The OGCleaner: Detecting False
... aligned together to form clusters. Homologous DNA (and those translated to amino acids) sequences can be further subdivided into two major classes: orthologs and paralogs. Orthologs are defined as homologous genes in different species that arose due to speciation events, whereas paralogs have evolve ...
... aligned together to form clusters. Homologous DNA (and those translated to amino acids) sequences can be further subdivided into two major classes: orthologs and paralogs. Orthologs are defined as homologous genes in different species that arose due to speciation events, whereas paralogs have evolve ...
Journal of Applied Phycology
... revealed that many of the domains and residues assigned functional roles in E. coli RecA are conserved in the Spirulina RecA. Numbering of the E. coli RecA residues begins with the first alanine (Dunkin & Wood, 1994). The ATP fold (R ..... G...SGKT) (Walker et al., 1982) is present in Spirulina RecA ...
... revealed that many of the domains and residues assigned functional roles in E. coli RecA are conserved in the Spirulina RecA. Numbering of the E. coli RecA residues begins with the first alanine (Dunkin & Wood, 1994). The ATP fold (R ..... G...SGKT) (Walker et al., 1982) is present in Spirulina RecA ...
supp - Springer Static Content Server
... HnRNP F is a 45 kDa protein composed of two N-terminal RRMs (residues 1 to 90 and 103 to 194) followed by a glycine-rich motif (residues 195 to 276), a third RRM (residues 277 to 366) and a second glycine-rich motif (residues 367 to 415). RRMs are among the most abundant protein domains in eukaryote ...
... HnRNP F is a 45 kDa protein composed of two N-terminal RRMs (residues 1 to 90 and 103 to 194) followed by a glycine-rich motif (residues 195 to 276), a third RRM (residues 277 to 366) and a second glycine-rich motif (residues 367 to 415). RRMs are among the most abundant protein domains in eukaryote ...
Sequence-based predictions of membrane-protein topology, homology and insertion
... 2001) and are responsible for numerous vital processes in the cell, but apart from their general biological significance, there are also specific reasons for why additional effort is being put into membrane protein predictions. First, the medical importance of membrane bound receptors, channels and ...
... 2001) and are responsible for numerous vital processes in the cell, but apart from their general biological significance, there are also specific reasons for why additional effort is being put into membrane protein predictions. First, the medical importance of membrane bound receptors, channels and ...
preprint - Human Genome Center
... Protein structure analysis is a very important research topic in the molecular biology of the postgenomic era. The RMSD (root mean square deviation) is the most frequently used measure for comparing two protein 3-D structures. In this paper, we deal with two fundamental problems related to the RMSD. ...
... Protein structure analysis is a very important research topic in the molecular biology of the postgenomic era. The RMSD (root mean square deviation) is the most frequently used measure for comparing two protein 3-D structures. In this paper, we deal with two fundamental problems related to the RMSD. ...
ProRule: a new database containing functional
... All the other information provided by the rule is conditional, depending on the presence of mandatory residues at some precise positions within the domain. A feature line for a predicted disulfide bond will only be created if cysteine residues are found at the two positions connected by the bond. He ...
... All the other information provided by the rule is conditional, depending on the presence of mandatory residues at some precise positions within the domain. A feature line for a predicted disulfide bond will only be created if cysteine residues are found at the two positions connected by the bond. He ...
Typically, to be “biologically related” means to share
... In practice, searching for sequence or structural similarity is one of the most powerful computational approaches for discovering functions for genes, since we can often glean many new insights about a protein based on what is known about its homologs. Here’s an example from my own lab, where we dis ...
... In practice, searching for sequence or structural similarity is one of the most powerful computational approaches for discovering functions for genes, since we can often glean many new insights about a protein based on what is known about its homologs. Here’s an example from my own lab, where we dis ...
Ribosome
... linked together by the ribosome. One by one, they bind to the ribosome, add their amino acid to the chain, and then depart 50S and 30S made primarily of RNA and are both larger than the average protein. 50S has rather rigid structure, while 30S has fairly ...
... linked together by the ribosome. One by one, they bind to the ribosome, add their amino acid to the chain, and then depart 50S and 30S made primarily of RNA and are both larger than the average protein. 50S has rather rigid structure, while 30S has fairly ...
2. Yi-Kuo Yu, John C. Wootton, and Stephen F. Altschul The compositional adjustment of amino acid substitution matrices PNAS 2003 100: 15688-15693.
... evolutionary divergence (3–10). Any such series implies a model of protein evolution, but current evolutionary theory provides no basis for calculating target frequencies a priori. Accordingly, methods have been developed to derive these target frequencies from large collections of alignments of hom ...
... evolutionary divergence (3–10). Any such series implies a model of protein evolution, but current evolutionary theory provides no basis for calculating target frequencies a priori. Accordingly, methods have been developed to derive these target frequencies from large collections of alignments of hom ...
Identification and Characterization of Two Temperature
... research on S. suis in recent years, little is known about pathogenesis and virulence factors. Studies on the pathogenicity of S. suis are complicated by the presence of multiple serotypes (of which currently 35 are known) based on the capsular polysaccharides (CPS) and by the high diversity in leve ...
... research on S. suis in recent years, little is known about pathogenesis and virulence factors. Studies on the pathogenicity of S. suis are complicated by the presence of multiple serotypes (of which currently 35 are known) based on the capsular polysaccharides (CPS) and by the high diversity in leve ...
Sample pages 2 PDF
... values of phi and psi. For each possible set of these dihedral angles, the distances between all pairs of nonbonded atoms can be compared using a set of minimum interatomic contact distances (Table 2.3); if the distance between any set of atoms is smaller than the minimum contact distance then that ...
... values of phi and psi. For each possible set of these dihedral angles, the distances between all pairs of nonbonded atoms can be compared using a set of minimum interatomic contact distances (Table 2.3); if the distance between any set of atoms is smaller than the minimum contact distance then that ...
Pvlea-18, a Member of a New Late-Embryogenesis
... expressed in yeast and found to confer improved resistance to high salinity and freezing (Imai et al., 1996). During normal seed development, most of the characterized LEA proteins have been located in all embryo cell types (Close et ...
... expressed in yeast and found to confer improved resistance to high salinity and freezing (Imai et al., 1996). During normal seed development, most of the characterized LEA proteins have been located in all embryo cell types (Close et ...
A Positive Selection Function for miRNA
... The combinations are then translated For example, miRNA let-7 (6) in the 5′ to 3′ has one open reading frame and three open reading frames in its antiparallel complement in the 5′ to 3′ direction. The antiparallel complement would correspond to coding sequences which would appear in mRNA which are ...
... The combinations are then translated For example, miRNA let-7 (6) in the 5′ to 3′ has one open reading frame and three open reading frames in its antiparallel complement in the 5′ to 3′ direction. The antiparallel complement would correspond to coding sequences which would appear in mRNA which are ...
PDB database http://www.pdb.org/
... The PDB archive contains macromolecular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses. Files in its holdings are deposited by the international user community and maintained by the RCSB PDB staff. Approximately 50-100 new structures are deposited each week. T ...
... The PDB archive contains macromolecular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses. Files in its holdings are deposited by the international user community and maintained by the RCSB PDB staff. Approximately 50-100 new structures are deposited each week. T ...
Beta Proteins - Two Important Folds : BCH 622 Worksheet
... Residues 110-136 (View3) are a long alpha helix (how many turns? __________ ) which forms the primary contact with the other subunit in the dimer. Residues 137-208 are the DNAbinding domain, a small open-face sandwich antiparallel beta sheet (View4). The pair of helices at residues 170-190 and their ...
... Residues 110-136 (View3) are a long alpha helix (how many turns? __________ ) which forms the primary contact with the other subunit in the dimer. Residues 137-208 are the DNAbinding domain, a small open-face sandwich antiparallel beta sheet (View4). The pair of helices at residues 170-190 and their ...
A Conversation about Central Dogma of Molecular
... of sequence-based information? After all the 3dimensional structure of a prion is dependent on its sequence, and a prion ‘converts’ the structure of only those ‘normal’ proteins that have the same sequence as the prion protein. Teacher: It is indeed true that the sequence of a prion protein is a per ...
... of sequence-based information? After all the 3dimensional structure of a prion is dependent on its sequence, and a prion ‘converts’ the structure of only those ‘normal’ proteins that have the same sequence as the prion protein. Teacher: It is indeed true that the sequence of a prion protein is a per ...
Protein sequence comparisons show that the
... lentivirus families and by poxviruses. These relationships suggest strongly that the 'pseudoproteases' actually are dUTPases, and have not arisen by duplication of an oncovirus protease gene as had been suggested. The herpesvirus dUTPase sequences differ from the others in that they are longer (abou ...
... lentivirus families and by poxviruses. These relationships suggest strongly that the 'pseudoproteases' actually are dUTPases, and have not arisen by duplication of an oncovirus protease gene as had been suggested. The herpesvirus dUTPase sequences differ from the others in that they are longer (abou ...
proposal for complex variants
... the accession.version number of the sequence submitted to GenBank. Please note that the purpose of the extended description is: 1) to reduce the necessity to submit new Genbank sequences for every small change observed within a larger change 2) to allow easy comparison between different complex chan ...
... the accession.version number of the sequence submitted to GenBank. Please note that the purpose of the extended description is: 1) to reduce the necessity to submit new Genbank sequences for every small change observed within a larger change 2) to allow easy comparison between different complex chan ...
Lipid–protein interactions probed by electron crystallography
... residues are often used to dictate lipid head group positioning because the positively charged indole ring on this amino acid may simultaneously interact with the electronegative glycerol backbone and acyl lipid tail [9]. It has now been determined that the central lipids are likely to be the archae ...
... residues are often used to dictate lipid head group positioning because the positively charged indole ring on this amino acid may simultaneously interact with the electronegative glycerol backbone and acyl lipid tail [9]. It has now been determined that the central lipids are likely to be the archae ...
Molecular Evolution and Structure of a
... The aligned sequences were analyzed using the PHYLIP, MEGA2, and MrBayes packages. The program SEQBOOT was used to create 1,000 bootstrapped data set and PROTPARS was used to calculate the phylogeny estimate. The maximum-parsimony tree obtained is shown in figure 2. Phylogenetic analysis based on ne ...
... The aligned sequences were analyzed using the PHYLIP, MEGA2, and MrBayes packages. The program SEQBOOT was used to create 1,000 bootstrapped data set and PROTPARS was used to calculate the phylogeny estimate. The maximum-parsimony tree obtained is shown in figure 2. Phylogenetic analysis based on ne ...
The epidermal intermediate filament proteins of
... putative start codons in frame, of which only the start codon at positions 105 ± 107 fits into the Kozak sequence context required for translational initiation. This assumption was confirmed by expression in E. coli using the entire open reading frame between nucleotides 21 and 1389. Microsequencing ...
... putative start codons in frame, of which only the start codon at positions 105 ± 107 fits into the Kozak sequence context required for translational initiation. This assumption was confirmed by expression in E. coli using the entire open reading frame between nucleotides 21 and 1389. Microsequencing ...
AmpliScribe™ T7 High Yield Transcription Kit
... to obtain the maximum possible yields of RNA from an in vitro transcription reaction. The standard 2-hour, 20-µl AmpliScribe reaction will incorporate up to 90% of input NTPs and produce up to 150 µg of RNA from 1 µg of the control template. These yields are made possible by the high-performance pro ...
... to obtain the maximum possible yields of RNA from an in vitro transcription reaction. The standard 2-hour, 20-µl AmpliScribe reaction will incorporate up to 90% of input NTPs and produce up to 150 µg of RNA from 1 µg of the control template. These yields are made possible by the high-performance pro ...
Homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the ""target"" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the ""template""). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure.It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone.The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity usually imply significant structural similarity.The quality of the homology model is dependent on the quality of the sequence alignment and template structure. The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. Model quality declines with decreasing sequence identity; a typical model has ~1–2 Å root mean square deviation between the matched Cα atoms at 70% sequence identity but only 2–4 Å agreement at 25% sequence identity. However, the errors are significantly higher in the loop regions, where the amino acid sequences of the target and template proteins may be completely different.Regions of the model that were constructed without a template, usually by loop modeling, are generally much less accurate than the rest of the model. Errors in side chain packing and position also increase with decreasing identity, and variations in these packing configurations have been suggested as a major reason for poor model quality at low identity. Taken together, these various atomic-position errors are significant and impede the use of homology models for purposes that require atomic-resolution data, such as drug design and protein–protein interaction predictions; even the quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid. Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds. The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection. Like other methods of structure prediction, current practice in homology modeling is assessed in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP.