Enantioselective Ethylation of Various Aldehydes Catalyzed by Readily Accessible Chiral Diols

Four chiral C₂‐symmetric diols were synthesized in a straightforward three‐step reaction and demonstrated excellent enantioselectivities and good overall yields. Their catalytic activities were examined via the addition of diethylzinc to various aldehydes. The enantioselective addition of diethylzinc to 2‐methoxybenzaldehyde gave the corresponding chiral secondary alcohol with high yields (up to 95%) and moderate to good enantiomeric excess (up to 88%). All synthesized ligands were evaluated in the addition of diethylzinc to various aldehydes in the presence of an additional metal such as Ti(IV) complexes. Chirality 28:593–598, 2016. © 2016 Wiley Periodicals, Inc.     

Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis

Pol η belongs to the important Y family of DNA polymerases that can catalyze translesion synthesis across sites of damaged DNA. This activity involves the reduced fidelity of Pol η for 8‐oxo‐7,8‐dhyedro‐2′‐deoxoguanosin(8‐oxoG). The fundamental interest in Pol η has grown recently with the demonstration of the importance of a 3rd Mg2+ ion. The current work explores both the fidelity of Pol η and the role of the 3rd metal ion, by using empirical valence bond (EVB) simulations. The simulations reproduce the observed trend in fidelity and shed a new light on the role of the 3rd metal ion. It is found that this ion does not lead to a major catalytic effect, but most probably plays an important role in reducing the product release barrier. Furthermore, it is concluded, in contrast to some implications, that the effect of this metal does not violate transition state theory, and the evaluation of the catalytic effect must conserve the molecular composition upon moving from the reactant to the transition state. Proteins 2017; 85:1446–1453. © 2017 Wiley Periodicals, Inc.     

A Nonadiabatic Theory for Ultrafast Catalytic Electron Transfer: A Model for the Photosynthetic Reaction Center

A non-adiabatic theory of Electron Transfer (ET), which improves the standard theory near the inversion point and becomes equivalent to it far from the inversion point, is presented. The complex amplitudes of the electronic wavefunctions at different sites are used as Kramers variables for describing the quantum tunneling of the electron in the deformable potential generated by its environment (nonadiabaticity) which is modeled as a harmonic classical thermal bath. After exact elimination of the bath, the effective electron dynamics is described by a discrete nonlinear Schrödinger equation with norm preserving dissipative terms and a Langevin random force, with a frequency cut-off, due to the thermalized phonons. This theory reveals the existence of a specially interesting marginal case when the linear and nonlinear coefficients of a two electronic states system are appropriately tuned for forming a Coherent Electron-Phonon Oscillator (CEPO). An electron injected on one of the electronic states of a CEPO generates large amplitude charge oscillations (even at zero temperature) associated with coherent phonon oscillations and electronic level oscillations. This fluctuating electronic level may resonate with a third site which captures the electron so that Ultrafast Electron Transfer (UFET) becomes possible. Numerical results are shown where two weakly interacting sites, a donor and a catalyst, form a CEPO that triggers an UFET to an acceptor. Without a catalytic site, a very large energy barrier prevents any direct ET. This UFET is shown to have many qualitative features similar to those observed in the primary charge separation in photosynthetic reaction centers. We suggest that more generally, CEPO could be a paradigm for understanding many selective chemical reactions involving electron transfer in biosystems.     

A glimpse into the active site of a group II intron and maybe the spliceosome, too

The X-ray crystal structure of an excised group II self-splicing intron was recently solved by the Pyle group. Here we review some of the notable features of this structure and what they may tell us about the catalytic active site of the group II ribozyme and potentially the spliceosome. The new structure validates the central role of domain V in both the structure and catalytic function of the ribozyme and resolves several outstanding puzzles raised by previous biochemical, genetic and structural studies. While lacking both exons as well as the cleavage sites and nucleophiles, the structure reveals how a network of tertiary interactions can position two divalent metal ions in a configuration that is ideal for catalysis.     

Structural basis for executioner caspase recognition of P5 position in substrates

Caspase-3, -6 and -7 cleave many proteins at specific sites to induce apoptosis. Their recognition of the P5 position in substrates has been investigated by kinetics, modeling and crystallography. Caspase-3 and -6 recognize P5 in pentapeptides as shown by enzyme activity data and interactions observed in the crystal structure of caspase-3/LDESD and in a model for caspase-6. In caspase-3 the P5 main-chain was anchored by interactions with Ser209 in loop-3 and the P5 Leu side-chain interacted with Phe250 and Phe252 in loop-4 consistent with 50% increased hydrolysis of LDEVD relative to DEVD. Caspase-6 formed similar interactions and showed a preference for polar P5 in QDEVD likely due to interactions with polar Lys265 and hydrophobic Phe263 in loop-4. Caspase-7 exhibited no preference for P5 residue in agreement with the absence of P5 interactions in the caspase-7/LDESD crystal structure. Initiator caspase-8, with Pro in the P5-anchoring position and no loop-4, had only 20% activity on tested pentapeptides relative to DEVD. Therefore, caspases-3 and -6 bind P5 using critical loop-3 anchoring Ser/Thr and loop-4 side-chain interactions, while caspase-7 and -8 lack P5-binding residues.     

A mild, efficient, and selective procedure for transprotection of acetonides to acetates catalyzed with HClO4-SiO2

The transformation of acetonides into acetates is frequently required in synthetic chemistry. An efficient procedure for direct conversion of acetonides into acetates in the presence of HClO₄-SiO₂ under mild conditions was developed. The acetonides of primary hydroxy groups are directly converted to diacetates, and the anomeric acetonides of furanosides are stereoselectively transformed into the corresponding acetyl β-d-furanosides with a 2-acetoxyisopropyl group.     

Enantioselective addition of phenylacetylene to N-aryl arylimines catalyzed by Cu(II)-pyridine containing N-tosylatedaminoimine ligand complex

Chiral tridentate N-tosylated pyridine-containing ligands were prepared and used in the Cu(II)-catalyzed enantioselective addition of phenylacetylene to N-aryl arylimines. Moderate to high enantioselectivities (up to 95% ee) were obtained in very mild reaction conditions.     

Formation of an active site in trans by interaction of two complete Varkud Satellite ribozymes

The complete VS ribozyme comprises seven helical segments, connected by three three-way RNA junctions. In the presence of Mg²⁺ ions, cleavage occurs within the internal loop of helix I. This requires the participation of a guanine (G638) within the helix I loop, and a remote adenine (A756) within an internal loop of helix VI. Previous structural studies have suggested that helix I docks into the fold of the remaining part of the ribozyme, bringing A756 and G638 close to the scissile phosphate to allow the cleavage reaction to proceed. We show here that while either A756C or G638A individually exhibit very low cleavage activity, a mixture of the two variants leads to cleavage of the A756C RNA, but not the G638A RNA. The rate of cleavage depends on the concentration of the VS G638A RNA, as expected for a bimolecular interaction. This regaining of cleavage activity by complementation indicates that helix I of one VS RNA can interact with another VS RNA molecule to generate a functional active site in trans.     

Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling

Caspase-3 recognition of various P4 residues in its numerous protein substrates was investigated by crystallography, kinetics, and calculations on model complexes. Asp is the most frequent P4 residue in peptide substrates, although a wide variety of P4 residues are found in the cellular proteins cleaved by caspase-3. The binding of peptidic inhibitors with hydrophobic P4 residues, or no P4 residue, is illustrated by crystal structures of caspase-3 complexes with Ac-IEPD-Cho, Ac-WEHD-Cho, Ac-YVAD-Cho, and Boc-D(OMe)-Fmk at resolutions of 1.9–2.6 Å. The P4 residues formed favorable hydrophobic interactions in two separate hydrophobic regions of the binding site. The side chains of P4 Ile and Tyr form hydrophobic interactions with caspase-3 residues Trp206 and Trp214 within a non-polar pocket of the S4 subsite, while P4 Trp interacts with Phe250 and Phe252 that can also form the S5 subsite. These interactions of hydrophobic P4 residues are distinct from those for polar P4 Asp, which indicates the adaptability of caspase-3 for binding diverse P4 residues. The predicted trends in peptide binding from molecular models had high correlation with experimental values for peptide inhibitors. Analysis of structural models for the binding of 20 different amino acids at P4 in the aldehyde peptide Ac-XEVD-Cho suggested that the majority of hydrophilic P4 residues interact with Phe250, while hydrophobic residues interact with Trp206, Phe250, and Trp214. Overall, the S4 pocket of caspase-3 exhibits flexible adaptation for different residues and the new structures and models, especially for hydrophobic P4 residues, will be helpful for the design of caspase-3 based drugs.     

Organic solvent tolerance of an alkaline protease from salt-tolerant alkaliphilic <Emphasis Type="Italic">Streptomyces clavuligerus</Emphasis> strain Mit-1

A salt-tolerant alkaliphilic actinomycete, Mit-1 was isolated from Mithapur, coastal region of Gujarat, India. The strain was identified as Streptomyces clavuligerus and based on 16S rRNA gene sequence (EU146061) homology; it was related to Streptomyces sp. (AY641538.1). The organism could grow with up to 15% salt and pH 11, optimally at 5% and pH 9. It was able to tolerate and secrete alkaline protease in the presence of a number of organic solvents including xylene, ethanol, acetone, butanol, benzene and chloroform. Besides, it could also utilize these solvents as the sole source of carbon with significant enzyme production. However, the organism produced spongy cell mass with all solvents and an orange brown soluble pigment was evident with benzene and xylene. Further, the enzyme secretion increased by 50-fold in the presence of butanol. With acetone and ethanol; the enzyme was highly active at 60–80°C and displayed optimum activity at 70°C. The protease was significantly stable and catalyzed the reaction in the presence of xylene, acetone and butanol. However, ethanol and benzene affected the catalysis of the enzyme adversely. Crude enzyme preparation was more stable at 37°C in solvents as compared to partially purified and purified enzymes. The study holds significance as only few salt-tolerant alkaliphilic actinomycetes are explored and information on their enzymatic potential is still scares. To the best of our knowledge this is the first report on organic solvent tolerant protease from salt-tolerant alkaliphilic actinomycetes.