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C-terminal Residues (c-terminal + residue)
Selected AbstractsUnusual binding interactions in PDZ domain crystal structures help explain binding mechanismsPROTEIN SCIENCE, Issue 4 2010Jonathan M. Elkins Abstract PDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domain's "binding groove". We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here allow comparison with canonical binding for the PDLIM PDZ domain family. Although influenced by crystal packing arrangements, the structures nevertheless show that changes in the positions of PDZ domain side-chains and the ,B helix allow noncanonical binding interactions. These interactions may be indicative of intermediate states between unbound and fully bound PDZ domain and target protein. The noncanonical "perpendicular" binding observed potentially represents the general form of a kinetic intermediate. Comparison with canonical binding suggests that the rearrangement during binding involves both the PDZ domain and its ligand. [source] Negative ion dissociation of peptides containing hydroxyl side chainsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 2 2008Dan Pu The dissociation of deprotonated peptides containing hydroxyl side chains was studied by electrospray ionization coupled with Fourier transform ion cyclotron resonance (ESI-FTICR) via sustained off-resonance irradiation collision induced dissociation (SORI-CID). Dissociation under post-source decay (PSD) conditions was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). This work included hexapeptides with one residue of serine, threonine, or tyrosine and five inert alanine residues. During SORI-CID and PSD, dissociation of [M,H], yielded c- and y-ions. Side-chain losses of formaldehyde (HCHO) from serine-containing peptides, acetaldehyde (CH3CHO) from threonine-containing peptides, and 4-methylene-2,5-cycohexadienone (C7H6O) from tyrosine-containing peptides were generally observed in the negative ion PSD and SORI-CID spectra. Side-chain loss occurs much less from tyrosine-containing peptides than from serine- and threonine-containing peptides. This is probably due to the bulky side chain of tyrosine, resulting in steric hindrance and poor geometry for dissociation reactions. Additionally, a selective cleavage leading to the elimination of the C-terminal residue from [M,H], was observed from the peptides with serine and threonine at the C-terminus. This cleavage does not occur in the dissociation of peptides with an amide group at the C-terminus or peptides with neutral or basic residues at the C-terminus. It also does not occur with tyrosine at the C-terminus. Both the C-terminal carboxylic acid group and the hydroxyl side chain of the C-terminal residue must play important roles in the mechanism of C-terminal residue loss. A mechanism involving both the C-terminal carboxylic acid group and a hydroxyl side chain of serine and threonine is proposed. Copyright © 2007 John Wiley & Sons, Ltd. [source] Chemotactic activity of oligopeptides containing an EWS motif on Tetrahymena pyriformis: the effect of amidation of the C-terminal residueCELL BIOCHEMISTRY AND FUNCTION, Issue 2 2003László Köhidai Abstract Chemotactic properties of 3,7-mer peptides containing an EWS motive and their peptide amides synthesized and characterized by us were investigated in Tetrahymena pyriformis GL model. Analysis of the peptide acids shows that SEWS possesses exceptionally strong (660%±21; 430%±18) chemoattractant ability at 10,12 and 10,11m respectively. The shorter peptide (EWS) possesses chemorepellent activity, while longer peptides display neutral (WSEWS) or moderate chemoattractant (EWSEWS and GEWSEWS) chemotactic ability. Amidation of the C-terminus can significantly modify the character of peptides: it points to the conclusion that a free ,-COOH group at this position is required for the high efficiency of SEWS, while in the shorter (EWS) and longer peptides (WSEWS and EWSEWS) amidation can result in chemoattractant ligands. Evaluation of the structure,function relationship of these compounds establishes the significance of Glu (E) with its high surface-exposed area and negatively-charged side chain. The high discriminative ability and good chemotactic responsiveness of Tetrahymena support the theory that a chemotactic signalling mechanism working in higher levels of phylogeny is a well conserved and inducible one even in protozoa. Copyright © 2002 John Wiley & Sons, Ltd. [source] Mouse cytosolic sulfotransferase SULT2B1b interacts with cytoskeletal proteins via a proline/serine-rich C-terminusFEBS JOURNAL, Issue 18 2010Katsuhisa Kurogi Cytosolic sulfotransferase (SULT) SULT2B1b had previously been characterized as a cholesterol sulfotransferase. Like human SULT2B1, mouse SULT2B1b contains a unique, 31 amino acid C-terminal sequence with a proline/serine-rich region, which is not found in members of other SULT families. To gain insight into the functional relevance of this proline/serine-rich region, we constructed a truncated mouse SULT2B1b lacking the 31 C-terminal amino acids, and compared it with the wild-type enzyme. Enzymatic characterization indicated that the catalytic activity was not significantly affected by the absence of those C-terminal residues. Glutathione S -transferase pulldown assays showed that several proteins interacted with mouse SULT2B1b specifically through this C-terminal proline/serine-rich region. Peptide mass fingerprinting revealed that of the five SULT2B1b-binding proteins analyzed, three were cytoskeletal proteins and two were cytoskeleton-binding molecular chaperones. Furthermore, wild-type mouse SULT2B1b, but not the truncated enzyme, was associated with the cytoskeleton in experiments with a cytoskeleton-stabilizing buffer. Collectively, these results suggested that the unique, extended proline/serine-rich C-terminus of mouse SULT2B1b is important for its interaction with cytoskeletal proteins. Such an interaction may allow the enzyme to move along microfilaments such as actin filaments, and catalyze the sulfation of hydroxysteroids, such as cholesterol and pregnenolone, at specific intracellular locations. Structured digital abstract ,,MINT-7975854: Sult2B1b (uniprotkb:O35400) physically interacts (MI:0914) with Myosin-Ic (uniprotkb:Q9WTI7), Alpha-actinin-1 (uniprotkb:Q7TPR4), Alpha-actinin-4 (uniprotkb:P57780), HSP 90-beta (uniprotkb:P11499), Hsc70, (uniprotkb:P63017), Beta-actin (uniprotkb:P60710) and Gamma-actin (uniprotkb:P63260) by pull down (MI:0096) [source] The C-terminus of viral vascular endothelial growth factor-E partially blocks binding to VEGF receptor-1FEBS JOURNAL, Issue 1 2008Marie K. Inder Vascular endothelial growth factor (VEGF) family members play important roles in embryonic development and angiogenesis during wound healing and in pathological conditions such as tumor formation. Parapoxviruses express a new member of the VEGF family which is a functional mitogen that specifically activates VEGF receptor (VEGFR)-2 but not VEGFR-1. In this study, we show that deletion from the viral VEGF of a unique C-terminal region increases both VEGFR-1 binding and VEGFR-1-mediated monocyte migration. Enzymatic removal of O -linked glycosylation from the C-terminus also increased VEGFR-1 binding and migration of THP-1 monocytes indicating that both the C-terminal residues and O -linked sugars contribute to blocking viral VEGF binding to VEGFR-1. The data suggest that conservation of the C-terminal residues throughout the viral VEGF subfamily may represent a means of reducing the immunostimulatory activities associated with VEGFR-1 activation while maintaining the ability to induce angiogenesis via VEGFR-2. [source] Secretion of the Escherichia coli K-12 SheA hemolysin is independent of its cytolytic activityFEMS MICROBIOLOGY LETTERS, Issue 2 2001Francisco J del Castillo Abstract The Escherichia coli K-12 sheA gene encodes a pore-forming hemolysin that is secreted to the medium by a hitherto unidentified mechanism. To study SheA secretion, we constructed fusions between SheA and the mature form of the periplasmic enzyme ,-lactamase, and performed site-directed mutagenesis on these constructs. The SheA-Bla and Bla-SheA hybrid proteins displayed hemolytic activity and were efficiently exported to the extracellular medium. Our results with mutant hybrid proteins show that secretion of SheA is independent of its cytolytic activity, that secretion is paralleled by a transient leakage of periplasmic contents to the extracellular medium, and that deletion of the 11 C-terminal residues of SheA has no effect on its secretion and cytolytic activity. [source] A role of the C-terminus of aquaporin 4 in its membrane expression in cultured astrocytesGENES TO CELLS, Issue 7 2002Ken-ichi Nakahama Background: Aquaporin 4 (AQP4) is a predominant water channel protein in mammalian brains, which is localized in the astrocyte plasma membrane. Membrane targeting of AQP4 is essential to perform its function. The mechanism(s) of membrane targeting is not clear in astrocytes. Results: We investigated the role of the C-terminus of AQP4 (short isoform) in its membrane targeting by an expression study of C-terminal mutants of AQP4 in cultured astrocytes. The deletion of 26 C-terminal residues of AQP4 (AQP4,276,301aa) results in the intracellular localization of the protein. However, smaller deletions than 21 C-terminal residues did not alter its plasma membrane localization. These results suggest that C-terminal residues between Val276 and Ile280 play an important role in the expression of AQP4 in the plasma membrane. However, the plasma membrane localization of the AQP4(A276AAAA280) mutant (alanine substitution of Val276 -Ile280 of AQP4) suggests that another signal for membrane targeting exists in the C-terminus of AQP4. The deletion or point mutations of the PDZ binding motif of the AQP4(A276AAAA280) mutant resulted in the intracellular localization of the proteins. These results suggest that the PDZ binding motif may also be involved in the membrane targeting of AQP4. Conclusions: We found that the C-terminal sequence of AQP4 contains two important signals for membrane expression of AQP4 in cultured astrocytes. One is a hydrophobic domain and the other is a PDZ binding motif that exists in the C-terminus. [source] Protein tyrosine phosphatase SHP-1 specifically recognizes C-terminal residues of its substrates via helix ,0JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 1 2001Jian Yang Abstract The catalytic domain of protein tyrosine phosphatase SHP-1 possesses distinct substrate specificity. It recognizes the P-3 to P-5 residues of its substrates via the ,5-loop-,6 region. To study the substrate specificity further, we determined the structure of the catalytic domain of SHP-1 (C455S) complexed with a less-favorable-substrate peptide originated from SIRP,. The complex has disordered N-terminal peptide structure and reduced interactions between the N-terminal peptide and the ,5-loop-,6 region. This could be the basis for the lower affinity of peptide pY427 for the catalytic domain of SHP-1. In addition, by comparing the SHP-1/less-favorable peptide complex structure with the SHP-1/substrate complex structures, we identified a novel substrate-recognition site in the catalytic domain of SHP-1. This site was formed by helix ,0 and the ,5-loop-,6 motif of SHP-1, and specifically bound residues at the P,+,4 and further C-terminal positions of peptide substrates. © 2001 Wiley-Liss, Inc. [source] Neural network-based prediction of transmembrane ,-strand segments in outer membrane proteinsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2004M. Michael Gromiha Abstract Prediction of transmembrane ,-strands in outer membrane proteins (OMP) is one of the important problems in computational chemistry and biology. In this work, we propose a method based on neural networks for identifying the membrane-spanning ,-strands. We introduce the concept of "residue probability" for assigning residues in transmembrane ,-strand segments. The performance of our method is evaluated with single-residue accuracy, correlation, specificity, and sensitivity. Our predicted segments show a good agreement with experimental observations with an accuracy level of 73% solely from amino acid sequence information. Further, the predictive power of N- and C-terminal residues in each segments, number of segments in each protein, and the influence of cutoff probability for identifying membrane-spanning ,-strands will be discussed. We have developed a Web server for predicting the transmembrane ,-strands from the amino acid sequence, and the prediction results are available at http://psfs.cbrc.jp/tmbeta-net/. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 762,767, 2004 [source] The strong dimerization of the transmembrane domain of the fibroblast growth factor receptor (FGFR) is modulated by C-terminal juxtamembrane residuesPROTEIN SCIENCE, Issue 2 2009Weng Chuan Peng Abstract The fibroblast growth factor receptor 3 (FGFR3) is a member of the FGFR subfamily of the receptor tyrosine kinases (RTKs) involved in signaling across the plasma membrane. Generally, ligand binding leads to receptor dimerization and activation. Dimerization involves the transmembrane (TM) domain, where mutations can lead to constitutive activation in certain cancer types and also in skeletal malformations. Thus, it has been postulated that FGFR homodimerization must be inherently weak to allow regulation, a feature reminiscent of , and , integrin TM interactions. However, we show herein that in FGFR3-TM, four C-terminal residues, CRLR, have a profound destabilizing effect in an otherwise strongly dimerizing TM peptide. In the absence of these four residues, the dimerizing propensity of FGFR3-TM is comparable to glycophorin, as shown using various detergents. In addition, the expected enhanced dimerization induced by the mutation associated to the Crouzon syndrome A391E, was observed only when these four C-terminal residues were present. In the absence of these four residues, A391E was dimer-destabilizing. Finally, using site specific infrared dichroism and convergence with evolutionary conservation data, we have determined the backbone model of the FGFR3-TM homodimer in model lipid bilayers. This model is consistent with, and correlates with the effects of, most known pathological mutations found in FGFR-TM. [source] Structure of the Escherichia coli RNA polymerase , subunit C-terminal domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Samuel Lara-González The , subunit C-terminal domain (,CTD) of RNA polymerase (RNAP) is a key element in transcription activation in Escherichia coli, possessing determinants responsible for the interaction of RNAP with DNA and with transcription factors. Here, the crystal structure of E. coli,CTD (, subunit residues 245,329) determined to 2.0,Ĺ resolution is reported. Crystals were obtained after reductive methylation of the recombinantly expressed domain. The crystals belonged to space group P21 and possessed both pseudo-translational symmetry and pseudo-merohedral twinning. The refined coordinate model (R factor = 0.193, Rfree = 0.236) has improved geometry compared with prior lower resolution determinations of the ,CTD structure [Jeon et al. (1995), Science, 270, 1495,1497; Benoff et al. (2002), Science, 297, 1562,1566]. An extensive dimerization interface formed primarily by N- and C-terminal residues is also observed. The new coordinates will facilitate the improved modeling of ,CTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction. [source] | |||||||||||||