Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure

The performance of the self-consistent mean field theory (SCMFT) method for side-chain modeling, employing rotamer energies calculated with the flexible rotamer model (FRM), is evaluated in the context of comparative modeling of protein structure. Predictions were carried out on a test set of 56 model backbones of varying accuracy, to allow side-chain prediction accuracy to be analyzed as a function of backbone accuracy. A progressive decrease in the accuracy of prediction was observed as backbone accuracy decreased. However, even for very low backbone accuracy, prediction was substantially higher than random, indicating that the FRM can, in part, compensate for the errors in the modeled tertiary environment. It was also investigated whether the introduction in the FRM-SCMFT method of knowledge-based biases, derived from a backbone-dependent rotamer library, could enhance its performance. A bias derived from the backbone-dependent rotamer conformations alone did not improve prediction accuracy. However, a bias derived from the backbone-dependent rotamer probabilities improved prediction accuracy considerably. This bias was incorporated through two different strategies. In one (the indirect strategy), rotamer probabilities were used to reject unlikely rotamers a priori, thus restricting prediction by FRM-SCMFT to a subset containing only the most probable rotamers in the library. In the other (the direct strategy), rotamer energies were transformed into pseudo-energies that were added to the average potential energies of the respective rotamers, thereby creating hybrid energy-based/knowledge-based average rotamer energies, which were used by the FRM-SCMFT method for prediction. For all degrees of backbone accuracy, an optimal strength of the knowledge-based bias existed for both strategies for which predictions were more accurate than pure energy-based predictions, and also than pure knowledge-based predictions. Hybrid knowledge-based/energy-based methods were obtained from both strategies and compared with the SCWRL method, a hybrid method based on the same backbone-dependent rotamer library. The accuracy of the indirect method was approximately the same as that of the SCWRL method, but that of the direct method was significantly higher.     

Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins

An alpha-helix and a beta-strand are said to be interactively packed if at least one residue in each of the secondary structural elements loses 10% of its solvent accessible contact area on association with the other secondary structural element. An analysis of all such 5,975 nonidentical alpha/beta units in protein structures, defined at < or = 2.5 A resolution, shows that the interaxial distance between the alpha-helix and the beta-strand is linearly correlated with the residue-dependent function, log[(V/nda)/n-int], where V is the volume of amino acid residues in the packing interface, nda is the normalized difference in solvent accessible contact area of the residues in packed and unpacked secondary structural elements, and n-int is the number of residues in the packing interface. The beta-sheet unit (beta u), defined as a pair of adjacent parallel or antiparallel hydrogen-bonded beta-strands, packing with an alpha-helix shows a better correlation between the interaxial distance and log(V/nda) for the residues in the packing interface. This packing relationship is shown to be useful in the prediction of interaxial distances in alpha/beta units using the interacting residue information of equivalent alpha/beta units of homologous proteins. It is, therefore, of value in comparative modeling of protein structures.     

MICAS: a fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences

MICAS is a web server for extracting microsatellite information from completely sequenced prokaryote and viral genomes, or user-submitted sequences. This server provides an integrated platform for MICdb (database of prokaryote and viral microsatellites), W-SSRF (simple sequence repeat finding program) and Autoprimer (primer design software). MICAS, through dynamic HTML page generation, helps in the systematic extraction of microsatellite information from selected genomes hosted on MICdb or from user-submitted sequences. Further, it assists in the design of primers with the help of Autoprimer, for sequences containing selected microsatellite tracts.     

Influence of solvent molecules on the stereochemical code of glycyl residues in proteins

The Ramachandran steric map and energy diagrams of the glycyl residue are symmetric. A plot of (phi,psi) angles of glycyl residues in 250 nonhomologous and high-resolution protein structures is also largely symmetric. However, there is a clear aberration in the symmetry. Although there is a cluster of points corresponding to the right-handed alpha-helical region, the "equivalent" cluster is clearly shifted to in and around the (phi,psi) values of (90 degrees, 0 degrees ) instead of being centered at the left-handed alpha-helical region of (60 degrees, 40 degrees ). This lack of symmetry exists even in the (phi,psi) distribution of residues from non-alpha-helical regions in proteins. Here we provide an explanation for this observation. An analysis of glycyl conformations in small peptide structures and in "coil" proteins, which are largely devoid of helical and sheet regions, shows that glycyl residues prefer to adopt conformations around (+/-90 degrees, 0 degrees ) instead of right- and left-handed alpha-helical regions. By using theoretical calculations, such conformations are shown to have highest solvent accessibility in a system of two-linked peptide units with glycyl residue at the central C(alpha) atom. This finding is consistent with the observations from 250 nonhomologous protein structures where glycyl residues with conformations close to (+/-90 degrees, 0 degrees ) are seen to have high solvent accessibility. Analysis of a subset of nonhomologous structures with very high resolution (1.5 A or better) shows that water molecules are indeed present at distances suitable for hydrogen bond interaction with glycyl residues possessing conformations close to (+/-90 degrees, 0 degrees ). It is suggested that water molecules play a key role in determining and stabilizing these conformations of glycyl residues and explain the aberration in the symmetry of glycyl conformations in proteins.     

Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments

Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates'' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the ‘burial and isolation'' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development.     

基因工程改善植物生物质能利用的研究进展

利用植物木质纤维资源发酵产乙醇越来越受到人们的重视,但是要达到工业生产仍然存在很多难题。最近在利用植物基因工程技术改善植物自身性状,以利于能源植物的研究方面取得了一定的进展,这些研究包括减少植物自身细胞壁中的木质素含量、细胞中积累表达纤维素酶和木聚耱酶等的方法,使产生的生物质更利于降解利用。     

IMEx: Imperfect Microsatellite Extractor

MOTIVATION: Microsatellites, also known as simple sequence repeats, are the tandem repeats of nucleotide motifs of the size 1-6 bp found in every genome known so far. Their importance in genomes is well known. Microsatellites are associated with various disease genes, have been used as molecular markers in linkage analysis and DNA fingerprinting studies, and also seem to play an important role in the genome evolution. Therefore, it is of importance to study distribution, enrichment and polymorphism of microsatellites in the genomes of interest. For this, the prerequisite is the availability of a computational tool for extraction of microsatellites (perfect as well as imperfect) and their related information from whole genome sequences. Examination of available tools revealed certain lacunae in them and prompted us to develop a new tool. RESULTS: In order to efficiently screen genome sequences for microsatellites (perfect as well as imperfect), we developed a new tool called IMEx (Imperfect Microsatellite Extractor). IMEx uses simple string-matching algorithm with sliding window approach to screen DNA sequences for microsatellites and reports the motif, copy number, genomic location, nearby genes, mutational events and many other features useful for in-depth studies. IMEx is more sensitive, efficient and useful than the available widely used tools. IMEx is available in the form of a stand-alone program as well as in the form of a web-server. AVAILABILITY: A World Wide Web server and the stand-alone program are available for free access at http://203.197.254.154/IMEX/ or http://www.cdfd.org.in/imex.     

Double intratibial injection of human tonsil-derived mesenchymal stromal cells recovers postmenopausal osteoporotic bone mass

Background and aims

Osteoporosis, which is a disease characterized by weakening of the bone, affects a large portion of the senior population. The current therapeutic options for osteoporosis have side effects, and there is no effective treatment for severe osteoporosis. Thus, we urgently need new treatment strategies, such as topical therapies and/or safe and effective stem cell therapies.