It has been known that there are more than 100 proteins which contain tandem repeats of oligopeptide with a variation of sequence and of length. Some methods and procedures including molecular modeling by computer graphics, energy minimization and molecular dynamics simulations have been proposed for the three-dimensional structure prediction of these tandem repeats. Our molecular modeling studies are described in some detail and then novel supersecondary structures are proposed.
Orientation and location of retinal in bovine rhodopsin have been determined by cross-linking studies with a photoactivatable analog of 11-cis retinal and by site-directed mutagenesis. The two approaches are corroborative and we identified Glu-122 and Trp-126 in helix C and Trp-265 and Tyr-268 in helix F as a part of retinal binding pocket. Our results also suggest that the β-ionone ring of retinal orients towards helices C and F from the Schiff base end in helix G. Recent mutagenesis studies regarding the counter ion to the protonated Schiff base were also discussed.
Many nuclear-encoded mitochondrial proteins, which are synthesized as precursors bearing an amino-terminal presequence, have to move across one or two mitochondrial mambranes to reach their destinations. Our physicochemical studys on a model precursor protein, pCOX IV-DHFR, suggest that the initial binding of this protein to the mitochondrial outer surface requires lipid-mediated partial unfolding of the polypeptide chain. Then the presequence of the precursor protein moves across the outer and inner membranes via contact sites in a membrane potential-dependent manner, and the traslocation of the mature part across the two membranes follows.
Sporulation of Bacillus subtilis is induced by the deprivation of the nutrients in the medium. During sporulation more than 50 sporulation qenes (spo) are expressed sequentially. The sequential expression of spo genes is regulated mainly at the level of transcription, which is governed by the cascades of five sporulation-specific sigma factors, σH, σF, σE, σG, and σK, At the initiation of sporulation, the first sporulation specific sigma factor σH is activated, which then activates spoIIA operon encoding the second sigma factor σF. Expression of spoIIA and spoIIE operons is required for the activation of the pro-σE, the inactive precursor of the third sigma factor σE, which is required for the expression of the fourth sigma factor σG. σG is present only in the forespore, but its function is required for the activation of the pro-σK, which is present only in the mother cell. sigK gene encoding σK is construted by the mother cell-specific DNA rearrangement occurring during the middle stage of sporuation.
When the color of a visual stimulus is changed, neurons in the lateral geniculate nucleus and non-oriented cells in the primary visual cortex (V1) of the monkey behave linearly in the color space. This indicates that these neurons combine signals from different types of cones linearly. A major difference between cells in these two structures is the increase of variability of the weights on the inputs from different types of cones seen in V1. In contrast, in the inferior temporal cortex, the behavior of many color selective neurons in the color space is highly non-linear. Such deviation from linear to non-linear behavior seems important to generate a sharp sensitivity to particular hues.
A growing root of the higher plant exhibits the spatial pattern and the self-sustained oscillation of the electric potentials near the surface. The electric potential along the root showed a stable banding pattern. This pattern of the electric potential was caused by the transcellular ionic current loops surrounding the root. The phase of the oscillation in the elongation region differed by 180 degrees from those in the mature region and the root tip. The change in the elongation velocity occurred several minutes after the application of the electric field together with the change in patterns of electric potential and pH.
The partial molar quantities of biomolecules in water were discussed from the view point of the hydration. These quantities will not always show a correlation with the water accessible surface area of the biomolecules, but show a good correlation with the dynamic hydration number. Namely, the details of motion and structure of hydration water can play a deterministic role both in static and in dynamic properties of aqueous solutions of biomolecules.