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Protein structural class prediction using predicted secondary
Protein structural class prediction using predicted secondary

... protein accurately. Generally if a method follows the SCOP classification scheme [3], then it classifies a protein into one of the following main four structural classes: all-α, all-β, α+β, and α/β. If a method follows CATH classification scheme [4] then it classifies a protein into one of the follo ...
Amino Acid Sequence of a Platelet-Binding Human Anti
Amino Acid Sequence of a Platelet-Binding Human Anti

... HF3 16/6, and HF2 l8/2). The first 40 residues these light chains ...
Proteomic analysis of the signaling pathway mediated by the
Proteomic analysis of the signaling pathway mediated by the

... Penicillium chrysogenum has had a key historical role in the development of industrial microbiology, and is currently one of the most important species in the biotechnological industry as producer of penicillin [5] and other β-lactam antibiotic precursors [6]. The P. chrysogenum heterotrimeric Gα pr ...
Representation and High-Quality Annotation of
Representation and High-Quality Annotation of

... not find a matching partner in the initial clustering phase remain as singlet sequences after the procedure. Sometimes not all sequences which were initially grouped into a cluster can be assembled into contig sequences. Hence, there can be multiple contigs and also so-called clustered singlets pres ...
Structure of the Coat Protein-binding Domain of
Structure of the Coat Protein-binding Domain of

... charged residues (K286, D288), and is followed by a solvent-exposed hydrophobic residue, V289, which is the ®rst residue in the second helix. Electrostatic interactions are somewhat nonspeci®c, especially when they do not involve a single pair of oppositely charged residues. However, this type of in ...
Sequence Alignment
Sequence Alignment

... Guide to the Analysis of Genes and Proteins) For nucleotide based searches, one should look for hits with E-values of 10-6 or less and sequence identity of 70% or more For protein based searches, one should look for hits with E-values of 10-3 or less and sequence identity of 25% or more ...
Local protein synthesis in neuronal axons: why and
Local protein synthesis in neuronal axons: why and

... protein on site by local mRNA translation (2). This idea led to a series of important discoveries that have firmly established local protein synthesis as one of key mechanisms underlying activity-dependent structural changes in the synapse (3). In contrast to the dendrite, however, polyribosomes wer ...
Prediction of mitochondrial proteins of malaria parasite
Prediction of mitochondrial proteins of malaria parasite

... proteins. This means that mitochondrial and non-mitochondrial proteins can be predicted based on their amino acid composition. We developed a SVM model using amino acid composition and got maximum MCC 0.38 with accuracy of 74.14%. Similarly, SVM models were developed using dipeptide composition whic ...
Journal of Bacteriology
Journal of Bacteriology

... frame is a structural gene (data not shown). The open reading frame is preceded by a possible ribosome-binding site (Fig. 2). This gene, which we designated nodO, codes for a protein of 284 amino acids with a predicted molecular size of 30,002 daltons. To test whether the gene identified above codes ...
Cloning and characterization of CmGPD1, the Candida magnoliae
Cloning and characterization of CmGPD1, the Candida magnoliae

... gene encodes a polypeptide of 360 amino acids, which shows high homology with known NADH-dependent GPDHs of other species. The CmGPD1 gene was expressed in recombinant Escherichia coli with the maltose-binding protein (MBP) fusion system and purified to homogeneity using simple affinity chromatograp ...
Primary sequence analysis of Xac catalases
Primary sequence analysis of Xac catalases

... pathogens X. campestris pv. vesicatoria (97% identity) [5] and X. oryzae pv. oryzae (96% ...
Alternative Splicing: How to Get More than One Protein from a Gene
Alternative Splicing: How to Get More than One Protein from a Gene

... Description: Use the word key from the “Protein Synthesis and Words” activity to demonstrate how eukaryotic cells may use one DNA sequence to code for multiple proteins. Eukaryotic cells might use the same gene or DNA sequence differently depending on where the gene is located. A brain cell might ma ...
Heat shock response in hyperthermophilic microorganisms
Heat shock response in hyperthermophilic microorganisms

... In vivo evidence for heat shock in hyperthermophiles When a culture of microorganisms is exposed to super-optimal growth temperatures, the number of viable cells decreases exponentially with time, and this rate of decline increases exponentially with increasing temperature [32]. However, if a cultur ...
Dream Protein - Greens First
Dream Protein - Greens First

... Amino Acids are the chemical units or commonly known as the building blocks that make up proteins. Because they contain about 16 percent nitrogen, this is what distinguishes them from the other two basic nutrients, sugars and fatty acids. Protein provides the structure for all living things, necessa ...
NMR Analysis of Protein
NMR Analysis of Protein

... overlay spectra in presence/absence of ligand  changes in peak position indicate binding  identity of peaks that change identifies binding site on protein surface  if a defined residue cluster is not observed  non-specific binding  if a majority of the peaks incur changes detrimental interacti ...
Synaptonemal complex proteins - Journal of Cell Science
Synaptonemal complex proteins - Journal of Cell Science

... fusion proteins (accession number L32978; Moens et al., 1992) proved that these represent overlapping cDNAs of the hamster homologue of the rat SCP1 gene that encodes a 125 kDa SC protein (Meuwissen et al., 1992). The hamster and rat proteins are 90% identical. We therefore adopt for Syn1 the number ...
How do non-enyzmatic domains become enzymes
How do non-enyzmatic domains become enzymes

... domain) with an identical core set of catalytic residues. Two distinct reactions: nucleotidyltransferase (transferase; class 2 according to the EC classification) and topoisomerase (isomerase; class 5 according to the EC classification) A more dramatic case of exploration of the reaction space is se ...
The synthesis of peptides and proteins containing non
The synthesis of peptides and proteins containing non

... domain, forming a thioester as the active acylating agent. This formally corresponds to the activation of acyl groups as thioesters of Coenzyme A in polyketide synthesis, and utilises the capability of thioesters to act as relatively active acylating agents whilst retaining a degree of stability aga ...
Supplemental Methods 1. Amino acid conformation clustering Amino
Supplemental Methods 1. Amino acid conformation clustering Amino

... conformation of each of the clusters was determined as the center of mass of the vectors in the cluster. The number of clusters, the torsion angles of the centroid conformations, and the distribution information of the members in the clusters are listed in Table S6. 2. Protein atomistic non-covalen ...
Comparison of Rumen Amino Acid Protection Technologies
Comparison of Rumen Amino Acid Protection Technologies

... Glutamic acid Glutamine Glycine Proline Serine Tyrosine ...
A perturbation-based method for calculating explicit likelihood of
A perturbation-based method for calculating explicit likelihood of

... All alignments that did not have a >95% match to a crystal structure in the Protein Data Bank (PDB) database were removed from the analysis set. In an attempt to correct for apparent co-variation due to a common phylogenetic origin of closely related sequences, duplicate sequences with greater than ...
Poster
Poster

... Bacteria are the cause of many diseases. Normally our bodies fight these infections, but sometimes assistance is necessary through prescription antibiotics. Antibiotics kill or inhibit the growth of bacteria by interfering with enzymes or processes specific to bacterial function. For instance, many ...
Sample Questions 1 - U of L Class Index
Sample Questions 1 - U of L Class Index

... Solute that diffuses into a bead flows more slowly through the column as the pores restrict flow down the column. Thus, smaller solutes are retarded relative to larger solutes which do not enter the pores. (27) The unknown protein must be exposed to conditions that (1) disrupt quaternary structure a ...
Constructing High Complexity Synthetic Libraries of Long ORFs
Constructing High Complexity Synthetic Libraries of Long ORFs

... Hospital, Boston, MA 02114, USA ...
Identification and expression of the first nonmammalian amyloid‐β
Identification and expression of the first nonmammalian amyloid‐β

... Phylogenetic analysis of the APP superfamily To reveal the evolutionary history of the APP superfamily, we used maximum likelihood and Bayesian methods to construct a phylogenetic tree of the members of the APP superfamily that now includes Xenopus APLP2 (X-APLP2) as the first nonmammalian APLP2 prot ...
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Ancestral sequence reconstruction

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