Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.     

聚丙烯酸载体用于青霉素酰化酶的固定

以反应性单体丙烯酸和交联剂二乙烯基苯,以石油醚为致孔剂,通过悬浮聚合制备固定化酶的载体,并用于对青霉素酰化酶的固定。研究了丙烯酸与二乙烯基苯以不同摩尔比对青霉素酰化酶固定活性的影响,以及悬浮聚合时水油相比例的不同所合成的载体对固定化酶性能的影响。当丙烯酸和二乙烯基苯摩尔比为84.2:4时合成的载体固定青霉素酰化酶的酶活为2784U/g,而水油相比为2.75:1（丙烯酸和二乙烯基苯摩洋比为84.2:5）时固定青霉素酰化酶活达到2183U/g。固定青霉素酰化酶可使青霉素转化,得到半合成青霉素的中间体6-氨基青霉烷酸,由此可制成高效、广谱、服用方便的新青霉素。     

血管紧张素转化酶活性抑制剂──丝素肽的分离、纯化和结构鉴定

 可溶性丝素粉末经碱性蛋白酶Alcalase水解后 ,其酶解产物对血管紧张素转化酶 (ACE)的活性有很强的抑制作用。采用凝胶过滤色谱SephadexG 15和反相高效液相色谱 (RP HPLC)对水解度为 2 0 %的酶解产物进行分离纯化 ,利用质谱鉴定其中一种ACE抑制剂是肽 ,其结构为Gly Tyr。     

Cobalt activation of Bacillus BR449 thermostable nitrile hydratase expressed in Escherichia coli

Expression of nitrile hydratase enzymes utilized in a new “green” process for acrylamide production has proven difficult in Escherichia coli owing to lack of a cobalt transport system to introduce the required cobaltion into this host. We describe the expression of a thermostable nitrile hydratase from a moderatethermophile Bacillus sp. BR449 in E. coli in which the cobaltrequired for enzyme activation is introduced by incubation, of the apoenzyme in the presence of Co⁺⁺ ion at 50°C, yielding active and thermostable, enzyme.     

Relationship between the hydration degree of poly-N-isopropylacrylamide gel and activity of immobilized α-chymotrypsin

The influence of the pH, temperature, and dimethyl sulfoxide concentration on the hydration degree of the poly-N-isopropylacrylamide gel and the activity of -chymotrypsin immobilized into the polymer was studied. The behavior of more hydrophilic preparations based on polyacrylamide and copolymer of acrylamide and acrylic acid was studied for comparison. An increase in both the temperature and dimethyl sulfoxide content decreases the hydration of the poly-N-isopropylacrylamide, which correlates with a decrease in the activity of the immobilized enzyme. The use of substrates with different structures and an irreversible inhibitor proves that the change in the properties of -chymotrypsin immobilized into the poly-N-isopropylacrylamide gel is related to the change in the rate constants of enzymatic reactions. Comparison of all experimental data obtained suggested an opportunity of local interactions between the protein globule and polymeric chains with a change in the hydration degree of poly-N-isopropylacrylamide during its phase transition.     

New supports for enzyme immobilization based on copolymers of vinylene carbonate and acrylamide

In this study, a series of beadlike and hydrophilic supports containing reactive cyclic carbonate groups for enzyme immobilization were prepared via reverse-phase suspension copolymerization of the aqueous solutions of vinylene carbonate (VCA), acrylamide (AA), and N,N′-methylene bisacrylamide in paraffin oil. The supports were used as a matrix for immobilization of trypsin and showed a considerable capacity to couple with trypsin and reasonable retention of activity for the immobilized trypsin, depending on the immobilization conditions, such as the content of VCA structural units, reaction time, and pH of the medium.     

Terminal Hydride Species in [FeFe]‐Hydrogenases Are Vibrationally Coupled to the Active Site Environment

A combination of nuclear resonance vibrational spectroscopy (NRVS), FTIR spectroscopy, and DFT calculations was used to observe and characterize Fe?H/D bending modes in CrHydA1 [FeFe]‐hydrogenase Cys‐to‐Ser variant C169S. Mutagenesis of cysteine to serine at position 169 changes the functional group adjacent to the H‐cluster from a ‐SH to ‐OH, thus altering the proton transfer pathway. The catalytic activity of C169S is significantly reduced compared to that of native CrHydA1, presumably owing to less efficient proton transfer to the H‐cluster. This mutation enabled effective capture of a hydride/deuteride intermediate and facilitated direct detection of the Fe?H/D normal modes. We observed a significant shift to higher frequency in an Fe?H bending mode of the C169S variant, as compared to previous findings with reconstituted native and oxadithiolate (ODT)‐substituted CrHydA1. On the basis of DFT calculations, we propose that this shift is caused by the stronger interaction of the ‐OH group of C169S with the bridgehead ‐NH‐ moiety of the active site, as compared to that of the ‐SH group of C169 in the native enzyme.     

Purification of angiotensin‐converting enzyme from human plasma and investigation of the effect of some active ingredients isolated from Nigella sativa L. extract on the enzyme activity

In the present study, one‐step purification of angiotensin‐converting enzyme (ACE, peptidyldipeptidase A, EC 3.4.15.1), responsible for regulation of blood pressure, was achieved using affinity chromatography from human plasma. The enzyme was purified 12,860‐fold with a specific activtiy of 5080 EU/mg protein. Optimum temperature and pH were determined for the enzyme as 35–40°C and pH 7.4–7.5, respectively. The purity of ACE was determined by SDS–PAGE and the enzyme showed two bands at 60 and 70 kDa on the gel. The native molecular weight of ACE was found to be 260 kDa by gel filtration chromatography, demonstrating that the enzyme has a heterodimeric structure. Natural fatty acids of Nigella sativa (Ranunculaceae) were isolated by means of column chromatography. The structures of these compounds were determined using NMR and GC‐MS. The results showed that high concentrations of linoleic, oleic and palmitic acids were isolated from the plant. The effect of six fractions (Fr 1–6) on ACE activity was examined. Fraction 3 increased the ACE activity while the other fractions decreased the enzyme activity. The concentrations of the fractions inhibiting the half‐maximum activity of the enzyme were calculated as 1.597 mg/mL for Fr 1, 0.053 mg/mL for Fr 2, 0.527 mg/mL for Fr 4, 0.044 mg/mL for Fr 5 and 0.136 mg/mL for Fr 6 using a Lineweaver–Burk graph.     

Enzyme Catalysis Induced Polymer Growth in Nanochannels: A New Approach to Regulate Ion Transport and to Study Enzyme Kinetics in Nanospace

Method that could regulate the ion transport in nanochannel in an efficient and rapid manner is still a challenge. Here, we introduced enzyme‐catalysis‐induced polymer growth in nanochannels to develop a new method to regulate the ion transport and evaluate the enzyme catalysis kinetics in nano‐space. As a model enzyme, Horseradish peroxidase (HRP) was immobilized in the nanochannels through a volume‐controlled‐drying method. In the presence of H₂O₂, HRP catalyzed o‐phenylenediamine (o‐PD) to trigger its polymer growth, in turn blocked the ion transport and led to the decrease of the ion current. Taking advantages of the high efficiency of enzyme catalysis and the nano‐confinement of nanochannels, the system readily achieved blocking ratios of ion current even reaching 99.6 % of the initial. Based on above concept, we developed a new method to evaluate the enzyme catalysis kinetics in nano‐confined space. By comparing with those in free state in solution and absorbed on planar surface, HRP confined in nanochannels presented similar apparent Michaelis constant (K_m) values for the substrate H₂O₂ but much higher K_m values for the substrate o‐PD, due to the steric hindrance and diffusion suppression. The enzyme‐catalysis‐induced polymerization in nanochannels might lead to new concept for the nano‐blocking/switching and provide a new platform for single molecule analysis and detection.