Optimization of combinatorial mutagenesis

Protein engineering by combinatorial site-directed mutagenesis evaluates a portion of the sequence space near a target protein, seeking variants with improved properties (e.g., stability, activity, immunogenicity). In order to improve the hit-rate of beneficial variants in such mutagenesis libraries, we develop methods to select optimal positions and corresponding sets of the mutations that will be used, in all combinations, in constructing a library for experimental evaluation. Our approach, OCoM (Optimization of Combinatorial Mutagenesis), encompasses both degenerate oligonucleotides and specified point mutations, and can be directed accordingly by requirements of experimental cost and library size. It evaluates the quality of the resulting library by one- and two-body sequence potentials, averaged over the variants. To ensure that it is not simply recapitulating extant sequences, it balances the quality of a library with an explicit evaluation of the novelty of its members. We show that, despite dealing with a combinatorial set of variants, in our approach the resulting library optimization problem is actually isomorphic to single-variant optimization. By the same token, this means that the two-body sequence potential results in an NP-hard optimization problem. We present an efficient dynamic programming algorithm for the one-body case and a practically-efficient integer programming approach for the general two-body case. We demonstrate the effectiveness of our approach in designing libraries for three different case study proteins targeted by previous combinatorial libraries--a green fluorescent protein, a cytochrome P450, and a beta lactamase. We found that OCoM worked quite efficiently in practice, requiring only 1 hour even for the massive design problem of selecting 18 mutations to generate 10? variants of a 443-residue P450. We demonstrate the general ability of OCoM in enabling the protein engineer to explore and evaluate trade-offs between quality and novelty as well as library construction technique, and identify optimal libraries for experimental evaluation.     

Searching for the Pareto frontier in multi-objective protein design

The goal of protein engineering and design is to identify sequences that adopt three-dimensional structures of desired function. Often, this is treated as a single-objective optimization problem, identifying the sequence–structure solution with the lowest computed free energy of folding. However, many design problems are multi-state, multi-specificity, or otherwise require concurrent optimization of multiple objectives. There may be tradeoffs among objectives, where improving one feature requires compromising another. The challenge lies in determining solutions that are part of the Pareto optimal set—designs where no further improvement can be achieved in any of the objectives without degrading one of the others. Pareto optimality problems are found in all areas of study, from economics to engineering to biology, and computational methods have been developed specifically to identify the Pareto frontier. We review progress in multi-objective protein design, the development of Pareto optimization methods, and present a specific case study using multi-objective optimization methods to model the tradeoff between three parameters, stability, specificity, and complexity, of a set of interacting synthetic collagen peptides.     

Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate

The immunogenicity of biotherapeutics can bottleneck development pipelines and poses a barrier to widespread clinical application. As a result, there is a growing need for improved deimmunization technologies. We have recently described algorithms that simultaneously optimize proteins for both reduced T cell epitope content and high-level function. In silico analysis of this dual objective design space reveals that there is no single global optimum with respect to protein deimmunization. Instead, mutagenic epitope deletion yields a spectrum of designs that exhibit tradeoffs between immunogenic potential and molecular function. The leading edge of this design space is the Pareto frontier, i.e. the undominated variants for which no other single design exhibits better performance in both criteria. Here, the Pareto frontier of a therapeutic enzyme has been designed, constructed, and evaluated experimentally. Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions. These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates. Given this capacity to rapidly assess and design for tradeoffs between protein immunogenicity and functionality, these algorithms may prove useful in augmenting, accelerating, and de-risking experimental deimmunization efforts.     

Systematic design for trait introgression projects

Key message

Using an Operations Research approach, we demonstrate design of optimal trait introgression projects with respect to competing objectives.

Abstract

We demonstrate an innovative approach for designing Trait Introgression (TI) projects based on optimization principles from Operations Research. If the designs of TI projects are based on clear and measurable objectives, they can be translated into mathematical models with decision variables and constraints that can be translated into Pareto optimality plots associated with any arbitrary selection strategy. The Pareto plots can be used to make rational decisions concerning the trade-offs between maximizing the probability of success while minimizing costs and time. The systematic rigor associated with a cost, time and probability of success (CTP) framework is well suited to designing TI projects that require dynamic decision making. The CTP framework also revealed that previously identified ‘best’ strategies can be improved to be at least twice as effective without increasing time or expenses.

     

丁酰胆碱酯酶结构研究新进展

丁酰胆碱酯酶(butyrylcholinesterase, BChE, EC 3.1.1.8),能与有机磷毒剂或杀虫剂结合,并能水解许多酯类、肽类及酰胺类化合物,对这些化合物的中毒具有防治作用.近年来通过计算机模拟技术及定点突变技术对其结构研究取得了重要进展,对人BChE外周阴离子部位的结构有了新的认识, 并通过氨基酸替换使BChE获得了水解有机磷酸酐的新功能.     

枯草杆菌蛋白酶基因工程的研究进展

本文介绍了枯草杆菌蛋白酶(Subtilisin)的研究现状,即利用定位诱变和体外重组等技术改变酶的性质,包括催化活性、底物特异性、稳定性、低温适应性以及酶在有机相中的性能等。对枯草杆菌蛋白酶的成功改造不仅有可观的商业价值,而且为蛋白质工程的发展作出了重要的贡献 。     

Robust design and optimization of retroaldol enzymes

Enzyme catalysts of a retroaldol reaction have been generated by computational design using a motif that combines a lysine in a nonpolar environment with water-mediated stabilization of the carbinolamine hydroxyl and β-hydroxyl groups. Here, we show that the design process is robust and repeatable, with 33 new active designs constructed on 13 different protein scaffold backbones. The initial activities are not high but are increased through site-directed mutagenesis and laboratory evolution. Mutational data highlight areas for improvement in design. Different designed catalysts give different borohydride-reduced reaction intermediates, suggesting a distribution of properties of the designed enzymes that may be further explored and exploited.     

Structure of the tetrameric form of human L-Xylulose reductase: probing the inhibitor-binding site with molecular modeling and site-directed mutagenesis

L-Xylulose reductase (XR) is a member of the short-chain dehydrogenase/reductase (SDR) superfamily. In this study we report the structure of the biological tetramer of human XR in complex with NADP(+) and a competitive inhibitor solved at 2.3 A resolution. A single subunit of human XR is formed by a centrally positioned, seven-stranded, parallel beta-sheet surrounded on either side by two arrays of three alpha-helices. Two helices located away from the main body of the protein form the variable substrate-binding cleft, while the dinucleotide coenzyme-binding motif is formed by a classical Rossmann fold. The tetrameric structure of XR, which is held together via salt bridges formed by the guanidino group of Arg203 from one monomer and the carboxylate group of the C-terminal residue Cys244 from the neighboring monomer, explains the ability of human XR to prevent the cold inactivation seen in the rodent forms of the enzyme. The orientations of Arg203 and Cys244 are maintained by a network of hydrogen bonds and main-chain interactions of Gln137, Glu238, Phe241, and Trp242. These interactions are similar to those defining the quaternary structure of the closely related carbonyl reductase from mouse lung. Molecular modeling and site-directed mutagenesis identified the active site residues His146 and Trp191 as forming essential contacts with inhibitors of XR. These results could provide a structural basis in the design of potent and specific inhibitors for human XR.     

A single proline substitution is critical for the thermostabilization of Clostridium beijerinckii alcohol dehydrogenase

Analysis of the three-dimensional structures of three closely related mesophilic, thermophilic, and hyperthermophilic alcohol dehydrogenases (ADHs) from the respective microorganisms Clostridium beijerinckii (CbADH), Entamoeba histolytica (EhADH1), and Thermoanaerobacter brockii (TbADH) suggested that a unique, strategically located proline residue (Pro100) might be crucial for maintaining the thermal stability of EhADH1. To determine whether proline substitution at this position in TbADH and CbADH would affect thermal stability, we used site-directed mutagenesis to replace the complementary residues in both enzymes with proline. The results showed that replacing Gln100 with proline significantly enhanced the thermal stability of the mesophilic ADH: DeltaT(1/2) (60 min) = + 8 degrees C (temperature of 50% inactivation after incubation for 60 min), DeltaT(1/2) (CD) = +11.5 degrees C (temperature at which 50% of the original CD signal at 218 nm is lost upon heating between 30 degrees and 98 degrees C). A His100 --> Pro substitution in the thermophilic TbADH had no effect on its thermostability. An analysis of the three-dimensional structure of the crystallized thermostable mutant Q100P-CbADH suggested that the proline residue at position 100 stabilized the enzyme by reinforcing hydrophobic interactions and by reducing the flexibility of a loop at this strategic region.     

Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activity

Simvastatin is the active pharmaceutical ingredient of the blockbuster cholesterol lowering drug Zocor. We have previously developed an Escherichia coli based whole-cell biocatalytic platform towards the synthesis of simvastatin sodium salt (SS) starting from the precursor monacolin J sodium salt (MJSS). The centerpiece of the biocatalytic approach is the simvastatin synthase LovD, which is highly prone to misfolding and aggregation when overexpressed from E. coli. Increasing the solubility of LovD without decreasing its catalytic activity can therefore elevate the performance of the whole-cell biocatalyst. Using a combination of homology structural prediction and site-directed mutagenesis, we identified two cysteine residues in LovD that are responsible for nonspecific intermolecular crosslinking, which leads to oligomer formation and protein aggregation. Replacement of Cys40 and Cys60 with alanine residues resulted in marked gain in both protein solubility and whole-cell biocatalytic activities. Further mutagenesis experiments converting these two residues to small or polar natural amino acids showed that C40A and C60N are the most beneficial, affording 27% and 26% increase in whole cell activities, respectively. The double mutant C40A/C60N combines the individual improvements and displayed approximately 50% increase in protein solubility and whole-cell activity. Optimized fed-batch high-cell-density fermentation of the double mutant in an E. coli strain engineered for simvastatin production quantitatively (>99%) converted 45 mM MJSS to SS within 18 h, which represents a significant improvement over the performance of wild-type LovD under identical conditions. The high efficiency of the improved whole-cell platform renders the biocatalytic synthesis of SS an attractive substitute over the existing semisynthetic routes.     

Modulation of human cytidine deaminase by specific aminoacids involved in the intersubunit interactions

An investigation was made of the role exerted by some residues supposed to be involved in the intersubunit interaction and also in the catalytic site of homotetrameric human cytidine deaminase (T-CDA). Attention was focused on Y33, Y60, R68, and F137 residues that are a part of a conserved region in most T-CDAs. Hence, a series of site-directed mutagenesis experiments was set up obtaining seven mutants: Y60G, Y33G, Y33F Y33S, F137A, R68G, and R68Q. Each active purified mutant protein was characterized kinetically, with a series of substrates and inhibitors, and the effect of temperature on enzyme activity and stability was also investigated. Circular dichroism (CD) experiments at different temperatures and in presence of small amounts of sodium dodecyl sulphate (SDS) were performed in all the soluble mutant CDAs. The results obtained by site-directed mutagenesis studies were compared to the crystallographic data of B. subtilis CDA and E. coli CDA and to molecular modeling studies previously performed on human CDA. The mutation of Y60 to glycine produced an enzyme with a more compact quaternary structure with respect to the wild-type; this mutation did not have a dramatic effect on cytidine deamination, but it slightly affected the binding with the substrate. None of the mutant CDAs in Y33 showed enzymatic activity; they existed only as monomers, indicating that this residue, located at the intersubunit interface, may be responsible for the correct folding of human CDA. The insertion of an alanine instead of phenylalanine at position 137 led to a soluble but completely inactive enzyme unable to form a tetramer, suggesting that F137 residue may be important for the assembling of the tetramer and also for the arrangement of the CDA active site. Finally, R68G and R68Q mutations revealed that the presence of the amino group seems to be important for the catalytic process but not for substrate binding, as already shown in B. subtilis CDA. The quaternary structure of R68Q was not affected by the mutation, as shown by the SDS-induced dissociation experiments and CD studies, whereas R68G dissociated very easily in presence of small amounts of SDS. These experiments indicated that in the human CDA, the side chain of arginine 68 involved in the catalytic process in one subunit active site might come from another subunit. The data obtained from these studies confirmed the presence of a complicated set of intersubunit interactions in the active site of human CDA, as shown in other T-CDAs.     

Engineering aromatic L-amino acid transaminase for the asymmetric synthesis of constrained analogs of L-phenylalanine

An enzymatic asymmetric synthesis was carried out for the preparation of enantiomerically pure L-diphenylalanine using the rationally engineered aromatic L-amino acid transaminase (eAroATEs) obtained from Enterobacter sp. BK2K-1. To rationally redesign the enzyme, structural model was constructed by the homology modeling. The structural model was experimentally validated by the site-directed mutagenesis of the predicted pyridoxal-5'-phosphate (PLP) binding site and the substrate-recognition region, and the cell-free protein synthesis of mutated enzymes. It was suggested that Arg281 and Arg375 were the key residues to recognize the distal carboxylate and alpha-carboxylate group of the substrates, respectively. The model also predicted that Tyr66 forms hydrogen bond with the phosphate moiety of PLP and interacts with the side chain attached to beta-carbon of the amino acid substrate. Among the various site-directed mutants, Y66L variant was able to synthesize L-diphenylalanine with 23% conversion yield for 10 h, whereas the wild-type AroATEs was inactive for the transamination between diphenylpyruvate and L-phenylalanine as amino acceptor and amino donor, respectively.     

Docking of human interleukin-15 to its specific receptor alpha chain: correlation between molecular modeling and mutagenesis experimental data

A structural model of the sushi domain of IL-15Ralpha was first obtained by homology modeling to study its interactions with IL-15 by means of molecular modeling, peptide scanning, and site-directed mutagenesis. From these experimental data, a putative interacting surface of IL-15Ralpha with a previously published IL-15 model was inferred: Leu25, Leu44, and Glu46 of IL-15 and Arg35 of IL-15Ralpha were found to be key interfacial residues and were subsequently used as filters for the construction of docking solutions. Human IL-15/IL-15Ralpha complexes were constructed in two stages, with a preliminary docking procedure, treating the two partners as rigid bodies and using these filters. In this first stage, two classes of docking solutions were characterized. From a topological point of view, each solution could be derived from the other by reverse orientation of one partner in relation to the other. In a second stage, several further energy refinements clearly favored one solution. Moreover, this unique docking solution was confirmed by molecular modeling of IL-15 mutants previously built and tested in our laboratory. Finally, this complex model, which is a useful tool to study the IL-15/IL-15Ralpha interface, was topologically compared to IL-2/IL-2Ralpha complexes (previous model in the literature and recent crystal structure).     

Optimizing the location of watercraft inspection stations to slow the spread of aquatic invasive species

The accidental spread of aquatic invasive species (AIS) by recreational boaters is a major concern of state and county environmental planners in the USA. While programs for watercraft inspection to educate boaters and slow AIS spread are common practice, large numbers of boats and waterbodies, together with limited budgets, make program design difficult. To facilitate program design, we developed an integer programming model for allocation of scarce inspection resources among lakes. Our model uses species-specific infestation status of lakes and estimates of boat movement between lakes. The objective is to select lakes for inspection stations to maximize the number of risky boats inspected, where risky boats are ones that move from infested to uninfested lakes. We apply our model in Stearns County in central Minnesota, USA, to prioritize lakes for inspection stations and evaluate alternative management objectives. With an objective of protecting uninfested lakes within and outside Stearns County, the optimal policy is to locate stations at infested lakes having the most boats departing for uninfested lakes inside and outside the county. With an objective of protecting only Stearns County lakes, the optimal policy is to locate stations at both infested and uninfested lakes having the riskiest boats arriving from within and outside the county and departing to in-county lakes. The tradeoff between these objectives is significant.

     

Consequential LCA and LCC using linear programming: an illustrative example of biorefineries

Purpose

This paper aims to demonstrate how LCA can be improved by the use of linear programming (LP) (i) to determine the optimal choice between new technologies, (ii) to identify the optimal region for supplying the feedstock, and (iii) to deal with multifunctional processes without specifying a certain main product. Furthermore, the contribution of LP in the context of consequential LCA and LCC is illustrated.

Methods

We create a mixed integer linear program (MILP) for the environmental and economic assessment of new technologies. The model is applied in order to analyze two residual beech wood-based biorefinery concepts in Germany. In terms of the optimal consequences for the system under study, the principle of the program is to find a scaling vector that minimizes the life cycle impact indicator results of the system. We further transform the original linear program to extend the assessment by life cycle costing (LCC). Thereby, two multi-objective programming methods are used, weighted goal programming and epsilon constraint method.

Results and discussion

The consequential case studies demonstrate the possibility to determine optimal locations of newly developed technologies. A high number of potential system modifications can be studied simultaneously without matrix inversion. The criteria for optimal choices are represented by the objective functions and the additional constraints such as the available feedstock in a region. By combining LCA and LCC targets within a multi-objective programming approach, it is possible to address environmental and economic trade-offs in consequential decision-making.

Conclusions

This article shows that linear programming can be used to extend standard LCA in the field of technological choices. Additional consequential research questions can be addressed such as the determination of the optimal number of new production plants and the optimal regions for supplying the resources. The modifications of the program by additional profit requirements (LCC) into a goal program and Pareto optimization problem have been identified as promising steps toward a comprehensive multi-objective LCSA.

     

Pareto front analysis of flight time and energy use in long-distance bird migration

Optimality models are frequently used in studies of long distance bird migration to help understand and predict migration routes, stopover strategies and fuelling behaviour in a spatially varying environment. These models typically evaluate bird behaviour by focusing on a single optimization currency, such as total migration time or energy-use, without explicitly considering trade-offs between the involved objectives. In this paper, we demonstrate that this classic single-objective approach downplays the importance of variability in bird behaviour. In the light of these considerations, we therefore propose to use a full multi-criteria optimization method to isolate the set of non-dominated, efficient or Pareto optimal solutions. Unlike single-objective optimization where there is only one combination of bird behaviour maximizing fitness, the Pareto solution set represents a range of optimal solutions to conflicting objectives. Our results demonstrate that this multi-objective approach provides important new ways of analyzing how environmental factors and behavioural constraints have driven the evolution of migratory behaviour.     

Improvement of Yersinia frederiksenii phytase performance by a single amino acid substitution

A new phytase (APPA) with optimum pH 2.5—substantially lower than that of most of microbial phytases (pH 4.5–6.0)—was cloned from Yersinia frederiksenii and heterologously expressed in Escherichia coli. Containing the highly conserved motifs typical of histidine acid phosphatases, APPA has the highest identity (84%) to the Yersinia intermedia phytase (optimal pH 4.5), a member of histidine acid phosphatase family. Based on sequence alignment and molecular modeling of APPA and related phytases, APPA has only one divergent residue, Ser51, in close proximity to the catalytic site. To understand the acidic adaptation of APPA, five mutants (S51A, S51T, S51D, S51K, and S51I) were constructed by site‐directed mutagenesis, expressed in E. coli, purified, and characterized. Mutants S51T and S51I exhibited a shift in the optimal pH from 2.5 to 4.5 and 5.0, respectively, confirming the role of Ser51 in defining the optimal pH. Thus, a previously unrecognized factor other than electrostatics—presumably the side‐chain structure near the active site—contributes to the optimal pH for APPA activity. Compared with wild‐type APPA, mutant S51T showed higher specific activity, greater activity over pH 2.0–5.5, and increased thermal and acid stability. These properties make S51T a better candidate than the wild‐type APPA for use in animal feed. Biotechnol. Bioeng. 2009;103: 857–864. © 2009 Wiley Periodicals, Inc.     

Multi-criterion optimization for heel-toe running

This paper presents an optimization procedure for multi-criterion analysis essential in many biomechanical studies. The optimization is illustrated with a heel-toe running analysis wherein the rate of load and the passive load on support leg are minimized concurrently. The goal of multi-criterion optimization is achieved by incorporating the criterion of Pareto optimality in the genetic algorithm. The proposed procedure can replace the popular weighted-sum approach for problems with multiple objectives. The selection of a final design from the Pareto optimum points (non-dominated designs) can be determined, based on the min-max objective deviation criterion. Nevertheless, a different decision can be made in the final selection without incurring recalculations. The scheme is readily adoptable for parallel computing, which deserves further study to reduce the execution time in a complex biomechanical analysis.     

Identifying Lowest‐Emission Choices and Environmental Pareto Frontiers for Wastewater Treatment Wastewater Treatment Input‐Output Model based Linear Programming

This article proposes a linear programming model that is based on the wastewater treatment input‐output model (W²IO) to identify the lowest‐emission choice among alternative feasible options for wastewater treatment; this model can be considered as an application of the waste input‐output linear programming model (WIO‐LP) to wastewater issues. Using the data of the Tokyo metropolitan W²IO table, I apply this model to obtain the optimal wastewater treatment options under alternative scenarios. The Pareto frontiers of environmental loads are derived to show the trade‐off relationships among various types of environmental load and the effect of the introduction of high‐temperature incineration of dewatered sludge on the generation of environmental loads. The main conclusion of the study is that when all three types of environmental load (landfill level, global warming potential, and chemical oxygen demand) are considered, the introduction of high‐temperature incineration causes the widening of the Pareto frontier of environmental loads and also causes it to move closer to the origin.