Candida parapsilosis carbonyl reductases (CpRCR) have been widely used for the reductive conversion of ketone precursors and chiral alcohol products in pharmaceutical industries. The enzymatic enantioselectivity is believed to be related to the shape complementation between the cavities in the enzymes and the substitutions of the ketone substrates. In this work, we reported an unexpected enantioselectivity in the enzyme reductions of dihydrofuran-3(2H)-one (DHF) to (S)-tetrahydrofuran-3-ol (DHF-ol, enantiomeric excess: 96.4%), while dihydrothiophen-3(2H)-one substrate (DHT) was unproductive under the same experimental conditions. To rationalize the exclusive S-configuration and the specific reactivity of DHF, we carried out molecular dynamics simulations for the reacting complexations of DHF with CpRCR, and DHT with CpRCR. Our calculations indicate that DHF preferentially binds to the small cavity near L119, F285, and W286, while the large cavity near the α1 helix was mainly occupied by solvent water molecules. Moreover, the pre-reaction state analysis suggests that the pro-S conformations were more abundant than the pro-R, in particular for DHF. This suggests that the non-polar interaction of substrate C4-C5 methylene contacting the hydrophobic side-chains of L119-F285-W286, and the polar interaction of funanyl oxygen exposing the solvent environment play important roles in the enantioselectivity and reactivity. The phylogenetic tree of CpRCR homologues implies that a variety of amino acid combinations at positions 285 and 286 were available and thereby potentially useful for redesigning enantioselective reductions of 5-membered-ring heterocyclic ketones.
Complex networks have been extensively studied across many fields, especially in interdisciplinary areas. It has since long been recognized that topological structures and dynamics are important aspects for capturing the essence of complex networks. The recent years have also witnessed the emergence of several new elements which play important roles in network study. By combining the results of different research orientations in our group, we provide here a review of the recent advances in regards to spectral graph theory, opinion dynamics, interdependent networks, graph energy theory and temporal networks. We hope this will be helpful for the newcomers of those fields to discover new intriguing topics.
A new mechanism, the forget-remember mechanism, is proposed for studying the spreading process in 2-state model. Such mechanism exhibits behaviors of message spreading influenced by some kinds of functions about time and history caring about the individuals of the spreading system, holding message or being out of message. To demonstrate the mechanism, both linear and exponential forms for forget-function and remember-function are simulated and show that a great impact on the saturation of message-spreading and the relative phase transformation.
This paper presents a comprehensive cryptoanalysis of a multiple-image encryption scheme based on amplitude truncation (AT) and phase truncation (PT) in the Fourier domain. In contrast to the conventional single-image cryptosystem based on phase-truncated Fourier transform (PTFT), the enhanced PTFT-based cryptosystem was proposed to encode multiple images efficiently and to augment the security strength by expanding the key space. Nevertheless, we found that the amplitude key exhibits low sensitivity, which has a restricted impact on the security enhancement and makes the scheme vulnerable. Moreover, the two random phase masks (RPMs) employed as private keys are uncorrelated with the plaintexts, which can be recovered through a devised known-plaintext attack (KPA). Once these additional private keys are recovered, the number of unknown keys is reduced to two, making it possible to recover plaintext information encrypted by this advanced PTFT-based cryptosystem using an iterative attack without any knowledge of the private keys. Based on these findings, a hybrid attack consisting of two cascaded KPAs and chosen-ciphertext attacks (CCAs) is proposed to successfully crack the improved PTFT-based cryptosystem. Numerical simulations have been performed to validate the feasibility and effectiveness of the proposed hybrid attack.
Abstract Short‐chain dehydrogenases (SDRs) are powerful catalysts for the asymmetric reduction of prochiral ketones in pharmaceutical products. Herein, through gene mining and evolutionary analysis, we obtained two major types of SDRs (SDR‐1 and SDR‐2) for the enantioselective complementary reduction of N‐Boc‐piperidone, which gives the corresponding product ( R )‐ or ( S)‐ N‐Boc‐piperidol, an intermediate of the interleukin inhibitor and lymphoma treatment drug (imbruvica), respectively. By integrating multiple sequence alignment, site‐directed mutagenesis and computational modeling, we proposed a “loop regulation” mechanism for the enantioselective control of SDRs, through which residues in the loop region could potentially fine‐tune their enantioselectivity. Further, site‐directed mutagenesis assays showed that two key residues (L201 and F205 for SDR‐1, F92 and H93 for SDR‐2) in the loop and its adjacent region played critical roles in fine‐tuning the enantioselectivity of SDRs. Understanding this mechanism of SDR stereo preference in catalyzing asymmetric reduction, we further switched the enantioselectivity of the homologous enzymes. The obtained enzymes catalyzed the enantiodivergent synthesis of chiral heterocyclic alcohols with different ring sizes and substituents (25–99% conversion and 25–99% ee ( R/S )), including piperidols, 4‐hydroxy azepanes, 3‐hydroxy azepanes and pyrrolidinols. These findings could potentially guide future attempts at protein engineering of stereoselective SDRs.
Perturbations in protein structure define the mechanism of allosteric regulation and biological information transfer. In cytochrome c (cyt c), ligation of Met80 to the heme iron is critical for the protein's electron-transfer (ET) function in oxidative phosphorylation and for suppressing its peroxidase activity in apoptosis. The hard base Lys is a better match for the hard ferric iron than the soft base Met is, suggesting the key role of the protein scaffold in favoring Met ligation. To probe the role of the protein structure in the maintenance of Met ligation, mutations T49V and Y67R/M80A were designed to disrupt hydrogen bonding and packing of the heme coordination loop, respectively. Electronic absorption, nuclear magnetic resonance, and electron paramagnetic resonance spectra reveal that ferric forms of both variants are Lys-ligated at neutral pH. A minor change in the tertiary contacts in T49V, away from the heme coordination loop, appears to be sufficient to execute a change in ligation, suggesting a cross-talk between the different regions of the protein structure and a possibility of built-in conformational switches in cyt c. Analyses of thermodynamic stability, kinetics of Lys binding and dissociation, and the pH-dependent changes in ligation provide a detailed characterization of the Lys coordination in these variants and relate these properties to the extent of structural perturbations. The findings emphasize the importance of the hydrogen-bonding network in controlling ligation of the native Met80 to the heme iron.
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