Classification of 29 families of secondary transport proteins into a single structural class using hydropathy profile analysis

A classification scheme for membrane proteins is proposed that clusters families of proteins into structural classes based on hydropathy profile analysis. The averaged hydropathy profiles of protein families are taken as fingerprints of the 3D structure of the proteins and, therefore, are able to detect more distant evolutionary relationships than amino acid sequences. A procedure was developed in which hydropathy profile analysis is used initially as a filter in a BLAST search of the NCBI protein database. The strength of the procedure is demonstrated by the classification of 29 families of secondary transporters into a single structural class, termed ST[3]. An exhaustive search of the database revealed that the 29 families contain 568 unique sequences. The proteins are predominantly from prokaryotic origin and most of the characterized transporters in ST[3] transport organic and inorganic anions and a smaller number are Na(+)/H(+) antiporters. All modes of energy coupling (symport, antiport, uniport) are found in structural class ST[3]. The relevance of the classification for structure/function prediction of uncharacterised transporters in the class is discussed.     

CARBANA: Carbon analysis program forprotein sequences

There are lots of works gone into proteins to understand the nature of proteins. Hydrophobic interaction is the dominant force that drives the proteins to carry out the biochemical reactions in all living system. Carbon is the only element that contributes towards this hydrophobic interaction. Studies find that globular proteins prefer to have 31.45% of carbon for its stability. Taking this as standard, a carbon analysis program has been developed to study the carbon distribution profile of protein sequences. This carbon analysis program has been made available online. This can be accessed at www.rajasekaran.net.in/tools/carbana.html. This new program is hoped to help in identification and development of active sites, study of protein stability, evolutionary understating of proteins, gene identification, ligand binding site identification, and to solve the long-standing problem of protein-protein and protein-DNA interactions.     

氨基酸组成聚类、蛋白质结构型和结构型的预测

用信息聚类方法对蛋白质的氨基酸组成进行聚类,发现存在梯级成团（大集团分解成小集团）现象,６４５个蛋白质可分成１５个小集团,每一个小集团与蛋白质二级结构含量决定的结构型有一定相关性,但与蛋白质五大结构型相关性不明显。指出了由氨基酸成分和二级结构含量预测结构型的方案中存在的问题。提出了由蛋白质二级结构序列预测蛋白质结构型的新方法,并给出了预测蛋白质结构型的简明预测规则     

Public services from the European Bioinformatics Institute

The European Bioinformatics Institute (EBI) provides numerous free-of-charge, publicly available bioinformatics services that can be divided into the following categories: ftp downloads; data submissions processing and biological database production; access to query; analysis and retrieval systems and tools; user support; training and education and industry support through EBI's SME program. These services are all available at the website. It is imperative that EBI's data as well as the tools to analyse it efficiently are made available in a free and unambiguous way to the scientific community. An important part of the EBI's mission is to make this happen in a fast, reliable and efficient manner. This paper serves as a brief introduction to each of these services.     

一种新的蛋白质结构类预测方法

基于氨基酸的16种分类模型,给出蛋白质序列的派生序列,进而结合加权拟熵和LZ复杂度构造出34维特征向量来表示蛋白质序列。借助于贝叶斯分类器对同源性不超过25%的640数据集进行蛋白质结构类预测,准确度达到71.28%。     

Primary structure of the hemoglobin alpha-chain of rose-ringed parakeet (Psittacula krameri)

The structure of the hernoglobin -chain of Rose-ringed Parakeet was determined by sequence degradations of the intact subunit, the CNBr fragments, and peptides obtained by digestion with staphylococcal Glu-specific protease and trypsin. Using this analysis, the complete -chain structure of 21 avian species is known, permitting comparisons of the protein structure and of avian relationships. The structure exhibits differences from previously established avian -chains at a total of 61 positions, five of which have residues unique to those of the parakeet (Ser-12, Gly-65, Ser-67, Ala-121, and Leu-134). The analysis defines hemoglobin variation within an additional avian order (Psittaciformes), demonstrates distant patterns for evaluation of relationships within other avian orders, and lends support to taxonomic conclusions from molecular data.     

Recognition of distantly related proteins through energy calculations

A new method to detect remote relationships between protein sequences and known three-dimensional structures based on direct energy calculations and without reliance on statistics has been developed. The likelihood of a residue to occupy a given position on the structural template was represented by an estimate of the stabilization free energy made after explicit prediction of the substituted side chain conformation. The profile matrix derived from these energy values and modified by increasing the residue self-exchange values successfully predicted compatibility of heatshock protein and globin sequences with the three-dimensional structures of actin and phycocyanin, respectively, from a full protein sequence databank search. The high sensitivity of the method makes it a unique tool for predicting the three-dimensional fold for the rapidly growing number of protein sequences. © 1994 Wiley-Liss, Inc.     

Combinatorial complexity of pathway analysis in metabolic networks

Elementary flux mode analysis is a promising approach for a pathway-oriented perspective of metabolic networks. However, in larger networks it is hampered by the combinatorial explosion of possible routes. In this work we give some estimations on the combinatorial complexity including theoretical upper bounds for the number of elementary flux modes in a network of a given size. In a case study, we computed the elementary modes in the central metabolism of Escherichia coli while utilizing four different substrates. Interestingly, although the number of modes occurring in this complex network can exceed half a million, it is still far below the upper bound. Hence, to a certain extent, pathway analysis of central catabolism is feasible to assess network properties such as flexibility and functionality.     

Resistance to ship-induced waves of benthic invertebrates in various littoral habitats

1. Ship‐induced waves disturb benthic invertebrate assemblages colonizing littoral zones of lakes and rivers. However, the impact of ship‐induced waves on invertebrates has rarely been quantified, and the influencing factors have not been addressed. 2. In an experimental wave tank, five benthic invertebrate species, Bithynia tentaculata, Calopteryx splendens, Dikerogammarus villosus, Gammarus roeseli and Laccophilus hyalinus, were exposed to waves of increasing shear stress (0.43–2.19 N m^?2). Mean number of detached individuals was recorded for five littoral habitats [coarse woody debris (CWD), reeds, sand, stones and tree roots], representing different levels of structural complexity as quantified by their fractal dimensions (FD). 3. Results showed that detachment of invertebrates was significantly related to shear stress in all habitats except tree roots. Detachments averaged for the five species were significantly lower in habitats with a high degree of structural complexity, decreasing in the habitat sequence: sand, CWD, stones, reeds and tree roots. 4. Consistent with their different morphologies and methods of attachment to substrates, the five species displayed differences in their response to hydraulic stress that were dependent on habitat. 5. The increasing sheltering effect of structural habitat complexity was mirrored by increasing dissipation of the kinetic energy of waves; i.e. the FD of the habitat was positively correlated with shear stress reduction due to the flow resistance of the habitat. 6. Network habitats such as tree roots provided the best sheltering conditions against hydraulic disturbance, because they combined good refuge availability for all studied invertebrate species and maximal dissipation of kinetic wave energy. Consequently, persistent anthropogenic impacts, such as lakeshore modification or long‐term exposure to ship‐induced waves, which cause disappearance of complex littoral habitats such as tree roots or dense reed belts, will drastically increase the adverse effects of boating and ship traffic on littoral invertebrate assemblages.     

Aggregate Measures of Complex Economic Structure and Evolution

It is perhaps in the nature of complex systems that they call for aggregate measures that enable analysts to grasp their structure and evolution without being overwhelmed by their very complexity. Complex interindustry theory and models are a typical case, where the underlying database—an input−output table—routinely contains thousands of data points for a single year. Within input−output analysis, quantitative measures have been developed that describe and characterize interindustry interactions and that have been used to compare economies, both in a static taxonomy and through their evolution over time. First, we review and critically discuss a number of concepts that have been proposed and applied to interindustry systems, such as interconnectedness, interrelatedness, linkages, and economic landscapes. Second, we apply these concepts to a case study of the Australian economy between 1975 and 1999 in terms of environmental headline indicators. Our results enable the reader to judge the usefulness and ability of the measures in capturing the key structural elements and evolutionary processes governing the interaction between the economy and the environment. For the Australian case study, the measures showed a diversifying economy occurring together with a specialization of environmental flows.