Structure-based method for analyzing protein-protein interfaces.

Hydrogen bond, hydrophobic and vdW interactions are the three major non-covalent interactions at protein-protein interfaces. We have developed a method that uses only these properties to describe interactions between proteins, which can qualitatively estimate the individual contribution of each interfacial residue to the binding and gives the results in a graphic display way. This method has been applied to analyze alanine mutation data at protein-protein interfaces.

Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase.

The 3C-like proteinase of severe acute respiratory syndrome (SARS) coronavirus has been proposed to be a key target for structural-based drug design against SARS. In order to understand the active form and the substrate specificity of the enzyme, we have cloned, expressed, and purified SARS 3C-like proteinase. Analytic gel filtration shows a mixture of monomer and dimer at a protein concentration of 4 mg/ml and mostly monomer at 0.

[Modeling of the SARS coronavirus main proteinase and conformational flexibility of the active site].

SARS coronavirus 3CL proteinase is the key enzyme for virus replication which may serve as the target for drug discovery against SARS. A 3D structure model has been built for SARS coronavirus 3CL proteinase by comparative protein modeling. A homodimer model of the proteinase was also built.

On the mechanism of chaperone activity of the small heat-shock protein of Methanococcus jannaschii.

The small heat-shock protein (sHSP) from Methanococcus jannaschii (Mj HSP16.5) forms a homomeric complex of 24 subunits and has an overall structure of a multiwindowed hollow sphere with an external diameter of approximately 120 A and an internal diameter of approximately 65 A with six square "windows" of approximately 17 A across and eight triangular windows of approximately 30 A across. This sHSP has been known to protect other proteins from thermal denaturation.

Direct observations of the cleavage reaction of an L-DPPC monolayer catalyzed by phospholipase A2 and inhibited by an indole inhibitor at the air/water interface.

The enzymatic hydrolysis of an L-dipalmitoylphosphatidylcholine (L-DPPC) monolayer at the air/water interface, catalyzed by phospholipase A(2) (PLA(2)), serves as a model for biospecific interfacial reactions. The cleavage of L-DPPC was investigated by Brewster angle microscopy. Different types of domain defects were observed to form in the coexisting liquid expanded and liquid condensed phases during the hydrolysis reaction.

Thermodynamic characterization of the folding coupled DNA binding by the monomeric transcription activator GCN4 peptide.

Dimerization is a widely believed critical requirement for the yeast transcriptional activator GCN4 specifically recognizing its DNA target sites. Nonetheless, the binding of the monomeric GCN4 to DNA target sites AP-1 and ATF/CREB was recently detected by kinetic studies. Here, for the first time, we present a detailed description of the thermodynamics of a monomeric peptide GCN4-br, the basic region (226-252) of GCN4, binding to AP-1, and ATF/CREB.

Metal ion binding and enzymatic mechanism of Methanococcus jannaschii RNase HII.

RNase H degrades the RNA moiety in DNA:RNA hybrid in a divalent metal ion dependent manner. It is essential to understand the role of metal ion in enzymatic mechanism. One of the key points in this study is how many metal ions are involved in the enzyme catalysis.

Beyond the rotamer library: genetic algorithm combined with the disturbing mutation process for upbuilding protein side-chains.

The disturbing genetic algorithm, incorporating the disturbing mutation process into the genetic algorithm flow, has been developed to extend the searching space of side-chain conformations and to improve the quality of the rotamer library. Moreover, the growing generation amount idea, simulating the real situation of the natural evolution, is introduced to improve the searching speed. In the calculations using the pseudo energy scoring function of the root mean squared deviation, the disturbing genetic algorithm method has been shown to be highly efficient.

Monitoring the kinetics and thermodynamics of interfacial enzymatic catalysis by differential scanning calorimetry.

Using phase transition profile as an indicator of thermodynamic property and phase transition heat as the second indicator of the percentage of substrates unhydrolyzed, differential scanning calorimetry has been used to observe in detail the kinetics and thermodynamics of phospholipase A(2)-catalyzed 1,2-dipalmitoyl-sn-glycero-3-phosphocholine large unilamellar vesicle (LUV) hydrolysis. Phase transition profiles show that the original LUV almost completely changes into a novel aggregate at the end of the latency, followed by an abrupt activation of the reaction. The phase transition profiles are asymmetric between the heating and cooling curves, indicating a thermodynamic mesostatic property of the system.

Further development and validation of empirical scoring functions for structure-based binding affinity prediction.

New empirical scoring functions have been developed to estimate the binding affinity of a given protein-ligand complex with known three-dimensional structure. These scoring functions include terms accounting for van der Waals interaction, hydrogen bonding, deformation penalty, and hydrophobic effect. A special feature is that three different algorithms have been implemented to calculate the hydrophobic effect term, which results in three parallel scoring functions.

CH...O hydrogen bonds at protein-protein interfaces.

For the first time, a statistical potential has been developed to quantitatively describe the CH.O hydrogen bonding interaction at the protein-protein interface. The calculated energies of the CH.

Synthesis, fungicidal activity, and 3D-QSAR of pyridazinone-substituted 1,3,4-oxadiazoles and 1,3,4-thiadiazoles.

A series of novel 5-[1-aryl-1,4-dihydro-6-methylpyridazin-4-one-3-yl] -2-arylamino-1,3,4-oxadiazoles, fungicidally active, were synthesized based on bioisosterism and tested in vivo against wheat leaf rust, Puccinia recondita. These compounds were shown to be fungicidally active, and their activity was influenced by the nature of the substituents. By using the three-dimensional quantitative structure-activity relationships (3D-QSAR) method of comparative molecular field analysis (CoMFA), we have studied the structure and activity relationship of the compounds containing both pyridazinone-substituted 1,3,4-thiadiazoles and pyridazinone-substituted 1,3,4-oxadiazoles.

Linear correlation between thermal stability and folding kinetics of lysozyme.

We have studied the refolding and thermal denaturation of hen egg white lysozyme in a wide range of pH values (from 1.5 to 9.4) using stopped-flow circular dichroism (CD) and differential scanning calorimetry (DSC).

Potential of mean force for protein-protein interaction studies.

Calculating protein-protein interaction energies is crucial for understanding protein-protein associations. On the basis of the methodology of mean-field potential, we have developed an empirical approach to estimate binding free energy for protein-protein interactions. This knowledge-based approach has been used to derive distance-dependent free energies of protein complexes from a nonredundant training set in the Protein Data Bank (PDB), with a careful treatment of homology.