Click Here to download this tutorial as a PDF
... Each structure hosted on the Protein Databank has a unique four character long alpha-numeric identifier, referred to as the structure's PDB ID. Often more than one .pdb file will exist for a specific type of protein. For example, there are hundreds of .pdb file entries for the relatively common prot ...
... Each structure hosted on the Protein Databank has a unique four character long alpha-numeric identifier, referred to as the structure's PDB ID. Often more than one .pdb file will exist for a specific type of protein. For example, there are hundreds of .pdb file entries for the relatively common prot ...
of Pseudomonas aeruginosa - BMC Microbiology
... Penicillin-Binding Proteins (PBPs) are acyl-serin transferases, initially identified by their ability to form covalent bonds with penicillin [10]. They are located on the external face of the inner membrane and share common D,D-peptidase activities (D,D-transpeptidase, D,D-carboxypeptidase or D,D-en ...
... Penicillin-Binding Proteins (PBPs) are acyl-serin transferases, initially identified by their ability to form covalent bonds with penicillin [10]. They are located on the external face of the inner membrane and share common D,D-peptidase activities (D,D-transpeptidase, D,D-carboxypeptidase or D,D-en ...
mechanism of the flagellar export system and its potential
... that the N-terminal part of flagellin contains the signal used about the same fragment size. These 18 constructs were expressed in a flagellin-deficient S. typhimurium strain and the export of the given fusion proteins was investigated. It is important to note that protein degradation, inclusion bod ...
... that the N-terminal part of flagellin contains the signal used about the same fragment size. These 18 constructs were expressed in a flagellin-deficient S. typhimurium strain and the export of the given fusion proteins was investigated. It is important to note that protein degradation, inclusion bod ...
2.7. Future of plant-based protein sources
... so that one doesn’t pay attention to them. Package sizes often form a barrier. Most people would like to try new products in a small package when they are not sure about how much they like it. Singles and couples without children prefer small packages at all times. On the other hand people with chil ...
... so that one doesn’t pay attention to them. Package sizes often form a barrier. Most people would like to try new products in a small package when they are not sure about how much they like it. Singles and couples without children prefer small packages at all times. On the other hand people with chil ...
Amino Acids, Proteins, and Enzymes
... - Each polypeptide chain starts on the left side by free amino group of the first amino acid enter in chain formation . It is termed ...
... - Each polypeptide chain starts on the left side by free amino group of the first amino acid enter in chain formation . It is termed ...
Cell and Molecular Biology
... actin filament or promote disassembly. They may have a role in determining filament length. For example: Tropomodulins cap the minus end, preventing dissociation of actin monomers. CapZ capping protein binds to the plus end, inhibiting polymerization. If actin monomers continue to dissociate from th ...
... actin filament or promote disassembly. They may have a role in determining filament length. For example: Tropomodulins cap the minus end, preventing dissociation of actin monomers. CapZ capping protein binds to the plus end, inhibiting polymerization. If actin monomers continue to dissociate from th ...
Tyrosine phosphorylation of the BRI1 receptor kinase occurs via a
... the Flag-BRI1 protein from uninduced E. coli cells had fivefold higher staining with ProQ Diamond than did the kinase-inactive Flag-BRI1 (K911E) directed mutant, referred to as mBRI1, that is completely unphosphorylated (Wang et al., 2005a). These results suggested that the BRI1 protein present in u ...
... the Flag-BRI1 protein from uninduced E. coli cells had fivefold higher staining with ProQ Diamond than did the kinase-inactive Flag-BRI1 (K911E) directed mutant, referred to as mBRI1, that is completely unphosphorylated (Wang et al., 2005a). These results suggested that the BRI1 protein present in u ...
Protein Function and Classification (Cont.) - EMBL-EBI
... Figure 3. Examples of hierarchical relationships between InterPro entries. Both family entries and domain entries are able to form hierarchical relationships, although family and domain hierarchies are kept separate in the database and do not overlap (for example, a subclass of a particular domain c ...
... Figure 3. Examples of hierarchical relationships between InterPro entries. Both family entries and domain entries are able to form hierarchical relationships, although family and domain hierarchies are kept separate in the database and do not overlap (for example, a subclass of a particular domain c ...
Kinesin superfamily proteins and their various functions and dynamics
... Fig. 2. KIFs and their cargoes. (a) Scheme of KIFs and their cargo organelles in neurons. Motors and cargoes in axonal and dendritic transports are shown. On the right, the axon is shown. In the axon, microtubules (shown in green) are unipolar and the plus ends (+) point to the synaptic terminal. KI ...
... Fig. 2. KIFs and their cargoes. (a) Scheme of KIFs and their cargo organelles in neurons. Motors and cargoes in axonal and dendritic transports are shown. On the right, the axon is shown. In the axon, microtubules (shown in green) are unipolar and the plus ends (+) point to the synaptic terminal. KI ...
bioinformatics - Noble Research Lab
... These methods include the yeast two-hybrid screen and methods based on mass spectrometry (see von Mering et al., 2002 and references therein). The data obtained by these methods are partial: each experimental assay can identify only a subset of the interactions, and it has been estimated that for th ...
... These methods include the yeast two-hybrid screen and methods based on mass spectrometry (see von Mering et al., 2002 and references therein). The data obtained by these methods are partial: each experimental assay can identify only a subset of the interactions, and it has been estimated that for th ...
Ro52: Structure and interactions of constructs of RING and B-box
... The ubiquitination process is vital to maintain the protein homeostasis in the cell. With high specificity it regulates degradation of proteins by tagging them with a small protein called ubiquitin. Four proteins are involved to perform the process and in this thesis one of these proteins is studied ...
... The ubiquitination process is vital to maintain the protein homeostasis in the cell. With high specificity it regulates degradation of proteins by tagging them with a small protein called ubiquitin. Four proteins are involved to perform the process and in this thesis one of these proteins is studied ...
Identification of an estrogen receptor a non covalent ubiquitin
... Monoubiquitinated proteins are often Ub receptors that possess at least one UBD (Woelk et al., 2006). Although many different UBDs exist, no specific conservation in terms of UBDs 3Dstructure has been recognized. In fact, UBDs appear to share a common ‘shape’: structural folds that have a regular se ...
... Monoubiquitinated proteins are often Ub receptors that possess at least one UBD (Woelk et al., 2006). Although many different UBDs exist, no specific conservation in terms of UBDs 3Dstructure has been recognized. In fact, UBDs appear to share a common ‘shape’: structural folds that have a regular se ...
Investigation of the interactions between MreB, the
... allosteric communication, also differs from GroEL. Furthermore, TRiC is larger than GroEL with a broader opening of the chaperonin chamber. (5) Despite these differences, TRiC and GroEL are in many ways similar. As mentioned in the introduction to this report, studies on actin by Villebeck et al. (5 ...
... allosteric communication, also differs from GroEL. Furthermore, TRiC is larger than GroEL with a broader opening of the chaperonin chamber. (5) Despite these differences, TRiC and GroEL are in many ways similar. As mentioned in the introduction to this report, studies on actin by Villebeck et al. (5 ...
Communication - Department of Molecular Physiology and Biophysics
... muscular dystrophy (DMD) patients suggests that syntrophincontaining dystrophin-glycoprotein complex is important in maintaining the normal structure and function of muscle sarcolemma (8, 11, 13, 14). Several lines of biochemical evidence suggest that dystrophin and syntrophin may directly interact ...
... muscular dystrophy (DMD) patients suggests that syntrophincontaining dystrophin-glycoprotein complex is important in maintaining the normal structure and function of muscle sarcolemma (8, 11, 13, 14). Several lines of biochemical evidence suggest that dystrophin and syntrophin may directly interact ...
trisphosphate specifically interacts with the phox homology domain
... cell survival (Stephens et al., 1998). However, PtdInsspecific cellular functions, especially PtdIns(3,4,5)P3-induced molecular activation and signaling events, are not fully understood. The Phox homology (PX) domain is named after its presence in the p40phox and p47phox subunits of the NADPH oxidas ...
... cell survival (Stephens et al., 1998). However, PtdInsspecific cellular functions, especially PtdIns(3,4,5)P3-induced molecular activation and signaling events, are not fully understood. The Phox homology (PX) domain is named after its presence in the p40phox and p47phox subunits of the NADPH oxidas ...
Sequential steps in clathrin-mediated synaptic vesicle endocytosis
... Diagram of proteins implicated in clathrinmediated synaptic vesicle endocytosis. Clathrin occurs as a triskelion consisting of three heavy and three light chains of clathrin. Triskelia assemble together into a lattice of pentagons and hexagons [1,11], which are connected to the plasma membrane via t ...
... Diagram of proteins implicated in clathrinmediated synaptic vesicle endocytosis. Clathrin occurs as a triskelion consisting of three heavy and three light chains of clathrin. Triskelia assemble together into a lattice of pentagons and hexagons [1,11], which are connected to the plasma membrane via t ...
Current Topics Intrinsic Disorder and Protein Function†
... transitions upon binding. A common theme is a coil-to-helix transition concomitant with binding to another molecule (5). Molecular crowding could certainly shift a disordered region’s equilibrium from coil to helix. However, in the absence of its binding partner, a helix induced by excluded volume e ...
... transitions upon binding. A common theme is a coil-to-helix transition concomitant with binding to another molecule (5). Molecular crowding could certainly shift a disordered region’s equilibrium from coil to helix. However, in the absence of its binding partner, a helix induced by excluded volume e ...
Engineering and Identifying Supercharged Proteins
... functional protein molecules directly into cells by translational fusion to supercharged proteins (Cronican et al., 2010). We initially demonstrated delivery of mCherry, ubiquitin, and Cre recombinase into multiple cell types using þ36 GFP (Cronican et al., 2010). These three proteins provide separa ...
... functional protein molecules directly into cells by translational fusion to supercharged proteins (Cronican et al., 2010). We initially demonstrated delivery of mCherry, ubiquitin, and Cre recombinase into multiple cell types using þ36 GFP (Cronican et al., 2010). These three proteins provide separa ...
Nucleolar localization of an isoform of the IGF
... A nucleolar localization signal in the Eb domain To test the role of IGF-I domains in the nuclear and nucleolar localization, chimeras were constructed that deleted part of exon 3 encoding the B and C domains (2-G-4-5 and 1-G-4-5). The clear nuclear and nucleolar localization remained when the 2-G-4 ...
... A nucleolar localization signal in the Eb domain To test the role of IGF-I domains in the nuclear and nucleolar localization, chimeras were constructed that deleted part of exon 3 encoding the B and C domains (2-G-4-5 and 1-G-4-5). The clear nuclear and nucleolar localization remained when the 2-G-4 ...
Fragment Screening by WAC - Transientic Interactions
... than when present in solution. Proteins such as thrombin and Hsp90 has proven to maintain 90% activity for several months and >200 injections(1,2). The activity of the target protein can ...
... than when present in solution. Proteins such as thrombin and Hsp90 has proven to maintain 90% activity for several months and >200 injections(1,2). The activity of the target protein can ...
Recombinant human insulin-11. Size-exclusion HPLC of
... molecules may lead to partial adsorption, especially in case of high molecular mass or the formation of complexes of water-soluble biopolymers, for which adsorption may by sufficiently high due to a great number of contacts, in addition to secondary effects. In order to reduce the contribution of hy ...
... molecules may lead to partial adsorption, especially in case of high molecular mass or the formation of complexes of water-soluble biopolymers, for which adsorption may by sufficiently high due to a great number of contacts, in addition to secondary effects. In order to reduce the contribution of hy ...
Peroxisome degradation requires catalytically active sterol
... many GRAM-domain proteins harbour additional lipidbinding motifs, e.g. FYVE or pleckstrin homology (PH) domains, they are thought to be associated with intracellular membranes. The physiological and biochemical functions of GRAM domains, however, have not been determined at either the cellular or mo ...
... many GRAM-domain proteins harbour additional lipidbinding motifs, e.g. FYVE or pleckstrin homology (PH) domains, they are thought to be associated with intracellular membranes. The physiological and biochemical functions of GRAM domains, however, have not been determined at either the cellular or mo ...
Cell dynamics of folding in two
... (henceforth we denote the maximally compact conformation as a cell), i.e. fit on a 4 × 4 lattice, and is amenable to exact enumeration. This allows for an exact evaluation of equilibrium parameters, such as Tf or the radius of gyration. We compare folding characteristics for three sequences: the cha ...
... (henceforth we denote the maximally compact conformation as a cell), i.e. fit on a 4 × 4 lattice, and is amenable to exact enumeration. This allows for an exact evaluation of equilibrium parameters, such as Tf or the radius of gyration. We compare folding characteristics for three sequences: the cha ...
Protein domain
A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. One domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. Domains vary in length from between about 25 amino acids up to 500 amino acids in length. The shortest domains such as zinc fingers are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be ""swapped"" by genetic engineering between one protein and another to make chimeric proteins.