DRF90: a polarizable force field

The direct reaction field (DRF) approach has proven to be a useful tool to investigate the influence of solvents on the quantum/classical behaviour of solute molecules. In this paper, we report the latest extension of this DRF approach, which consists of the gradient of the completely classical energy expressions of this otherwise QM/MM method. They can be used in (completely classical) molecular dynamics (MD) simulations and geometry optimizations, that can be followed by a number of single point QM/MM calculations on configurations obtained in these simulations/optimizations. We report all energy and gradient expressions, and results for a number of interesting (model) systems. They include geometry optimization of the benzene dimer as well as MD simulations of some solvents. The most stable configuration for the benzene dimer is shown to be the parallel-displaced form, which is slightly more stable (0.3 kcal/mol) than the T-shaped dimer.     

遮荫对峦大杉1年生苗木生长的影响及动态优化

以当年播种的峦大杉(Cunninghamia konishii)幼苗为材料,采用单因素试验设计3个遮荫处理(50%、75%、100%光照),每隔7 d监测地径、苗高等生长进程;应用Logistic方程拟合苗高、地径生长过程并分析其生长节律。结果表明,遮荫显著促进峦大杉幼苗全生长季的苗高、地径生长,以50%光照表现最好;不同生长阶段遮荫对峦大杉苗高、地径生长量的影响有所不同,进行动态优化十分必要。Logistic方程能较好地拟合峦大杉苗木生长动态。50%光照处理显著提高峦大杉苗高、地径的线性生长速率、最大线性生长速率和线性生长量,显著提前苗高线性生长终期、缩短线性生长持续时间,显著推迟地径线性生长始期。峦大杉苗期光照强度动态优化方案：在t≤133 d前阶段宜采用50%光照,在t＞133 d期间宜采用100%光照。     

Enzymatic synthesis of cetyl oleate in a solvent-free medium using microwave irradiation and physicochemical evaluation

Abstract

A cosmetic ester, cetyl oleate was synthesized using microwave irradiated system. The esterification reaction was carried using Candida antarctica lipase B in a solvent-free media. The influence of various reaction parameters was studied, and the efficiency of Fermase CALB^TM10000 was compared with other enzymes. Equilibrium conversion of 97.5% was obtained within 20?min at 60?°C temperature, 1:2 oleic acid to cetyl alcohol molar ratio and 4% w/w dose of lipase. A comparative study showed that microwave irradiation is a much more efficient method than ultrasound irradiation and conventional heating. Fermase CALB^TM10000 was reusable over 6 enzymatic cycles as its stability improved under microwave system. Physicochemical parameters of cetyl oleate were tested in order to analyze its suitability for further cosmetic use.     

Enhancement of extracellular bispecific anti‐MUC1 nanobody expression in E. coli BL21 (DE3) by optimization of temperature and carbon sources through an autoinduction condition

Escherichia coli is one of the most suitable hosts for production of antibodies and antibody fragments. Antibody fragment secretion to the culture medium improves product purity in cell culture and diminishes downstream costs. In this study, E. coli strain BL21 (DE3) harboring gene encoding bispecific anti‐MUC1 nanobody was selected, and the autoinduction methodology for expression of bispecific anti‐MUC1 nanobody was investigated. Due to the replacement of IPTG by lactose as inducer, less impurity and toxicity in the final product were observed. To increase both intracellular and extracellular nanobody production, initially, the experiments were performed for the key factors including temperature and duration of protein expression. The highest amount of nanobody was produced after 21 h at 33°C. The effect of different carbon sources, glycerol, glucose, lactose, and glycine as a medium additive at optimum temperature and time were also assessed by using response surface methodology. The optimized concentrations of carbon sources were obtained as 0.75% (w/v), 0.03% (w/v), 0.1% (w/v), and 0.75% (w/v) for glycerol, glucose, lactose, and glycine, respectively. Finally, the production of nanobody in 2 L fermenter under the optimized autoinduction conditions was evaluated. The results show that the total titer of 87.66 µg/mL anti‐MUC1 nanobody, which is approximately seven times more than the total titer of nanobody produced in LB culture medium, is 12.23 µg/L .     

Resource recovery from low strength wastewater in a bioelectrochemical desalination process

In this research, low strength synthetic wastewaters with chemical oxygen demand less than 300 mg L^?1 were treated at different concentrations in a bioelectrochemical desalination process. A process optimization model was utilized to study the performance of the photosynthetic bioelectrochemical desalination process. The variables include substrate (chemical oxygen demand) concentration, total dissolved solids, and microalgae biomass concentration in the cathode chamber. Relationships between the chemical oxygen demand concentration, microalgae, and salt concentrations were evaluated. Power densities and potential energy benefits from microalgal biomass growth were discussed. The results from this study demonstrated the reliability and reproducibility of the photosynthetic microbial desalination process performance followed by a response surface methodology optimization. This study also confirms the suitability of bioelectrochemical desalination process for treating low substrate wastewaters such as agricultural wastewaters, anaerobic digester effluents, and septic tank effluents for net energy production and water desalination.     

Antibody humanization by structure-based computational protein design

Antibodies derived from non-human sources must be modified for therapeutic use so as to mitigate undesirable immune responses. While complementarity-determining region (CDR) grafting-based humanization techniques have been successfully applied in many cases, it remains challenging to maintain the desired stability and antigen binding affinity upon grafting. We developed an alternative humanization approach called CoDAH (“Computationally-Driven Antibody Humanization”) in which computational protein design methods directly select sets of amino acids to incorporate from human germline sequences to increase humanness while maintaining structural stability. Retrospective studies show that CoDAH is able to identify variants deemed beneficial according to both humanness and structural stability criteria, even for targets lacking crystal structures. Prospective application to TZ47, a murine anti-human B7H6 antibody, demonstrates the approach. Four diverse humanized variants were designed, and all possible unique VH/VL combinations were produced as full-length IgG1 antibodies. Soluble and cell surface expressed antigen binding assays showed that 75% (6 of 8) of the computationally designed VH/VL variants were successfully expressed and competed with the murine TZ47 for binding to B7H6 antigen. Furthermore, 4 of the 6 bound with an estimated K_D within an order of magnitude of the original TZ47 antibody. In contrast, a traditional CDR-grafted variant could not be expressed. These results suggest that the computational protein design approach described here can be used to efficiently generate functional humanized antibodies and provide humanized templates for further affinity maturation.     

Generation of “LYmph Node Derived Antibody Libraries” (LYNDAL) for selecting fully human antibody fragments with therapeutic potential

The development of efficient strategies for generating fully human monoclonal antibodies with unique functional properties that are exploitable for tailored therapeutic interventions remains a major challenge in the antibody technology field. Here, we present a methodology for recovering such antibodies from antigen-encountered human B cell repertoires. As the source for variable antibody genes, we cloned immunoglobulin G (IgG)-derived B cell repertoires from lymph nodes of 20 individuals undergoing surgery for head and neck cancer. Sequence analysis of unselected “LYmph Node Derived Antibody Libraries” (LYNDAL) revealed a naturally occurring distribution pattern of rearranged antibody sequences, representing all known variable gene families and most functional germline sequences. To demonstrate the feasibility for selecting antibodies with therapeutic potential from these repertoires, seven LYNDAL from donors with high serum titers against herpes simplex virus (HSV) were panned on recombinant glycoprotein B of HSV-1. Screening for specific binders delivered 34 single-chain variable fragments (scFvs) with unique sequences. Sequence analysis revealed extensive somatic hypermutation of enriched clones as a result of affinity maturation. Binding of scFvs to common glycoprotein B variants from HSV-1 and HSV-2 strains was highly specific, and the majority of analyzed antibody fragments bound to the target antigen with nanomolar affinity. From eight scFvs with HSV-neutralizing capacity in vitro, the most potent antibody neutralized 50% HSV-2 at 4.5 nM as a dimeric (scFv)₂. We anticipate our approach to be useful for recovering fully human antibodies with therapeutic potential.     

Systematic optimization model and algorithm for binding sequence selection in computational enzyme design

A systematic optimization model for binding sequence selection in computational enzyme design was developed based on the transition state theory of enzyme catalysis and graph‐theoretical modeling. The saddle point on the free energy surface of the reaction system was represented by catalytic geometrical constraints, and the binding energy between the active site and transition state was minimized to reduce the activation energy barrier. The resulting hyperscale combinatorial optimization problem was tackled using a novel heuristic global optimization algorithm, which was inspired and tested by the protein core sequence selection problem. The sequence recapitulation tests on native active sites for two enzyme catalyzed hydrolytic reactions were applied to evaluate the predictive power of the design methodology. The results of the calculation show that most of the native binding sites can be successfully identified if the catalytic geometrical constraints and the structural motifs of the substrate are taken into account. Reliably predicting active site sequences may have significant implications for the creation of novel enzymes that are capable of catalyzing targeted chemical reactions.     

基于CA-Markov模型和多目标优化的大连市土地利用格局

运用马尔科夫转移矩阵、多准则评估以及元胞自动机耦合的CA-Markov模型,基于1990、2000、2010年土地利用图、地形因子和地理要素等,模拟大连市未来土地利用景观格局变化趋势.基于大连市土地利用结构、经济社会、自然环境等特点,结合大连市城市总体规划和土地利用规划,建立经济、社会、环境3个目标导向的模糊多目标优化模型,优化配置了大连市未来土地利用格局.结果表明:1990-2010年,大连的快速发展呈现出建设用地持续扩张而耕地、林地面积缩小的特点,以现有城市化速度发展,到2020年大连市景观格局土地覆盖将发生很大变化,景观破碎化程度将加剧.优化调整土地利用数量结构,能满足未来大连可持续发展的要求.