共查询到20条相似文献,搜索用时 15 毫秒
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Background
The database of protein structures contains representatives from organisms with a range of growth temperatures. Various properties have been studied in a search for the molecular basis of protein adaptation to higher growth temperature. Charged groups have emerged as key distinguishing factors for proteins from thermophiles and mesophiles. 相似文献3.
Dan M Bolser Ioannis Filippis Henning Stehr Jose Duarte Michael Lappe 《BMC structural biology》2008,8(1):53
Background
For over 30 years potentials of mean force have been used to evaluate the relative energy of protein structures. The most commonly used potentials define the energy of residue-residue interactions and are derived from the empirical analysis of the known protein structures. However, single-body residue 'environment' potentials, although widely used in protein structure analysis, have not been rigorously compared to these classical two-body residue-residue interaction potentials. Here we do not try to combine the two different types of residue interaction potential, but rather to assess their independent contribution to scoring protein structures. 相似文献4.
Background
Bioactive cyclic peptides derived from natural sources are well studied, particularly those derived from non-ribosomal synthetases in fungi or bacteria. Ribosomally synthesised bioactive disulphide-bonded loops represent a large, naturally enriched library of potential bioactive compounds, worthy of systematic investigation.Results
We examined the distribution of short cyclic loops on the surface of a large number of proteins, especially membrane or extracellular proteins. Available three-dimensional structures highlighted a number of disulphide-bonded loops responsible for the majority of the likely binding interactions in a variety of protein complexes, due to their location at protein-protein interfaces. We find that disulphide-bonded loops at protein-protein interfaces may, but do not necessarily, show biological activity independent of their parent protein. Examining the conservation of short disulphide bonded loops in proteins, we find a small but significant increase in conservation inside these loops compared to surrounding residues. We identify a subset of these loops that exhibit a high relative conservation, particularly among peptide hormones.Conclusions
We conclude that short disulphide-bonded loops are found in a wide variety of biological interactions. They may retain biological activity outside their parent proteins. Such structurally independent peptides may be useful as biologically active templates for the development of novel modulators of protein-protein interactions.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-305) contains supplementary material, which is available to authorized users. 相似文献5.
Background
An efficient building block for protein structure prediction can be tripeptides. 8000 different tripeptides from a dataset of 1220 high resolution (≤ 2.0°A) structures from the Protein Data Bank (PDB) have been looked at, to determine which are structurally rigid and non-rigid. This data has been statistically analyzed, discussed and summarized. The entire data can be utilized for the building of protein structures. 相似文献6.
Background
Template-target sequence alignment and loop modeling are key components of protein comparative modeling. Short loops can be predicted with high accuracy using structural fragments from other, not necessairly homologous proteins, or by various minimization methods. For longer loops multiscale approaches employing coarse-grained de novo modeling techniques should be more effective. 相似文献7.
Background
Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins, but so far there has been less focus on the objective comparison between the alignments produced by different methods. 相似文献8.
Background
The use of knowledge-based potential function is a powerful method for protein structure evaluation. A variety of formulations that evaluate single or multiple structural features of proteins have been developed and studied. The performance of functions is often evaluated by discrimination ability using decoy structures of target proteins. A function that can evaluate coarse-grained structures is advantageous from many aspects, such as relatively easy generation and manipulation of model structures; however, the reduction of structural representation is often accompanied by degradation of the structure discrimination performance. 相似文献9.
Jussi T Koivumäki Topi Korhonen Jouni Takalo Matti Weckström Pasi Tavi 《BMC physiology》2009,9(1):16-20
Background
The cardiomyocyte is a prime example of inherently complex biological system with inter- and cross-connected feedback loops in signalling, forming the basic properties of intracellular homeostasis. Functional properties of cells and tissues have been studied e.g. with powerful tools of genetic engineering, combined with extensive experimentation. While this approach provides accurate information about the physiology at the endpoint, complementary methods, such as mathematical modelling, can provide more detailed information about the processes that have lead to the endpoint phenotype. 相似文献10.
Background
Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues) with special emphasis to protein interfaces. 相似文献11.
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Background
Methods that can automatically assess the quality of computationally predicted protein structures are important, as they enable the selection of the most accurate structure from an ensemble of predictions. Assessment methods that determine the quality of a predicted structure by comparing it against the various structures predicted by different servers have been shown to outperform approaches that rely on the intrinsic characteristics of the structure itself. 相似文献13.
Background
Recent advances on high-throughput technologies have produced a vast amount of protein sequences, while the number of high-resolution structures has seen a limited increase. This has impelled the production of many strategies to built protein structures from its sequence, generating a considerable amount of alternative models. The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both. 相似文献14.
Claire Gaillard Luda S Shlyakhtenko Yuri L Lyubchenko Fran?ois Strauss 《BMC structural biology》2002,2(1):7-13
Background
We have previously isolated a stable alternative DNA structure, which was formed in vitro by reassociation of the strands of DNA fragments containing a 62 bp tract of the CA-microsatellite poly(CA)·poly(TG). In the model which was proposed for this structure the double helix is folded into a loop, the base of the loop consists of a DNA junction in which one of the strands of one duplex passes between the two strands of the other duplex, forming a DNA hemicatenane in a hemiknot structure. The hemiknot DNA structures obtained with long CA/TG inserts have been imaged by AFM allowing us to directly visualize the loops. 相似文献15.
Background
Since many of the new protein structures delivered by high-throughput processes do not have any known function, there is a need for structure-based prediction of protein function. Protein 3D structures can be clustered according to their fold or secondary structures to produce classes of some functional significance. A recent alternative has been to detect specific 3D motifs which are often associated to active sites. Unfortunately, there are very few known 3D motifs, which are usually the result of a manual process, compared to the number of sequential motifs already known. In this paper, we report a method to automatically generate 3D motifs of protein structure binding sites based on consensus atom positions and evaluate it on a set of adenine based ligands. 相似文献16.
Ian Walsh Alberto JM Martin Catherine Mooney Enrico Rubagotti Alessandro Vullo Gianluca Pollastri 《BMC bioinformatics》2009,10(1):195-19
Background
Proteins, especially larger ones, are often composed of individual evolutionary units, domains, which have their own function and structural fold. Predicting domains is an important intermediate step in protein analyses, including the prediction of protein structures. 相似文献17.
Background
Annotation of protein functions is an important task in the post-genomic era. Most early approaches for this task exploit only the sequence or global structure information. However, protein surfaces are believed to be crucial to protein functions because they are the main interfaces to facilitate biological interactions. Recently, several databases related to structural surfaces, such as pockets and cavities, have been constructed with a comprehensive library of identified surface structures. For example, CASTp provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities. 相似文献18.
Background
Proteins of the tetraspanin family contain four transmembrane domains (TM1-4) linked by two extracellular loops and a short intracellular loop, and have short intracellular N- and C-termini. While structure and function analysis of the larger extracellular loop has been performed, the organization and role of transmembrane domains have not been systematically assessed. 相似文献19.
Marcin von Grotthuss Dariusz Plewczynski Krzysztof Ginalski Leszek Rychlewski Eugene I Shakhnovich 《BMC bioinformatics》2006,7(1):53
Background
The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. 相似文献20.