When you search "hemoglobin" at PDBj site, you will find various types of molecule shapes in the search result list (Figure 1). The variety means the molecule may be folded into different form for each situation as well as the included atomic coordinates (asymmetric unit, AU) don't always equal to the biological functional unit (biological unit, BU) (Figure 2). Then I illustrated some examples of hemoglobin molecules. The Figure 3 shows two states of hemoglobin molecules from human: one is oxidized form, and the other is reduced form. Figure 4 shows two types: one is normal type, and the other is hemoglobin S which causes sickle-cell anemia. Finally I introduce another feature of PDBj search that the search target includes not only PDB entries but also PDBj websites, such as news, help and Molecule of the Month articles (Figure 5).
The phase diagram for a Lennard-Jones system was estimated using conventional NPH molecular dynamics (MD) simulations. Standard periodic boundaries were assumed for unit cells containing 1000 molecules. An elongated unit cell with both solid and vacuum sections was found to be suitable for the NPH MD simulations when calculating both the melting and vapor pressure curves under pressures lower than the critical one. Under high pressures, a unit cell with both solid and liquid sections was used as the initial configuration to obtain the melting temperature. The results of these simulations were compared with the phase transition point given by the reported equations of state.
OmpF porin is one of the major components of the outer membrane proteins in Escherichia coli, and it facilitates the transport of small hydrophilic molecules across the outer membrane. The conductance values of various alkali metal ions for OmpF porin show a trend of Li+ < Na+ < K+ < Rb+ ~ Cs+ (C. Danelon, A. Suenaga, M. Winterhalter, and I. Yamato, Molecular origin of the cation selectivity in OmpF porin: single channel conductances vs. free energy calculation. Biophysical chemistry 104 (2003) 591–603.) On the other hand, permeability ratios of the alkali metal ions to chloride anions, estimated by zero-current membrane potential measurements, show an opposite trend at low salt concentrations, that is, Li+ > Na+ > K+ > Rb+ > Cs+, meaning that the protein has a small cation selectivity. In order to elucidate the physico-chemical mechanisms responsible for the conductance and selectivity of OmpF porin, we performed all-atom molecular dynamics (MD)/free energy calculations of the protein. In MD simulations at low salt concentrations under an electric field; simultaneous binding of two Na+ ions to Asp113 in the constriction zone of OmpF porin was observed in the Na+ permeation processes, which is consistent with a previous simulation study (A. Suenega, Y. Komeiji, M. Uebayasi, T. Meguro, M. Saito, and I. Yamato, Computational observation of an ion permeation through a channel protein. Bioscience reports 18 (1998) 39–48.) Then, we hypothesized that the stability of the two-cation bound states plays an important role in determining the conductance sequence of monovalent cations. Driven by this idea, we estimated the binding affinities of two Li+, Na+, and K+ ions to Asp113 in the bound state by a free energy calculation technique, showing that the affinity decreases with their atomic radii, that is, Li+ > Na+ >> K+. This result is qualitatively consistent with the experimental observation of the protein under the electric field and offers new insights into understanding the ion permeation mechanism of OmpF porin.