Search results for "Energy landscape"
showing 7 items of 37 documents
Single-molecule FRET studies of counterion effects on the free energy landscape of human mitochondrial lysine tRNA.
2011
The folding energy landscape of RNA is greatly affected by interactions between the RNA and counterions that neutralize the backbone negative charges and may also participate in tertiary contacts. Valence, size, coordination number, and electron shell structure can all contribute to the energetic stabilization of specific RNA conformations. Using single-molecule fluorescence resonance energy transfer (smFRET), we have examined the folding properties of the RNA transcript of human mitochondrial tRNA(Lys), which possesses two different folded states in addition to the unfolded one under conditions of thermodynamic equilibrium. We have quantitatively analyzed the degree of RNA tertiary structu…
Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute
1999
AbstractMolecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the syst…
Nonequilibrium thermodynamics of the RNA-RNA interaction underlying a genetic transposition program
2021
Thermodynamic descriptions are powerful tools to formally study complex gene expression programs evolved in living cells on the basis of macromolecular interactions. While transcriptional regulations are often modeled in the equilibrium, other interactions that occur in the cell follow a more complex pattern. Here, we adopt a nonequilibrium thermodynamic scheme to explain the RNA-RNA interaction underlying IS10 transposition. We determine the energy landscape associated with such an interaction at the base-pair resolution, and we present an original scaling law for expression prediction that depends on different free energies characterizing that landscape. Then, we show that massive experim…
Aging in a free-energy landscape model for glassy relaxation
2005
The aging properties of a simple free-energy landscape model for the primary relaxation in supercooled liquids are investigated. The intermediate scattering function and the rotational correlation functions are calculated for the generic situation of a quench from a high temperature to below the glass transition temperature. It is found that the re-equilibration of molecular orientations takes longer than for translational degrees of freedom. The time scale for re-equilibration is determined by that of the primary relaxation as an intrinsic property of the model.
Quaternary structure dependence of kinetic hole burning and conformational substates interconversion in hemoglobin.
2003
Using a sol-gel encapsulation technique, we have prepared samples of CO saturated human adult hemoglobin locked in the R or T quaternary conformation. We report time-resolved spectra of these samples in the Soret region following flash photolysis, in the time interval ranging from 250 ns to 200 ms and in the temperature interval of 100-170 K. A suitable analysis of the measured difference spectra enables us to obtain the spectral contribution of deoxyHb and HbCO molecules as a function of time and/or of the fraction N(t) of deoxyHb molecules. In our experimental time window geminate CO rebinding to hemoglobin in the T quaternary conformation is about 2 orders of magnitude slower than to hem…
Early stages of beta2-microglobulin aggregation and the inhibiting action of alphaB-crystallin
2008
The interest of nucleation of protein crystals and aggregates (including oligomerization) spans from basic physics theory all the way to biophysics, nanophysics, clinical sciences, biotechnologies, food technologies and polymer-solvent interactions. Understanding nucleation within a theoretical framework capable of providing quantitative predictions and control of nucleation rates, or even the very occurrence of crystallization, is a long-sought goal of remarkable relevance to each of the above fields. A large amount of work has been aimed at such goal, but success has been so far rather limited. Work at our laboratory has more recently highlighted a direct link between nucleation rates and…
Future rural landscapes : the necessary co-evolution between agricultural landscape and energy landscape
2022
This article explores the ongoing transformation process affecting the agricultural and energy landscape. The complexity of the landscape (natural and artificial) in which we live, calls for urgent reflection on how to achieve effective integration between vegetation and the built environment. The landscape has always been subject to mutation. Man and the consequences of his actions have often been the trigger for it. Today we are in a necessary transition phase, especially from an energy point of view. The landscape will change again and this time more quickly because of the urgency imposed by the new policies implemented (European Green Deal, NRRP, etc.). The article emphasises the indisp…