Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function

Unexpected alkyl isomerization at the silicon ligand of an unsaturated Rh complex: combined experiment and theory

The formation of dimer [(μ-Cl)Rh-(κ3(P,Si,Si)PhP(o-C6H4CH2SiiPr2)(o-C6H4CH2SiiPrnPr))]2 (Rh-3) with an n-propyl group on one of the silicon atoms as a minor product was affected by the reaction of [RhCl(COD)]2 with proligand PhP(o-C6H4CH2SiHiPr2)2, L1. The major product of the reaction was monomeric 14-electron Rh(III) complex [ClRh(κ3(P,Si,Si)PhP(o-C6H4CH2SiiPr2)2)] (Rh-1). Computations revealed that the monomer-dimer equilibrium is shifted toward the monomer with four isopropyl substituents on the two Si atoms of the ligand as in Rh-1; conversely, the dimer is favored with only one n-propyl as in Rh-3, and with less bulky alkyl substituents such as in [ClRh(κ3(P,Si,Si)PhP(o-C6H4CH2SiMe2)2]2 (Rh-2). Computations on the mechanism of formation of Rh-3 directly from [RhCl(COD)]2 are in agreement with the experimental findings and it is found to be less energetic than if stemming from Rh-1. Additionally, a Si-O-Si complex, [μ-Cl-Rh{κ3(P,Si,C)PPh(o-C6H4CH2SiiPrO SiiPr2CH-o-C6H4)}]2, Rh-4, is generated from the reaction of Rh-1 with adventitious water as a result of intramolecular C-H activation.

Genome-Wide Analysis of the Peptidase M24 Superfamily in Triticum aestivum Demonstrates That TaM24-9 Is Involved in Abiotic Stress Response

The peptidase M24 (Metallopeptidase 24, M24) superfamily is essential for plant growth, stress response, and pathogen defense. At present, there are few systematic reports on the identification and classification of members of the peptidase M24 proteins superfamily in wheat. In this work, we identified 53 putative candidate TaM24 genes. According to the protein sequences characteristics, these members can be roughly divided into three subfamilies: I, II, III. Most TaM24 genes are complex with multiple exons, and the motifs are relatively conserved in each sub-group. Through chromosome mapping analysis, we found that the 53 genes were unevenly distributed on 19 wheat chromosomes (except 3A and 3D), of which 68% were in triads. Analysis of gene duplication events showed that 62% of TaM24 genes in wheat came from fragment duplication events, and there were no tandem duplication events to amplify genes. Analysis of the promoter sequences of TaM24 genes revealed that cis-acting elements were rich in response elements to drought, osmotic stress, ABA, and MeJA. We also studied the expression of TaM24 in wheat tissues at developmental stages and abiotic stress. Then we selected TaM24-9 as the target for further analysis. The results showed that TaM24-9 genes strengthened the drought and salt tolerance of plants. Overall, our analysis showed that members of the peptidase M24 genes may participate in the abiotic stress response and provided potential gene resources for improving wheat resistance.

Two-domain aminopeptidase of M1 family: Structural features for substrate binding and gating in absence of C-terminal domain

Zinc metallopeptidases of the M1 family (M1 peptidases) with unique metal binding motif HEXXH(X)₁₈E regulate many important biological processes such as tumor growth, angiogenesis, hormone regulation, and immune cell development. Typically, these enzymes exist in three-domain [N-terminal domain (N-domain), catalytic domain, and C-terminal domain (C-domain)] or four-domain (N-domain, catalytic domain, middle domain, and C-domain) format in which N-domain and catalytic domain are more conserved. The C-domain plays important roles in substrate binding and gating. In this study we report the first structure of a two-domain (N-domain and catalytic domain) M1 peptidase at 2.05 Å resolution. Despite the lack of C-domain, the enzyme is active and prefers peptide substrates with large hydrophobic N-terminal residues. Its substrate-bound structure was determined at 1.9 Å resolution. Structural analyses supported by site directed mutagenesis and molecular dynamics simulations reveal structural features that could compensate for the lack of C-domain. A unique loop insertion (loop A) in the N-domain has important roles in gating and desolvation of active site. Three Arg residues of the catalytic domain are involved in substrate-binding roles typically played by positively charged residues of C-domain in other M1 peptidases. Further, its unique exopeptidase sequence motif, LALET, creates a more hydrophobic environment at the S1 subsite (which binds N-terminal residue of the substrate in aminopeptidases) than the more common GXMEN motif in the family. This leads to high affinity for large hydrophobic residues in the S1 subsite, which contributes towards efficient substrate binding in absence of C-domain.