the lateral spreading but have little influence on the penetration time and depth. The direct numerical method proposed in this study can be applied to predict the actual spreading and penetration status in the droplet-powder system and further insight into the droplet-powder interaction.

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Structural analysis of free and liganded forms of the Fab fragment of a high-affinity anti-cocaine antibody, h2E2

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x19013608 ◽

2019 ◽

Vol 75 (11) ◽

pp. 697-706

Author(s):

Kemin Tan ◽

Min Zhou ◽

Angela J. Ahrendt ◽

Norma E. C. Duke ◽

Nassif Tabaja ◽

...

Keyword(s):

Monoclonal Antibody ◽

Cocaine Abuse ◽

Phase 1 ◽

Complex Structure ◽

Van Der Waals Interactions ◽

Binding Studies ◽

Fab Fragment ◽

Aromatic Residues ◽

High Affinity ◽

Insight Into

A high-affinity anti-cocaine monoclonal antibody, designated h2E2, is entering phase 1 clinical trials for cocaine abuse therapy. To gain insight into the molecular details of its structure that are important for binding cocaine and cocaine metabolites, the Fab fragment was generated and crystallized with and without ligand. Structures of the unliganded Fab and the Fab fragment bound to benzoylecgonine were determined, and were compared with each other and with other crystallized anti-cocaine antibodies. The affinity of the h2E2 antibody for cocaine is 4 nM, while that of the cocaine metabolite benzoylecgonine is 20 nM. Both are higher than the reported affinity for cocaine of the two previously crystallized anti-cocaine antibodies. Consistent with cocaine fluorescent quenching binding studies for the h2E2 mAb, four aromatic residues in the CDR regions of the Fab (TyrL32, TyrL96, TrpL91 and TrpH33) were found to be involved in ligand binding. The aromatic side chains surround and trap the tropane moiety of the ligand in the complex structure, forming significant van der Waals interactions which may account for the higher affinity observed for the h2E2 antibody. A water molecule mediates hydrogen bonding between the antibody and the carbonyl group of the benzoyl ester. The affinity of binding to h2E2 of benzoylecgonine differs only by a factor of five compared with that of cocaine; therefore, it is suggested that h2E2 would bind cocaine in the same way as observed in the Fab–benzoylecgonine complex, with minor rearrangements of some hypervariable segments of the antibody.

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