枫香叶片衰老过程中光合能力的变化

利用Li-6400XT便携式光合作用测定系统,于2014年10—12月测定枫香叶片衰老过程中光合作用光响应曲线,采用叶氏模型和非直角双曲线模型进行模拟,分析枫香叶片衰老过程中光合能力的变化.结果表明: 随着枫香叶片逐渐变黄变红,其净光合速率的光响应能力逐渐降低,实测的最大净光合速率从叶片开始泛黄时的2.88 μmol CO₂·m^-2·s^-1下降到叶片衰老后期(12月8日)的0.95 μmol CO₂·m^-2·s^-1.2种光响应模型均较好地模拟了观测的光响应数据,其中叶氏模型表现更优.模拟得到的最大净光合速率、表观量子效率、光补偿点的量子效率、暗呼吸速率等参数均随枫香叶片衰老凋落而逐渐下降,反映出枫香叶片衰老过程中光合能力缓慢下降的过程.在树梢红叶未落期间,枫香叶片仍具有一定的净光合作用能力,这有利于增加秋冬季节的碳吸收量.     

基于流域水环境响应的城市建设用地面积阈值模拟

城市扩张影响流域水环境质量.从水环境响应出发,模拟预测流域范围内城市建设用地的扩张阈值,可为城市建设用地规划提供客观依据.本文选取完全城市化的筼筜湖流域、半城市化的马銮湾流域和城市化起步阶段的杏林湾流域作为对比研究对象,结合2009—2012年实测数据,运用区域污染物管理模型(ReNuMa),计算3个流域水体污染物总氮(TN)和总磷(TP)环境容量上限,确定流域内城市建设用地面积阈值,并预测城市景观格局演变产生的水环境效应.结果表明: 筼筜湖、马銮湾和杏林湾的TN年负荷上限值分别为12900、42800和43120 kg,TP年负荷上限值分别为340、420和450 kg;现实情境下,筼筜湖水体污染物环境容量尚未饱和,马銮湾与杏林湾的污染物年负荷均接近上限值,杏林湾的TN和TP年负荷存在明显的上升趋势;3个流域污染物年负荷均在模拟情境1下未超标、情境3下超标,情境2下,筼筜湖污染物年负荷均未超标,而马銮湾TN与TP年负荷均处于超标;筼筜湖、马銮湾和杏林湾流域的城市建设用地面积阈值分别为1320、5600和4750 hm²,并据此提出景观格局调整对策建议.     

Introducing folding stability into the score function for computational design of RNA‐binding peptides boosts the probability of success

A computational strategy that integrates our peptide search algorithm with atomistic molecular dynamics simulation was used to design rational peptide drugs that recognize and bind to the anticodon stem and loop domain (ASL^Lys3) of human for the purpose of interrupting HIV replication. The score function of the search algorithm was improved by adding a peptide stability term weighted by an adjustable factor λ to the peptide binding free energy. The five best peptide sequences associated with five different values of λ were determined using the search algorithm and then input in atomistic simulations to examine the stability of the peptides' folded conformations and their ability to bind to ASL^Lys3. Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASL^Lys3. Thus, addition of a peptide stability term significantly improves the success rate for our peptide design search. Proteins 2016; 84:700–711. © 2016 Wiley Periodicals, Inc.     

Pressure‐induced conformational switch of an interfacial protein

A special class of proteins adopts an inactive conformation in aqueous solution and activates at an interface (such as the surface of lipid droplet) by switching their conformations. Lipase, an essential enzyme for breaking down lipids, serves as a model system for studying such interfacial proteins. The underlying conformational switch of lipase induced by solvent condition is achieved through changing the status of the gated substrate‐access channel. Interestingly, a lipase was also reported to exhibit pressure activation, which indicates it is drastically active at high hydrostatic pressure. To unravel the molecular mechanism of this unusual phenomenon, we examined the structural changes induced by high hydrostatic pressures (up to 1500 MPa) using molecular dynamics simulations. By monitoring the width of the access channel, we found that the protein undergoes a conformational transition and opens the access channel at high pressures (>100 MPa). Particularly, a disordered amphiphilic α5 region of the protein becomes ordered at high pressure. This positive correlation between the channel opening and α5 ordering is consistent with the early findings of the gating motion in the presence of a water–oil interface. Statistical analysis of the ensemble of conformations also reveals the essential collective motions of the protein and how these motions contribute to gating. Arguments are presented as to why heightened sensitivity to high‐pressure perturbation can be a general feature of switchable interfacial proteins. Further mutations are also suggested to validate our observations. Proteins 2016; 84:820–827. © 2016 Wiley Periodicals, Inc.     

Intrinsic disorder accelerates dissociation rather than association

The intrinsically disordered protein (IDP) has distinct properties both physically and biologically: it often becomes folded when binding to the target and is frequently involved in signal transduction. The physical property seems to be compatible with the biological property where fast association and dissociation between IDP and the target are required. While fast association has been well studied, fueled by the fly‐casting mechanism, the dissociation kinetics has received less attention. We here study how the intrinsic disorder affects the dissociation kinetics, as well as the association kinetics, paying attention to the interaction strength at the binding site (i.e., the quality of the “fly lure”). Coarse‐grained molecular dynamics simulation of the pKID‐KIX system, a well‐studied IDP system, shows that the association rate becomes larger as the disorder‐inducing flexibility that was imparted to the model is increased, but the acceleration is marginal and turns into deceleration as the quality of the fly lure is worsened. In contrast, the dissociation rate is greatly enhanced as the disorder is increased, indicating that intrinsic disorder serves for rapid signal switching more effectively through dissociation than association. Proteins 2016; 84:1124–1133. © 2016 Wiley Periodicals, Inc.     

Mechanical properties of armchair silicene nanoribbons with edge cracks: a molecular dynamics study

Silicene has been proven to be a promising material with attractive electronic properties. During the synthesis of silicene, structural defects such as edge crack are likely to be generated and such defects in silicene have impacts on its properties. Herein, molecular dynamics simulations were performed to investigate the mechanical properties of the armchair silicene nanoribbons (ASiNRs) with edge cracks. Our results showed that the mechanical properties of the ASiNRs decrease because of the existence of edge crack. Both the pristine ASiNRs and the ASiNRs with edge cracks show brittle fracture behaviours. The crack length plays an important role in determining the critical strain and fracture strength of the ASiNRs. Moreover, we investigated the effects of strain rate and temperature on the mechanical properties of the ASiNRs with edge cracks. We observed that the increasing strain rate increases the critical strain and fracture strength while decreasing the Young’s modulus. Low-strain rates also changes the expanded directions of cracks in the ASiNRs. We also found that the increasing temperature could significantly decrease the mechanical properties of the ASiNRs with edge cracks.     

Investigation of the role of disulphide bond in modulating internal motions of BmK AGAP protein by molecular dynamics simulation

Elucidating structural determinants in the functional regions of toxins can provide useful knowledge for designing novel analgesic peptides. A series of 100 ns MD simulations were performed on the scorpion toxin BmK AGAP in native and disulphide bond broken states. The comparison of disulphide bond broken states with the native state showed the α-helix was found to be the key to the analgesic activity. Furthermore, our results revealed disulphide bonds have considerable influence on the functionally important essential modes of motions and the correlations between the motions of the Core domain and the C-terminal region which are involved in the analgesic activity. Therefore, we can conclude that disulphide bonds have a crucial role in modulating the function via adjusting the dynamics of scorpion toxin BmK AGAP molecule.