Proteins
... The measurement of globulins based on their tryptophan content has never come into common use because of the ease and simplicity of the dye-binding methods for albumin. ...
... The measurement of globulins based on their tryptophan content has never come into common use because of the ease and simplicity of the dye-binding methods for albumin. ...
Top down - The Fenyo Lab
... high affinity for antigen without light chain • Aimed to clone individual single-domain VHH antibodies against GFP – only ~15 kDa, can be recombinantly expressed, used as bait for pullouts, etc. • To identify full repertoire, will identify GFP binders through combination of high-throughput DNA seque ...
... high affinity for antigen without light chain • Aimed to clone individual single-domain VHH antibodies against GFP – only ~15 kDa, can be recombinantly expressed, used as bait for pullouts, etc. • To identify full repertoire, will identify GFP binders through combination of high-throughput DNA seque ...
2. CYCLIC AMINOACIDS 2.1. Aromatic
... Specific features: – The conformation is determined by the properties of the sidechain radicals and medium – The molecule tends to adopt an energetically favorable configuration corresponding to the minimum of free energy ...
... Specific features: – The conformation is determined by the properties of the sidechain radicals and medium – The molecule tends to adopt an energetically favorable configuration corresponding to the minimum of free energy ...
Histidine protonation and the activation of viral fusion proteins
... Experimentally, protein-mediated membrane fusion cannot be observed with either the spatial or temporal resolution required to investigate the role of specific histidine residues. Instead, to selectively test the effect of histidine protonation, MD simulations have been performed of the DEN2 sE prot ...
... Experimentally, protein-mediated membrane fusion cannot be observed with either the spatial or temporal resolution required to investigate the role of specific histidine residues. Instead, to selectively test the effect of histidine protonation, MD simulations have been performed of the DEN2 sE prot ...
A High Yield Method for the Removal of Detergents from Low
... mass spectrometric analysis of 2.5-10 ug of BSA enzymatic digests at 25-100 µg/mL prepared in the presence of detergents and processed to remove detergent revealed sequence coverage and MASCOT scores as good as or better than control BSA samples processed without detergent. The method significantly ...
... mass spectrometric analysis of 2.5-10 ug of BSA enzymatic digests at 25-100 µg/mL prepared in the presence of detergents and processed to remove detergent revealed sequence coverage and MASCOT scores as good as or better than control BSA samples processed without detergent. The method significantly ...
The Crystal Structure of Arabidopsis thaliana Allene Oxide Cyclase
... The barrel forms an elongated cavity, which is lined mostly by aromatic and hydrophobic residues and reaches ;14 Å into the protein (Figure 2C). Three areas of the cavity surface are noteworthy. First, the conserved Glu-23 is positioned at the very bottom of the cavity, introducing a negative charg ...
... The barrel forms an elongated cavity, which is lined mostly by aromatic and hydrophobic residues and reaches ;14 Å into the protein (Figure 2C). Three areas of the cavity surface are noteworthy. First, the conserved Glu-23 is positioned at the very bottom of the cavity, introducing a negative charg ...
Membrane pore architecture of the CslF6
... expressed in N. benthamiana leaf (Fig. 1C). Conversely, the group of species (maize, oat, rice, and sorghum) with low DP3/DP4 ratio (1-3,1-4)-b-glucan in their grain have CslF6 genes that produce (1-3,1-4)b-glucan with a relatively low DP3/DP4 ratio (about 1.0) when expressed in N. benthamiana leaf ...
... expressed in N. benthamiana leaf (Fig. 1C). Conversely, the group of species (maize, oat, rice, and sorghum) with low DP3/DP4 ratio (1-3,1-4)-b-glucan in their grain have CslF6 genes that produce (1-3,1-4)b-glucan with a relatively low DP3/DP4 ratio (about 1.0) when expressed in N. benthamiana leaf ...
tutorial5_12
... • Motif discovery from unaligned sequences Genomic or protein sequences • Flexible model of motif presence (Motif can be absent in some sequences or appear several times in one sequence) ...
... • Motif discovery from unaligned sequences Genomic or protein sequences • Flexible model of motif presence (Motif can be absent in some sequences or appear several times in one sequence) ...
appendix 1
... prepared or processed to reduce their gluten content and this must not exceed 20mg / kg (20 ppm) These foods will be subject to future review ...
... prepared or processed to reduce their gluten content and this must not exceed 20mg / kg (20 ppm) These foods will be subject to future review ...
Structures of nucleotide-bound and free aIF2γ from Sulfolobus
... excluding these flexible regions yields an rms deviation of 0.39 Å. Since the model of SsoaIF2γ-GDP was determined with a higher resolution, hereafter we refer to this structure unless stated otherwise. Two molecules of Sso-aIF2γ-GDP in the asymmetric unit of the crystal are slightly different in so ...
... excluding these flexible regions yields an rms deviation of 0.39 Å. Since the model of SsoaIF2γ-GDP was determined with a higher resolution, hereafter we refer to this structure unless stated otherwise. Two molecules of Sso-aIF2γ-GDP in the asymmetric unit of the crystal are slightly different in so ...
Supplemental Methods 1. Amino acid conformation clustering Amino
... and the distribution information of the members in the clusters are listed in Table S6. 2. Protein atomistic non-covalent interacting database Atomistic contact interactions in proteins of known structures were organized into a database containing non-covalent atomistic interaction information for a ...
... and the distribution information of the members in the clusters are listed in Table S6. 2. Protein atomistic non-covalent interacting database Atomistic contact interactions in proteins of known structures were organized into a database containing non-covalent atomistic interaction information for a ...
Statistically Significant Patterns in DNA Sequences
... a sequence or set of sequences is expected to have similar/higher/lower/more regular a.o. distribution of motifs than another sequence or set of sequences How many motif occurences are expected? ...
... a sequence or set of sequences is expected to have similar/higher/lower/more regular a.o. distribution of motifs than another sequence or set of sequences How many motif occurences are expected? ...
a server for analyzing and predicting RNA
... RNABindR provides two main services: (i) identification of RNA-binding residues, given the structure of a protein– RNA complex and (ii) prediction of RNA-binding residues given a protein sequence. An overview of RNABindR is provided in Figure 2. Calculation of RNA-binding residues in protein–RNA comp ...
... RNABindR provides two main services: (i) identification of RNA-binding residues, given the structure of a protein– RNA complex and (ii) prediction of RNA-binding residues given a protein sequence. An overview of RNABindR is provided in Figure 2. Calculation of RNA-binding residues in protein–RNA comp ...
Cloning, sequence and in vitro transcription/translation analysis of a
... beginning of ORF I (.5’-GTATGAGT) and the 1-nt overlap between the end of ORF 1 and the beginning of ORF E (5’-CTTAATGGC) suggest possible translational coupling of these ORFs during translation from a single polycistronic transcript (Normark et al.. 1983) derived from an AIE operon. The presence of ...
... beginning of ORF I (.5’-GTATGAGT) and the 1-nt overlap between the end of ORF 1 and the beginning of ORF E (5’-CTTAATGGC) suggest possible translational coupling of these ORFs during translation from a single polycistronic transcript (Normark et al.. 1983) derived from an AIE operon. The presence of ...
The Dock and Lock Method: A Novel
... regulatory (R) subunits of protein kinase A (PKA) and the anchoring domain (AD) of A-kinase anchoring proteins (AKAP; refs. 8, 9). PKA, which plays a central role in one of the best studied signal transduction pathway triggered by the binding of the second messenger cyclic AMP to the R subunits, was ...
... regulatory (R) subunits of protein kinase A (PKA) and the anchoring domain (AD) of A-kinase anchoring proteins (AKAP; refs. 8, 9). PKA, which plays a central role in one of the best studied signal transduction pathway triggered by the binding of the second messenger cyclic AMP to the R subunits, was ...
i PRODUCTION OF NATURAL PROTEIN USING CHICKEN
... sources, including waste products. Feathers are bio-resource with high protein content (more than 750 g kg-1 crude protein). Keratin is the main component of feathers, representing nearly 90% of feather weight. Feather keratin shows an elevated content of the amino acids glycine, alanine, serine, cy ...
... sources, including waste products. Feathers are bio-resource with high protein content (more than 750 g kg-1 crude protein). Keratin is the main component of feathers, representing nearly 90% of feather weight. Feather keratin shows an elevated content of the amino acids glycine, alanine, serine, cy ...
Conservation and relative importance of residues across protein
... that retain partial accessibility (24, 25). The core possesses more hydrophobic residues and has a composition that is distinct from the rim or the rest of the protein surface. With the division into core and rim residues one can ask the question of whether as two groups these residues have differen ...
... that retain partial accessibility (24, 25). The core possesses more hydrophobic residues and has a composition that is distinct from the rim or the rest of the protein surface. With the division into core and rim residues one can ask the question of whether as two groups these residues have differen ...
With-the-great-explosion-of-use-of
... biological data and genomic information for development of computational methods. There are available all kind of information to elucidate peptide/protein structures obtained by experimental approaches like CD, EPR, FTIR, NMR, and X ray crystallography. This data show the enormous structural diversi ...
... biological data and genomic information for development of computational methods. There are available all kind of information to elucidate peptide/protein structures obtained by experimental approaches like CD, EPR, FTIR, NMR, and X ray crystallography. This data show the enormous structural diversi ...
Elements of Systemic..
... 100 nm). Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino acids, also referred to as residues. For chains under 40 residues the term peptide is frequently used instead of protein. To be able to perform their biological function, proteins f ...
... 100 nm). Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino acids, also referred to as residues. For chains under 40 residues the term peptide is frequently used instead of protein. To be able to perform their biological function, proteins f ...
Bioinformatics - Department of Computer Science
... Xi {A,R,N,D,C,E,Q,G,H,I,L,K, M,F,P,S,T,W,Y,V} ...
... Xi {A,R,N,D,C,E,Q,G,H,I,L,K, M,F,P,S,T,W,Y,V} ...
Evolutionary rate at the protein domain level is
... In 1968 Motoo Kimura proposed the neutral theory of evolution which provides a theoretical framework for understanding the molecular clock as well as the apparent differences in the rate of evolution that arise within proteins and across different lineages [13]. Because the mechanism of DNA replicat ...
... In 1968 Motoo Kimura proposed the neutral theory of evolution which provides a theoretical framework for understanding the molecular clock as well as the apparent differences in the rate of evolution that arise within proteins and across different lineages [13]. Because the mechanism of DNA replicat ...
Thermodynamic prediction of protein neutrality
... natural protein evolution, developing protein engineering strategies, and understanding the basis of genetic diseases. Computational and experimental studies have demonstrated that both protein stability and structure affect a protein’s tolerance to substitutions. Simulations have shown that more st ...
... natural protein evolution, developing protein engineering strategies, and understanding the basis of genetic diseases. Computational and experimental studies have demonstrated that both protein stability and structure affect a protein’s tolerance to substitutions. Simulations have shown that more st ...
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.