Do salt bridges stabilize proteins? A continuum electrostatic analysis

The electrostatic contribution to the free energy of folding was calculated for 21 salt bridges in 9 protein X-ray crystal structures using a continuum electrostatic approach with the DELPHI computer-program package. The majority (17) were found to be electrostatically destabilizing; the average free energy change, which is analogous to mutation of salt bridging side chains to hydrophobic isosteres, was calculated to be 3.5 kcal/mol. This is fundamentally different from stability measurements using pKa shifts, which effectively measure the strength of a salt bridge relative to 1 or more charged hydrogen bonds. The calculated effect was due to a large, unfavorable desolvation contribution that was not fully compensated by favorable interactions within the salt bridge and between salt-bridge partners and other polar and charged groups in the folded protein. Some of the salt bridges were studied in further detail to determine the effect of the choice of values for atomic radii, internal protein dielectric constant, and ionic strength used in the calculations. Increased ionic strength resulted in little or no change in calculated stability for 3 of 4 salt bridges over a range of 0.1-0.9 M. The results suggest that mutation of salt bridges, particularly those that are buried, to "hydrophobic bridges" (that pack at least as well as wild type) can result in proteins with increased stability. Due to the large penalty for burying uncompensated ionizable groups, salt bridges could help to limit the number of low free energy conformations of a molecule or complex and thus play a role in determining specificity (i.e., the uniqueness of a protein fold or protein-ligand binding geometry).     

Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories.

This paper explores the dependence of the molecular dynamics (MD) trajectory of a protein molecule on the titration state assigned to the molecule. Four 100-ps MD trajectories of bovine pancreatic trypsin inhibitor (BPTI) were generated, starting from two different structures, each of which was held in two different charge states. The two starting structures were the X-ray crystal structure and one of the solution structures determined by NMR, and the charge states differed only in the ionization state of N terminus. Although it is evident that the MD simulations were too short to sample fully the equilibrium distribution of structures in each case, standard Poisson-Boltzmann titration state analysis of the resulting configurations shows general agreement between the overall titration behavior of the protein and the charge state assumed during MD simulation: at pH 7, the total net charge of the protein resulting from the titration analysis is consistently lower for the protein with the N terminus assumed to be neutral than for the protein with the N terminus assumed to be charged. For most of the ionizable residues, the differences in the calculated pKaS among the four trajectories are statistically negligible and remain in good agreement with the data obtained by crystal structure titration and by experiment. The exceptions include the N terminus, which responds directly to the change of its imposed charge; the C terminus, which in the NMR structure interacts strongly with the former; and a few other residues (Arg 1, Glu 7, Tyr 35, and Arg 42) whose pKaS reflect the initial structure and the limited trajectory lengths. This study illustrates the importance of the careful assignment of protonation states at the start of MD simulations and points to the need for simulation methods that allow for the variation of the protonation state in the calculation of equilibrium properties.     

香溪河河流连续统特征研究

以香溪河附石藻类密度、藻类叶绿素a浓度、Shannon-Wiener多样性指数及生态系统初级生产力随河流级别的变化为例探索该河流的连续统特征。结果表明,附石藻类密度、藻类叶绿素a浓度和Shannon-Wiener多样性指数总体上都有随着河流级别增加而增加的趋势,但在1～3级河段之间这种趋势并不明显,甚至出现了逆转。河流初级生产力也有随河流级别增加而增加的趋势,并在第4级河流达到最大,随后有所下降。在全水系范围内河流初级生产力(P)与群落呼吸(R)比值P／R均大于1,说明香溪河是一条以自养生产为主的河流。所研究的特征并不完全与连续统概念的预测相一致,表明河流已经受到了一定程度的人为干扰。     

基于可见光波段包络线去除的湿地植物叶片叶绿素估算

研究采用芦苇和香蒲叶片光谱及实测叶绿素含量数据,选取波段谱带范围为可见光波段400—760nm(为了避免近红外波段受叶片水分含量的影响,降低构建模型的稳定性),利用相关分析与逐步回归分析的统计学分析方法,建立叶面尺度下不同包络线去除衍生转换光谱:BD(band depth)、CRDR(continuum-removed derivative reflectance)、BDR(band depth ratio)、NBDI(normalized band depth index)与叶绿素含量估算模型。通过对入选波段的统计表明在550—750nm,特别是700—750nm(红边)波段范围内产生了较多的有效波段,是今后进行生物参量反演的重点波段范围。舍一交叉验证结果表明芦苇、香蒲和混合样本绿素含量估测的最佳模型分别为BD、CRDR和NBDI模型,其交叉验证决定系数依次为0.87、0.83和0.81,交叉验证均方根误差RMSE依次为0.16、0.15和0.33。并在此基础上利用独立样本非参数检验和多因子方差分析,探讨相关因素对于叶绿素含量估算模型精度的影响。结果表明物种差异、数据类型差异对于叶绿素回归模型的影响较大,而光谱类型差异及光谱数据与数据类型交互作用对于回归模型精度的影响较小。     

Changes in nitrogen cycling and retention processes in soils under spruce forests along a nitrogen enrichment gradient in Germany

A network of long-term monitoring sites on nitrogen (N) input and output of forests across Germany showed that a number of Germany's forests are subject to or are experiencing N saturation and that spruce (Picea abies) stands have high risk. Our study was aimed at (1) quantifying the changes in gross rates of microbial N cycling and retention processes in forest soils along an N enrichment gradient and (2) relating the changes in soil N dynamics to N losses. We selected spruce sites representing an N enrichment gradient (indicated by leaching : throughfall N ratios) ranging from 0.04–0.13 (low N),≤0.26 (intermediate N enrichment) to≥0.42 (highly N enriched). To our knowledge, our study is the first to report on mechanistic changes in gross rates of soil N cycling and abiotic NO₃⁻ retention under ambient N enrichment gradient. Gross N mineralization, NH₄⁺ immobilization, gross nitrification, and NO₃⁻ immobilization rates increased up to intermediate N enrichment level and somewhat decreased at highly N-enriched condition. The turnover rates of NH₄⁺ and microbial N pools increased while the turnover rates of the NO₃⁻ pool decreased across the N enrichment gradient. Abiotic immobilization of NH₄⁺ did not differ across sites and was lower than that of NO₃⁻. Abiotic NO₃⁻ immobilization decreased across the N enrichment gradient. Microbial assimilation and turnover appeared to contribute largely to the retention of NH₄⁺. The increasing NO₃⁻ deposition and decreasing turnover rates of the NO₃⁻ pool, combined with decreasing abiotic NO₃⁻ retention, possibly contributed to increasing NO₃⁻ leaching and gaseous emissions across the N enrichment gradient. The empirical relationships of changes in microbial N cycling across the N enrichment gradient may be integrated in models used to predict responses of forest ecosystems (e.g. spruce) to increasing N deposition.     

基于稳定同位素的SPAC水碳拆分及耦合研究进展

土壤-植被-大气连续体(SPAC)是陆地水文学、生态学和全球变化领域的重要研究对象,其水碳循环过程及耦合机制是前沿性问题.稳定同位素技术示踪、整合和指示的特征有助于评估分析生态系统固碳和耗水情况.本文在简述稳定同位素应用原理和技术的基础上,重点阐释了基于稳定同位素光学技术的SPAC系统水碳交换研究进展,包括:在净碳通量中拆分光合与呼吸量,在蒸散通量中拆分蒸腾与蒸发量,以及在系统尺度上的水碳耦合研究.新兴的技术和方法实现了生态系统尺度上长期高频的同位素观测,但在测量精准度、生态系统呼吸拆分、非稳态模型适应性、尺度转换和水碳耦合机制等方面存在挑战.本文探讨了现有主要研究成果、局限性以及未来研究展望,以期对稳定同位素生态学领域的新研究和技术发展有所帮助.     

植物根系吸水机理的研究进展

近年来,植物根系吸水机理在细胞、组织和整体水平上的研究进展非常迅速,对阐明植物抗旱机制及其高效利用有限水资源途径的探讨具有重要意义.本文主要对植物根的复合结构和根系在土壤中的分布、根系中水流性质等方面的最新研究状况进行了概述,特别详细地论述了水通道蛋白的表达及功能与根系中水分运动的关系、以及根系输水的调节和根系吸水过程中的信号传导方面的研究动态,并且评价了根的复合运输模型和根系吸水的数学模型等,最后就其可能生理意义及其应用前景作了评述.     

Is population subdivision different from speciation? From phylogeography to species delimitation

Species‐level diversity and the underlying mechanisms that lead to the formation of new species, that is, speciation, have often been confounded with intraspecific diversity and population subdivision. The delineation between intraspecific and interspecific divergence processes has received much less attention than species delimitation. The ramifications of confounding speciation and population subdivision are that the term speciation has been used to describe many different biological divergence processes, rendering the results, or inferences, between studies incomparable. Phylogeographic studies have advanced our understanding of how spatial variation in the pattern of biodiversity can begin, become structured, and persist through time. Studies of species delimitation have further provided statistical and model‐based approaches to determine the phylogeographic entities that merit species status. However, without a proper understanding and delineation between the processes that generate and maintain intraspecific and interspecific diversity in a study system, the delimitation of species may still not be biologically and evolutionarily relevant. I argue that variation in the continuity of the divergence process among biological systems could be a key factor leading to the enduring contention in delineating divergence patterns, or species delimitation, meriting future comparative studies to help us better understand the nature of biological species.     

人为干扰对溪流鱼类功能多样性及其纵向梯度格局的影响

溪流鱼类多样性沿着河流纵向梯度的空间分布规律已得到大量报道, 但这些研究大多聚焦基于物种组成的分类α多样性, 而有关分类β多样性和功能多样性的纵向梯度分布规律及其对人类干扰的响应研究较少。本文以青弋江上游3条人为干扰程度不同的河源溪流为研究区域, 比较研究了人为干扰对溪流鱼类功能α和β多样性及其纵向梯度分布格局的影响。结果显示, 人类干扰改变了河源溪流鱼类功能多样性的纵向梯度格局——由线性变化变为二项式分布。此外, 我们发现, 人为干扰导致土著种被本地入侵种取代, 且较强的土地利用和水污染排放可能增大环境的不连续性, 而群落周转和嵌套变化往往取决于环境的变化。尽管功能β多样性由嵌套成分主导, 但周转成分占比相对于人为干扰较小的溪流而言明显增加。人为干扰显著改变了受干扰溪流鱼类的物种组成和功能多样性, 且功能多样性的纵向梯度格局在不同的多样性指标上存在差异。本研究强调, 在评估人为干扰下多样性的变化时, 需要从多方面考虑, 包括空间尺度和多样性指标等。     

A mixed finite element formulation for a non-linear,transversely isotropic material model for the cardiac tissue

In this paper we present a mixed finite element method for modeling the passive properties of the myocardium. The passive properties are described by a non-linear, transversely isotropic, hyperelastic material model, and the myocardium is assumed to be almost incompressible. Single-field, pure displacement-based formulations are known to cause numerical difficulties when applied to incompressible or slightly compressible material cases. This paper presents an alternative approach in the form of a mixed formulation, where a separately interpolated pressure field is introduced as a primary unknown in addition to the displacement field. Moreover, a constraint term is included in the formulation to enforce (almost) incompressibility. Numerical results presented in the paper demonstrate the difficulties related to employing a pure displacement-based method, applying a set of physically relevant material parameter values for the cardiac tissue. The same problems are not experienced for the proposed mixed method. We show that the mixed formulation provides reasonable numerical results for compressible as well as nearly incompressible cases, also in situations of large fiber stretches. There is good agreement between the numerical results and the underlying analytical models.