mechanism of the flagellar export system and its potential
... flagellum. As every motor, it consists of a rotor and a stator. The MS ring and the adjoining Cring make up the rotor, while the stator is formed around it from MotA-MotB complexes. The T3SS is assembled at the base of the MS ring. At the cytoplasmic face of the T3SS the so-called soluble export com ...
... flagellum. As every motor, it consists of a rotor and a stator. The MS ring and the adjoining Cring make up the rotor, while the stator is formed around it from MotA-MotB complexes. The T3SS is assembled at the base of the MS ring. At the cytoplasmic face of the T3SS the so-called soluble export com ...
Co-translational Folding
... Folding intermediates having large part of its secondary structures formed and even with tertiary structure formation The final level of folding - outside the ribosome - ‘post translational’. But the released polypeptide chain received the instructions for folding from the ribosome (Fedorov, A. N., ...
... Folding intermediates having large part of its secondary structures formed and even with tertiary structure formation The final level of folding - outside the ribosome - ‘post translational’. But the released polypeptide chain received the instructions for folding from the ribosome (Fedorov, A. N., ...
Introduction to Protein Structure
... • Aminoacids form polypeptide chains • Chains fold into three-dimensional structure • Specific backbone angles are permitted or not: Ramachandran plot • Secundary structure elements: -helix, b-sheet • Common structural motifs: Helix-turn-helix, Calcium binding motif, Hairpin, Greek key motif, b--b ...
... • Aminoacids form polypeptide chains • Chains fold into three-dimensional structure • Specific backbone angles are permitted or not: Ramachandran plot • Secundary structure elements: -helix, b-sheet • Common structural motifs: Helix-turn-helix, Calcium binding motif, Hairpin, Greek key motif, b--b ...
The Amino Acid Sequences of the Myelin
... separated by preparative SDS PAGE (10% acrylamide) and the broad 100kD MAG band was excised and electroeluted (16). Antibodies were raised by injecting purified MAG (50 ~tg) into rabbit popliteal lymph nodes in complete Freund's adjuvant and boosting every other week with 100 Ixg of MAG in incomplet ...
... separated by preparative SDS PAGE (10% acrylamide) and the broad 100kD MAG band was excised and electroeluted (16). Antibodies were raised by injecting purified MAG (50 ~tg) into rabbit popliteal lymph nodes in complete Freund's adjuvant and boosting every other week with 100 Ixg of MAG in incomplet ...
2 Applications
... Since the completion of genome sequencing of several organisms including the human genome, attention has been directed from genome to proteome analysis. The term proteome was first introduced by Wilkins et al. in 1995 [1] and denotes the total number of proteins expressed by a genome at a given time ...
... Since the completion of genome sequencing of several organisms including the human genome, attention has been directed from genome to proteome analysis. The term proteome was first introduced by Wilkins et al. in 1995 [1] and denotes the total number of proteins expressed by a genome at a given time ...
Chapter 12 Role of tunnels, channels and gates in enzymatic catalysis
... followed by theoretical analyses using molecular dynamics (MD) simulations. In the last few decades, advances in biological chemistry were boosted by the determination of high-resolution three-dimensional structures of proteins by X-ray diffraction, which allowed a deeper understanding of the underl ...
... followed by theoretical analyses using molecular dynamics (MD) simulations. In the last few decades, advances in biological chemistry were boosted by the determination of high-resolution three-dimensional structures of proteins by X-ray diffraction, which allowed a deeper understanding of the underl ...
12 Molecular Visualization of an Enzyme, Acetylcholinesterase
... The MDR efflux pump is an integral membrane protein. As such, the protein structure has some common membrane protein structural characteristics. First, transmembrane helices comprise the bulk of the protein. These helices stretch the width of the lipid bilayer and expose hydrophobic amino acids to t ...
... The MDR efflux pump is an integral membrane protein. As such, the protein structure has some common membrane protein structural characteristics. First, transmembrane helices comprise the bulk of the protein. These helices stretch the width of the lipid bilayer and expose hydrophobic amino acids to t ...
The Genome-linked Protein of Picornaviruses. VIII. Complete Amino
... glycine. Recently, glutaminyl-glycine pairs have been shown to be cleavage sites for a virusspecific proteinase (Hanecak et al., 1982). Moreover, the glycine residue following the carboxyterminal glutamine of VPg is the amino terminus of P3-2, the cleavage product adjacent to VPg (Semler et al., 198 ...
... glycine. Recently, glutaminyl-glycine pairs have been shown to be cleavage sites for a virusspecific proteinase (Hanecak et al., 1982). Moreover, the glycine residue following the carboxyterminal glutamine of VPg is the amino terminus of P3-2, the cleavage product adjacent to VPg (Semler et al., 198 ...
exon junctions of Euglena gene(s) - DigitalCommons@University of
... photosystem II (LHCPLI) are a group of abundant, highly conserved thylakoid proteins. LHCPIIs are encoded by a nuclear multigene family comprising approximately 3-20 members depending upon the organism studied (1). LHCPIIs have been classified into three types based on the amino acids found at 14 po ...
... photosystem II (LHCPLI) are a group of abundant, highly conserved thylakoid proteins. LHCPIIs are encoded by a nuclear multigene family comprising approximately 3-20 members depending upon the organism studied (1). LHCPIIs have been classified into three types based on the amino acids found at 14 po ...
Gene Section LCK (lymphocyte-specific protein tyrosine kinase) Atlas of Genetics and Cytogenetics
... Lck associates with the inner face of the plasma membrane through its amino-terminus. This interaction is mediated by both myristic acid and palmitic acid that are bound to the amino terminal glycine and Cys-3 and/or Cys-5. The Unique region of Lck represents the domain possessing the greatest seque ...
... Lck associates with the inner face of the plasma membrane through its amino-terminus. This interaction is mediated by both myristic acid and palmitic acid that are bound to the amino terminal glycine and Cys-3 and/or Cys-5. The Unique region of Lck represents the domain possessing the greatest seque ...
311-320 - CiteSeerX
... 325 nm fluorescence emission is due to the buried tryptophan residues (Teale, 1960); quenching of the fluorescence is due to the exposure of the buried tryptophan residues. Thus the first event in the denaturation reaction appears to be perturbation of the aromatic amino acid residues. This is follo ...
... 325 nm fluorescence emission is due to the buried tryptophan residues (Teale, 1960); quenching of the fluorescence is due to the exposure of the buried tryptophan residues. Thus the first event in the denaturation reaction appears to be perturbation of the aromatic amino acid residues. This is follo ...
Computational Biology
... surfaces of TM proteins. Those residues will also be highly conserved, and the method will therefore fail. ...
... surfaces of TM proteins. Those residues will also be highly conserved, and the method will therefore fail. ...
The SWISS-PROT protein sequence data bank
... associated with that protein (OMIM), the 3D structure (PDB) or the pattern specific for that family of proteins (PROSITE). RECENT DEVELOPMENTS Model organisms We have selected a number of organisms that are the target of genome sequencing and/or mapping projects and for which we intend to: Be as c ...
... associated with that protein (OMIM), the 3D structure (PDB) or the pattern specific for that family of proteins (PROSITE). RECENT DEVELOPMENTS Model organisms We have selected a number of organisms that are the target of genome sequencing and/or mapping projects and for which we intend to: Be as c ...
Production of Polyclonal Antibodies against Sucrose Transporter
... which contained cell debris (insoluble fraction), was resuspended with NPI -10 buffer and centrifuged at 12000 rpm, at 4o C for 20 minutes. Supernatant was thrown away and pellet resuspended with DNPI-10 buffer pH 8.0 (50 mM NaH2PO4, 300 mM NaCl and 10 mM imidazole and 8 M urea) and sonicated for 3 ...
... which contained cell debris (insoluble fraction), was resuspended with NPI -10 buffer and centrifuged at 12000 rpm, at 4o C for 20 minutes. Supernatant was thrown away and pellet resuspended with DNPI-10 buffer pH 8.0 (50 mM NaH2PO4, 300 mM NaCl and 10 mM imidazole and 8 M urea) and sonicated for 3 ...
Protein splicing of PRP8 mini-inteins from species of the genus
... represents a negative control without DNA ...
... represents a negative control without DNA ...
embor2011116-sup-0001
... estimated repeatedly using a number of single or multiple mutations. Our review aimed at evaluating the correlation between such experimental data and those estimated in silico by several algorithms. The algorithms are, however, different in the type of predictions they provide. Two of the predictiv ...
... estimated repeatedly using a number of single or multiple mutations. Our review aimed at evaluating the correlation between such experimental data and those estimated in silico by several algorithms. The algorithms are, however, different in the type of predictions they provide. Two of the predictiv ...
Regulation of transcript encoding the 43K
... purified phage from 24 plaques and analysed DNA from these phage by Southern blots. Phage DNA was digested separately with EcoRl and Stul and Southern blots were probed with 32P-T43k.l cDNA. Based upon the restriction maps of cDNA clones that encode an incorrect C-terminal region (T43k.l) and a seco ...
... purified phage from 24 plaques and analysed DNA from these phage by Southern blots. Phage DNA was digested separately with EcoRl and Stul and Southern blots were probed with 32P-T43k.l cDNA. Based upon the restriction maps of cDNA clones that encode an incorrect C-terminal region (T43k.l) and a seco ...
Williams, Brandon: A Review on Common Applications Designed to Optimize the SEQUEST Search Algorithm With Respect to Limiting False Positive Identification
... individual proteins in the high molecular weight range, their modifications or protein complexes, suppressed the broad application of proteomics. This technological hurdle has for the most part been overcome through the application of mass spectrometry (MS) when used in combination with developing p ...
... individual proteins in the high molecular weight range, their modifications or protein complexes, suppressed the broad application of proteomics. This technological hurdle has for the most part been overcome through the application of mass spectrometry (MS) when used in combination with developing p ...
RELIC – A bioinformatics server for combinatorial
... Phage display technology provides a versatile tool for exploring the interactions between proteins, peptides and small molecule ligands. Quantitative analysis of peptide population sequence diversity and bias patterns has the power to significantly enhance the impact of these methods [1, 2]. We have ...
... Phage display technology provides a versatile tool for exploring the interactions between proteins, peptides and small molecule ligands. Quantitative analysis of peptide population sequence diversity and bias patterns has the power to significantly enhance the impact of these methods [1, 2]. We have ...
Evolution of b-type cytochromes in prokaryotes
... Figure S4: Multiple sequence alignment of eukaryotic and prokaryotic cytochrome b561. The alignment, including 22 eukaryotic cytochrome b561 (K08360) and 61 prokaryotic cytochrome b561 (K12262) sequences (dataset as in Figure 4), was generated using Muscle, and visualized in Jalview. The four helice ...
... Figure S4: Multiple sequence alignment of eukaryotic and prokaryotic cytochrome b561. The alignment, including 22 eukaryotic cytochrome b561 (K08360) and 61 prokaryotic cytochrome b561 (K12262) sequences (dataset as in Figure 4), was generated using Muscle, and visualized in Jalview. The four helice ...
Flavors of Protein Disorder
... Intrinsically disordered proteins are characterized by long regions lacking 3-D structure in their native states, yet they have been so far associated with 28 distinguishable functions. Previous studies showed that protein predictors trained on disorder from one type of protein often achieve poor ac ...
... Intrinsically disordered proteins are characterized by long regions lacking 3-D structure in their native states, yet they have been so far associated with 28 distinguishable functions. Previous studies showed that protein predictors trained on disorder from one type of protein often achieve poor ac ...
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.