Infrared spectroscopy: a tool for protein characterization Chenge Li
... which contains an amino group (-NH2), a carboxyl group (-COOH), along with a side chain that is specific for each amino acid. The side chain can be hydrophobic, polar, positively or negatively charged, depending on its composition, structure and properties. In total, there are mainly 20 natural prot ...
... which contains an amino group (-NH2), a carboxyl group (-COOH), along with a side chain that is specific for each amino acid. The side chain can be hydrophobic, polar, positively or negatively charged, depending on its composition, structure and properties. In total, there are mainly 20 natural prot ...
04_db_blast
... P-value is the probability of finding a seq. similarity as similar as the observed match if there were really no true matches in the database. E-value ≠ p-value E-value ~ p-value when it is small (say < 0.1) Since we are interested in unusual hits, it is safe to interchange E-value with p-value. E-v ...
... P-value is the probability of finding a seq. similarity as similar as the observed match if there were really no true matches in the database. E-value ≠ p-value E-value ~ p-value when it is small (say < 0.1) Since we are interested in unusual hits, it is safe to interchange E-value with p-value. E-v ...
Proteins and amino acids
... Primary structure Proteins are polymers The monomers (residues) are amino acids The sequence: ...
... Primary structure Proteins are polymers The monomers (residues) are amino acids The sequence: ...
Structure-Function Relationship and Regulation of Two Bacillus
... regions ranging from 30 to 120 base pairs (Strauch, 1995b). However, from these sequences no common motif can be deduced as an AbrB consensus sequence. Using an in vitro selection of random oligo nucleotides, seemingly optimal AbrB binding sites corresponding to a regularly spaced motif were selecte ...
... regions ranging from 30 to 120 base pairs (Strauch, 1995b). However, from these sequences no common motif can be deduced as an AbrB consensus sequence. Using an in vitro selection of random oligo nucleotides, seemingly optimal AbrB binding sites corresponding to a regularly spaced motif were selecte ...
Constitutive expression of Vitis vinifera thaumatin
... Induction of PR genes has been associated with incompatibility and overexpression of one or more PR proteins can delay disease development (Hammond-Kosack and Jones 1996). PR proteins are induced intra- and extracellularly by pathogens, chemical elicitors or, in some instances, environmental stresse ...
... Induction of PR genes has been associated with incompatibility and overexpression of one or more PR proteins can delay disease development (Hammond-Kosack and Jones 1996). PR proteins are induced intra- and extracellularly by pathogens, chemical elicitors or, in some instances, environmental stresse ...
Allantoin transport protein, PucI, from Bacillus subtilis
... restriction-digested PCR product was ligated into plasmid pTTQ18 (Stark, 1987) immediately upstream from a hexahistidine tag coding sequence and the resultant pTTQ18-pucI(His6) construct was used to transform E. coli BL21(DE3) cells. For full details of the cloning procedure see Supplementary Method ...
... restriction-digested PCR product was ligated into plasmid pTTQ18 (Stark, 1987) immediately upstream from a hexahistidine tag coding sequence and the resultant pTTQ18-pucI(His6) construct was used to transform E. coli BL21(DE3) cells. For full details of the cloning procedure see Supplementary Method ...
Molecular Interactions of Collagen-binding Proteins
... proteins. The most abundant structural fiber is collagen. A collagen-fiber is comprised of bundles of collagen-fibrils, which again are comprised of individual collagen-molecules that are bundled together in a process called fibrillogenesis (Figure 1) [1, 2]. The fibrillogenesis of collagen is a hig ...
... proteins. The most abundant structural fiber is collagen. A collagen-fiber is comprised of bundles of collagen-fibrils, which again are comprised of individual collagen-molecules that are bundled together in a process called fibrillogenesis (Figure 1) [1, 2]. The fibrillogenesis of collagen is a hig ...
Sample pages 2 PDF
... back to a speciation event. Paralogy indicates that the common ancestry of the sequences can be traced back to a gene-duplication event. A series of sequences that are either orthologs (comparing taxa) or paralogs (comparing lineages of genes), and which all share the same common ancestor, are said ...
... back to a speciation event. Paralogy indicates that the common ancestry of the sequences can be traced back to a gene-duplication event. A series of sequences that are either orthologs (comparing taxa) or paralogs (comparing lineages of genes), and which all share the same common ancestor, are said ...
The role of histidine residues in low-pH-mediated viral
... His244, His261 and His317 were located in the vicinity of positively charged residues, highlighted in Figure 4.1B. His261 and His317 form conserved salt bridges in the post-fusion structure. His244 does not form a salt bridge in the post-fusion structure of the dengue viral E protein, but in the tic ...
... His244, His261 and His317 were located in the vicinity of positively charged residues, highlighted in Figure 4.1B. His261 and His317 form conserved salt bridges in the post-fusion structure. His244 does not form a salt bridge in the post-fusion structure of the dengue viral E protein, but in the tic ...
Hydrodynamic Studies on the Manganese
... These values are in good agreement with the values obtained from the SVEDBERG program. Thus, analysis of the sedimentation velocity data by two independent methods [direct fitting and g(s) analysis] yielded very similar s values. Miyao and Murata (22) have also determined a sedimentation coefficient ...
... These values are in good agreement with the values obtained from the SVEDBERG program. Thus, analysis of the sedimentation velocity data by two independent methods [direct fitting and g(s) analysis] yielded very similar s values. Miyao and Murata (22) have also determined a sedimentation coefficient ...
Hamster Placental Lactogen-ll Contains a Structural Feature Unique
... to a significantly greater extent for haPL-II than for hPL and mPL-II. Although these experiments have not been performed with rPL-II, this protein probably behaves similarly to mPL-II, since no significant amount of high Mr forms are present in the placenta or in the blood (9). ...
... to a significantly greater extent for haPL-II than for hPL and mPL-II. Although these experiments have not been performed with rPL-II, this protein probably behaves similarly to mPL-II, since no significant amount of high Mr forms are present in the placenta or in the blood (9). ...
Identification of Surface Residues Involved in Protein
... rectly identified. With this level of success, predictions generated using this approach should be valuable for guiding experimental investigations into the roles of specific residues of a protein in its interaction with other proteins. Detailed examination of the predicted interface residues in th ...
... rectly identified. With this level of success, predictions generated using this approach should be valuable for guiding experimental investigations into the roles of specific residues of a protein in its interaction with other proteins. Detailed examination of the predicted interface residues in th ...
COMBINING MOLECULAR DOCKING WITH RECEPTOR DOMAIN
... MD of ATP-binding domain of Ca-ATPase was performed for 3 experimental models: 1EUL (“open” apo-form), 1IWO (another “open” apo-form), and 1T5S (“closed” holo-form). The GROMACS program and the GROMOS96 force field (Berendsen et al., 1995) were used. Molecules with uncharged N- and C-termini were pl ...
... MD of ATP-binding domain of Ca-ATPase was performed for 3 experimental models: 1EUL (“open” apo-form), 1IWO (another “open” apo-form), and 1T5S (“closed” holo-form). The GROMACS program and the GROMOS96 force field (Berendsen et al., 1995) were used. Molecules with uncharged N- and C-termini were pl ...
MOLECULAR EVOLUTION
... Many alignments are possible between sequences, and algorithms typically maximize the matching number of amino acids or nucleotides, invoking the smallest possible number of indel events. ...
... Many alignments are possible between sequences, and algorithms typically maximize the matching number of amino acids or nucleotides, invoking the smallest possible number of indel events. ...
Notes for using PROTPOL.f
... RESTYPE = name of residue contributing amino N NORES = no. of residue contributing amino N R = cartesian coords of atom (note that the RESTYPE and NORES for the CA, C, O are incorrectly given as those for the following residue – these parameters are only correct for the N) Followed by three lines wi ...
... RESTYPE = name of residue contributing amino N NORES = no. of residue contributing amino N R = cartesian coords of atom (note that the RESTYPE and NORES for the CA, C, O are incorrectly given as those for the following residue – these parameters are only correct for the N) Followed by three lines wi ...
CHMI 2227E Biochemistry I
... From a biological sample containing the protein of interest, a series of procedures are used sequentially to progressively obtain the protein in a « pure » form; ...
... From a biological sample containing the protein of interest, a series of procedures are used sequentially to progressively obtain the protein in a « pure » form; ...
Self-assembling Protein Cage Systems and - Wiley-VCH
... eukaryotic ferritins, their overall similarities are more important than their differences. Ferritins are large multi-subunit proteins (24 subunits) that self-assemble to form a cagelike architecture (Figure 1a) with a central cavity in which a hydrated ferric oxide (or phosphate) is mineralized. Va ...
... eukaryotic ferritins, their overall similarities are more important than their differences. Ferritins are large multi-subunit proteins (24 subunits) that self-assemble to form a cagelike architecture (Figure 1a) with a central cavity in which a hydrated ferric oxide (or phosphate) is mineralized. Va ...
CHAPTER 10 HOMOLOGY SEARCH METHODS
... optimized to be highly sensitive for alignments matching a particular model of alignments, which allows substantial improvement in sensitivity. In fact, one can use these spaced models to approach Smith-Waterman sensitivity at BLAST speed. This chapter takes you through this roun ...
... optimized to be highly sensitive for alignments matching a particular model of alignments, which allows substantial improvement in sensitivity. In fact, one can use these spaced models to approach Smith-Waterman sensitivity at BLAST speed. This chapter takes you through this roun ...
The cloning and overexpression of E coli acyl carrier protein (ACP)
... Acyl carrier protein (ACP) is a small (9kDa) protein which is essential for fatty acid synthesis. In bacteria [ l ] and plants [2] which use type I1 dissociable fatty acid synthetases, acyl chains are esterified to ACP through the 4'-phosphopantetheineprosthetic group, and ACP acts as a carrier duri ...
... Acyl carrier protein (ACP) is a small (9kDa) protein which is essential for fatty acid synthesis. In bacteria [ l ] and plants [2] which use type I1 dissociable fatty acid synthetases, acyl chains are esterified to ACP through the 4'-phosphopantetheineprosthetic group, and ACP acts as a carrier duri ...
Lecture 2 - Proteins_in_food
... the normal growth of rats and other small experimental animals (Osborne and Mendel, 1917). Soybeans contain a heat-labile protein that inhibits the proteolytic activity of trypsin (Bowman, 1944). The nutritive quality of soybean flour heated at various temperatures increased in proportion to the des ...
... the normal growth of rats and other small experimental animals (Osborne and Mendel, 1917). Soybeans contain a heat-labile protein that inhibits the proteolytic activity of trypsin (Bowman, 1944). The nutritive quality of soybean flour heated at various temperatures increased in proportion to the des ...
Large-scale identification of cytosolic mouse brain proteins by
... highly abundant proteins to one of the fractions [11]. It was the aim of this study to generate a mouse brain protein reference database by the use of DEAE-ion exchange chromatography (IEC) and hydrophobic interaction chromatography (HIC) followed by 2-DE MALDI-MS analysis, independent of antibody a ...
... highly abundant proteins to one of the fractions [11]. It was the aim of this study to generate a mouse brain protein reference database by the use of DEAE-ion exchange chromatography (IEC) and hydrophobic interaction chromatography (HIC) followed by 2-DE MALDI-MS analysis, independent of antibody a ...
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.