On the relationship between Pielou’s evenness and landscape dominance within the context of Hill’s diversity profiles

Entropy-related biodiversity indices deriving their conceptual basis from Shannon’s information theory have a long history of use in ecology for quantifying community structure and diversity. In addition, in the last two decades, numerous information–theoretical indices, such as the landscape dominance index, have been extensively applied to characterize landscape diversity in space and time. In this contribution, we offer a simple analytical relation between Pielou’s evenness J and landscape dominance D within the broader context of Hill’s parametric diversity family. Within this context, we recommend the use of Hill’s diversity number evenness E_1,0 to overcome the shortcomings both of Pielou’s evenness J and the landscape dominance index D.     

Evidence of α fluctuations in myoglobin's denaturation in the high temperature region: Average relaxation time from an Adam–Gibbs perspective

In this work, we derive an analytical expression for the relaxation time τ as a function of temperature T for myoglobin protein (Mb, PDB:1MBN) in the high temperature limit (T > T_g = 200 K). The method is based on a modified version of the Adam–Gibbs theory (AG theory) for the glass transition in supercooled liquids and an implementation of differential geometry techniques. This modified version of the AG theory takes into account that the entropic component in protein's denaturation has two major sources: a configurational contribution ΔS_c due to the unfolding of the highly ordered native state N and a hydration contribution ΔS^hyd arising from the exposure of non-polar residues to direct contact with solvent polar molecules. Our results show that the configurational contribution ΔS_c is temperature-independent and one order of magnitude smaller than its hydration counterpart ΔS^hyd in the temperature range considered. The profile obtained for log τ(T) from T = 200 K to T = 300 K exhibits a non-Arrhenius behavior characteristic of α relaxation mechanisms in hydrated proteins and glassy systems. This result is in agreement with recent dielectric spectroscopy data obtained for hydrated myoglobin, where at least two fast relaxation processes in the high temperature limit have been observed. The connection between the relaxation process calculated here and the experimental results is outlined.     

Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures

A new method, called Protonate3D, is presented for the automated prediction of hydrogen coordinates given the 3D coordinates of the heavy atoms of a macromolecular structure. Protonate3D considers side-chain "flip," rotamer, tautomer, and ionization states of all chemical groups, ligands, and solvent, provided suitable templates are available in a parameter file. The energy model includes van der Waals, Coulomb, solvation, rotamer, tautomer, and titration effects. The results of computational validation experiments suggest that Protonate3D can accurately predict the location of hydrogen atoms in macromolecular structures.     

Free‐energy function based on an all‐atom model for proteins

We have developed a free‐energy function based on an all‐atom model for proteins. It comprises two components, the hydration entropy (HE) and the total dehydration penalty (TDP). Upon a transition to a more compact structure, the number of accessible configurations arising from the translational displacement of water molecules in the system increases, leading to a water‐entropy gain. To fully account for this effect, the HE is calculated using a statistical‐mechanical theory applied to a molecular model for water. The TDP corresponds to the sum of the hydration energy and the protein intramolecular energy when a fully extended structure, which possesses the maximum number of hydrogen bonds with water molecules and no intramolecular hydrogen bonds, is chosen as the standard one. When a donor and an acceptor (e.g., N and O, respectively) are buried in the interior after the break of hydrogen bonds with water molecules, if they form an intramolecular hydrogen bond, no penalty is imposed. When a donor or an acceptor is buried with no intramolecular hydrogen bond formed, an energetic penalty is imposed. We examine all the donors and acceptors for backbone‐backbone, backbone‐side chain, and side chain‐side chain intramolecular hydrogen bonds and calculate the TDP. Our free‐energy function has been tested for three different decoy sets. It is better than any other physics‐based or knowledge‐based potential function in terms of the accuracy in discriminating the native fold from misfolded decoys and the achievement of high Z‐scores. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Computational protein design with side-chain conformational entropy

Recent advances in modeling protein structures at the atomic level have made it possible to tackle "de novo" computational protein design. Most procedures are based on combinatorial optimization using a scoring function that estimates the folding free energy of a protein sequence on a given main-chain structure. However, the computation of the conformational entropy in the folded state is generally an intractable problem, and its contribution to the free energy is not properly evaluated. In this article, we propose a new automated protein design methodology that incorporates such conformational entropy based on statistical mechanics principles. We define the free energy of a protein sequence by the corresponding partition function over rotamer states. The free energy is written in variational form in a pairwise approximation and minimized using the Belief Propagation algorithm. In this way, a free energy is associated to each amino acid sequence: we use this insight to rescore the results obtained with a standard minimization method, with the energy as the cost function. Then, we set up a design method that directly uses the free energy as a cost function in combination with a stochastic search in the sequence space. We validate the methods on the design of three superficial sites of a small SH3 domain, and then apply them to the complete redesign of 27 proteins. Our results indicate that accounting for entropic contribution in the score function affects the outcome in a highly nontrivial way, and might improve current computational design techniques based on protein stability.     

OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries

In this article, we present a de novo method for predicting protein domain boundaries, called OPUS-Dom. The core of the method is a novel coarse-grained folding method, VECFOLD, which constructs low-resolution structural models from a target sequence by folding a chain of vectors representing the predicted secondary-structure elements. OPUS-Dom generates a large ensemble of folded structure decoys by VECFOLD and labels the domain boundaries of each decoy by a domain parsing algorithm. Consensus domain boundaries are then derived from the statistical distribution of the putative boundaries and three empirical sequence-based domain profiles. OPUS-Dom generally outperformed several state-of-the-art domain prediction algorithms over various benchmark protein sets. Even though each VECFOLD-generated structure contains large errors, collectively these structures provide a more robust delineation of domain boundaries. The success of OPUS-Dom suggests that the arrangement of protein domains is more a consequence of limited coordination patterns per domain arising from tertiary packing of secondary-structure segments, rather than sequence-specific constraints.     

基于信息论k—modes聚类法的基因表达数据分析

k-均值聚类算法是一种广泛应用于基因表达数据聚类分析中的迭代变换算法,它通常用距离法来表示基因间的关系,但不能有效的反应基因间的相互依赖的关系。为此,提出基于信息论的k-modes聚类算法,克服了以上缺点。另外,还引入了伪F统计量,一方面,可以对空间中有部分重叠的点进行有效的分类;另一方面,可以给出最佳聚类数目,从而弥补了k-modes聚类法的不足。使其成为一种非常有效的算法,从而达到较优的聚类效果。     

芒和五节芒在中国的潜在分布

利用最大熵模型, 将我国现有芒(Miscanthus sinensis)和五节芒(M. floridulus)的地理分布信息与19个降水及温度等气候因子相拟合, 预测了芒和五节芒在我国的潜在分布区域, 并推测出芒和五节芒的基本生态位。结果显示: 芒的潜在适生区包括四川西部、陕西北部、宁夏、内蒙古中部、黑龙江、吉林西部、辽宁西部、青海东南部等地区, 其基本生态位参数为: 最暖季节降水量为400-1 000 mm, 平均8月降水量为100-350 mm, 7月平均最低气温为15 ℃, 平均7月降水量为100-350 mm, 11月平均最高气温为-10-22 ℃, 最干月平均气温为-15-20 ℃, 平均12月降水量为100 mm以下; 五节芒的潜在适生区为云南、陕西、山西、宁夏、河南、山东、吉林、辽宁以及四川西部、甘肃南部和内蒙古东部等地区, 其基本生态位参数为: 最暖季节降水量至少在400 mm以上, 平均6月降水量为150-550 mm, 7月平均最低气温在15-30 ℃之间, 6月平均最低气温为10 ℃, 平均4月降水量为50-100 mm。结果表明, 在进行遗传改良的前提下, 我国有丰富的适合栽植芒和五节芒的土地资源。     

Prediction of Potential Geological Distribution of Asarum in China by Maxent Model

Genus Asarum contains several plant species that are mostly used as precious drug resources. In this study, 126 distribution records of 3 Asarum species and relevant 28 environmental factors data were collected, then a geographical distribution model of the genus medicinal plants in China was made by Maxent and the ArcGIS spatial analysis technique. The results showed that the 3 Asarum species have a wide potential distribution region. High suitable region and suitable region were 3125km2 and 276042km2 respectively. Among the environmental factors, 3 precipitation factors (annual precipitation, precipitations in the most dry season and the most warm season) are the main ones that can affect the distribution of the 3 Asarum medicinal plants. This study can provide a useful reference for the collection and cultivation of Asarum medicinal plants.