Biomedical subjects

J Ferkinghoff-Borg

Publications and source records attributed to J Ferkinghoff-Borg.

3 recordsLinked to original sources

PubMed2006

Thermodynamic features characterizing good and bad folding sequences obtained using a simplified off-lattice protein model.

The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each beadlike amino acid interacts with the others through a contact potential controlled by a random matrix. Good folding sequences, characterized by a low native energy, display three main thermodynamical ensembles, namely, a coil-like ensemble, an unfolded globule, and a folded ensemble (plus two other states, frozen and random coils, populated only at extreme temperatures). Interestingly, the unfolded globule has some regions already structured. Poorly designed sequences, on the other hand, display a wide transition from the random coil to a frozen state. The comparison with the analytic theory of heteropolymers is discussed.

Amino Acid Sequence↗

PubMed2005

Design of amino acid sequences to fold into C(alpha)-model proteins.

In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting through a contact potential controlled by a 20x20 quenched random matrix. The goal of the present work is to design and characterize amino acid sequences folding to the SH3 conformation, a 60-residue recognition domain common to many regulatory proteins. We show that a number of sequences can fold, starting from a random conformation, to within a distance root-mean-square deviation between 2.6 and 4.0 A from the native state. Good folders are those sequences displaying in the native conformation an energy lower than a sequence-independent threshold energy.

Amino Acid Sequence↗

PubMed2004

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.

SmartCell has been developed to be a general framework for modelling and simulation of diffusion-reaction networks in a whole-cell context. It supports localisation and diffusion by using a mesoscopic stochastic reaction model. The SmartCell package can handle any cell geometry, considers different cell compartments, allows localisation of species, supports DNA transcription and translation, membrane diffusion and multistep reactions, as well as cell growth. Moreover, different temporal and spatial constraints can be applied to the model. A GUI interface that facilitates model making is also available. In this work we discuss limitations and advantages arising from the approach used in SmartCell and determine the impact of localisation on the behaviour of simple well-defined networks, previously analysed with differential equations. Our results show that this factor might play an important role in the response of networks and cannot be neglected in cell simulations.

Animals↗