The inverse hexagonal - inverse ribbon - lamellar gel phase transition sequence in low hydration DOPC:DOPE phospholipid mixtures

The inverse hexagonal to inverse ribbon phase transition in a mixed phosphatidylcholine-phosphatidylethanolamine system at low hydration is studied using small and wide angle X-ray scattering. It is found that the structural parameters of the inverse hexagonal phase are independent of temperature. By contrast the length of each ribbon of the inverse ribbon phase increases continuously with decreasing temperature over a range of 50 °C. At low temperatures the inverse ribbon phase is observed to have a transition to a gel lamellar phase, with no intermediate fluid lamellar phase. This phase transition is confirmed by differential scanning calorimetry.     

Emergence of scale-free distribution in protein–protein interaction networks based on random selection of interacting domain pairs

Recent analyses of biological and artificial networks have revealed a common network architecture, called scale-free topology. The origin of the scale-free topology has been explained by using growth and preferential attachment mechanisms. In a cell, proteins are the most important carriers of function, and are composed of domains as elemental units responsible for the physical interaction between protein pairs. Here, we propose a model for protein–protein interaction networks that reveals the emergence of two possible topologies. We show that depending on the number of randomly selected interacting domain pairs, the connectivity distribution follows either a scale-free distribution, even in the absence of the preferential attachment, or a normal distribution. This new approach only requires an evolutionary model of proteins (nodes) but not for the interactions (edges). The edges are added by means of random interaction of domain pairs. As a result, this model offers a new mechanistic explanation for understanding complex networks with a direct biological interpretation because only protein structures and their functions evolved through genetic modifications of amino acid sequences. These findings are supported by numerical simulations as well as experimental data.     

On the relation between native geometry and conformational plasticity

In protein folding the term plasticity refers to the number of alternative folding pathways encountered in response to free energy perturbations such as those induced by mutation. Here we explore the relation between folding plasticity and a gross, generic feature of the native geometry, namely, the relative number of local and non-local native contacts. The results from our study, which is based on Monte Carlo simulations of simple lattice proteins, show that folding to a structure that is rich in local contacts is considerably more plastic than folding to a native geometry characterized by having a very large number of long-range contacts (i.e., contacts between amino acids that are separated by more than 12 units of backbone distance). The smaller folding plasticity of native geometries is probably a direct consequence of their higher folding cooperativity that renders the folding reaction more robust against single- and multiple-point mutations.     

Characterization of protein-binding to the spinach chloroplast psbA mRNA 5' untranslated region.

RNA-binding proteins play a major role in regulating mRNA metabolism in chloroplasts. In this work we characterized two proteins, of 43 and 47 kDa, which bind to the spinach psbA mRNA 5' untranslated region (psbA encoding the D1 protein of photosystem II). The 43 kDa protein, which is present in the stroma and in membranes, co-sediments with a complex of 68S. It was purified, and the N-terminal sequence was determined. Upon homology search it was identified as the chloroplast homologue of the Escherichia coli ribosomal protein S1. The 47 kDa protein, which, in contrast with the 43 kDa protein, sediments with a small sedimentation coefficient, is only detected in the stromal fraction. It is soluble in an uncomplexed form. By deletion analysis, an element within the psbA mRNA 5' untranslated region was identified that is necessary but not sufficient for binding of stromal proteins. The 'central protein binding element' ranges from nucleotide -49 to -9 of the psbA mRNA 5' untranslated region. It comprises the Shine-Dalgarno-like GGAG motif and, 7 nucleotides upstream, an endonucleolytic cleavage site involved in psbA mRNA degradation in vitro . The mechanistic impacts of this region in relation to RNA-binding proteins are discussed.     

Extended Holstein small polaron model for charge transfer in dry DNA

In this paper, the charge transfer problem in dry DNA was investigated by employing an extended Holstein small polaron model with external potential traps being involved in consideration. The ground state energy and the probability amplitude of polaron in various DNA chains with different external trap potentials were obtained by variational method with the trial function being taken in coherent state form. The stability of transfered charges in various circumstances was discussed accordingly.