Local polarity analysis: a sensitive method that discriminates between native proteins and incorrectly folded models.

The evaluation of calculated protein structures is an important step in the protein design cycle. Known criteria for this assessment of proteins are the polar and apolar, accessible and buried surface area, electrostatic interactions and other interactions between the protein atoms (e.g. H..O, S..S), atomic packing, analysis of amino acid environment and surface charge distribution. We show that a powerful test of accuracy of protein structure can be derived by analysing the water contact of atoms and additionally taking into account their polarity. On the basis of estimated reference values of the polar fraction of typical globular proteins with known structure (mean, SD and distribution), the evaluation of misfolded structures can be improved significantly. The reference values are derived by moving windows of different length (3-99 amino acid residues) over the amino acid sequence. Model proteins, which are included in the Brookhaven protein structure databank, deliberately misfolded proteins, hypothetical proteins and predicted protein structures are diagnosed as at least partially incorrectly folded. The local fault, mostly observed, is that polar groups are buried too frequently in the interior of the protein. The database-derived quantities are useful in screening the designed proteins prior to experimentation and may also be useful in the assessment of errors in the experimentally determined protein structures.

The role of eye accommodation in the depth perception of common toads.

Distance estimation in prey catching was as exact in monocular toads (Bufo bufo (L.)) as in binocular ones. Application of Atropine or Miotic had no significant effect on binocular animals, whereas in monocular toads it made accurate distance estimation impossible. The accommodative state of the eye is decisive for depth estimation of monocular, but not of binocular toads.

The role of early sensory experience in the prey catching responses of Salamandra salamandra to stationary prey.

Two groups of newly metamorphosed Salamandra salamandra (L.) were raised with living and with stationary prey, respectively. One year later, the group which had experience exclusively with stationary prey was significantly better in responding to stationary prey than the group which only had experience with moving prey. This was the case both under light and dark conditions. The experiments show that prey-catching behavior in salamanders can be considerably modified by experience.

The influence of prey experience on movement pattern preference in Salamandra salamandra (L.).

Groups of juvenile Salamandra salamandra were raised selectively with different types of prey. The influence of these conditions on the movement pattern preference was studied during the first six months after metamorphosis. Responses to a black horizontal bar moving continuously or stepwise at step frequencies between 0.25 and 8 steps/s were tested. The differently raised groups showed significant differences in their respective preference for stimulus movement patterns which corresponded with the movement pattern of their food. At the same time, superimposed upon this learning process, a general increase in the relative efficiency of continuous stimulus movement with regard to stepwise stimulus movement could be observed.