1,100 research outputs found
The folding of knotted proteins: insights from lattice simulations
We carry out systematic Monte Carlo simulations of Go lattice proteins to investigate and compare the folding processes of two model proteins whose native structures differ from each other due to the presence of a trefoil knot located near the terminus of one of the protein chains. We show that the folding time of the knotted fold is larger than that of the unknotted protein and that this difference in folding time is particularly striking in the temperature region below the optimal folding temperature. Both proteins display similar folding transition temperatures, which is indicative of similar thermal stabilities. By using the folding probability reaction coordinate as an estimator of folding progression we have found out that the formation of the knot is mainly a late folding event in our shallow knot system
Pathways to folding, nucleation events and native geometry
We perform extensive Monte Carlo simulations of a lattice model and the Go
potential to investigate the existence of folding pathways at the level of
contact cluster formation for two native structures with markedly different
geometries. Our analysis of folding pathways revealed a common underlying
folding mechanism, based on nucleation phenomena, for both protein models.
However, folding to the more complex geometry (i.e. that with more non-local
contacts) is driven by a folding nucleus whose geometric traits more closely
resemble those of the native fold. For this geometry folding is clearly a more
cooperative process.Comment: Accepted in J. Chem. Phy
The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics
Protein folding is a universal process, very fast and accurate, which works
consistently (as it should be) in a wide range of physiological conditions. The
present work is based on three premises, namely: () folding reaction is a
process with two consecutive and independent stages, namely the search
mechanism and the overall productive stabilization; () the folding kinetics
results from a mechanism as fast as can be; and () at nanoscale
dimensions, local thermal fluctuations may have important role on the folding
kinetics. Here the first stage of folding process (search mechanism) is focused
exclusively. The effects and consequences of local thermal fluctuations on the
configurational kinetics, treated here in the context of non extensive
statistical mechanics, is analyzed in detail through the dependence of the
characteristic time of folding () on the temperature and on the
nonextensive parameter .The model used consists of effective residues
forming a chain of 27 beads, which occupy different sites of a D infinite
lattice, representing a single protein chain in solution. The configurational
evolution, treated by Monte Carlo simulation, is driven mainly by the change in
free energy of transfer between consecutive configurations. ...Comment: 19 pages, 3 figures, 1 tabl
Soft culture substrates favor stem-like cellular phenotype and facilitate reprogramming of human mesenchymal stem/stromal cells (hMSCs) through mechanotransduction
Fundação para a Ciência e a Tecnologia) - FCT - grant FCT-UID/NEU/04539/2019.
European Regional Development Fund (ERDF/FEDER) through the Operational Program Competitiveness Factors (Programa Operacional Factores de Competitividade) - COMPETE - funding through Project 'Stem cell based platforms for Regenerative and Therapeutic Medicine', Centro-07-ST24-FEDER-002008.
M.G. acknowledges funding by the ERDF/FEDER through COMPETE and by national funds by FCT through grant FCOMP-01-0124-FEDER-021150 - PTDC/SAU-889 ENB/119292/2010 and grant POCI-01-0145-FEDER-029516, co-financed by the ERDF/FEDER under the framework Competitiveness and Internationalization Operational Program (Programa Operacional Competitividade e Internacionalizacao -POCI),
national funds through FCT/'Ministerio da Ciencia, Tecnologia e Ensino Superior' (FCT/MCTES) through the Portuguese State Budget. Grant PTDC/SAU-ENB/113696/2009 was attributed to R.P.N.
R.D.M.T. and J.C. thank the support of FEDER funds through COMPETE and by national funds by FCT under the strategic project UID/FIS/04564/2016 and under POCI-01-0145-FEDER-031743 - PTDC/BIA-CEL/31743/2017.
R.D.M.T. acknowledges FCT's support through the FCT Researcher Program.Biophysical cues influence many aspects of cell behavior. Stiffness of the extracellular matrix is probed by cells and transduced into biochemical signals through mechanotransduction protein networks, strongly influencing stem cell behavior. Cellular stemness is intimately related with mechanical properties of the cell, like intracellular contractility and stiffness, which in turn are influenced by the microenvironment. Pluripotency is associated with soft and low-contractility cells. Hence, we postulated that soft cell culture substrates, presumably inducing low cellular contractility and stiffness, increase the reprogramming efficiency of mesenchymal stem/stromal cells (MSCs) into induced pluripotent stem cells (iPSCs). We demonstrate that soft substrates (1.5 or 15 kPa polydimethylsiloxane – PDMS) caused modulation of several cellular features of MSCs into a phenotype closer to pluripotent stem cells (PSCs). MSCs cultured on soft substrates presented more relaxed nuclei, lower maturation of focal adhesions and F-actin assembling, more euchromatic and less heterochromatic nuclear DNA regions, and increased expression of pluripotency-related genes. These changes correlate with the reprogramming of MSCs, with a positive impact on the kinetics, robustness of colony formation and reprogramming efficiency. Additionally, substrate stiffness influences several phenotypic features of iPS cells and colonies, and data indicates that soft substrates favor full iPSC reprogramming.publishersversionpublishe
Simulation of the spinodal phase separation dynamics of the Bi-Zn system
In the phase separation occurring at the miscibility gap (at the spinodal region) of an alloy a discrete symmetry is spontaneously broken and a domain wall network is formed. Field theory simulations are often used to study the dynamics of topological defects networks appearing in different physical contexts. In this work, we focus on the dynamics of the two immiscible liquids appearing on the phase diagram of the BiZn system, one of the basic systems of lead free solders. We use phase field simulations to quantitatively simulate the dynamics of the two liquids separation in the BiZn system, at different temperatures and for different concentrations. We obtain the miscibility gap curve and the domain morphologies of the system as a function of time, temperature and component concentrations using simulations
Ohta-Jasnow-Kawasaki Approximation for Nonconserved Coarsening under Shear
We analytically study coarsening dynamics in a system with nonconserved
scalar order parameter, when a uniform time-independent shear flow is present.
We use an anisotropic version of the Ohta-Jasnow-Kawasaki approximation to
calculate the growth exponents in two and three dimensions: for d=3 the
exponents we find are the same as expected on the basis of simple scaling
arguments, that is 3/2 in the flow direction and 1/2 in all the other
directions, while for d=2 we find an unusual behavior, in that the domains
experience an unlimited narrowing for very large times and a nontrivial
dynamical scaling appears. In addition, we consider the case where an
oscillatory shear is applied to a two-dimensional system, finding in this case
a standard t^1/2 growth, modulated by periodic oscillations. We support our
two-dimensional results by means of numerical simulations and we propose to
test our predictions by experiments on twisted nematic liquid crystals.Comment: 25 RevTeX pages, 7 EPS figures. To be published in Phys. Rev.
Nucleation phenomena in protein folding: The modulating role of protein sequence
For the vast majority of naturally occurring, small, single domain proteins
folding is often described as a two-state process that lacks detectable
intermediates. This observation has often been rationalized on the basis of a
nucleation mechanism for protein folding whose basic premise is the idea that
after completion of a specific set of contacts forming the so-called folding
nucleus the native state is achieved promptly. Here we propose a methodology to
identify folding nuclei in small lattice polymers and apply it to the study of
protein molecules with chain length N=48. To investigate the extent to which
protein topology is a robust determinant of the nucleation mechanism we compare
the nucleation scenario of a native-centric model with that of a sequence
specific model sharing the same native fold. To evaluate the impact of the
sequence's finner details in the nucleation mechanism we consider the folding
of two non- homologous sequences. We conclude that in a sequence-specific model
the folding nucleus is, to some extent, formed by the most stable contacts in
the protein and that the less stable linkages in the folding nucleus are solely
determined by the fold's topology. We have also found that independently of
protein sequence the folding nucleus performs the same `topological' function.
This unifying feature of the nucleation mechanism results from the residues
forming the folding nucleus being distributed along the protein chain in a
similar and well-defined manner that is determined by the fold's topological
features.Comment: 10 Figures. J. Physics: Condensed Matter (to appear
The variable finesse locking technique
Virgo is a power recycled Michelson interferometer, with 3 km long Fabry-Perot cavities in the arms. The locking of the interferometer has been obtained with an original lock acquisition technique. The main idea is to lock the instrument away from its working point. Lock is obtained by misaligning the power recycling mirror and detuning the Michelson from the dark fringe. In this way, a good fraction of light escapes through the antisymmetric port and the power build-up inside the recycling cavity is extremely low. The benefit is that all the degrees of freedom are controlled when they are almost decoupled, and the linewidth of the recycling cavity is large. The interferometer is then adiabatically brought on to the dark fringe. This technique is referred to as variable finesse, since the recycling cavity is considered as a variable finesse Fabry-Perot. This technique has been widely tested and allows us to reach the dark fringe in few minutes, in an essentially deterministic way
A Cross-correlation method to search for gravitational wave bursts with AURIGA and Virgo
We present a method to search for transient GWs using a network of detectors
with different spectral and directional sensitivities: the interferometer Virgo
and the bar detector AURIGA. The data analysis method is based on the
measurements of the correlated energy in the network by means of a weighted
cross-correlation. To limit the computational load, this coherent analysis step
is performed around time-frequency coincident triggers selected by an excess
power event trigger generator tuned at low thresholds. The final selection of
GW candidates is performed by a combined cut on the correlated energy and on
the significance as measured by the event trigger generator. The method has
been tested on one day of data of AURIGA and Virgo during September 2005. The
outcomes are compared to the results of a stand-alone time-frequency
coincidence search. We discuss the advantages and the limits of this approach,
in view of a possible future joint search between AURIGA and one
interferometric detector.Comment: 11 pages, 6 figures, submitted to CQG special issue for Amaldi 7
Proceeding
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