scholarly journals TOWARDS FAST 3D NANOPARTICLE LOCALIZATION FOR STUDYING MOLECULAR DYNAMICS IN LIVING CELLS

2011 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Living Cells

Crystal structures and snapshots along the reaction pathway of human phosphoserine phosphatase

2019 ◽  
Vol 75 (6) ◽  
pp. 592-604 ◽  
Author(s):  
Marie Haufroid ◽  
Manon Mirgaux ◽  
Laurence Leherte ◽  
Johan Wouters
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Crystal Structures ◽  
Reaction Pathway ◽  
Living Cells ◽  
Homocysteic Acid ◽  
Phosphoserine Phosphatase ◽  
Key Enzyme ◽  
The Subject ◽  
Dynamics Simulations

The equilibrium between phosphorylation and dephosphorylation is one of the most important processes that takes place in living cells. Human phosphoserine phosphatase (hPSP) is a key enzyme in the production of serine by the dephosphorylation of phospho-L-serine. It is directly involved in the biosynthesis of other important metabolites such as glycine and D-serine (a neuromodulator). hPSP is involved in the survival mechanism of cancer cells and has recently been found to be an essential biomarker. Here, three new high-resolution crystal structures of hPSP (1.5–2.0 Å) in complexes with phosphoserine and with serine, which are the substrate and the product of the reaction, respectively, and in complex with a noncleavable substrate analogue (homocysteic acid) are presented. New types of interactions take place between the enzyme and its ligands. Moreover, the loop involved in the open/closed state of the enzyme is fully refined in a totally unfolded conformation. This loop is further studied through molecular-dynamics simulations. Finally, all of these analyses allow a more complete reaction mechanism for this enzyme to be proposed which is consistent with previous publications on the subject.

Fluorescent Protein Biosensors: Measurement of Molecular Dynamics in Living Cells

1995 ◽  
Vol 24 (1) ◽  
pp. 405-434 ◽  
Author(s):  
K A Giuliano ◽  
P L Post ◽  
K M Hahn ◽  
D L Taylor
Keyword(s):  
Molecular Dynamics ◽  
Fluorescent Protein ◽  
Living Cells

scholarly journals Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

2019 ◽  
Vol 15 ◽  
pp. 1933-1944 ◽  
Author(s):  
Silvie Rimpelová ◽  
Michal Jurášek ◽  
Lucie Peterková ◽  
Jiří Bejček ◽  
Vojtěch Spiwok ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Biological Effects ◽  
Sesquiterpene Lactones ◽  
Living Cells ◽  
Calcium Atpase ◽  
Dynamics Simulation ◽  
Plant Metabolites ◽  
Cytotoxic Effects ◽  
Secondary Plant Metabolites ◽  
Fluorescent Derivative

Sesquiterpene lactones are secondary plant metabolites with sundry biological effects. In plants, they are synthesized, among others, for pesticidal and antimicrobial effects. Two such compounds, archangelolide and trilobolide of the guaianolide type, are structurally similar to the well-known and clinically tested lactone thapsigargin. While trilobolide has already been studied by us and others, there are only scarce reports on the biological activity of archangelolide. Here we present the preparation of its fluorescent derivative based on a dansyl moiety using azide–alkyne Huisgen cycloaddition having obtained the two sesquiterpene lactones from the seeds of Laserpitium archangelica Wulfen using supercritical CO2 extraction. We show that dansyl-archangelolide localizes in the endoplasmic reticulum of living cells similarly to trilobolide; localization in mitochondria was also detected. This led us to a more detailed study of the anticancer potential of archangelolide. Interestingly, we found that neither archangelolide nor its dansyl conjugate did exhibit cytotoxic effects in contrast to the structurally closely related counterparts trilobolide and thapsigargin. We explain this observation by a molecular dynamics simulation, in which, in contrast to trilobolide, archangelolide did not bind into the sarco/endoplasmic reticular calcium ATPase cavity utilized by thapsigargin. Last, but not least, archangelolide exhibited anti-inflammatory activity, which makes it promising compound for medicinal purposes.

Improved fabrication of zero-mode waveguides for monitoring specific molecular dynamics in living cells

2012 ◽  
Author(s):  
Chia-Fen Hsieh ◽  
Shui-Chin Lai ◽  
Chih-Ting Chen ◽  
Yii-Lih Lin ◽  
Kuo-Tang Liao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Zero Mode ◽  
Living Cells

scholarly journals Archangelolide: Sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

2019 ◽  
Author(s):  
Silvie Rimpelová ◽  
Michal Jurášek ◽  
Lucie Peterková ◽  
Jiří Bejček ◽  
Vojtěch Spiwok ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cytotoxic Effect ◽  
Biological Effects ◽  
Sesquiterpene Lactones ◽  
Living Cells ◽  
Calcium Atpase ◽  
Dynamics Simulation ◽  
Plant Metabolites ◽  
Secondary Plant Metabolites ◽  
Fluorescent Derivative

Sesquiterpene lactones are secondary plant metabolites with sundry biological effects. In plants, they are synthesized mainly for their pesticidal, antimicrobial and other effects. Two such compounds, archangelolide and trilobolide of the guaianolide type, are structurally similar to the well-known and clinically tested lactone thapsigargin. Here we present the development of a facile method for isolation of these two sesquiterpene lactones from the seeds of Laserpitium archangelica Wulfen using supercritical CO2 extraction. Furthermore, not much has been reported on biological activity of archangelolide. We prepared its fluorescent derivative based on a dansyl moiety using azide-alkyne Huisgen cycloaddition. We showed that dansyl-archangelolide localized in endoplasmic reticulum of living cells similarly to trilobolide; nevertheless, localization in mitochondria was also detected. This led us to study the anticancer potential of archangelolide. Interestingly, we found that neither archangelolide nor its dansyl conjugate did exhibit cytotoxic effect in contrast to its structurally closely related counterparts trilobolide and thapsigargin. We explain this observation by a molecular dynamics simulation, in which, in contrast to trilobolide, archangelolide did not bind into the sarco/endoplasmic reticular calcium ATPase cavity utilized by thapsigargin. Last, but not least, archangelolide exhibited anti-inflammatory activity, which makes it promising compound for medicinal purposes.

Transmembrane penetration mechanism of Cyclic Pollutants Inspected by Molecular Dynamics and Metadynamics. Case of Morpholine, Phenol, 1,4-Dioxane and Oxane.

2021 ◽  
Author(s):  
Zsófia Borbála Rózsa ◽  
Emma Szőri-Dorogházi ◽  
Béla Viskolcz ◽  
Milán Szőri
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Living Cells ◽  
Passive Transport ◽  
Penetration Mechanism ◽  
Dynamics Simulations

The presence of industrially produced chemicals in water is often not monitored while their passive transport and accumulation can cause serious damage in living cells. Molecular dynamics simulations make an...

Molecular dynamics imaging in micropatterned living cells

2005 ◽  
Vol 2 (10) ◽  
pp. 739-741 ◽  
Author(s):  
Kristiana Kandere-Grzybowska ◽  
Christopher Campbell ◽  
Yulia Komarova ◽  
Bartosz A Grzybowski ◽  
Gary G Borisy
Keyword(s):  
Molecular Dynamics ◽  
Living Cells

scholarly journals Polewards microtubule flux in the mitotic spindle: evidence from photoactivation of fluorescence.

1989 ◽  
Vol 109 (2) ◽  
pp. 637-652 ◽  
Author(s):  
T J Mitchison
Keyword(s):  
Molecular Dynamics ◽  
Tissue Culture ◽  
Strong Evidence ◽  
Mitotic Spindle ◽  
Living Cells ◽  
Structure And Function ◽  
Culture Cells ◽  
Tissue Culture Cells ◽  
And Function ◽  
Spindle Structure

I have synthesized a novel derivative of carboxyfluorescein that is nonfluorescent, but can be converted to a fluorescent form by exposure to 365-nm light. This photoactivable, fluorescent probe was covalently attached to tubulin and microinjected into mitotic tissue culture cells, where it incorporated into functional spindles. To generate a fluorescent bar across the mitotic spindle, metaphase cells were irradiated with a slit microbeam. This bar decreased in intensity over the first minute, presumably due to turnover of nonkinetochore microtubules. The remaining fluorescent zones, now presumably restricted to kinetochore microtubules, moved polewards at 0.3-0.7 microns/min. This result provides strong evidence for polewards flux in kinetochore microtubules. In conjunction with earlier biotin-tubulin incorporation experiments (Mitchison, T. J., L. Evans, E. Schulze, and M. Kirschner. 1986. Cell. 45:515-527), I conclude that microtubules polymerize at kinetochores and depolymerize near the poles throughout metaphase. The significance of this observation for spindle structure and function is discussed. Local photoactivation of fluorescence should be a generally useful method for following molecular dynamics inside living cells.

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