共查询到20条相似文献,搜索用时 921 毫秒
1.
A prominent feature of the interaction of MS2 coat protein with RNA is the quasi-symmetric insertion of a bulged adenine (A-10) and a loop adenine (A-4) into conserved pockets on each subunit of the coat protein dimer. Because of its presence in both of these adenine-binding pockets, Thr(45) is thought to play an important role in interaction with RNA on both subunits of the dimer. To test the significance of Thr(45), we introduced all 19 amino acid substitutions. However, we were initially unable to determine the effects of the mutations on RNA binding because every substitution compromised the ability of coat protein to fold correctly. Genetic fusion of coat protein subunits reverted these protein structural defects, allowing us to show that the RNA binding activity of coat protein tolerates substitution of Thr(45), but only on one or the other subunit of the dimer. Single-chain heterodimer complementation experiments suggest that the primary site of Thr(45) interaction with RNA is with A-4 in the translational operator. Either contact of Thr(45) with A-10 makes little contribution to stability of the RNA-protein complex, or the effects of Thr(45) substitution are offset by conformational adjustments that introduce new, favorable contacts at nearby sites. 相似文献
2.
Background
Identifying pockets on protein surfaces is of great importance for many structure-based drug design applications and protein-ligand docking algorithms. Over the last ten years, many geometric methods for the prediction of ligand-binding sites have been developed. 相似文献3.
Barbara Pauly Margherita Lasi Carol MacKintosh Nick Morrice Axel Imhof Jörg Regula Stephen Rudd Charles N David Angelika Böttger 《BMC cell biology》2007,8(1):31
Background
14-3-3 proteins have been implicated in many signalling mechanisms due to their interaction with Ser/Thr phosphorylated target proteins. They are evolutionarily well conserved in eukaryotic organisms from single celled protozoans and unicellular algae to plants and humans. A diverse array of target proteins has been found in higher plants and in human cell lines including proteins involved in cellular metabolism, apoptosis, cytoskeletal organisation, secretion and Ca2+ signalling. 相似文献4.
Gabriele Ausiello Federico Pier Gherardini Elena Gatti Ottaviano Incani Manuela Helmer-Citterich 《BMC bioinformatics》2009,10(1):182
Background
The structural analysis of protein ligand binding sites can provide information relevant for assigning functions to unknown proteins, to guide the drug discovery process and to infer relations among distant protein folds. Previous approaches to the comparative analysis of binding pockets have usually been focused either on the ligand or the protein component. Even though several useful observations have been made with these approaches they both have limitations. In the former case the analysis is restricted to binding pockets interacting with similar ligands, while in the latter it is difficult to systematically check whether the observed structural similarities have a functional significance. 相似文献5.
Martin Petřek Michal Otyepka Pavel Banáš Pavlína Košinová Jaroslav Koča Jiří Damborský 《BMC bioinformatics》2006,7(1):316-9
Background
The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. 相似文献6.
7.
Héctor Estrada-Medina Robert C. Graham Michael F. Allen Juan José Jiménez-Osornio Said Robles-Casolco 《Plant and Soil》2013,362(1-2):37-50
Background and Aims
With limited soil depth in northern Yucatán (<30 cm), roots grow deeper through rock fractures and dissolution karst features (i.e., cavities, including soil-filled ones known as soil pockets). We assessed the importance of limestone bedrock and dissolution karst features on tree root growth.Methods
Fieldwork was conducted in a limestone quarry where the relative proportions of rock matrix, empty cavities, and soil pockets were calculated by observing recently exposed walls. Physical properties of rocks, topsoil, and soil pockets were analyzed. Root distribution was assessed and roots identified.Results
Soil pockets represented 9% of the rock matrix. The physical properties of rock layers were different with depth. Available water capacity is higher in soil (0.11 m-3 m-3) than in rock layers (<0.05 m-3 m-3). But potential available water was much higher in subsurface features than top soil.Conclusions
Dissolution karts features allow roots to grow deep into the bedrock, tapping water stored there. Although the limestone upper layer in northern Yucatan is highly restrictive to root growth, subsurface limestone layers and soil pockets are not restrictive and can hold important amounts of water. 相似文献8.
Radha Venkatesan Dhanasekaran Bodhini Nagarajan Narayani Viswanathan Mohan 《Indian journal of human genetics》2014,20(1):37-42
BACKGROUND:
The ABCC8 gene which encodes the sulfonylurea receptor plays a major role in insulin secretion and is a potential candidate for type 2 diabetes. The -3c → t (rs1799854) and Thr759Thr (C → T, rs1801261) single nucleotide polymorphisms (SNPs) of the ABCC8 gene have been associated with type 2 diabetes in many populations. The present study was designed to investigate the association of these two SNPs in an Asian Indian population from south India.MATERIALS AND METHODS:
A total of 1,300 subjects, 663 normal glucose tolerant (NGT) and 637 type 2 diabetic subjects were randomly selected from the Chennai Urban Rural Epidemiology Study (CURES). The -3c → t and Thr759Thr were genotyped in these subjects using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and a few variants were confirmed by direct sequencing.RESULTS:
The frequency of the ‘t’ allele of the -3c → t SNP was found to be 0.27 in NGT and 0.29 in type 2 diabetic subjects (P = 0.44). There was no significant difference in the genotypic frequency between the NGT and type 2 diabetic group (P = 0.18). Neither the genotypic frequency nor the allele frequency of the Thr759Thr polymorphism was found to differ significantly between the NGT and type 2 diabetic groups.CONCLUSION:
The -3c → t and the Thr759Thr polymorphisms of the ABCC8 gene were not associated with type 2 diabetes in this study. However, an effect of these genetic variants on specific unidentified sub groups of type 2 diabetes cannot be excluded. 相似文献9.
Background
A retrospective study was made to demonstrate normal variations of the color and size of the tapetal area and color of the nontapetal area in the ocular fundus in dogs, correlating them to breed, age and coat color. 相似文献10.
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11.
Background
The Arabidopsis outer ovule integument is a simple two-cell layered structure that grows around the developing embryo and develops into the outer layer of the seed coat. As one of the functions of the seed coat is the protection of the plant embryo, the outer ovule integument is an example for a plant organ whose morphogenesis has to be precisely regulated. 相似文献12.
13.
Background
Dengue virus along with the other members of the flaviviridae family has reemerged as deadly human pathogens. Understanding the mechanistic details of these infections can be highly rewarding in developing effective antivirals. During maturation of the virus inside the host cell, the coat proteins E and M undergo conformational changes, altering the morphology of the viral coat. However, due to low resolution nature of the available 3-D structures of viral assemblies, the atomic details of these changes are still elusive. 相似文献14.
Sebastian Schlafer Birgit Riep Ann L Griffen Annett Petrich Julia Hübner Moritz Berning Anton Friedmann Ulf B Göbel Annette Moter 《BMC microbiology》2010,10(1):66
Background
Bacteria in periodontal pockets develop complex sessile communities that attach to the tooth surface. These highly dynamic microfloral environments challenge both clinicians and researchers alike. The exploration of structural organisation and bacterial interactions within these biofilms is critically important for a thorough understanding of periodontal disease. In recent years, Filifactor alocis, a fastidious, Gram-positive, obligately anaerobic rod was repeatedly identified in periodontal lesions using DNA-based methods. It has been suggested to be a marker for periodontal deterioration. The present study investigated the epidemiology of F. alocis in periodontal pockets and analysed the spatial arrangement and architectural role of the organism in in vivo grown subgingival biofilms. 相似文献15.
Dustin L Johnson Chris B Stone David C Bulir Brian K Coombes James B Mahony 《BMC microbiology》2009,9(1):218
Background
We have shown previously that Chlamydophila pneumoniae contains a dual-specific Ser/Thr protein kinase that phosphorylates CdsD, a structural component of the type III secretion apparatus. To further study the role of PknD in growth and development we sought to identify a PknD inhibitor to determine whether PknD activity is required for replication. 相似文献16.
Edward J Cargill Thomas R Famula Robert D Schnabel George M Strain Keith E Murphy 《BMC veterinary research》2005,1(1):1-3
Background
The distinctive coat pattern of a Dalmatian is the result of the interaction of several loci. While the encoded function of these genes is not fully understood, it is known the Piebald, Ticking, and Flecking loci interact to produce the Dalmatian's classic pigmented spots on a white background. The color of the pigmented spots in purebred Dalmatians can either be black or liver, but the locus responsible for color determination is unknown. Studies have been conducted to determine the underlying genes involved in coat color determination in the dog, e.g., in the Labrador Retriever, but none to date have addressed black versus liver in the Dalmatian. 相似文献17.
Arnljot Flaa Øivind Ekeberg Sverre Erik Kjeldsen Morten Rostrup 《BioPsychoSocial medicine》2007,1(1):1-8
Background
Possible mechanisms behind psychophysiological hyperreactivity may be located at a cognitive-emotional level. Several personality traits have been associated with increased cardiovascular reactivity. Subjects with white coat hypertension, which may constitute a kind of hyperreactivity, are found to suppress their emotions and adapt to the surroundings to a larger extent than controls. 相似文献18.
Background
Leucine rich repeats (LRRs) are present in over 60,000 proteins that have been identified in viruses, bacteria, archae, and eukaryotes. All known structures of repeated LRRs adopt an arc shape. Most LRRs are 20-30 residues long. All LRRs contain LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. Seven classes of LRRs have been identified. However, other LRR classes remains to be characterized. The evolution of LRRs is not well understood. 相似文献19.
Background
Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compounds. For SBVS, the identification of candidate pockets in protein structures is a key feature, and the recent years have seen increasing interest in developing methods for pocket and cavity detection on protein surfaces. 相似文献20.
Claudia Bănescu Mariana Tilinca Erzsebeth Lazar Benedek Smaranda Demian Ioan Macarie Carmen Duicu Minodora Dobreanu 《Gene》2013