Identification of a novel gene family, paralogs of inhibitor of apoptosis proteins present in plants, fungi, and animals.

Only few orthologs of animal apoptosis regulators have been found in plants. Recently, the ectopic expression of mammalian inhibitor of apoptosis proteins (IAPs) has been shown to affect plant programmed cell death. Here, we identified two novel proteins homologous to Arabidopsis thaliana IAP-like protein (AtILP) 1 and 2 by applying an improved motif searching method. Furthermore, homologs of AtILP1 were found to occur as a novel gene family in other organisms such as fungi and animals including Homo sapiens (HsILP1). Like baculovirus IAP repeats (BIRs) in IAPs, ILPs contain two highly conserved BIR-like domains (BLDs) with a putative C2HC-type zinc finger. Phylogenetic analyses indicated that ILPs are putative paralogs of IAPs. Homology modeling revealed that the three-dimensional structure of BLD in HsILP1 is similar to that of BIR. Transient expression of HsILP1 resulted in inhibition of etoposide-induced apoptosis in HEK293 and HeLaS3 cells. These findings suggest that ILPs are conserved in a wide range of eukaryotes including plants, and that their functions are closely related to those of IAPs.

Structure-based design of an agonistic peptide targeting Fas.

A small agonistic peptide FRAP-4 (WEWT, Fas reactive peptide-4) that binds to the human Fas molecule was discovered using our computer screening strategy named the Amino acid Complement Wave (ACW) method, which is based on the complementarities of interacting amino acids between comprehensive testing peptides and a target protein surface pocket. In silico docking studies demonstrated the specific interaction of FRAP-4 with the main Fas ligand (FasL) binding domain in the Fas molecule. An octamer of this peptide produced by carboxyl terminal linkages of polylysine branches (MAP), (FRAP-4)8-MAP, effectively induced apoptosis in human ovarian cancer cell line NOS4 cells that was associated with the activation of caspases-8, -9 and -3, and the cleavage of PARP. Alanine substitution of the N-terminal W in FRAP-4 resulted in complete loss of FasL-mimetic action of (FRAP-4)8-MAP, suggesting that the aromatic functionality at the N-terminal position W appears to play an essentially important role in Fas binding ability. These observations indicate that the FasL-mimetic peptide should serve as an excellent starting point for the design of effective compounds with FasL-mimetic activity. Furthermore, the ACW method for the structure-based design of optimized small peptides against receptor molecules such as Fas could open new avenues for the development of peptide mimetic and nonpeptidic organic forms to generate novel effective pharmaceuticals.

Bandwidth analysis of solvation dynamics in a simple liquid mixture.

The time-dependent energy distribution of solvation dynamics is studied by molecular dynamics simulations of a Lennard-Jones mixture. We calculate the response functions of the average and the variance which correspond to the spectral peak shift and bandwidth. Our calculation shows that the variance relaxation is slower than that of the average. The result agrees qualitatively with the experimental results. Dividing the obtained response functions into subcomponents caused by each solvent, we find that the relaxation is dominated by that solvent which strongly interacts with the solute. Extracting the redistribution component from the response functions, we find that it causes the slower relaxation of the response function. Thus, we conclude that the difference of the slower relaxations between the average and variance is caused by the redistribution process.

Cooling rate dependence of specific heat in systems out of equilibrium.

The anomaly of specific heat in systems out of equilibrium, especially the measurement procedure dependence of specific heat, is investigated by means of free energy landscape. Introducing measurement procedure which is based on experimental method, we propose a calculation method of specific heat in systems out of equilibrium and find an abrupt change in specific heat between annealed and quenched states. For longer observation time the change in specific heat occurs at lower temperature and becomes sharper. For slower cooling of a system the transition temperature becomes lower. This cooling rate dependence of the transition temperature is consistent with experiments and thus the abrupt change in specific heat can be regarded as the glass transition which is thermally identified.

Specific heat in nonequilibrium systems.

We propose a general framework of calculating the specific heat of the system in nonequilibrium, where the dynamics of the representative point can be separated into fast motion in a basin of energy landscape and the slow stochastic jump motion among basins. We apply this framework to gaseous hydrogen and obtain the observation time (t(obs)) dependence of the specific heat. We find that the specific heat gives the quenched and the annealed one in the limit of t(obs)-->0 and t(obs)-->infinity, respectively. We also investigate the waiting time and the observation time dependence of the specific heat and show that, for shorter waiting time, the observation time must be longer to obtain the same degree of annealing. This tendency is consistent with the observation that the glass transition temperature is higher for faster quenching.

Automatic epitope recognition in proteins oriented to the system for macromolecular interaction assessment MIAX.

In the present work we evaluate the performance of an algorithm for the automatic recognition of binding sites in proteins as well as in other macromolecules whose interactions are involved in many cellular and physiological processes. The algorithm is a combination of an unsupervised learning algorithm - based on Kohonen self organizing maps - to characterize the properties of patches of protein solvent accessible surfaces and a filtering algorithm to establish both the physical boundaries of the patches as well as the level of contribution of different and distant atoms involved in the interaction. We have found that the algorithm performs extremely well in a set of randomly selected protein complexes for which the interaction interfaces are extracted and compared with the results of the algorithm. A statistical evaluation of the algorithm is additionally performed by analysis of the degree of hydrophobicity and hydrophilicity of the output patches and comparison with that of the observed interface constituent amino acids.

MIAX: a system for assessment of macromolecular interaction. 3) A parallel hybrid GA for flexible protein docking.

We propose a parallel hybrid genetic algorithm for flexible protein-protein docking in order to improve the conventional rigid-body models to manipulate protein-protein interactions. The proposed hybrid algorithm is a combination of an evolutionary algorithm with a simulated annealing one, yielding a powerful protein-complex conformation-searching engine. Parallelization of the procedure makes possible to reach high algorithm performance, in both, execution times and size of treated monomers and complexes. Knowledge on side chain flexibility is extracted by means of an exhaustive analysis of crystallographic data on proteins and protein complexes. Results demonstrate the competency of the algorithm since comparison of calculated and crystallographic data accounts for a maximum of 2.5A in RMS difference, including side chain conformation. The system allows routine analysis of this fundamental molecular biology problem important to elucidate bio-macromolecular function in biophysical and biochemical mechanisms involving molecular recognition and interaction, yielding simultaneously clues for designing new proteins and enzymes directed to different purposes.

Nonlinear Langevin equations and the time dependent density functional method.

To study the time dependent density functional method (TDDFM), two streaming velocity (reversible) terms are reformulated in the nonlinear Langevin equation. Mori's [Prog. Theor. Phys. 33, 423 (1965)] projection operator method shows a variety of nonlinear Langevin equations. This is because the equations depend on the choice of phase space functions employed in the projection. If phase space functions include particular functions, however, the streaming velocity term has an invariable form. The form is independent of the choice of other phase space functions. Since the invariable streaming velocity term does not introduce the TDDFM, the second viewpoint is presented. In this, the linearization of the streaming velocity term agrees with the frequency term in the linear Langevin equation. Since only the second streaming velocity term introduces the TDDFM, one needs to be cautious in the derivation of the TDDFM.

MIAX: A Novel System for Assessment of Macromolecular Interaction in Condensed Phases. 1) Description of the Interaction Model and Simulation Algorithm.

We describe a novel computer system directed to evaluate protein complex formation in a liquid environment. The relevant feature of the system is a potential function expressing the main thermodynamic and kinetic factors leading to protein interaction in solution. The protein interaction model expresses the interaction energy as basically composed of three forces: electrostatic (hydrogen bond), van der Waals, and hydrophobic. The latter is defined in function of the forces that the solvent molecules exert on the surface of the complex, and the van der Waals forces between the monomers and the solvent. The interaction model implemented in the system has proven a high discrimination ability between different protein dockings, scoring high those close to the observed crystal structures. These results have led to the establishment of the basic principles underlying protein interaction, which constitutes the main way of expression of the biological function of these macromolecules.