Search results for " Dynamics"

A Perspective : Active Role of Lipids in Neurotransmitter Dynamics

2019

AbstractSynaptic neurotransmission is generally considered as a function of membrane-embedded receptors and ion channels in response to the neurotransmitter (NT) release and binding. This perspective aims to widen the protein-centric view by including another vital component—the synaptic membrane—in the discussion. A vast set of atomistic molecular dynamics simulations and biophysical experiments indicate that NTs are divided into membrane-binding and membrane-nonbinding categories. The binary choice takes place at the water-membrane interface and follows closely the positioning of the receptors’ binding sites in relation to the membrane. Accordingly, when a lipophilic NT is on route to a m…

Monitoring of ticks and tick-borne pathogens through a nationwide research station network in Finland.

2020

In 2015 a long-term, nationwide tick and tick-borne pathogen (TBP) monitoring project was started by the Finnish Tick Project and the Finnish Research Station network (RESTAT), with the goal of producing temporally and geographically extensive data regarding exophilic ticks in Finland. In the current study, we present results from the first four years of this collaboration. Ticks were collected by cloth dragging from 11 research stations across Finland in May September 2015-2018 (2012-2018 in Seili). Collected ticks were screened for twelve different pathogens by qPCR: Borrelia afzelii, Borrelia garinii, Borrelia valaisiana, Borrelia burgdorferi sensu stricto, Borrelia miyamotoi, Babesia sp…

Protoparvovirus Knocking at the Nuclear Door

2017

Protoparvoviruses target the nucleus due to their dependence on the cellular reproduction machinery during the replication and expression of their single-stranded DNA genome. In recent years, our understanding of the multistep process of the capsid nuclear import has improved, and led to the discovery of unique viral nuclear entry strategies. Preceded by endosomal transport, endosomal escape and microtubule-mediated movement to the vicinity of the nuclear envelope, the protoparvoviruses interact with the nuclear pore complexes. The capsids are transported actively across the nuclear pore complexes using nuclear import receptors. The nuclear import is sometimes accompanied by structural chan…

Ubiquitous Structural Signaling in Bacterial Phytochromes

2015

The phytochrome family of light-switchable proteins has long been studied by biochemical, spectroscopic and crystallographic means, while a direct probe for global conformational signal propagation has been lacking. Using solution X-ray scattering, we find that the photosensory cores of several bacterial phytochromes undergo similar large-scale structural changes upon red-light excitation. The data establish that phytochromes with ordinary and inverted photocycles share a structural signaling mechanism and that a particular conserved histidine, previously proposed to be involved in signal propagation, in fact tunes photoresponse.

Atomistic Simulations of Functional Gold Nanoparticles Au144(Sr)60 Interacting with Membranes

2013

Gold nanoparticles (AuNps) are used in nanomedicine in, e.g., drug delivery and bio-imaging. However, it is regrettable that the understanding of nanoparticle properties in cellular surroundings is incompletely understood. Here, we have complemented our previous studies [1] by performing extensive atomistic molecular dynamics simulations of lipid membranes interacting with charged gold nanoparticles. We have elucidated the action of these nanoparticles on membranes characterized by lipid compositional asymmetry in the two leaflets, thereby unraveling the interactions of AuNPs with both the extracellular and the cytosolic sides of plasma membranes of eukaryotic cells. We have found that ther…

An exploration of digital ride-hailing multisided platforms' market dynamics: empirical evidence from the Uber case study

2020

PurposeThe purpose of this paper is to experiment a dynamic performance management (DPM) approach to explore and assess the business dynamics of digital ride-hailing platforms with a focus on both supply and demand sides, and related interplays.Design/methodology/approachThe research adopts the DPM framework supported by simulation-based experimentations for developing a systemic case interpretation of Uber Inc. and its specific business complexity.FindingsThe emerging scenario analysis reveals that changes in the commission percentage for drivers and cutting prices for customers (car hailers) by competitors have significant impacts on the car-hailing industry.Originality/valueDPM and assoc…

2021

A substantial body of research has shown worse health conditions for East- vs. West-Germany in the wake of reunification. In the present study, we investigate how these differences between the two formerly divided regions developed and what maintains them. Specifically, we consider the associations between health status, income satisfaction, and health-related locus of control. In a quasi-experimental and longitudinal study design, we are particularly interested in the differences between individuals who stayed in East-Germany and those who were born in the East but migrated to West-Germany. To this end, we examined data from seven waves of the Saxony Longitudinal Study (2003–2009). Specifi…

Modeling of Particle Number Fluctuations in Entire Cells

2012

In a recent study we developed a method to model protein diffusion in cells [1], where special attention was given to generating from image data of the measured cell a realistic digital model cell in which protein dynamics were simulated. The method was shown to be well suited for modeling non-equilibrium situations that arise, e.g., in photobleaching experiments, and to be capable of producing more detailed information about protein motion than traditional modeling.Another experimental way to assess protein dynamics is to study fluctuations in the local protein number, as it is done, e.g., in fluorescence correlation spectroscopy (FCS), or in similar measurements that apply single-plane il…

A Microscopic Description of SARS-CoV-2 Main Protease Inhibition with Michael Acceptors. Strategies for Improving Inhibitors Design

2020

The irreversible inhibition of the main protease of SARS-CoV-2 by a Michael acceptor known as N3 has been investigated using multiscale methods. The noncovalent enzyme–inhibitor complex was simulated using classical molecular dynamics techniques and the pose of the inhibitor in the active site was compared to that of the natural substrate, a peptide containing the Gln–Ser scissile bond. The formation of the covalent enzyme–inhibitor complex was then simulated using hybrid QM/MM free energy methods. After binding, the reaction mechanism was found to be composed of two steps: (i) the activation of the catalytic dyad (Cys145 and His41) to form an ion pair and (ii) a Michael addition where the …

2019

So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution…