Biology subjects

Falo, F.

Publications and source records attributed to Falo, F..

4 recordsLinked to original sources

bioRxiv2025

Telomeric G-quadruplex Intermediates unveiled by Complex Markov Network Analysis.

G-quadruplexes are secondary, non-canonical RNA/DNA structures formed by guanine-rich sequences assembled into four-stranded helical structures by the progressive stacking of G-Tetrads, planar arrangements of guanines stabilised by monovalent ions such as K+ or Na+. Their stability plays a very important role in the prevention of DNA degradation, leading to the promotion or inhibition of specific biological pathways upon formation. In this work, we explore the occurrences of intermediates originating from the unfolding of these structures by using all-atom simulations, analyzing a small number of significant reaction coordinates to follow the evolution of the system by applying a mesoscopic simplification of the structures followed by two different dimensionality reduction techniques: Principal Component Analysis (PCA) and time-Independent Component Analysis (tICA). The data of the reduced trajectories are then encoded into a Complex Markov Network which, in conjunction with an Stochastic Steepest Descent, provides a hierarchical organization of the different nodes into basins of attraction. This procedure is able to reveal the main intermediates and the most relevant transitions the system undergoes in its denaturation path.

biophysics↗

bioRxiv2019

Thermal versus Mechanical Unfolding in a Model Protein

Force spectroscopy techniques are often used to learn about the free energy landscape of single biomolecules, typically by recovering free energy quantities that, extrapolated to zero force, are compared to those measured in bulk experiments. However, it is not always clear how the information obtained from a mechanically perturbed system can be related to that obtained using other denaturants, since tensioned molecules unfold and refold along a reaction coordinate imposed by the force, which is unlikely meaningful in its absence. Here, we explore this dichotomy by investigating the unfolding landscape of a model protein, which is first unfolded mechanically through typical force spectroscopy-like protocols, and next thermally. When unfolded by non-equilibrium force extension and constant force protocols, we recover a simple two-barrier landscape, as the protein reaches the extended conformation through a metastable intermediate. Interestingly, folding-unfolding equilibrium simulations at low forces suggested a totally different scenario, where this metastable state plays little role in the unfolding mechanism, and the protein unfolds through two competing pathways27. Finally, we use Markov state models to describe the configurational space of the unperturbed protein close to the critical temperature. The thermal dynamics is well understood by a one-dimensional landscape along an appropriate reaction coordinate, however very different from the mechanical picture. In this sense, in our protein model the mechanical and thermal descriptions provide incompatible views of the folding/unfolding landscape of the system, and the estimated quantities to zero force result hard to interpret.

biophysics↗

bioRxiv2018

Exact analytical solution of the extensible freely jointed chain model

Based on classical statistical mechanics, we calculate analytically the length extension under a pulling force of a polymer modeled as a freely jointed chain with extensible bonds, the latter being considered as harmonic springs. We obtain an exact formula for the extension curve, as well as an independent high force approximation. These formulas can reproduce with high precision the experimental extension/force curves also at low values of the elastic constant of the spring, where previous proposals differ substantially. We successfully validate the analytical results together with the phenomenological expressions used in the literature by analyzing the precision of their fit on data obtained from Langevin simulations.

biophysics↗

bioRxiv2017

Mesoscopic Model For DNA G-Quadruplex Unfolding

Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been reported to date by all-atom simulations, which cannot dissect the major physical interactions responsible for their cohesion. Here, we propose a mesoscopic model to describe both the mechanical and thermal stability of DNA G-quadruplexes, where each nucleotide of the structure, as well as each central cation located at the inner channel, is mapped onto a single bead. In this framework we are able to simulate loading rates similar to the experimental ones, which are not reachable in simulations with atomistic resolution. In this regard, we present single-molecule force-induced unfolding experiments by a high-resolution optical tweezers on a DNA telomeric sequence capable of forming a G-quadruplex conformation. Fitting the parameters of the model to the experiments we find a correct prediction of the rupture-force kinetics and a good agreement with previous near equilibrium measurements. Since G-quadruplex unfolding dynamics is halfway in complexity between secondary nucleic acids and tertiary protein structures, our model entails a nanoscale paradigm for non-equilibrium processes in the cell.

biophysics↗