In the theoretical viewpoints, three-dimensional structure of proteins determines their functions, therefore we should be able to identify the function of proteins when the structures of proteins are provided, but it has not been realized. Here we describe our trials of the structure-based function identification of proteins. We focus our attention on the shape and electrostatic potential of molecular surface where the function of proteins is exhibited. Our approach is based on the similarity search of those properties against the functional site database of known proteins. As an application to hypothetical proteins, one successful result for the case of MJ0226 is described.
From chemical point of view, the NO reduction to N2O is one of the most attractive subjects, since it contains the N-O bond cleavage and N-N bond formation with aid of two electrons and two protons. Nitric oxide reductase (NOR) is a key enzyme for this reaction in biological denitrification processes. Two types of NORs have been isolated from some microorganisms and characterized; one is a soluble cytochrome P450-type enzyme from fungi, whereas the other is a membrane-bound cytochrome bc-type complex from denitrifying bacteria. These NORs effectively catalyze the NO reduction in a quite different mechanism. Here we summarize the current results in the mechanistic study of NO reduction reaction conducted by each enzyme, and discuss their molecular mechanism based on their structural and functional information.
The membrane proteins require lipids in order to express their function. The function is under the influence of structure and physical properties of the lipid membrane surrounding the proteins. The non-bilayer structure induced by non-bilayer forming lipids is concerned in various membrane functions, such as membrane fusion during endocytosis. The physical properties of non-bilayer forming lipids are investigated by fluorescence measurements using an environment-sensitive probe, laurdan, differential scanning calorimetry and density meter. The results suggest relationship between the physical properties of non-bilayer forming lipid and the membrane functions.
Double whole cell recordings and voltage-sensitive dye imaging from the dendrites of pyramidal neurons revealed that the membrane of the apical dendrites is electrically leakier than that of other locations. A theoretical analysis predicts that the impact of synaptic inputs on the distal part of the dendrites can be more effective when the membrane resistivity is lower towards the end of the dendrite than when the resistivity is uniform. The distribution of resistivity along the soma-dendritic axis may have important implications on synaptic integration much as the active electrical properties of the dendrites.