Haruo Abe

Conformational change of a globular protein elucidated at atomic resolution: Theoretical and nuclear magnetic resonance study*

A powerful method of conformational energy minimization which uses both first and second derivatives of the energy function is applied both to a small globular protein, bovine pancreatic trypsin inhibitor (BPTI), consisting of 58 amino acid residues and to its chemical derivative obtained by carboxamidomethylation of cysteinyl residues of the 14-38 disulphide bond. Conformational fluctuations are also calculated from the second derivative matrix obtained at the respective minimum energy conformations. Appreciable conformational changes upon chemical modification are observed only in the vicinity of the site of the modification. The nuclear magnetic resonance data on both BPTI and the modified BPTI are analyzed to compare with the calculated conformational changes upon chemical modification. Good correlations are found between the theoretically predicted and experimentally deduced conformational changes. The theoretical method employed here has a general application for the calculation of small conformational changes of globular proteins upon their chemical modification or an amino acid substitution.

Application of a statistical mechanical model for protein folding to a three-dimensional lattice protein

A statistical mechanical model for protein folding is applied to the three-dimensional lattice protein using a foldable amino acid sequence. The key to the model lies in the concept of its local structure, defined as a continuous region which takes the same local conformation as in the native conformation, and in the assumption of the absence of interactions between local structures. The partition function is precisely calculated for a given native conformation without any adjustable parameters. The model can well reproduce the equilibrium thermodynamic quantities obtained from the simulation.

Single Amino Acid Substitutions in Lattice Proteins Using Statistical Mechanical Model for Protein Folding

The folding of lattice proteins with single amino acid substitutions was studied using a statistical mechanical model for protein folding. All possible single amino acid substitutions were analyzed for two different native conformations, and two amino acid sequences foldable to the given native conformation were considered for each native conformation. First, the transition temperature change Δ T m (ξ i ) with the conformational energy change Δ E (ξ i ) caused by the substitution of the amino acid residue type ξ i at the i -th residue was examined. Although both Δ E (ξ i ) and Δ T m (ξ i ) strongly depend on the amino acid sequence (as a result, these two changes for the two proteins with different amino acid sequences foldable to the same native conformation differ considerably from each other), it is indicated that the correlations between Δ E (ξ i ) and Δ T m (ξ i ) for the given residue i of the two proteins are mainly determined by their native conformations and are less dependent on their amino acid...

Characterization of protein folding by a Φ-value calculation with a statistical-mechanical model

The Φ-value analysis approach provides information about transition-state structures along the folding pathway of a protein by measuring the effects of an amino acid mutation on folding kinetics. Here we compared the theoretically calculated Φ values of 27 proteins with their experimentally observed Φ values; the theoretical values were calculated using a simple statistical-mechanical model of protein folding. The theoretically calculated Φ values reflected the corresponding experimentally observed Φ values with reasonable accuracy for many of the proteins, but not for all. The correlation between the theoretically calculated and experimentally observed Φ values strongly depends on whether the protein-folding mechanism assumed in the model holds true in real proteins. In other words, the correlation coefficient can be expected to illuminate the folding mechanisms of proteins, providing the answer to the question of which model more accurately describes protein folding: the framework model or the nucleation-condensation model. In addition, we tried to characterize protein folding with respect to various properties of each protein apart from the size and fold class, such as the free-energy profile, contact-order profile, and sensitivity to the parameters used in the Φ-value calculation. The results showed that any one of these properties alone was not enough to explain protein folding, although each one played a significant role in it. We have confirmed the importance of characterizing protein folding from various perspectives. Our findings have also highlighted that protein folding is highly variable and unique across different proteins, and this should be considered while pursuing a unified theory of protein folding.