Protein structure
... and β-sheets are referred to as turns and loops Other secondary substructure classifications exist, but are rarely seen in practice Sub-units that do not fit into any other classification are known as random coils ...
... and β-sheets are referred to as turns and loops Other secondary substructure classifications exist, but are rarely seen in practice Sub-units that do not fit into any other classification are known as random coils ...
Document
... The C-terminal domain mediates the interactions of two repressor dimers to operator sites, O64 and OL. The N-terminal domain mediates the interaction with RNA polymerase (lysogenic promoter for repressor maintenance) and thus, activating the CI gene. (Bell et al.) Therefore, above reasons are why th ...
... The C-terminal domain mediates the interactions of two repressor dimers to operator sites, O64 and OL. The N-terminal domain mediates the interaction with RNA polymerase (lysogenic promoter for repressor maintenance) and thus, activating the CI gene. (Bell et al.) Therefore, above reasons are why th ...
Protein Data Bank Contents Guide: Atomic Coordinate Entry
... The Protein Data Bank (PDB) is an archive of experimentally determined threedimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, bibliographic citations, primary and s ...
... The Protein Data Bank (PDB) is an archive of experimentally determined threedimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, bibliographic citations, primary and s ...
How to study proteins by circular dichroism
... report this also in terms of the ellipticity (h) in degrees. It should be noted that h = tan1 (b/a) where b and a are the minor and major axes of the resulting ellipse (Fig. 1). There is a simple numerical relationship between DA and ellipticity (in degrees), namely h = 32.98 DA. The CD spectrum is ...
... report this also in terms of the ellipticity (h) in degrees. It should be noted that h = tan1 (b/a) where b and a are the minor and major axes of the resulting ellipse (Fig. 1). There is a simple numerical relationship between DA and ellipticity (in degrees), namely h = 32.98 DA. The CD spectrum is ...
How to study proteins by circular dichroism
... report this also in terms of the ellipticity (h) in degrees. It should be noted that h = tan1 (b/a) where b and a are the minor and major axes of the resulting ellipse (Fig. 1). There is a simple numerical relationship between DA and ellipticity (in degrees), namely h = 32.98 DA. The CD spectrum is ...
... report this also in terms of the ellipticity (h) in degrees. It should be noted that h = tan1 (b/a) where b and a are the minor and major axes of the resulting ellipse (Fig. 1). There is a simple numerical relationship between DA and ellipticity (in degrees), namely h = 32.98 DA. The CD spectrum is ...
Section III - Designing Models for 3D Printing
... 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 ...
Thermodynamic analysis of the unfolding and stability of the dimeric
... quite similar in a considerable number of species [10]. It is essential in the assembly of supramolecular nucleoprotein complexes and is also involved in a variety of DNA metabolic events, such as replication, transcription and transposition [11,12]. Its ability to repair DNA [13,14] and to prevent ...
... quite similar in a considerable number of species [10]. It is essential in the assembly of supramolecular nucleoprotein complexes and is also involved in a variety of DNA metabolic events, such as replication, transcription and transposition [11,12]. Its ability to repair DNA [13,14] and to prevent ...
translation
... 2. The codon a) There are 20 amino acids and 4 nucleotide bases (1) Obviously single nucleotides cannot code for amino acids (2) There is 16 combinations possible for 4 nucleotides read 2 at a time, not enough to code for 20 amino acids (3) There are 64 combinations possible for 4 nucleotides read 3 ...
... 2. The codon a) There are 20 amino acids and 4 nucleotide bases (1) Obviously single nucleotides cannot code for amino acids (2) There is 16 combinations possible for 4 nucleotides read 2 at a time, not enough to code for 20 amino acids (3) There are 64 combinations possible for 4 nucleotides read 3 ...
Conserved Positions for Ribose Recognition: Importance of Water
... govern ribose recognition by proteins is sketchy because tertiary and even secondary structural elements involved in nucleotide recognition are very diverse among proteins having different folds.1 Furthermore, although some sequence motifs have been identified within ligand binding folds, in general ...
... govern ribose recognition by proteins is sketchy because tertiary and even secondary structural elements involved in nucleotide recognition are very diverse among proteins having different folds.1 Furthermore, although some sequence motifs have been identified within ligand binding folds, in general ...
Feature-Based Classification of Amino Acid Substitutions outside
... polymorphisms (SNPs) of which 24 000 are in GENCODE regions [1, 2]. More than 500 SNPs per exome affect protein sequence [3, 4], leading to amino acid substitutions (AASs). The major focus is on identification of genetic variants that disrupt molecular functions and cause human diseases. This is a p ...
... polymorphisms (SNPs) of which 24 000 are in GENCODE regions [1, 2]. More than 500 SNPs per exome affect protein sequence [3, 4], leading to amino acid substitutions (AASs). The major focus is on identification of genetic variants that disrupt molecular functions and cause human diseases. This is a p ...
The CS2 fimbrial antigen from escherichia coli, purification
... As the N-terminal region does not appear to constitute an antigenic determinant (if it did the two proteins would show immunological cross-reactivity) large parts or perhaps all of this segment of the molecule might not be situated on the surface of the molecule. Furthermore, since the N-terminal se ...
... As the N-terminal region does not appear to constitute an antigenic determinant (if it did the two proteins would show immunological cross-reactivity) large parts or perhaps all of this segment of the molecule might not be situated on the surface of the molecule. Furthermore, since the N-terminal se ...
Number 53, 2006 5 m sh4
... eukaryotic splice sites (figure 2). Using either human or Arabidopsis parameters gave very similar results. Analysis of the predicted 871 amino acid sequence using Motifs (GCG: W isconsin Package TM) identified a potential gene with an ATP/GTP binding site and a DNA MMR motif. Use of a CD search, wh ...
... eukaryotic splice sites (figure 2). Using either human or Arabidopsis parameters gave very similar results. Analysis of the predicted 871 amino acid sequence using Motifs (GCG: W isconsin Package TM) identified a potential gene with an ATP/GTP binding site and a DNA MMR motif. Use of a CD search, wh ...
Spinalin, a new glycine- and histidine
... which punches a hole in the prey’s integument. Nematocyst discharge is driven by the very high osmotic pressure (15 MPa; Weber, 1989) in the resting capsule, which results from the high concentration of poly-γ-glutamic acid and the corresponding cations in the matrix (Weber, 1990, 1991). The high os ...
... which punches a hole in the prey’s integument. Nematocyst discharge is driven by the very high osmotic pressure (15 MPa; Weber, 1989) in the resting capsule, which results from the high concentration of poly-γ-glutamic acid and the corresponding cations in the matrix (Weber, 1990, 1991). The high os ...
Structural and Functional Implications of an Unusual Foraminiferal b
... from that species (X96478). None of the b-tubulin sequences that we obtained from any species are Type 1; all resemble the more divergent Type 2. The inferred amino acid sequences of these genes were compared with homologous sequences retrieved from GenBank. The a-tubulin sequences contained almost ...
... from that species (X96478). None of the b-tubulin sequences that we obtained from any species are Type 1; all resemble the more divergent Type 2. The inferred amino acid sequences of these genes were compared with homologous sequences retrieved from GenBank. The a-tubulin sequences contained almost ...
Application 1
... nanoparticles can serve as useful detection and targeting agents. These AuNPs when encapsulated with carbohydrate ligands can serve as a useful affinity probe for rapid, efficient separation of target proteins followed by on-probe analysis using mass spectroscopy. This technique of protein targeting ...
... nanoparticles can serve as useful detection and targeting agents. These AuNPs when encapsulated with carbohydrate ligands can serve as a useful affinity probe for rapid, efficient separation of target proteins followed by on-probe analysis using mass spectroscopy. This technique of protein targeting ...
Review Structural Insights into Biological Roles of Protein
... trasted with that of DNA (4 building blocks) and proteins (20 building blocks). The high information density of GAGs in terms of their sequence diversity arises from their biosynthesis, which is a complex non-template-driven process involving several enzymes with tissue-specific isoforms [16, 18]. H ...
... trasted with that of DNA (4 building blocks) and proteins (20 building blocks). The high information density of GAGs in terms of their sequence diversity arises from their biosynthesis, which is a complex non-template-driven process involving several enzymes with tissue-specific isoforms [16, 18]. H ...
Predicting the Secondary Structure of Globular Proteins Using
... protein structures to help predict the secondary structure of proteins for which no homologous structures are available. The known structures implicitly contain information about the biophysical properties of amino acids and their interactions. This approach is not meant to be an alternative to othe ...
... protein structures to help predict the secondary structure of proteins for which no homologous structures are available. The known structures implicitly contain information about the biophysical properties of amino acids and their interactions. This approach is not meant to be an alternative to othe ...
As listed in the Compendium of Pharmaceuticals and Specialties
... Pregnancy ‐ No adverse effects have been reported. A health care practitioner should be consulted prior to use if the patient is pregnant or has reason to believe she is. ...
... Pregnancy ‐ No adverse effects have been reported. A health care practitioner should be consulted prior to use if the patient is pregnant or has reason to believe she is. ...
Characterisation of hexon and fibre genes of a novel strain of
... Figure 1 Restriction patterns obtained after cleavage of Ad35p (P) and M86 (C). (A) Restriction endonucleases Xho1, BstEII, EcoRI, SalI, and SmaI; (B) XbaI, PstI, BamHI, HindIII, and BglII. The samples were electrophoresed on a 1.2% agarose gel. A HindIII digest of l DNA (lane ...
... Figure 1 Restriction patterns obtained after cleavage of Ad35p (P) and M86 (C). (A) Restriction endonucleases Xho1, BstEII, EcoRI, SalI, and SmaI; (B) XbaI, PstI, BamHI, HindIII, and BglII. The samples were electrophoresed on a 1.2% agarose gel. A HindIII digest of l DNA (lane ...
PDF - School of Chemistry
... “stripped-down” sequences; i.e., only the residues important for structural specification and stabilization are defined, leaving the remainder as agnostic side chains (e.g., alanine (Ala, A) or glutamine (Gln, Q)) and free for substitution later in the design process. The basis-set peptides are fully ...
... “stripped-down” sequences; i.e., only the residues important for structural specification and stabilization are defined, leaving the remainder as agnostic side chains (e.g., alanine (Ala, A) or glutamine (Gln, Q)) and free for substitution later in the design process. The basis-set peptides are fully ...
Cloning and structure of three rainbow trout C3
... acid sequence and binding to various complement activators. To study the structural elements that determine the observed functional dierences, we have cloned and sequenced the three C3 isoforms. Comparison of the deduced amino acid sequences showed that the sequence identity/similarity of C3-3 to C ...
... acid sequence and binding to various complement activators. To study the structural elements that determine the observed functional dierences, we have cloned and sequenced the three C3 isoforms. Comparison of the deduced amino acid sequences showed that the sequence identity/similarity of C3-3 to C ...
PPT - Bioinformatics.ca
... (from Koster and Klumperman, Nat Rev Mol Cell Biol, Sep 2003, S6-10) ...
... (from Koster and Klumperman, Nat Rev Mol Cell Biol, Sep 2003, S6-10) ...
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.