THE THREE-DIMENSIONAL STRUCTURE OF PROTEINS
... prominent are the helix and conformations described below. Using fundamental chemical principles and a few experimental observations, Pauling and Corey predicted the existence of these secondary structures in 1951, several years before the first complete protein ...
... prominent are the helix and conformations described below. Using fundamental chemical principles and a few experimental observations, Pauling and Corey predicted the existence of these secondary structures in 1951, several years before the first complete protein ...
Primary Structure of Diphtheria Toxin Fragment B
... fragment B (40,700 daltons) binds to specific eukaryotic cellmembrane receptors and mediates the entry of the enzymically active N-terminal fragment A (21,150 daltons) into the cytoplasm where A catalytically ADP-ribosylates elongation factor 2 and, thereby, inhibits protein synthesis of the cell (9 ...
... fragment B (40,700 daltons) binds to specific eukaryotic cellmembrane receptors and mediates the entry of the enzymically active N-terminal fragment A (21,150 daltons) into the cytoplasm where A catalytically ADP-ribosylates elongation factor 2 and, thereby, inhibits protein synthesis of the cell (9 ...
Adv. Protein Chem. Struct. Biol.
... flexibility. For example, almost any interaction between a protein and another molecule is associated with conformational changes. Ligand recognition and binding, protein–protein interactions, and processes as complicated as signal transduction and assembly of multiprotein machines are based on prot ...
... flexibility. For example, almost any interaction between a protein and another molecule is associated with conformational changes. Ligand recognition and binding, protein–protein interactions, and processes as complicated as signal transduction and assembly of multiprotein machines are based on prot ...
The Protein Data Bank (PDB) & PDB Files
... • Recall what the PDB is and what is stores • Recall what a PDB file is and what its contents stand for • Summarize two (2) ways to obtain PDB files associated with an article • Summarize how to find articles associated with a PDB file ...
... • Recall what the PDB is and what is stores • Recall what a PDB file is and what its contents stand for • Summarize two (2) ways to obtain PDB files associated with an article • Summarize how to find articles associated with a PDB file ...
Derivation and testing of pair potentials for protein folding. When is
... the quasichemical approximation that treats the residues in a protein as being disconnected and expresses the side-chain contact probability as being proportional to the product of the mole fractions of the pair of residues would appear to be rather severe. To investigate the validity of this approx ...
... the quasichemical approximation that treats the residues in a protein as being disconnected and expresses the side-chain contact probability as being proportional to the product of the mole fractions of the pair of residues would appear to be rather severe. To investigate the validity of this approx ...
Ternary complex structure of Aristaless and Clawless bound to DNA
... binary complex of Al-DNA, and the ternary complex of Al-Cll-DNA The crystal structures of the Al and Hox11L1 homeodomains were determined at 1.00 Å and 1.54 Å, respectively, with good stereochemistry (Supplementary Figure 2AB). These structures were refined to R/Rfree values of 17.3/18.4% and 20.1/2 ...
... binary complex of Al-DNA, and the ternary complex of Al-Cll-DNA The crystal structures of the Al and Hox11L1 homeodomains were determined at 1.00 Å and 1.54 Å, respectively, with good stereochemistry (Supplementary Figure 2AB). These structures were refined to R/Rfree values of 17.3/18.4% and 20.1/2 ...
Strain in Protein Structures as Viewed Through Nonrotameric Side
... preference to be in the vicinity of ligands, the distance (Dnonrot) between each cluster and its nearest ligand was taken as the smallest separation between any ligand atom and any side-chain atom of the cluster. We also determined such distances for all rotameric clusters with a number of residues ...
... preference to be in the vicinity of ligands, the distance (Dnonrot) between each cluster and its nearest ligand was taken as the smallest separation between any ligand atom and any side-chain atom of the cluster. We also determined such distances for all rotameric clusters with a number of residues ...
Supporting Information Heim et al. 10.1073/pnas.1413018111
... DNA encoding full-length recombinant P1 lacking the signal sequence (rP1, amino acids 39–1566) was cloned into the pQE-30 vector and used to transform Escherichia coli M15-pREP4 cells as described previously (2, 3). In a previous study, the P1 mutant PC967, in which Cla1 restriction sites had been i ...
... DNA encoding full-length recombinant P1 lacking the signal sequence (rP1, amino acids 39–1566) was cloned into the pQE-30 vector and used to transform Escherichia coli M15-pREP4 cells as described previously (2, 3). In a previous study, the P1 mutant PC967, in which Cla1 restriction sites had been i ...
Structure, function and evolution of armless mitochondrial tRNAs
... cloverleaf, which is composed of 4 arms: the amino acid accepting arm, the D-arm, the anticodon arm and the T-arm. The tertiary structure resembles the letter L. The secondary and tertiary structures are recognized by numerous maturation and modification enzymes as well as specific aminoacyl-tRNA sy ...
... cloverleaf, which is composed of 4 arms: the amino acid accepting arm, the D-arm, the anticodon arm and the T-arm. The tertiary structure resembles the letter L. The secondary and tertiary structures are recognized by numerous maturation and modification enzymes as well as specific aminoacyl-tRNA sy ...
Prediction of protease substrates using sequence
... 1999; Dix et al., 2008; Mahrus et al., 2008). However, different datasets overlap only partially, indicating that many substrates remain to be identified. For example, two proteomics studies, respectively, reported 261 and 292 caspase cleavage sequences, although the high-confidence overlap between ...
... 1999; Dix et al., 2008; Mahrus et al., 2008). However, different datasets overlap only partially, indicating that many substrates remain to be identified. For example, two proteomics studies, respectively, reported 261 and 292 caspase cleavage sequences, although the high-confidence overlap between ...
lecture notes
... a tripeptide of proline, which has a covalently constrained N-Cα dihedral (φ), has even more restricted conformation. In Figure 2.2, it was noted that proline and glycine are a structurally distinct pair of amino acids – they can have substantial impact on the conformation of the polypeptide, and th ...
... a tripeptide of proline, which has a covalently constrained N-Cα dihedral (φ), has even more restricted conformation. In Figure 2.2, it was noted that proline and glycine are a structurally distinct pair of amino acids – they can have substantial impact on the conformation of the polypeptide, and th ...
Site-specific functionalization of proteins and their applications to
... is via the primary amino groups on lysine residues and at the Nterminus. In general, multiple accessible lysines and thus reactive amines are present on the protein surface, resulting in efficient labeling but inevitably leading to heterogeneous mixtures. Whether this method is applicable depends on ...
... is via the primary amino groups on lysine residues and at the Nterminus. In general, multiple accessible lysines and thus reactive amines are present on the protein surface, resulting in efficient labeling but inevitably leading to heterogeneous mixtures. Whether this method is applicable depends on ...
The Complement of Protein Phosphatase
... phosphatases (PPEFs) sequences and the Drosophila melanogaster protein RdgC. A PP5 cluster (sequences 13–25) contains one Arabidopsis sequence. Sequences 26 through 29 form a cluster consisting of three bacterial sequences plus an Arabidopsis sequence. The latter contains a chloroplast motif, and to ...
... phosphatases (PPEFs) sequences and the Drosophila melanogaster protein RdgC. A PP5 cluster (sequences 13–25) contains one Arabidopsis sequence. Sequences 26 through 29 form a cluster consisting of three bacterial sequences plus an Arabidopsis sequence. The latter contains a chloroplast motif, and to ...
Making sense of Sequences: Comparative Genomics and the New GIS
... Another Genomic Revolution An explosion in genomic data The rise of population genomics & proteomics ...
... Another Genomic Revolution An explosion in genomic data The rise of population genomics & proteomics ...
Эволюция генетического кода
... In the table of the universal genetic code there are two amino acids, each of which is encoded by one codon only: tryptophan (Trp), encoded by the UGG codon, and methionine (Met), encoded by AUG. This feature can be consistently explained based upon the same arguments that have been used to explain ...
... In the table of the universal genetic code there are two amino acids, each of which is encoded by one codon only: tryptophan (Trp), encoded by the UGG codon, and methionine (Met), encoded by AUG. This feature can be consistently explained based upon the same arguments that have been used to explain ...
This presentation introduces the topics we will
... physical and chemical parameters. There is no particular reason to assume that a big peak is interesting and a small peak is less interesting. The main use of intensity information is to distinguish signal from noise. Mass accuracy is important, but so is coverage. Better to have a large number of m ...
... physical and chemical parameters. There is no particular reason to assume that a big peak is interesting and a small peak is less interesting. The main use of intensity information is to distinguish signal from noise. Mass accuracy is important, but so is coverage. Better to have a large number of m ...
WHAT_CHECK report for 1BFX
... Nomenclature problems seem, at first, rather unimportant. After all who cares if we call the δ atoms in leucine δ 2 and δ 1 rather than the other way around. Chemically speaking that is correct. But structures have not been solved and deposited just for chemists to look at them. Most times a structu ...
... Nomenclature problems seem, at first, rather unimportant. After all who cares if we call the δ atoms in leucine δ 2 and δ 1 rather than the other way around. Chemically speaking that is correct. But structures have not been solved and deposited just for chemists to look at them. Most times a structu ...
slides - DTU CBS
... CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS TECHNICAL UNIVERSITY OF DENMARK DTU ...
... CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS TECHNICAL UNIVERSITY OF DENMARK DTU ...
Introduction to Database Searching using MASCOT
... PMF, but with an added stage of selectivity and fragmentation. Again, we start with protein, which can now be a single protein or a complex mixture of proteins. We use an enzyme such as trypsin to digest the proteins to peptides. If it is a complex mixture, such as a whole cell lysate, we will proba ...
... PMF, but with an added stage of selectivity and fragmentation. Again, we start with protein, which can now be a single protein or a complex mixture of proteins. We use an enzyme such as trypsin to digest the proteins to peptides. If it is a complex mixture, such as a whole cell lysate, we will proba ...
Protein structure
... to the underlying arrangement of atoms by a mathematical summation known as the Fourier transform (FIGURE 1.3). The intensities of the reflections are simply the Fourier transform of the electron density around each atom; the pattern that they form on the detector (photographic film in the case of B ...
... to the underlying arrangement of atoms by a mathematical summation known as the Fourier transform (FIGURE 1.3). The intensities of the reflections are simply the Fourier transform of the electron density around each atom; the pattern that they form on the detector (photographic film in the case of B ...
Computer-Based Design of Novel Protein Structures
... loops) to be defined by six adjustable parameters: three values to specify the displacement of the helical monomer and three to specify its orientation (79). A variety of four-helix diiron proteins can be rebuilt with idealized helices to less than 1.5 Å rmsd by optimizing only these six parameters ...
... loops) to be defined by six adjustable parameters: three values to specify the displacement of the helical monomer and three to specify its orientation (79). A variety of four-helix diiron proteins can be rebuilt with idealized helices to less than 1.5 Å rmsd by optimizing only these six parameters ...
Iboga – mit in resničnost
... effects last longer than the presence of ibogaine in the body fat deposits of lipophillic metabolite cannot directly cause the effect for weeks or months ...
... effects last longer than the presence of ibogaine in the body fat deposits of lipophillic metabolite cannot directly cause the effect for weeks or months ...
Sequence Searching and Alignments
... to recognise what is similar, to identify what is different and from there to investigate whether differences are significant and biologically meaningful. Biological research tries to recognise patterns in order to infer relationships with previously-characterised sequences. It is essential to keep ...
... to recognise what is similar, to identify what is different and from there to investigate whether differences are significant and biologically meaningful. Biological research tries to recognise patterns in order to infer relationships with previously-characterised sequences. It is essential to keep ...
Structural alignment
Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which multiple unrelated amino acid sequences converge on a common tertiary structure.Structural alignments can compare two sequences or multiple sequences. Because these alignments rely on information about all the query sequences' three-dimensional conformations, the method can only be used on sequences where these structures are known. These are usually found by X-ray crystallography or NMR spectroscopy. It is possible to perform a structural alignment on structures produced by structure prediction methods. Indeed, evaluating such predictions often requires a structural alignment between the model and the true known structure to assess the model's quality. Structural alignments are especially useful in analyzing data from structural genomics and proteomics efforts, and they can be used as comparison points to evaluate alignments produced by purely sequence-based bioinformatics methods.The outputs of a structural alignment are a superposition of the atomic coordinate sets and a minimal root mean square deviation (RMSD) between the structures. The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple protein domains within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.