Molecular Weight Estimation - Bio-Rad
... systems possess a wider dynamic range and are easier to quantitate by densitometry compared to colorimetric detection or film-based techniques. Protein standards are a key component in the analysis of a western blotting experiment. Standards used for western blots can provide reliable MW estimation ...
... systems possess a wider dynamic range and are easier to quantitate by densitometry compared to colorimetric detection or film-based techniques. Protein standards are a key component in the analysis of a western blotting experiment. Standards used for western blots can provide reliable MW estimation ...
Methods of Protein Analysis
... sis, a 95 per cent probability that the value would be within ± 2 S.D.; wheat of 14.0 per cent protein could show a range from 13.68 to 14.32 per cent protein (14.0 ± 0.32). What about the 5 per cent of the time when the variation is greater than ± 2 S.D.? There is a 0.26 per cent probability that t ...
... sis, a 95 per cent probability that the value would be within ± 2 S.D.; wheat of 14.0 per cent protein could show a range from 13.68 to 14.32 per cent protein (14.0 ± 0.32). What about the 5 per cent of the time when the variation is greater than ± 2 S.D.? There is a 0.26 per cent probability that t ...
Alpha-Domain Structures
... • Leucines (“knobs”) of one helix sit in hydrophobic “holes” of other helix ...
... • Leucines (“knobs”) of one helix sit in hydrophobic “holes” of other helix ...
PowerPoint - Oregon State University
... • Identification of ToxB homologs will be carried out by PCR. • Screening of several ascomycete isolates • Primers have been designed for the Internal Transcribed Spacer (ITS) sequence and the Ptr ToxB sequence within the ORF ...
... • Identification of ToxB homologs will be carried out by PCR. • Screening of several ascomycete isolates • Primers have been designed for the Internal Transcribed Spacer (ITS) sequence and the Ptr ToxB sequence within the ORF ...
Short review - BioPublisher
... was significantly more accurate than the other two tools in predicting secreted proteins. The Mathews' correlation coefficient (MCC) (Matthews, 1975) values for prediction of all other subcellular locations by all three tools were lower than 50%. Thus, an improvement in prediction accuracies for the ...
... was significantly more accurate than the other two tools in predicting secreted proteins. The Mathews' correlation coefficient (MCC) (Matthews, 1975) values for prediction of all other subcellular locations by all three tools were lower than 50%. Thus, an improvement in prediction accuracies for the ...
Site-specific functionalization of proteins and their applications to
... the application. In the case of monoclonal antibodies, random labeling with fluorescent molecules hardly affects the antigen binding since many primary amines are present and only a small fraction may be important for this interaction. Smaller proteins such as antibody fragments are more likely to s ...
... the application. In the case of monoclonal antibodies, random labeling with fluorescent molecules hardly affects the antigen binding since many primary amines are present and only a small fraction may be important for this interaction. Smaller proteins such as antibody fragments are more likely to s ...
University of Groningen Structure and mechanism of the ECF
... proteins (BioY, NikM and CbiM) were very different. A link between BioY, FolT and ThiT was made when an orthologue of the bioY gene was found in the L. casei genome, but without the additional bioMN (ecfAT) genes. Instead, an operon encoding BioMNhomologues was found at a different location in the g ...
... proteins (BioY, NikM and CbiM) were very different. A link between BioY, FolT and ThiT was made when an orthologue of the bioY gene was found in the L. casei genome, but without the additional bioMN (ecfAT) genes. Instead, an operon encoding BioMNhomologues was found at a different location in the g ...
Function and biotechnology of extremophilic enzymes in low water
... side chains buried and better ordered than those from non-halophiles (Figure 3). In halophilic proteins, lysine residues are often replaced by arginines, likely due to the greater hydrophilicity of the guanidinyl side chain, with a substantial role in maintaining the active protein structure [11,30, ...
... side chains buried and better ordered than those from non-halophiles (Figure 3). In halophilic proteins, lysine residues are often replaced by arginines, likely due to the greater hydrophilicity of the guanidinyl side chain, with a substantial role in maintaining the active protein structure [11,30, ...
2-D Quant Kit - GE Healthcare Life Sciences
... electrophoresis as well as any sample that contains substances that otherwise interfere with protein quantification. The procedure uses a combination of a unique precipitant and co-precipitant to quantitatively precipitate sample protein while leaving interfering contaminants in solution. The protei ...
... electrophoresis as well as any sample that contains substances that otherwise interfere with protein quantification. The procedure uses a combination of a unique precipitant and co-precipitant to quantitatively precipitate sample protein while leaving interfering contaminants in solution. The protei ...
Lecture 5
... Structural hierarchy in proteins • Primary structure (1º structure)-for a protein is the amino acid sequence of its polypeptide chain(s). • Secondary structure (2º structure)-the local spatial arrangement of a polypeptide’s backbone atoms without regard to the conformations of their side chains. • ...
... Structural hierarchy in proteins • Primary structure (1º structure)-for a protein is the amino acid sequence of its polypeptide chain(s). • Secondary structure (2º structure)-the local spatial arrangement of a polypeptide’s backbone atoms without regard to the conformations of their side chains. • ...
Section III (pdf)
... atoms in the Display Window (see section 1.5 for more information on identifying atom numbers). Once you know the two atom numbers, you must select only those two atoms using the select atomno= command. Finally, use the struts 1.0 command to add a strut or the strut off command to remove the bond be ...
... atoms in the Display Window (see section 1.5 for more information on identifying atom numbers). Once you know the two atom numbers, you must select only those two atoms using the select atomno= command. Finally, use the struts 1.0 command to add a strut or the strut off command to remove the bond be ...
Structural Investigation of the Antibiotic and ATP
... X-ray Data Collection and Processing. X-ray diffraction data were collected to 2.5 A resolution at 4 "C with a Siemens XlOOOD area detector system equipped with doublefocusing mirrors. The X-ray source was Cu K a radiation from a Rigaku RU200 rotating anode generator operated at 50 kV and 50 mA. The ...
... X-ray Data Collection and Processing. X-ray diffraction data were collected to 2.5 A resolution at 4 "C with a Siemens XlOOOD area detector system equipped with doublefocusing mirrors. The X-ray source was Cu K a radiation from a Rigaku RU200 rotating anode generator operated at 50 kV and 50 mA. The ...
BMC Microbiology
... 407 amino acids. The invariant amino acids required by serine/threonine protein kinases are shaded in red. The potential autophosphorylation sites containing the consensus sequence {R, K}-X-X-{T, S} are shaded in light blue. The calmodulin-binding domain is shaded in gray. ...
... 407 amino acids. The invariant amino acids required by serine/threonine protein kinases are shaded in red. The potential autophosphorylation sites containing the consensus sequence {R, K}-X-X-{T, S} are shaded in light blue. The calmodulin-binding domain is shaded in gray. ...
EVIDENCE FOR TWO DISTINCT CLASSES OF STREPTOCOCCAL
... conserved surface-exposed domain, and those serotypes previously described as having MAP I antigen (10). Included in the group that share a conserved domain with M6 protein are the ARRassociated serotypes . Furthermore, most isolates that lack the conserved domain on their surface give a positive se ...
... conserved surface-exposed domain, and those serotypes previously described as having MAP I antigen (10). Included in the group that share a conserved domain with M6 protein are the ARRassociated serotypes . Furthermore, most isolates that lack the conserved domain on their surface give a positive se ...
Protein sequence alignment
... 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 di ...
... 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 di ...
Know Your Feed Terms - Alberta Agriculture and Forestry
... bound with the fibre is unavailable to the animal. Feed labs may report acid detergent fibre protein (ADF-P%) or acid detergent insoluble protein (ADIP% or ADICP%), which can be expressed as a per cent of total dry matter or as a percentage of total nitrogen/protein. The concentration of ADIN is use ...
... bound with the fibre is unavailable to the animal. Feed labs may report acid detergent fibre protein (ADF-P%) or acid detergent insoluble protein (ADIP% or ADICP%), which can be expressed as a per cent of total dry matter or as a percentage of total nitrogen/protein. The concentration of ADIN is use ...
Cloning, Purification, and Partial Characterization of the
... more slowly than predicted from their calculated molecular mass. The protein with intein migrates as a 123 kDa instead of 90 kDa molecule and the recombinant protein without intein migrates as 98 kDa instead of 71 kDa molecule. To confirm that the purified proteins are indeed the MCM proteins MALDI- ...
... more slowly than predicted from their calculated molecular mass. The protein with intein migrates as a 123 kDa instead of 90 kDa molecule and the recombinant protein without intein migrates as 98 kDa instead of 71 kDa molecule. To confirm that the purified proteins are indeed the MCM proteins MALDI- ...
Assessing Side-chain Perturbations of the Protein Backbone: A
... Classification of the 20 amino acids simplifies analysis and helps uncover relationships that are important to protein structure, folding and function. Such an understanding is especially important in explaining the less-than-straightforward plasticity found between sequence and structure space. Man ...
... Classification of the 20 amino acids simplifies analysis and helps uncover relationships that are important to protein structure, folding and function. Such an understanding is especially important in explaining the less-than-straightforward plasticity found between sequence and structure space. Man ...
Unit 4 proteins
... 4.1 Proteins as Biotechnology Products • Proteins – large molecules that are required for the structure, function, and regulation of living cells • 2000 NIH launched Protein Structure Initiative – Effort to identify the structure of human proteins – 2010 began using high throughput structure determ ...
... 4.1 Proteins as Biotechnology Products • Proteins – large molecules that are required for the structure, function, and regulation of living cells • 2000 NIH launched Protein Structure Initiative – Effort to identify the structure of human proteins – 2010 began using high throughput structure determ ...
proteinstructure
... Nonetheless, it’s hard to visualize what’s happening at the active site at any instant Hydrogens sometimes well-located; they’re often the least defined atoms in an Xray structure The NMR structure is obtained in solution! Hard to make NMR work if MW > 25 kDa ...
... Nonetheless, it’s hard to visualize what’s happening at the active site at any instant Hydrogens sometimes well-located; they’re often the least defined atoms in an Xray structure The NMR structure is obtained in solution! Hard to make NMR work if MW > 25 kDa ...
A bioinformatics study concerning the structural and functional
... The structural and functional characteristics of caveolin proteins have not yet been well defined, but some useful information can be obtained through sequence based predictions using structural bioinformatics tools. In the present study, a bioinformatics investigation was performed in which, to the ...
... The structural and functional characteristics of caveolin proteins have not yet been well defined, but some useful information can be obtained through sequence based predictions using structural bioinformatics tools. In the present study, a bioinformatics investigation was performed in which, to the ...
The Plant Cell
... was identified from the GenBank database. These proteins contained predicted coiled-coil and Src homology 3 (SH3) domains that are similar to animal and yeast proteins involved in the formation, fission, and uncoating of clathrin-coated vesicles. Subcellular fractionation and immunolocalization stud ...
... was identified from the GenBank database. These proteins contained predicted coiled-coil and Src homology 3 (SH3) domains that are similar to animal and yeast proteins involved in the formation, fission, and uncoating of clathrin-coated vesicles. Subcellular fractionation and immunolocalization stud ...
The RAGNYA fold: a novel fold with multiple topological variants
... Several recent structural studies indicate that a number of protein folds have been repeatedly deployed as scaffolds for a biochemically diverse set of interactions with nucleic acids. Some notable examples of such folds are the RNA recognition motif (RRM)-like fold, double c-beta barrel (and the rel ...
... Several recent structural studies indicate that a number of protein folds have been repeatedly deployed as scaffolds for a biochemically diverse set of interactions with nucleic acids. Some notable examples of such folds are the RNA recognition motif (RRM)-like fold, double c-beta barrel (and the rel ...
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.