Thermodynamics and molecular simulation analysis of hydrophobic substrate recognition by aminotransferases

Rational Protein Engineering Guided by Deep Mutational Scanning

Sequence-function relationship in a protein is commonly determined by the three-dimensional protein structure followed by various biochemical experiments. However, with the explosive increase in the number of genome sequences, facilitated by recent advances in sequencing technology, the gap between protein sequences available and three-dimensional structures is rapidly widening. A recently developed method termed deep mutational scanning explores the functional phenotype of thousands of mutants via massive sequencing. Coupled with a highly efficient screening system, this approach assesses the phenotypic changes made by the substitution of each amino acid sequence that constitutes a protein. Such an informational resource provides the functional role of each amino acid sequence, thereby providing sufficient rationale for selecting target residues for protein engineering. Here, we discuss the current applications of deep mutational scanning and consider experimental design.

Molecular Determinants for the Interaction of the Valvulopathic Anorexigen Norfenfluramine with the 5-HT2B Receptor

S-(+)-Norfenfluramine (SNF)-an active metabolite of the now-banned anorexigen fenfluramine-has been implicated in the drug's appetite-suppressing actions and its life-threatening cardiovascular side effects. SNF reduces appetite through serotonin 5-HT(2C) receptor activation; it causes cardiopulmonary side effects through 5-HT(2B) receptor activation. Thus, we attempted to identify molecular determinants of SNF binding to 5-HT(2B) receptors distinct from those underlying SNF-5-HT(2C/2A) receptor interactions. Mutagenesis implicated Val2.53 in SNF binding to 5-HT(2B) receptors. Ligand docking simulations suggested both Val2.53 gamma-methyl groups form stabilizing van der Waals' (vdW) interactions with the alpha-methyl group of SNF. A V2.53L mutation induced a 17-fold decrease in affinity; molecular dynamics (MD) simulations suggested that this decrease resulted from the loss of one 2.53-alpha-methyl group vdW interaction. Supporting this, 1) the binding of norfenfluramine (NF) analogs lacking an S-(+) alpha-methyl group (RNF and alpha-desmethyl-NF) was less sensitive to the V2.53L mutation, and 2) a V2.53A mutation decreased SNF affinity 190-fold, but decreased RNF and alpha-desmethyl-NF affinities only 16- and 45-fold, respectively. We next addressed whether the alpha-methyl group of SNF contributes to 5-HT(2C/2A) receptor affinity. Removal of the alpha-methyl group (RNF and alpha-desmethyl-NF), which reduced 5-HT(2B) receptor binding 3-fold, did not affect 5-HT(2C/2A) receptor binding. An alpha-ethyl substituent (alpha-ethyl-NF), which decreased 5-HT(2B) receptor affinity 46-fold, reduced 5-HT(2C) and 5-HT(2A) receptor binding by 14- and 5-fold, respectively. Finally, we determined that residue 2.53 affects SNF potency and efficacy at 5-HT(2B) receptors but not at 5-HT(2C) and 5-HT(2A) receptors. In conclusion, vdW interactions between residue 2.53 and the alpha-methyl group of SNF contribute to the ligand's 5-HT(2) receptor subtype-selective pharmacology.

Analyses of microbial desulfurization reaction of alkylated dibenzothiophenes dissolved in oil phase

The kinetics of the oil/water two-phase reaction system was analyzed, and the reaction was carried out with the desulfurization of alkylated dibenzothiophenes (Cx-DBTs) using the desulfurizing microorganism Mycobacterium sp. G3. In the water-phase reaction system, the desulfurization activities were constant with respect to species of Cx-DBTs as substrates. However, the desulfurization activities in the oil/water two-phase reaction system against DBT, 4,6-dimethyl DBT, 4,6-diethyl DBT, 4,6-dipropyl DBT, and 4,6-dibutyl DBT were 49.0, 45.9, 11.5, 1.35, and 0.00 micromol g DCW(-1) h(-1), respectively. The kinetic parameters for the degradation of DBT, 4,6-dimethyl DBT, and 4,6-diethyl DBT were also obtained (V(max) values 90.0, 68.7, and 22.7 micromol g DCW(-1) h(-1) and K(m) values 0.21, 0.70, and 3.03 mM, respectively). The reason for the decrease in activity against Cx-DBTs of high molecular weight was a decrease in the V(max) value and an increase in the K(m) value, the latter being a particularly serious problem. Furthermore, the hydrophobicity of the substrate was evaluated as the capacity factor measured by high-performance liquid chromatography (HPLC). The correlation between substrate hydrophobicity and desulfurization activity indicated that the desulfurization reaction in the oil/water two-phase reaction system is greatly influenced by the hydrophobicity of the substrates. In addition, the influence of the solvent on desulfurization activity was examined, and it was found that not only the hydrophobicity of substrates, but also that of solvents, affected the desulfurization reaction.

Free energy requirement for domain movement of an enzyme

Domain movement is sometimes essential for substrate recognition by an enzyme. X-ray crystallography of aminotransferase with a series of aliphatic substrates showed that the domain movement of aspartate aminotransferase was changed dramatically from an open to a closed form by the addition of only one CH(2) to the side chain of the C4 substrate CH(3)(CH(2))C((alpha))H(NH(3)(+))COO(-). These crystallographic results and reaction kinetics (Kawaguchi, S., Nobe, Y., Yasuoka, J., Wakamiya, T., Kusumoto, S., and Kuramitsu, S. (1997) J. Biochem. (Tokyo) 122, 55-63; Kawaguchi, S. and Kuramitsu, S. (1998) J. Biol. Chem. 273, 18353-18364) enabled us to estimate the free energy required for the domain movement.

Thermodynamics of Fab-ssDNA interactions: contribution of heavy chain complementarity determining region 3

The recombinant anti-ssDNA Fab, DNA-1, and 16 heavy chain complementarity determining region 3 (HCDR3) mutant variants were selected for thermodynamic characterization of ssDNA binding. The affinity of Fab to (dT)(15) under different temperatures and cation concentrations was measured by equilibrium fluorescence quenching titration. Changes in the standard Gibbs free binding energy (DeltaG degrees ), enthalpy (DeltaH degrees ), entropy (DeltaS degrees ), and the number of ionic pairs (Z) formed upon interaction were determined. All Fab possessed an enthalpic nature of interaction with ssDNA, that was opposite to the previously reported entropically driven binding to dsDNA [Tanha, J., and Lee, J. S. (1997) Nucleic Acids Res. 25, 1442-1449]. The contribution of separate residues of HCDR3 to ssDNA interaction was investigated. Analysis of the changes in DeltaH degrees and TDeltaS degrees, induced by substitutions in HCDR3, revealed a complete entropy/enthalpy compensation. Mutations R98A and D108A at the ends of the HCDR3 loop produced increases in TDeltaS degrees ( )()by 10.4 and 15.9 kcal/mol, respectively. Substitution of proline for arginine at the top of HCDR3 resulted in a new electrostatic contact with (dT)(15). The observed linear correlation of Z and DeltaG degrees ( )()of nonelectrostatic interactions (DeltaG degrees (nonel)) at the anti-ssDNA combining site was used for the estimation of the specific DeltaG degrees (nonel) [-20 to -25 cal/(mol.A(2))], the average contact area (450-550 A(2)), the maximal Z (6-7), and the limit in affinity under standard cation concentrations [(0.5-1) x 10(8) M(-)(1)] for this family of Fab. Results suggested that rational engineering of HCDR3 could be utilized to control the affinity and likely the specificity of Ab-DNA interactions.