An Engineered Aryl Acid Adenylation Domain with an Enlarged Substrate Binding Pocket

Adenylation (A) domains act as the gatekeepers of non‐ribosomal peptide synthetases (NRPSs), ensuring the activation and thioesterification of the correct amino acid/aryl acid building blocks. Aryl acid building blocks are most commonly observed in iron‐chelating siderophores, but are not limited to them. Very little is known about the reprogramming of aryl acid A‐domains. We show that a single asparagine‐to‐glycine mutation in an aryl acid A‐domain leads to an enzyme that tolerates a wide range of non‐native aryl acids. The engineered catalyst is capable of activating non‐native aryl acids functionalized with nitro, cyano, bromo, and iodo groups, even though no enzymatic activity of wild‐type enzyme was observed toward these substrates. Co‐crystal structures with non‐hydrolysable aryl‐AMP analogues revealed the origins of this expansion of substrate promiscuity, highlighting an enlargement of the substrate binding pocket of the enzyme. Our findings may be exploited to produce diversified aryl acid containing natural products and serve as a template for further directed evolution in combinatorial biosynthesis.     

Surface Display of Bacterial Metallothioneins and a Chitin Binding Domain on Escherichia coli Increase Cadmium Adsorption and Cell Immobilization

To increase the level of adsorption of cadmium ions to the surface of Escherichia coli, we fused cyanobacterial metallothioneins, SmtA (from Synechococcus elongatus PCC 3601) and MtnA (from Synechococcus vulcanus) to the E. coli cell surface using a Lpp??-OmpA-based display system. E. coli strains expressing Lpp??-OmpA?CSmtA-linker-ChBD (chitin-binding domain from Bacillus pumillus SG2 chitinase S; chiS) and Lpp??-OmpA?CMtnA-linker-ChBD on their surface adsorbed more cadmium compared to the E. coli cells expressing only the Lpp??-OmpA-linker-ChBD hybrid. These constructs also were bound to chitin through their chitin-binding domain, allowing them to be immobilized on a chitin matrix. We assessed surface presentation of Lpp??-OmpA?CSmtA-linker-ChBD, Lpp??-OmpA?CMtnA-linker-ChBD, and Lpp??-OmpA-linker-ChBD using immunostaining. The Lpp??-OmpA?CSmtA-linker-ChBD chimera adsorbed metal and was bound to chitin with the highest efficiency compared to the other chimeras, suggesting that it is an effective bioadsorbent. This is the first example of coupling metal adsorption with cell immobilization using a whole-cell bioadsorbent.     

Improved Thermostability of Lipase B from Candida antarctica by Directed Evolution and Display on Yeast Surface

To expand the functionality of lipase B from Candida antarctica (CALB), we used the multi-site saturation mutagenesis methods to create CALB mutants with improved thermal stability. The times of residual activity of the mutants mCALB168 and mCALB7 were 14 and 6 times higher than that of the displayed WT-CALB at 60 °C. Amino acid substitutions at positions 218, 219, 220, and 221 in mCALB7 introduced two additional hydrogen bonds and altered part of the surface domain from 217 to 224. In mCALB168, we introduced mutations T57A/R168K, which formed three additional hydrogen bonds. The mutants displayed on yeast significantly increased the thermostability in an aqueous system at 60 °C. These results indicate that yeast surface display technology could dramatically improve the stability of CALB.     

Engineering the Substrate Specificity of a P450 Dimerase Enables the Collective Biosynthesis of Heterodimeric Tryptophan-Containing Diketopiperazines

Heterodimeric tryptophan-containing diketopiperazines (HTDKPs) are an important class of bioactive secondary metabolites. Biosynthesis offers a practical opportunity to access their bioactive structural diversity, however, it is restricted by the limited substrate scopes of the HTDKPs-forming P450 dimerases. Herein, by genome mining and investigation of the sequence-product relationships, we unveiled three important residues (F387, F388 and E73) in these P450s that are pivotal for selecting different diketopiperazine (DKP) substrates in the upper binding pocket. Engineering these residues in Nas_F5053 significantly expanded its substrate specificity and enabled the collective biosynthesis, including 12 self-dimerized and at least 81 cross-dimerized HTDKPs. Structural and molecular dynamics analysis of F387G and E73S revealed that they control the substrate specificity via reducing steric hindrance and regulating substrate tunnels, respectively.     

Engineering Substrate Topography at the Micro‐ and Nanoscale to Control Cell Function

The interaction of mammalian cells with nanoscale topography has proven to be an important signaling modality in controlling cell function. Naturally occurring nanotopographic structures within the extracellular matrix present surrounding cells with mechanotransductive cues that influence local migration, cell polarization, and other functions. Synthetically nanofabricated topography can also influence cell morphology, alignment, adhesion, migration, proliferation, and cytoskeleton organization. We review the use of in vitro synthetic cell–nanotopography interactions to control cell behavior and influence complex cellular processes, including stem‐cell differentiation and tissue organization. Future challenges and opportunities in cell–nanotopography engineering are also discussed, including the elucidation of mechanisms and applications in tissue engineering.     

Construction of Copper Removing Bacteria Through the Integration of Two-Component System and Cell Surface Display

Synthetic biological systems are becoming more and more feasible for commercial and medical purposes through the genetic engineering of several components. The simple assembly of a genetic circuit was shown to stimulate the removal of copper by bacteria through the engineering of a two-component system. The CusSR two-component systems is a regulator of Escherichia coli copper homeostatic system. In this system, genetic circuits of CusSR were fused to a cell surface display system for metal adsorption; this system is suitable for the display of a copper binding peptide through outer membrane protein C (OmpC). E. coli ompC codes for an outer membrane pore protein (porin) are induced at high osmolarity and temperature, which can also be used as an anchoring motif to accept the passenger proteins. The bacteria that produce the chimeric OmpC containing the copper binding peptide adsorbed maximum concentrations of 92.2 μmol of Cu(2+)/gram dry weight of bacterial cells. This synthetic bacterial system senses the specific heavy metal and activates a cell surface display system that acts to remove the metal.     

Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density

Many enzymes, particularly in one single family, with highly conserved structures and folds exhibit rather distinct substrate specificities. The underlying mechanism remains elusive, the resolution of which is of great importance for biochemistry, biophysics, and bioengineering. Here, we performed a neutron scattering experiment and molecular dynamics (MD) simulations on two structurally similar CYP450 proteins; CYP101 primarily catalyzes one type of ligands, then CYP2C9 can catalyze a large range of substrates. We demonstrated that it is the high density of salt bridges in CYP101 that reduces its structural flexibility, which controls the ligand access channel and the fluctuation of the catalytic pocket, thus restricting its selection on substrates. Moreover, we performed MD simulations on 146 different kinds of CYP450 proteins, spanning distinct biological categories including Fungi, Archaea, Bacteria, Protista, Animalia, and Plantae, and found the above mechanism generally valid. We demonstrated that, by fine changes of chemistry (salt-bridge density), the CYP450 superfamily can vary the structural flexibility of its member proteins among different biological categories, and thus differentiate their substrate specificities to meet the specific biological needs. As this mechanism is well-controllable and easy to be implemented, we expect it to be generally applicable in future enzymatic engineering to develop proteins of desired substrate specificities.     

Construction of a Laccase Chimerical Gene: Recombinant Protein Characterization and Gene Expression via Yeast Surface Display

The ERY4 laccase gene from Pleurotus eryngii was expressed in Saccharomyces cerevisiae and the recombinant laccase resulted to be not biologically active. This gene was thus modified to obtain chimerical enzymes derived from the substitution of N–, C– and both N- and C-terminal regions with the corresponding regions of Ery3 laccase, another laccase isoform of P. eryngii. The chimerical isoform named 4NC3, derived from the substitution of both N- and C-terminal regions, showed the best performances in terms of enzymatic activities, affinities for different substrates and stability at a broad range of temperatures and pHs. The chimerical 4NC3 laccase isoform was displayed on the cell surface of S. cerevisiae using the N-terminal fusion with either the Pir2 or the Flo1 S. cerevisiae proteins as anchor attachment sequence. Immunofluorescence microscopy and Western blot analyses confirmed the localization of 4NC3 on the yeast cell surface. The enzyme activity on specific laccase substrates revealed that 4NC3 laccase was immobilized in active form on the cell surface. To our knowledge, this is the first example of expression of a chimerical fungal laccase by yeast cell display.     

Recent Advances in DNA-Based Cell Surface Engineering for Biological Applications

Due to its excellent programmability and biocompatibility, DNA molecule has unique advantages in cell surface engineering. Recent progresses provide a reliable and feasible way to engineer cell surfaces with diverse DNA molecules and DNA nanostructures. The abundant form of DNA nanostructures has greatly expanded the toolbox of DNA-based cell surface engineering and gave rise to a variety of novel and fascinating applications. In this review, we summarize recent advances in DNA-based cell surface engineering and its biological applications. We first introduce some widely used methods of immobilizing DNA molecules on cell surfaces and their application features. Then we discuss the approaches of employing DNA nanostructures and dynamic DNA nanotechnology as elements for creating functional cell surfaces. Finally, we review the extensive biological applications of DNA-based cell surface engineering and discuss the challenges and prospects of DNA-based cell surface engineering.     

Surface Properties of Yeast Cells

Surface properties of Torulopsis (Candida) kefir var kumis and Saccharomyces cerevisiae yeast cells are studied. It is shown that the cells are characterized by the high values of potential and carry the negative charge, which does not vary within pH 2–10 range, that is explained by the presence of ionized carboxyl and phosphoric acid groups on the surface. Based on the results of electrokinetic studies, the wettability of cell surface, and the cell distribution between the aqueous and organic phases, it was concluded that the properties of organic phase, in particular the size of the molecules of this phase, play an important role in determining the hydrophilic-hydrophobic characteristics of the cell surface.     

Effects of Various Cell Surface Engineering Reactions on the Biological Behavior of Mammalian Cells

Cell surface engineering technologies can regulate cell function and behavior by modifying the cell surface. Previous studies have mainly focused on investigating the effects of cell surface engineering reactions and materials on cell activity. However, they do not comprehensively analyze other cellular processes. This study exploits covalent bonding, hydrophobic interactions, and electrostatic interactions to modify the macromolecules succinimide ester-methoxy polyethylene glycol (NHS-mPEG), distearoyl phosphoethanolamine-methoxy polyethylene glycol (DSPE-mPEG), and poly-L -lysine (PLL), respectively, on the cell surface. This work systematically investigates the effects of the three surface engineering reactions on the behavior of human umbilical vein endothelial cells (HUVECs) and human skin fibroblasts, including viability, growth, proliferation, cell cycle, adhesion, and migration. The results reveals that the PLL modification method notably affects cell viability and G2/M arrest and has a short modification duration. However, the DSPE-mPEG and NHS-mPEG modification methods have little effect on cell viability and proliferation but have a prolonged modification duration. Moreover, the DSPE-mPEG modification method highly affects cell adherence. Further, the NHS-mPEG modification method can significantly improve the migration ability of HUVECs by reducing the area of focal adhesions. The findings of this study will contribute to the application of cell surface engineering technology in the biomedical field.     

Substrate Specificity Analysis and Novel Substrates of the Protein Lysine Methyltransferase NSD1

1. Download : Download high-res image (365KB)
2. Download : Download full-size image

     

聚合物表面自组装电极的制备

采用在聚合物表面制备选择性化学镀电极的方法, 将具有电极结构的模板置于聚萘二甲酸乙二醇酯(PEN)基片表面上, 用紫外光进行照射, 使辐照区域表面形成羧基, 然后通过配位作用使银离子附着到表面上, 再经过紫外光照射还原出金属银颗粒, 最后以表面的金属银颗粒为催化剂进行特定区域化学镀铜形成电极. 利用四探针法测得电极的电阻率为5.063×10-2 Ω·mm2/m, 与纯金属铜的电阻率的数量级相同.     

Enhanced Activity and Substrate Specificity by Site-Directed Mutagenesis for the P450 119 Peroxygenase Catalyzed Sulfoxidation of Thioanisole

P450 119 peroxygenase was found to catalyze the sulfoxidation of thioanisole and the sulfonation of sulfoxide in the presence of tert-butyl hydroperoxide (TBHP) for the first time with turnover rates of 1549 min⁻¹ and 196 min⁻¹ respectively. Several mutants were designed to improve the peroxygenation activity and thioanisole specificity by site-directed mutagenesis. The F153G/T213G mutant gave an increase of sulfoxide yield and a decrease of sulfone yield. Moreover the S148P/I161T/K199E/T214V mutant and the K199E mutant with acidic Glu residue contributed to improving the product ratio of sulfoxide to sulfone. Addition of short-alkyl-chain organic acids to the P450 119 peroxygenase-catalyzed sulfur oxidation of thioanisole was investigated. Octanoic acid was found to induce a preferred sulfoxidation of thioanisole catalyzed by the F153G/T213G mutant to give approximately 2.4-fold increase in turnover rate with a k_cat value of 3687 min⁻¹ relative to that of the wild-type, and by the F153G mutant to give the R-sulfoxide up to 30 % ee. The experimental control and the proposed mechanism for the P450 119 peroxygenase-catalyzed sulfoxidation of thioanisole in the presence of octanoic acid suggested that octanoic acid could partially occupy the substrate pocket; meanwhile the F153G mutation could enhance the substrate specificity, which could lead to efficiently regulate the spatial orientation of thioanisole and facilitate the formation of Compound I. This is the most effective catalytic system for the P450 119 peroxygenase-catalyzed sulfoxidation of thioanisole.     

材料表面性质调控细胞黏附

生物医用材料旨在通过调控材料和细胞之间的相互作用来实现组织的再生和修复。黏附过程直接决定了细胞是否能够充分发挥生物学性能,因此通过对材料表面的物理和化学改性来调控细胞黏附,对于生物材料具有至关重要的意义,也是非常活跃的研究热点。材料表面物理改性通常通过对包括表面粗糙度、形貌、模量和多孔结构等物理性质的调控,为细胞构建适合黏附的材料表面。而化学改性则借助于表面电荷及亲疏水性调控、促黏分子修饰等化学手段来提高材料表面与细胞间的相互作用力,进而促进细胞黏附。近年来,材料表面调控细胞黏附的研究取得了许多新的突破性进展。例如在传统的促黏分子表面修饰之外,人们逐步发现对促黏分子序构的精准调控也可以有效地提高材料表面的促黏性能。而刺激响应性表面则可以根据外界信号的刺激,使得材料表面在促黏和抗黏之间实现智能的转换。本文从物理改性、化学修饰、刺激响应性表面构建等角度出发,全面总结和讨论了材料表面性质对细胞黏附的调控作用,梳理了材料表面的设计思路,多种材料表面的修饰改性方法等最新进展,并展望了未来材料表面对细胞黏附的调控思路。     

Substrate Specificity of Chimeric Enzymes Formed by Interchange of the Catalytic and Specificity Domains of the 5′-Nucleotidase UshA and the 3′-Nucleotidase CpdB

The 5′-nucleotidase UshA and the 3′-nucleotidase CpdB from Escherichia coli are broad-specificity phosphohydrolases with similar two-domain structures. Their N-terminal domains (UshA_Ndom and CpdB_Ndom) contain the catalytic site, and their C-terminal domains (UshA_Cdom and CpdB_Cdom) contain a substrate-binding site responsible for specificity. Both enzymes show only partial overlap in their substrate specificities. So, it was decided to investigate the catalytic behavior of chimeras bearing the UshA catalytic domain and the CpdB specificity domain, or vice versa. UshA_Ndom–CpdB_Cdom and CpdB_Ndom–UshA_Cdom were constructed and tested on substrates specific to UshA (5′-AMP, CDP-choline, UDP-glucose) or to CpdB (3′-AMP), as well as on 2′,3′-cAMP and on the common phosphodiester substrate bis-4-NPP (bis-4-nitrophenylphosphate). The chimeras did show neither 5′-nucleotidase nor 3′-nucleotidase activity. When compared to UshA, UshA_Ndom–CpdB_Cdom conserved high activity on bis-4-NPP, some on CDP-choline and UDP-glucose, and displayed activity on 2′,3′-cAMP. When compared to CpdB, CpdB_Ndom–UshA_Cdom conserved phosphodiesterase activities on 2′,3′-cAMP and bis-4-NPP, and gained activity on the phosphoanhydride CDP-choline. Therefore, the non-nucleotidase activities of UshA and CpdB are not fully dependent on the interplay between domains. The specificity domains may confer the chimeras some of the phosphodiester or phosphoanhydride selectivity displayed when associated with their native partners. Contrarily, the nucleotidase activity of UshA and CpdB depends strictly on the interplay between their native catalytic and specificity domains.     

Kinetic Involvement of Acetaldehyde Substrate Inhibition on the Rate Equation of Yeast Aldehyde Dehydrogenase

In order to evaluate the effectiveness of aldehyde dehydrogenase (ALDH) from Saccharomyces cerevisiae as a catalyst for the conversion of acetaldehyde into its physiologically and biologically less toxic acetate, the kinetics over broad concentrations were studied to develop a suitable kinetic rate expression. Even with literature accounts of the binding complexations, the yeast ALDH currently lacks a quantitative kinetic rate expression accounting for simultaneous inhibition parameters under higher acetaldehyde concentrations. Both substrate acetaldehyde and product NADH were observed as individual sources of inhibition with the combined effect of a ternary complex of acetaldehyde and the coenzyme leading to experimental rates as little as an eighth of the expected activity. Furthermore, the onset and strength of inhibition from each component were directly affected by the concentration of the co-substrate NAD. While acetaldehyde inhibition of ALDH is initiated below concentrations of 0.05?mM in the presence of 0.5?mM NAD or less, the acetaldehyde inhibition onset shifts to 0.2?mM with as much as 1.6?mM NAD. The convenience of the statistical software package JMP allowed for effective determination of experimental kinetic constants and simplification to a suitable rate expression: $$ v = \frac{{Vmax\left( {{\text A}{\text B}} \right)}}{{KiaKb + KbA + KaB + AB + \frac{{{B^2}}}{{KI-Ald}} + \frac{{{B^2}Q}}{{KI-Ald-NADH}} + \frac{{BQ}}{{KI-NADH}}}} $$ where the last three terms represent the inhibition complex terms for acetaldehyde, acetaldehyde?CNADH, and NADH, respectively. The corresponding values of K _I?CAld, K _I?CAld?CNADH, and K _I?CNADH for yeast ALDH are 2.55, 0.0269, and 0.162?mM at 22?°C and pH?7.8.     

improvement of the Specificity of Surface Plasmon Resonance with BSA-modified Chip

Recently, surface plasmon resonance (SPR) become more and more popular without the need of the label technology1-3. However, sometimes, a number of experimental artifacts complicate the final biosensor analysis4-7. The utilization of a reference surface c…