molecular dynamics simulation
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... Numerical Methods for Stochastic Molecular Dynamics -- 8. ...
Interdisciplinary Applied Mathematics, ISSN 0939-6047 39
1st edition XXII, 443 stran : ilustrace ; 24 cm
- MeSH
- matematika MeSH
- simulace molekulární dynamiky MeSH
- Publikační typ
- monografie MeSH
- Konspekt
- Matematika
- NLK Obory
- přírodní vědy
Intense pulsed electric fields are known to act at the cell membrane level and are already being exploited in biomedical and biotechnological applications. However, it is not clear if electric pulses within biomedically-attainable parameters could directly influence intra-cellular components such as cytoskeletal proteins. If so, a molecular mechanism of action could be uncovered for therapeutic applications of such electric fields. To help clarify this question, we first identified that a tubulin heterodimer is a natural biological target for intense electric fields due to its exceptional electric properties and crucial roles played in cell division. Using molecular dynamics simulations, we then demonstrated that an intense - yet experimentally attainable - electric field of nanosecond duration can affect the bβ-tubulin's C-terminus conformations and also influence local electrostatic properties at the GTPase as well as the binding sites of major tubulin drugs site. Our results suggest that intense nanosecond electric pulses could be used for physical modulation of microtubule dynamics. Since a nanosecond pulsed electric field can penetrate the tissues and cellular membranes due to its broadband spectrum, our results are also potentially significant for the development of new therapeutic protocols.
- MeSH
- elektrická stimulace * metody MeSH
- lidé MeSH
- simulace molekulární dynamiky * MeSH
- statická elektřina MeSH
- tubulin fyziologie MeSH
- vazebná místa MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Kinesin is a biological molecular nanomotor which converts chemical energy into mechanical work. To fulfill various nanotechnological tasks in engineered environments, the function of biological molecular motors can be altered by artificial chemical modifications. The drawback of this approach is the necessity of designing and creating a new motor construct for every new task. We propose that intense nanosecond-scale pulsed electric field could modify the function of nanomotors. To explore this hypothesis, we performed molecular dynamics simulation of a kinesin motor domain docked on a subunit of its microtubule track - a single tubulin heterodimer. In the simulation, we exposed the kinesin motor domain to intense (100 MV/m) electric field up to 30 ns. We found that both the magnitude and angle of the kinesin dipole moment are affected. Furthermore, we found that the electric field affects contact surface area between kinesin and tubulin, the structure and dynamics of the functionally important kinesin segments, including microtubule binding motifs as well as nucleotide hydrolysis site which power the nanomotor. These findings indicate that external intense nanosecond-scale electric field could alter kinesin behavior. Our results contribute to developing novel electromagnetic methods for modulating the function of biomolecular matter at the nanoscale.
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
- MeSH
- DNA chemie MeSH
- G-kvadruplexy * MeSH
- guanin chemie MeSH
- konformace nukleové kyseliny MeSH
- ligandy MeSH
- RNA chemie MeSH
- rozpouštědla chemie MeSH
- simulace molekulární dynamiky * MeSH
- telomery chemie MeSH
- vodíková vazba MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
The tear film is a thin multilayered structure covering the cornea. Its outermost layer is a lipid film underneath of which resides on an aqueous layer. This tear film lipid layer (TFLL) is itself a complex structure, formed by both polar and nonpolar lipids. It was recently suggested that due to tear film dynamics, TFLL contains inhomogeneities in the form of polar lipid aggregates. The aqueous phase of tear film contains lachrymal-origin proteins, whereby lysozyme is the most abundant. These proteins can alter TFLL properties, mainly by reducing its surface tension. However, a detailed nature of protein-lipid interactions in tear film is not known. We investigate the interactions of lysozyme with TFLL in molecular details by employing coarse-grained molecular dynamics simulations. We demonstrate that lysozyme, due to lateral restructuring of TFLL, is able to penetrate the tear lipid film embedded in inverse micellar aggregates.
- MeSH
- adsorpce MeSH
- estery cholesterolu chemie MeSH
- fosfatidylcholiny chemie MeSH
- fosfatidylethanolaminy chemie MeSH
- kinetika MeSH
- lidé MeSH
- muramidasa chemie MeSH
- povrchové napětí MeSH
- sfingomyeliny chemie MeSH
- simulace molekulární dynamiky * MeSH
- slzy chemie MeSH
- sulfoglykosfingolipidy chemie MeSH
- termodynamika MeSH
- triolein chemie MeSH
- voda chemie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Pregnenolone (P5) is synthesized as the first bioactive steroid in the mitochondria from cholesterol. Clusters of differentiation 4 (CD4+) and Clusters of differentiation 8 (CD8+) immune cells synthesize P5 de novo; P5, in turn, play important role in immune homeostasis and regulation. However, P5's biochemical mode of action in immune cells is still emerging. We envisage that revealing the complete spectrum of P5 target proteins in immune cells would have multifold applications, not only in basic understanding of steroids biochemistry in immune cells but also in developing new therapeutic applications. We employed a CLICK-enabled probe to capture P5-binding proteins in live T helper cell type 2 (Th2) cells. Subsequently, using high-throughput quantitative proteomics, we identified the P5 interactome in CD4+ Th2 cells. Our study revealed P5's mode of action in CD4+ immune cells. We identified novel proteins from mitochondrial and endoplasmic reticulum membranes to be the primary mediators of P5's biochemistry in CD4+ and to concur with our earlier finding in CD8+ immune cells. Applying advanced computational algorithms and molecular simulations, we were able to generate near-native maps of P5-protein key molecular interactions. We showed bonds and interactions between key amino acids and P5, which revealed the importance of ionic bond, hydrophobic interactions, and water channels. We point out that our results can lead to designing of novel molecular therapeutics strategies.
Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreement with ab initio calculations obtained in the Gaussian03 program. Dihedral torsions of active groups of betulin were determined for both procedures, and related calculated structures were compared successfully. The selected force field was used for subsequent optimization of betulin in a water environment, and a conformational search was performed using quench molecular dynamics. The total energies of betulin and its interactions in water bulk were calculated, and the influence of water on betulin structure was investigated.
The pandemic of COVID-19 caused by SARS-CoV-2 has made a worldwide health emergency. Despite the fact that current vaccines are readily available, several SARSCoV-2 variants affecting the existing vaccine are to be less effective due to the mutations in the structural proteins. Furthermore, the appearance of the new variants cannot be easily predicted in the future. Therefore, the attempts to construct new vaccines or to modify the current vaccines are still pivotal works for preventing the spread of the virus. In the present investigation, the computational analysis through immunoinformatics, molecular docking, and molecular dynamics (MD) simulation is employed to construct an effective vaccine against SARS-CoV2. The structural proteins of SARS-CoV2 are utilized to create a multiepitope-based vaccine (MEV). According to our findings presented by systematic procedures in the current investigation, the MEV construct may be able to trigger a strong immunological response against the virus. Therefore, the designed MEV could be a potential vaccine candidate against SARS-CoV-2, and also it is expected to be effective for other variants.
- MeSH
- COVID-19 * prevence a kontrola MeSH
- epitopy B-lymfocytární chemie genetika MeSH
- epitopy T-lymfocytární chemie genetika MeSH
- imunogenicita vakcíny MeSH
- kvantitativní vztahy mezi strukturou a aktivitou MeSH
- lidé MeSH
- RNA virová MeSH
- SARS-CoV-2 * MeSH
- simulace molekulární dynamiky MeSH
- simulace molekulového dockingu MeSH
- subjednotkové vakcíny chemie MeSH
- vakcíny proti COVID-19 MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Coxiella burnetii is a gram-negative bacterium able to infect several eukaryotic cells, mainly monocytes and macrophages. It is found widely in nature with ticks, birds, and mammals as major hosts. C. burnetii is also the biological warfare agent that causes Q fever, a disease that has no vaccine or proven chemotherapy available. Considering the current geopolitical context, this fact reinforces the need for discovering new treatments and molecular targets for drug design against C. burnetii. Among the main molecular targets against bacterial diseases reported, the enzyme dihydrofolate reductase (DHFR) has been investigated for several infectious diseases. In the present work, we applied molecular modeling techniques to evaluate the interactions of known DHFR inhibitors in the active sites of human and C. burnetii DHFR (HssDHFR and CbDHFR) in order to investigate their potential as selective inhibitors of CbDHFR. Results showed that most of the ligands studied compete for the binding site of the substrate more effectively than the reference drug trimethoprim. Also the most promising compounds were proposed as leads for the drug design of potential CbDHFR inhibitors.
- MeSH
- antagonisté kyseliny listové chemie farmakologie MeSH
- bakteriální proteiny antagonisté a inhibitory MeSH
- Coxiella burnetii účinky léků metabolismus MeSH
- dihydrofolátreduktasa chemie metabolismus MeSH
- katalytická doména MeSH
- lidé MeSH
- ligandy MeSH
- racionální návrh léčiv MeSH
- simulace molekulární dynamiky MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
