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Protein Structure (protein + structure)
Kinds of Protein Structure Terms modified by Protein Structure Selected AbstractsAzidohomoalanine: A Conformationally Sensitive IR Probe of Protein Folding, Protein Structure, and Electrostatics,ANGEWANDTE CHEMIE, Issue 41 2010Humeyra Taskent-Sezgin Hoch empfindlich: Das Azido-Analogon von Methionin, Azidohomoalanin (siehe Bild), ist eine empfindliche IR-Sonde für die Analyse der Struktur, Faltung und Elektrostatik von Proteinen, wie am Beispiel des Proteins NTL9 demonstriert wird. Die Sonde lässt sich leicht in Proteine einbauen, und die Azido-Frequenz im thermisch entfalteten Zustand ist deutlichen blauverschoben. [source] Prediction of the Candida antarctica Lipase A Protein Structure by Comparative Modeling and Site-Directed MutagenesisCHEMBIOCHEM, Issue 12 2007Alex Kasrayan Dr. Abstract A number of model structures of the CalA suggested by comparative modeling were tested by site-directed mutagenesis. Enzyme variants were created where amino acids predicted to play key roles for the lipase activity in the different models were replaced by an inert amino acid (alanine). The results from activity measurements of the overproduced and purified mutant enzymes indicate a structure where the active site consists of amino acid residues Ser184, His366, and Asp334 and in which there is no lid. This model can be used for future targeted modifications of the enzyme to obtain new substrate acceptance, better thermostability, and higher enantioselectivity. [source] 18O Isotope Substitution, Vibrational Coupling and Protein Structure: A Theoretical ApproachCHEMPHYSCHEM, Issue 2 2004Thorsten Koslowski Prof. Dr. Site-specific 18O substitution of two amino acids that are in a close spatial vicinity, but far apart in the primary sequence, exhibits characteristic IR fingerprints; the corresponding spectral shifts of the absorption bands are shown color-coded in the figure. This approach can be used to obtain detailed structural information, for example, about membrane proteins which are difficult to crystallize. [source] Sunflower proteins: overview of their physicochemical, structural and functional propertiesJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 12 2007Sergio González-Pérez Abstract There is increasing worldwide demand for proteins of both animal and plant origin. However, animal proteins are expensive in terms of both market price and environmental impact. Among alternative plant proteins, sunflower seeds are particularly interesting in view of their widespread availability in areas where soy is not or only sparsely produced. Compared with other sources of vegetable proteins, sunflower seeds have been reported to have a low content of antinutritional factors. Although the absence of these factors is important, the functionality of the protein preparations will mainly determine their applicability. This review provides detailed information about sunflower seed composition and processing, including processes to remove phenolic compounds from meals. The main part of the review concerns the structure and functionality of the two major protein fractions, helianthinin and 2S albumins. Regarding functionality, emphasis is on solubility, thermal behaviour and surface activity. Protein structure and functionality are discussed as a function of extrinsic factors such as pH, ionic strength, temperature and the presence of other seed components, particularly chlorogenic acid. In addition, sunflower proteins are compared from a structural and functional point of view with other plant proteins, particularly soy proteins. Copyright © 2007 Society of Chemical Industry [source] New structural insights from Raman spectroscopy of proteins and their assembliesBIOPOLYMERS, Issue 4-5 2002George J. Thomas Jr.Article first published online: 9 MAY 200 Abstract Protein structure and stability are sensitive to and dependent on the local interactions of amino acid side chains. A diverse and important type of side-chain interaction is the hydrogen bond. Although numerous hydrogen bonds are resolved in protein 3-dimensional structures, those of the cysteine sulfhydryl group (S H) are elusive to high-resolution X-ray and NMR methods. However, the nature and strength of sulfhydryl hydrogen bonds (SH,X) are amenable to investigation by Raman spectroscopy. The power of the Raman method for characterizing SH,X interactions is illustrated by resolving the Raman SH stretching band for each of the eight cysteines per 666-residue subunit in the trimeric tailspike of icosahedral bacteriophage P22. The Raman sulfhydryl signatures of the wild-type tailspike and eight single-site cysteine to serine mutants reveal a heretofore unrecognized diversity of SH hydrogen bonds in a native protein. The use of Raman spectroscopy to identify the non-hydrogen-bonded state of the tyrosine phenoxyl group is also described. This unusual and unexpected state occurs for all tyrosines in the assembled capsids of filamentous viruses Ff and Pf1. The Raman spectral signature of the non-hydrogen-bonded tyrosine phenoxyl, which is characterized by an extraordinary Raman Fermi doublet intensity ratio (I850/I830 = 6.7), extends and refines the existing correlation for hydrogen-bonded tyrosines. Finally, a novel Raman signature for tryptophan in the Pf3 filamentous virus is identified, which is proposed as diagnostic of "cation,, interaction" involving the guanidinium group of Arg 37 as a cation donor and the indolyl ring of Trp 38 as a ,-electron acceptor. These studies demonstrate the power of Raman spectroscopy for investigating the interactions of key side chains in native protein assemblies. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 67: 214,225, 2002 [source] Structure of purine nucleoside phosphorylase (DeoD) from Bacillus anthracisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2005Rosa Grenha Protein structures from the causative agent of anthrax (Bacillus anthracis) are being determined as part of a structural genomics programme. Amongst initial candidates for crystallographic analysis are enzymes involved in nucleotide biosynthesis, since these are recognized as potential targets in antibacterial therapy. Purine nucleoside phosphorylase is a key enzyme in the purine-salvage pathway. The crystal structure of purine nucleoside phosphorylase (DeoD) from B. anthracis has been solved by molecular replacement at 2.24,Å resolution and refined to an R factor of 18.4%. This is the first report of a DeoD structure from a Gram-positive bacterium. [source] Structure and function of AMP-activated protein kinaseACTA PHYSIOLOGICA, Issue 1 2009J. S. Oakhill Abstract AMP-activated protein kinase (AMPK) regulates metabolism in response to energy demand and supply. AMPK is activated in response to rises in intracellular AMP or calcium-mediated signalling and is responsible for phosphorylating a wide variety of substrates. Recent structural studies have revealed the architecture of the ,,, subunit interactions as well as the AMP binding pockets on the , subunit. The , catalytic domain (1,280) is autoinhibited by a C-terminal tail (313,335), which is proposed to interact with the small lobe of the catalytic domain by homology modelling with the MARK2 protein structure. Two direct activating drugs have been reported for AMPK, the thienopyridone compound A769662 and PTI, which may activate by distinct mechanisms. [source] How do crystal lattice contacts reveal protein crystallization mechanism?CRYSTAL RESEARCH AND TECHNOLOGY, Issue 9 2008Christo N. Nanev Abstract The nature of crystal lattice contacts is discussed because they reflect the selection of the most appropriate (for the given set of conditions) contact patches on the surface of protein molecules. The conclusion is that, along with chemical composition, the protein structure at the crystal lattice contacts is the key to crystallization behavior. The reason is that most stable are conformations, which do not only maximize the number of the bonds but simultaneously minimize van der Waals repulsions. A plausible explanation of the crystallization slot that exists for proteins is given on this basis. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Electroactivity of Nonconjugated Proteins and Peptides.ELECTROANALYSIS, Issue 23 2007Towards Electroanalysis of All Proteins Abstract Present proteomics and biomedicine require sensitive analytical methods for all proteins. Recent progress in electrochemical analysis of peptides and proteins based on their intrinsic electroactivity is reviewed. Tyrosine and/or tryptophan-containing proteins are oxidizable at carbon electrodes. At mercury electrodes all peptides and proteins (about 13 peptides and >25 proteins were tested) produce chronopotentiometric peak H at nanomolar concentrations. This peak is sensitive to changes in protein structure. Microliter sample volumes are sufficient for the analysis. Electrochemical methods can be used in studies of nucleic acid-protein interactions and can be applied in biomedicine. Examples of such applications in neurogenerative diseases and cancer are presented. [source] Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspectiveELECTROPHORESIS, Issue S1 2009Nicolas Guex Abstract SWISS-MODEL pioneered the field of automated modeling as the first protein modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-MODEL Repository, it provides a fully integrated sequence to structure analysis and modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative protein modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper. [source] Compound heterozygosity of two missense mutations in the NADH-cytochrome b5 reductase gene of a Polish patient with type I recessive congenital methaemoglobinaemiaEUROPEAN JOURNAL OF HAEMATOLOGY, Issue 6 2003Dorota Grabowska Abstract: A case of type I methaemoglobinaemia observed in a Polish subject with compound heterozygosity for two mutations in the reduced nicotinamide adenine dinucleotide (NADH) cytochrome b5 reductase (b5R) gene is described. One is a novel mutation 647T,C which leads to substitution of isoleucine by threonine at position 215 (I215T). This maternal mutation was found in several family members. A previously known mutation, 757G,A, leads to the replacement of valine by methionine at position 252 (V252M). The latter mutation was found also in the father and one of the two brothers. The effects of these mutations were analysed on a model of the human b5R protein obtained by homology modelling. Although both amino acid substitutions are located in the NADH-binding domain, the whole protein structure, especially the region between the flavin adenine dinucleotide and NADH-binding domains, is disturbed. The structural changes in the I215T mutant are less prominent than those in the V252M mutant. We presume that the 647T,C mutation is a type I mutation, however, it has not been observed in the homozygous state. [source] LRRN6A/LERN1 (leucine-rich repeat neuronal protein 1), a novel gene with enriched expression in limbic system and neocortexEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 12 2003Laura Carim-Todd Abstract Human chromosome 15q24-q26 is a very complex genomic region containing several blocks of segmental duplications to which susceptibility to anxiety disorders has been mapped (Gratacos et al., 2001, Cell, 106, 367,379; Pujana et al., 2001, Genome Res., 11, 98,111). Through an in silico gene content analysis of the 15q24-q26 region we have identifie1d a novel gene, LRRN6A (leucine-rich repeat neuronal 6A), and confirmed its location to the centromeric end of this complex region. LRRN6A encodes a transmembrane leucine-rich repeat protein, LERN1 (leucine-rich repeat neuronal protein 1), with similarity to proteins involved in axonal guidance and migration, nervous system development and regeneration processes. The identification of homologous genes to LRRN6A on chromosomes 9 and 19 and the orthologous genes in the mouse genome and other organisms suggests that LERN proteins constitute a novel subfamily of LRR (leucine-rich repeat)-containing proteins. The LRRN6A expression pattern is specific to the central nervous system, highly and broadly expressed during early stages of development and gradually restricted to forebrain structures as development proceeds. Expression level in adulthood is lower in general but remains stable and significantly enriched in the limbic system and cerebral cortex. Taken together, the confirmation of LRRN6A's expression profile, its predicted protein structure and its similarity to nervous system-expressed LRR proteins with essential roles in nervous system development and maintenance suggest that LRRN6A is a novel gene of relevance in the molecular and cellular neurobiology of vertebrates. [source] Mechanisms of channel gating of the ligand-gated ion channel superfamily inferred from protein structureEXPERIMENTAL PHYSIOLOGY, Issue 2 2004Nathan L. Absalom The nicotinic-like ligand-gated ion channel superfamily consists of a group of structurally related receptors that activate an ion channel after the binding of extracellular ligand. The recent publications of the crystal structure of an acetylcholine binding protein and a refined electron micrograph structure of the membrane-bound segment of an acetylcholine receptor have led to insights into the molecular determinants of receptor function. Although the structures confirmed much biochemical and electrophysiological data obtained about the receptors, they also provide opportunities to study further the mechanisms that allow channel activation stimulated by ligand-binding. Here we review the mechanisms of channel gating that have been elucidated by information gained from the structures of the acetylcholine binding protein and membrane-bound segment of the acetylcholine receptor. [source] Destabilization of psychrotrophic RNase HI in a localized fashion as revealed by mutational and X-ray crystallographic analysesFEBS JOURNAL, Issue 2 2009Muhammad S. Rohman The Arg97 , Gly and Asp136 , His mutations stabilized So-RNase HI from the psychrotrophic bacterium Shewanella oneidensis MR-1 by 5.4 and 9.7 °C, respectively, in Tm, and 3.5 and 6.1 kJ·mol,1, respectively, in ,G(H2O). These mutations also stabilized the So-RNase HI derivative (4×-RNase HI) with quadruple thermostabilizing mutations in an additive manner. As a result, the resultant sextuple mutant protein (6×-RNase HI) was more stable than the wild-type protein by 28.8 °C in Tm and 27.0 kJ·mol,1 in ,G(H2O). To analyse the effects of the mutations on the protein structure, the crystal structure of the 6×-RNase HI protein was determined at 2.5 Å resolution. The main chain fold and interactions of the side-chains of the 6×-RNase HI protein were basically identical to those of the wild-type protein, except for the mutation sites. These results indicate that all six mutations independently affect the protein structure, and are consistent with the fact that the thermostabilizing effects of the mutations are roughly additive. The introduction of favourable interactions and the elimination of unfavourable interactions by the mutations contribute to the stabilization of the 6×-RNase HI protein. We propose that So-RNase HI is destabilized when compared with its mesophilic and thermophilic counterparts in a localized fashion by increasing the number of amino acid residues unfavourable for protein stability. [source] Full-length prion protein aggregates to amyloid fibrils and spherical particles by distinct pathwaysFEBS JOURNAL, Issue 9 2008Driss El Moustaine As limited structural information is available on prion protein (PrP) misfolding and aggregation, a causative link between the specific (supra)molecular structure of PrP and transmissible spongiform encephalopathies remains to be elucidated. In this study, high pressure was utilized, as an approach to perturb protein structure, to characterize different morphological and structural PrP aggregates. It was shown that full-length recombinant PrP undergoes ,-sheet aggregation on high-pressure-induced destabilization. By tuning the physicochemical conditions, the assembly process evolves through two distinct pathways leading to the irreversible formation of spherical particles or amyloid fibrils, respectively. When the PrP aggregation propensity is enhanced, high pressure induces the formation of a partially unfolded aggregated protein, AggHP, which relaxes at ambient pressure to form amorphous aggregates. The latter largely retain the native secondary structure. On prolonged incubation at high pressure, followed by depressurization, AggHP transforms to a monodisperse population of spherical particles of about 20 nm in diameter, characterized by an essentially ,-sheet secondary structure. When the PrP aggregation propensity is decreased, an oligomeric reaction intermediate, IHP, is formed under high pressure. After pressure release, IHP relaxes to the original native structure. However, on prolonged incubation at high pressure and subsequent depressurization, it transforms to amyloid fibrils. Structural evaluation, using optical spectroscopic methods, demonstrates that the conformation adopted by the subfibrillar oligomeric intermediate, IHP, constitutes a necessary prerequisite for the formation of amyloids. The use of high-pressure perturbation thus provides an insight into the molecular mechanism of the first stages of PrP misfolding into amyloids. [source] Calcite-specific coupling protein in barnacle underwater cementFEBS JOURNAL, Issue 24 2007Youichi Mori The barnacle relies for its attachment to underwater foreign substrata on the formation of a multiprotein complex called cement. The 20 kDa cement protein is a component of Megabalanus rosa cement, although its specific function in underwater attachment has not, until now, been known. The recombinant form of the protein expressed in bacteria was purified in soluble form under physiological conditions, and confirmed to retain almost the same structure as that of the native protein. Both the protein from the adhesive layer of the barnacle and the recombinant protein were characterized. This revealed that abundant Cys residues, which accounted for 17% of the total residues, were in the intramolecular disulfide form, and were essential for the proper folding of the monomeric protein structure. The recombinant protein was adsorbed to calcite and metal oxides in seawater, but not to glass and synthetic polymers. The adsorption isotherm for adsorption to calcite fitted the Langmuir model well, indicating that the protein is a calcite-specific adsorbent. An evaluation of the distribution of the molecular size in solution by analytical ultracentrifugation indicated that the recombinant protein exists as a monomer in 100 mm to 1 m NaCl solution; thus, the protein acts as a monomer when interacting with the calcite surface. cDNA encoding a homologous protein was isolated from Balanus albicostatus, and its derived amino acid sequence was compared with that from M. rosa. Calcite is the major constituent in both the shell of barnacle base and the periphery, which is also a possible target for the cement, due to the gregarious nature of the organisms. The specificity of the protein for calcite may be related to the fact that calcite is the most frequent material attached by the cement. [source] Isolation, characterization, sequencing and crystal structure of charybdin, a type 1 ribosome-inactivating protein from Charybdis maritima agg.FEBS JOURNAL, Issue 12 2006Eleftherios Touloupakis A novel, type 1 ribosome-inactivating protein designated charybdin was isolated from bulbs of Charybdis maritima agg. The protein, consisting of a single polypeptide chain with a molecular mass of 29 kDa, inhibited translation in rabbit reticulocytes with an IC50 of 27.2 nm. Plant genomic DNA extracted from the bulb was amplified by PCR between primers based on the N-terminal and C-terminal sequence of the protein from dissolved crystals. The complete mature protein sequence was derived by partial DNA sequencing and terminal protein sequencing, and was confirmed by high-resolution crystal structure analysis. The protein contains Val at position 79 instead of the conserved Tyr residue of the ribosome-inactivating proteins known to date. To our knowledge, this is the first observation of a natural substitution of a catalytic residue at the active site of a natural ribosome-inactivating protein. This substitution in the active site may be responsible for the relatively low in vitro translation inhibitory effect compared with other ribosome-inactivating proteins. Single crystals were grown in the cold room from PEG6000 solutions. Diffraction data collected to 1.6 Å resolution were used to determine the protein structure by the molecular replacement method. The fold of the protein comprises two structural domains: an ,,+ , N-terminal domain (residues 4,190) and a mainly ,-helical C-terminal domain (residues 191,257). The active site is located in the interface between the two domains and comprises residues Val79, Tyr117, Glu167 and Arg170. [source] The crystal structure of a plant 2C -methyl- D -erythritol 4-phosphate cytidylyltransferase exhibits a distinct quaternary structure compared to bacterial homologues and a possible role in feedback regulation for cytidine monophosphateFEBS JOURNAL, Issue 5 2006Mads Gabrielsen The homodimeric 2C -methyl- d -erythritol 4-phosphate cytidylyltransferase contributes to the nonmevalonate pathway of isoprenoid biosynthesis. The crystal structure of the catalytic domain of the recombinant enzyme derived from the plant Arabidopsis thaliana has been solved by molecular replacement and refined to 2.0 Å resolution. The structure contains cytidine monophosphate bound in the active site, a ligand that has been acquired from the bacterial expression system, and this observation suggests a mechanism for feedback regulation of enzyme activity. Comparisons with bacterial enzyme structures, in particular the enzyme from Escherichia coli, indicate that whilst individual subunits overlay well, the arrangement of subunits in each functional dimer is different. That distinct quaternary structures are available, in conjunction with the observation that the protein structure contains localized areas of disorder, suggests that conformational flexibility may contribute to the function of this enzyme. [source] Conformational properties of bacterial DnaK and yeast mitochondrial Hsp70FEBS JOURNAL, Issue 12 2005-helical subdomain, Role of the divergent C-terminal Among the eukaryotic members of the Hsp70 family, mitochondrial Hsp70 shows the highest degree of sequence identity with bacterial DnaK. Although they share a functional mechanism and homologous co-chaperones, they are highly specific and cannot be exchanged between Escherichia coli and yeast mitochondria. To provide a structural basis for this finding, we characterized both proteins, as well as two DnaK/mtHsp70 chimeras constructed by domain swapping, using biochemical and biophysical methods. Here, we show that DnaK and mtHsp70 display different conformational and biochemical properties. Replacing different regions of the DnaK peptide-binding domain with those of mtHsp70 results in chimeric proteins that: (a) are not able to support growth of an E. coli DnaK deletion strain at stress temperatures (e.g. 42 °C); (b) show increased accessibility and decreased thermal stability of the peptide-binding pocket; and (c) have reduced activation by bacterial, but not mitochondrial co-chaperones, as compared with DnaK. Importantly, swapping the C-terminal ,-helical subdomain promotes a conformational change in the chimeras to an mtHsp70-like conformation. Thus, interaction with bacterial co-chaperones correlates well with the conformation that natural and chimeric Hsp70s adopt in solution. Our results support the hypothesis that a specific protein structure might regulate the interaction of Hsp70s with particular components of the cellular machinery, such as Tim44, so that they perform specific functions. [source] Insight into molecular changes of the FIX protein in a series of Italian patients with haemophilia BHAEMOPHILIA, Issue 3 2006M. P. BICOCCHI Summary., Deficiency or dysfunction of factor IX FIX leads to haemophilia B (HB), an X-linked, recessive, bleeding disorder. On a molecular basis, HB is due to a heterogeneous spectrum of mutations spread throughout the F9 gene. In several instances, a cause-effect relation has been elucidated, in others predicted possibilities have been offered by crystallography inspection and by software-constructed models of the protein. The aim of this study was to contribute to the understanding of HB molecular pathology. The F9 missense mutations we identified in 21 unrelated Italian HB patients by direct sequencing of the whole F9 coding regions were inspected for the causative effect they provoked on the ensuing transcript, and on the protein structure. Each alteration was studied in order to: (i) characterize the defect on the basis of the nature of the mutation; (ii) identify the predicted defect that is induced in the gene and (iii) speculate about the potential, detrimental effects which upset the protein functionality through an idealized FIX model. The resulting data may further contribute to the comprehension of the mechanisms underlying the disease. [source] Designer haem proteins: What can we learn from protein engineering?HETEROATOM CHEMISTRY, Issue 6 2002Emma Lloyd Raven Iron protoporphyrin(IX) is one of the most versatile and widespread pieces of catalytic machinery known in biology and is a key component of a multitude of proteins and enzymes. One of most challenging questions in this area has been to identify and understand the relationships that exist between different classes of haem proteins and to use protein engineering methods to rationalize the mechanisms by which the protein structure controls the specific chemical reactivity of the haem group. The application of this approach to the haem enzyme ascorbate peroxidase and the haem protein leghaemoglobin is discussed. © 2002 Wiley Periodicals, Inc. Heteroatom Chem 13:501,505, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.10094 [source] Novel method for genomic analysis of PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease,HUMAN MUTATION, Issue 2 2009Ying-Cai Tan Abstract Genetic testing of PKD1 and PKD2 is useful for diagnosis and prognosis of autosomal dominant polycystic kidney disease (ADPKD), particularly in asymptomatic individuals or those without a family history. PKD1 testing is complicated by the large transcript size, complexity of the gene region, and the extent of gene variations. A molecular assay was developed using Transgenomic's SURVEYOR Nuclease and WAVE Nucleic Acid High Sensitivity Fragment Analysis System to screen for PKD1 and PKD2 variants, followed by sequencing of variant gene segments, thereby reducing the sequencing reactions by 80%. This method was compared to complete DNA sequencing performed by a reference laboratory for 25 ADPKD patients from 22 families. The pathogenic potential of gene variations of unknown significance was examined by evolutionary comparison, effects of amino acid substitutions on protein structure, and effects of splice-site alterations. A total of 90 variations were identified, including all 82 reported by the reference laboratory (100% sensitivity). A total of 76 variations (84.4%) were in PKD1 and 14 (15.6%) in PKD2. Definite pathogenic mutations (seven nonsense, four truncation, and three splicing defects) were detected in 64% (14/22) of families. The remaining 76 variants included 26 missense, 33 silent, and 17 intronic changes. Two heterozygous nonsense mutations were incorrectly determined by the reference laboratory as homozygous. "Probably pathogenic" mutations were identified in an additional five families (overall detection rate 86%). In conclusion, the SURVEYOR nuclease method was comparable to direct sequencing for detecting ADPKD mutations, achieving high sensitivity with lower cost, providing an important tool for genetic analysis of complex genes. Hum Mutat 0, 1,10, 2008. © 2008 Wiley-Liss, Inc. [source] Mutations of the RDX gene cause nonsyndromic hearing loss at the DFNB24 locus,,HUMAN MUTATION, Issue 5 2007Shahid Y. Khan Abstract Ezrin, radixin, and moesin are paralogous proteins that make up the ERM family and function as cross-linkers between integral membrane proteins and actin filaments of the cytoskeleton. In the mouse, a null allele of Rdx encoding radixin is associated with hearing loss as a result of the degeneration of inner ear hair cells as well as with hyperbilirubinemia due to hepatocyte dysfunction. Two mutant alleles of RDX [c.1732G>A (p.D578N) and c.1404_1405insG (p.A469fsX487)] segregating in two consanguineous Pakistani families are associated with neurosensory hearing loss. Both of these mutant alleles are predicted to affect the actin-binding motif of radixin. Sequence analysis of RDX in the DNA samples from the original DFNB24 family revealed a c.463C>T transition substitution that is predicted to truncate the protein in the FERM domain (F for 4.1, E for ezrin, R for radixin, and M for moesin) (p.Q155X). We also report a more complete gene and protein structure of RDX, including four additional exons and five new isoforms of RDX that are expressed in human retina and inner ear. Further, high-resolution confocal microscopy in mouse inner ear demonstrates that radixin is expressed along the length of stereocilia of hair cells from both the organ of Corti and the vestibular system. Hum Mutat 28(5), 417,423, 2007. Published 2007 Wiley-Liss, Inc. [source] Phenotology of disease-linked proteins,HUMAN MUTATION, Issue 1 2005Jeffrey K. Myers Abstract Are there analogous sequence positions in families of related proteins where disease-linked mutations occur with unusually high frequency? We attempt to answer this question by examining sequence alignments for G-protein coupled receptors (GPCRs) and voltage-gated potassium channels that have a significant number of missense mutations linked to some form of human disease. When the disease-linked mutations are mapped onto the sequences for each family, there are a large number of aligned sites at which disease-linked mutations occur in more than one protein. The statistical significance of the aligned sites is judged by analysis of artificially-generated random datasets. There are a modest number of aligned sites that are statistically significant,we refer to these as "phenotologous" sequence positions. Phenotologous sites represent aligned positions at which mutations linked to disease phenotypes occur with high frequency within a family of proteins. The most interesting of these sites are those which are not conserved,such sites are apparently critical in defining structural or functional differences between related proteins. Phenotology may be used to make experimentally testable predictions regarding medical genetics, the molecular basis of disease, and protein structure,function relationships. Hum Mutat 25:90,97, 2005. © 2004 Wiley-Liss, Inc. [source] MHC Class II epitope predictive algorithmsIMMUNOLOGY, Issue 3 2010Morten Nielsen Summary Major histocompatibility complex class II (MHC-II) molecules sample peptides from the extracellular space, allowing the immune system to detect the presence of foreign microbes from this compartment. To be able to predict the immune response to given pathogens, a number of methods have been developed to predict peptide,MHC binding. However, few methods other than the pioneering TEPITOPE/ProPred method have been developed for MHC-II. Despite recent progress in method development, the predictive performance for MHC-II remains significantly lower than what can be obtained for MHC-I. One reason for this is that the MHC-II molecule is open at both ends allowing binding of peptides extending out of the groove. The binding core of MHC-II-bound peptides is therefore not known a priori and the binding motif is hence not readily discernible. Recent progress has been obtained by including the flanking residues in the predictions. All attempts to make ab initio predictions based on protein structure have failed to reach predictive performances similar to those that can be obtained by data-driven methods. Thousands of different MHC-II alleles exist in humans. Recently developed pan-specific methods have been able to make reasonably accurate predictions for alleles that were not included in the training data. These methods can be used to define supertypes (clusters) of MHC-II alleles where alleles within each supertype have similar binding specificities. Furthermore, the pan-specific methods have been used to make a graphical atlas such as the MHCMotifviewer, which allows for visual comparison of specificities of different alleles. [source] Developmental variation in epidermal growth factor receptor size and localization in the malaria mosquito, Anopheles gambiaeINSECT MOLECULAR BIOLOGY, Issue 6 2001G. Lycett Abstract The AGER gene encoding the epidermal growth factor receptor (EGFR) of the malaria mosquito Anopheles gambiae was cloned and sequenced. It represents a canonical member of this family of tyrosine kinase proteins exhibiting many similarities to orthologues from other species, both on the level of genomic organization and protein structure. The mRNA can be detected throughout development. Western analysis with an antibody raised against the extracellular domain of the mosquito protein suggests developmental variation in protein size and location that may be involved in the function of EGFR in the mosquito. [source] A review of physical and chemical protein-gel inductionINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 6 2002Alfonso Totosaus Summary Protein gelation is important to obtain desirable sensory and textural structures in foods. Gelation phenomenon requires a driving force to unfold the native protein structure, followed by an aggregation retaining a certain degree of order in the matrix formed by association between protein strands. Protein gelation has been traditionally achieved by heating, but some physical and chemical processes form protein gels in an analogous way to heat-induction. A physical means, besides heat, is high pressure. Chemical means are acidification, enzymatic cross-linking, and use of salts and urea, causing modifications in protein,protein and protein,medium interactions. The characteristics of each gel are different and dependent upon factors like protein concentration, degree of denaturation caused by pH, temperature, ionic strength and/or pressure. [source] Buffalo (Bubalus bubalis) interleukin-2: sequence analysis reveals high nucleotide and amino acid identity with interleukin-2 of cattle and other ruminantsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 4 2002E. Sreekumar Summary A 4400-bp genomic sequence and a 332-bp truncated cDNA sequence of the interleukin-2 (IL-2) gene of Indian water buffalo (Bubalus bubalis) were amplified by polymerase chain reaction and cloned. The coding sequence of the buffalo IL-2 gene was assembled from the 5, end of the genomic clone and the truncated cDNA clone. This sequence had 98.5% nucleotide identity and 98% amino acid identity with cattle IL-2. Three amino acid substitutions were observed at positions 63, 124 and 135. Comparison of the predicted protein structure of buffalo IL-2 with that of human and cattle IL-2 did not reveal significant differences. The putative amino acids responsible for IL-2 receptor binding were conserved in buffalo, cattle and human IL-2. The amino acid sequence of buffalo IL-2 also showed very high identity with that of other ruminants, indicating functional cross-reactivity. [source] Foundation of quantum similarity measures and their relationship to QSPR: Density function structure, approximations, and application examplesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2005Ramon Carbó-Dorca Abstract This work presents a schematic description of the theoretical foundations of quantum similarity measures and the varied usefulness of the enveloping mathematical structure. The study starts with the definition of tagged sets, continuing with inward matrix products, matrix signatures, and vector semispaces. From there, the construction and structure of quantum density functions become clear and facilitate entry into the description of quantum object sets, as well as into the construction of atomic shell approximations (ASA). An application of the ASA is presented, consisting of the density surfaces of a protein structure. Based on this previous background, quantum similarity measures are naturally constructed, and similarity matrices, composed of all the quantum similarity measures on a quantum object set, along with the quantum mechanical concept of expectation value of an operator, allow the setup of a fundamental quantitative structure,activity relationship (QSPR) equation based on quantum descriptors. An application example is presented based on the inhibition of photosynthesis produced by some naphthyridinone derivatives, which makes them good herbicide candidates. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] New computational algorithm for the prediction of protein folding typesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2001Nikola, tambuk Abstract We present a new computational algorithm for the prediction of a secondary protein structure. The method enables the evaluation of ,- and ,-protein folding types from the nucleotide sequences. The procedure is based on the reflected Gray code algorithm of nucleotide,amino acid relationships, and represents the extension of Swanson's procedure in Ref. 4. It is shown that six-digit binary notation of each codon enables the prediction of ,- and ,-protein folds by means of the error-correcting linear block triple-check code. We tested the validity of the method on the test set of 140 proteins (70 ,- and 70 ,-folds). The test set consisted of standard ,- and ,-protein classes from Jpred and SCOP databases, with nucleotide sequence available in the GenBank database. 100% accurate classification of ,- and ,-protein folds, based on 39 dipeptide addresses derived by the error-correcting coding procedure was obtained by means of the logistic regression analysis (p<0.00000001). Classification tree and machine learning sequential minimal optimization (SMO) classifier confirmed the results by means 97.1% and 90% accurate classification, respectively. Protein fold prediction quality tested by means of leave-one-out cross-validation was a satisfactory 82.1% for the logistic regression and 81.4% for the SMO classifier. The presented procedure of computational analysis can be helpful in detecting the type of protein folding from the newly sequenced exon regions. The method enables quick, simple, and accurate prediction of ,- and ,-protein folds from the nucleotide sequence on a personal computer. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 13,22, 2001 [source] | |||||||||||||||||||||||||||||||||||||||||||