Search results for "Landscape"

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

2013

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers however from the same limitation, i.e. the non trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachadran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates. We illustrate the robustness of this …

Curvature and Torsion of Protein Main Chain as Local Order Parameters of Protein Unfolding

2020

International audience; Thermal protein unfolding resembles a global (two-state) phase transition. At the local scale, protein unfolding is, however, heterogeneous and probe dependent. Here, we consider local order parameters defined by the local curvature and torsion of the protein main chain. Because chemical shift (CS) measured by NMR spectroscopy is extremely sensitive to the local atomic environment, CS has served as a local probe of thermal unfolding of proteins by varying the position of the atomic isotope along the amino-acid sequence. The variation of the CS of each C(alpha) atom along the sequence as a function of the temperature defines a local heat-induced denaturation curve. We…

Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods

2020

We present a detailed theoretical analysis of the reaction mechanism of proteolysis catalyzed by the main protease of SARS-CoV-2. Using multiscale simulation methods, we have characterized the interactions established by a peptidic substrate in the active site, and then we have explored the free energy landscape associated with the acylation and deacylation steps of the proteolysis reaction, characterizing the transition states of the process. Our mechanistic proposals can explain most of the experimental observations made on the highly similar ortholog protease of SARS-CoV. We point to some key interactions that may facilitate the acylation process and thus can be crucial in the design of …

Public provision versus private provision of industrial land: a hedonic approach

2005

Abstract This study examines the factors that explain the differences observed between the industrial land prices offered by the public sector and those offered by the private sector by means of estimating three hedonic pricing models. The results obtained show that location, defined as the distance to a highway, the distance to the city business district and the distance to the capital of the province, have an important impact on industrial land value. However, this impact is greater when private developers provide the land. Other variables considered, such as who is behind the provision of the industrial land, have an important impact on sale prices.

Perceptions of Cultural Ecosystem Services: spatial differences in urban and rural areas of Kokemäenjoki, Finland

2021

This study aims to identify and evaluate the spatial distribution of Cultural Ecosystem Services (CES) benefits perceived by people in both urban and rural areas. A public participation GIS (PPGIS)...

IL PROGETTO CONTEMPORANEO DEGLI SPAZI PUBBLICI AD ALCAMO

2021

Il saggio presenta alcuni progetti significativi nella città di Alcamo, in cui il tema dello spazio pubblico si presenta come una sorta di allestimento, che configura luoghi di qualità per la città contemporanea. Questi interventi manifestano la loro partecipazione a quello spirito contemporaneo che elabora l’architettura come sistema di relazioni spaziali e temporali: ricostruendo un ordine tra le cose – i pieni ed i vuoti, la vegetazione e le pietre, la città e il paesaggio – e un legame evidente tra contemporaneità e tradizione.

Ģeogrāfija. Ģeoloģija. Vides zinātne: referātu tēzes

2011

Shedding Light on the Dark Ages: Sketching Potential Trade Relationships in Early Medieval Romania through Mitochondrial DNA Analysis of Sheep Remains

2021

Southeast Europe has played an important role in shaping the genetic diversity of sheep due to its proximity to the Danubian route of transport from the Near East into Europe, as well as its possible role as a post-domestication migration network and long tradition of sheep breeding. The history of Romania and, in particular, the historical province of Dobruja, located on the shore of the Black Sea, has been influenced by its geographical position at the intersection between the great powers of the Near East and mainland Europe, with the Middle Ages being an especially animated time in terms of trade, migration, and conflict. In this study, we analyzed the mitochondrial control region of fi…

Mechanical unfolding pathway of a model β-peptide foldamer.

2015

Foldamers constructed from oligomers of β-peptides form stable secondary helix structures already for small chain lengths, which makes them ideal candidates for the investigation of the (un)folding of polypeptides. Here, the results of molecular simulations of the mechanical unfolding of a β-heptapeptide in methanol solvent revealing the detailed unfolding pathway are reported. The unfolding process is shown to proceed via a stable intermediate even for such a small system. This result is arrived at performing non-equilibrium force ramp simulations employing different pulling velocities and also using standard calculations of the potential of mean force, i.e., the free energy as a function …

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…