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Structural Basis (structural + basis)
Selected AbstractsStructural Basis of ,-Fucosidase Inhibition by Iminocyclitols with Ki Values in the Micro- to Picomolar Range,ANGEWANDTE CHEMIE, Issue 2 2010Hsing-Ju Wu Dr. Zwei Schleifen, die sich nach innen zum aktiven Zentrum von ,-Fucosidase bewegen, führen zu einer geschlossenen Konformation des Komplexes mit Inhibitoren mit Ki -Werten vom Mikro- bis zum Nanomolbereich. Bei Inhibitoren mit subnanomolaren Ki -Werten treten zwar keine weiteren Konformationsänderungen in den beiden Schleifen auf, aber die Schleifen werden durch Wasserstoffbrücken und hydrophobe Wechselwirkungen weiter stabilisiert. [source] ChemInform Abstract: Li+ Diffusion and Its Structural Basis in the Nanocrystalline and Amorphous Forms of Two-Dimensionally Ion-Conducting LixTiS2.CHEMINFORM, Issue 40 2001Rudolf Winter Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] ChemInform Abstract: Structural Basis of Binding of High-Affinity Ligands to Protein Kinase C: Prediction of the Binding Modes Through a New Molecular Dynamics Method and Evaluation by Site-Directed Mutagenesis.CHEMINFORM, Issue 35 2001Youngshang Pak Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] MBSJ MCC Young Scientist Award 2009 REVIEW: Structural basis of protein disulfide bond generation in the cellGENES TO CELLS, Issue 9 2010Kenji Inaba The formation of protein disulfide bonds is an oxidative reaction that is crucial for the folding and maturation of many secreted and membrane proteins. Both prokaryotic and eukaryotic cells possess various disulfide oxidoreductases and redox-active cofactors to accelerate this oxidative reaction in a correct manner. Crystal or solution structures have been solved for some of the oxidoreductases in the past 10 years, leading to remarkable progress in the field of thiol-based redox cell biology. Consequently, structural and mechanistic similarities in the disulfide bond formation pathways have been uncovered. This review highlights the molecular basis of the elaborate oxidative systems operating in the Escherichia coli periplasm, the endoplasmic reticulum lumen and the mitochondrial intermembrane space. The accumulated knowledge provides important insights into how protein and redox homeostasis are maintained in the cell. [source] Structural basis of target recognition by Atg8/LC3 during selective autophagyGENES TO CELLS, Issue 12 2008Nobuo N. Noda Autophagy is a non-selective bulk degradation process in which isolation membranes enclose a portion of cytoplasm to form double-membrane vesicles, called autophagosomes, and deliver their inner constituents to the lytic compartments. Recent studies have also shed light on another mode of autophagy that selectively degrades various targets. Yeast Atg8 and its mammalian homologue LC3 are ubiquitin-like modifiers that are localized on isolation membranes and play crucial roles in the formation of autophagosomes. These proteins are also involved in selective incorporation of specific cargo molecules into autophagosomes, in which Atg8 and LC3 interact with Atg19 and p62, receptor proteins for vacuolar enzymes and disease-related protein aggregates, respectively. Using X-ray crystallography and NMR, we herein report the structural basis for Atg8,Atg19 and LC3,p62 interactions. Remarkably, Atg8 and LC3 were shown to interact with Atg19 and p62, respectively, in a quite similar manner: they recognized the side-chains of Trp and Leu in a four-amino acid motif, WXXL, in Atg19 and p62 using hydrophobic pockets conserved among Atg8 homologues. Together with mutational analyses, our results show the fundamental mechanism that allows Atg8 homologues, in association with WXXL-containing proteins, to capture specific cargo molecules, thereby endowing isolation membranes and/or their assembly machineries with target selectivity. [source] Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chainsGENES TO CELLS, Issue 10 2004Takeshi Tenno Ubiquitination, a modification in which single or multiple ubiquitin molecules are attached to a protein, serves as a signalling function that controls a wide variety of cellular processes. To date, two major forms of polyubiquitin chain have been functionally characterized, in which the isopeptide bond linkages involve Lys48 or Lys63. Lys48-linked polyubiquitin tagging is mostly used to target proteins for degradation by the proteasome, whereas Lys63-linked polyubiquitination has been linked to numerous cellular events that do not rely on degradative signalling via the proteasome. Apparently linkage-specific conformations of polyubiquitin chains are important for these cellular functions, but the structural bases distinguishing Lys48- and Lys63-linked chains remain elusive. Here, we report NMR and small-angle X-ray scattering (SAXS) studies on the intersubunit interfaces and conformations of Lys63- and Lys48-linked di- and tetraubiquitin chains. Our results indicate that, in marked contrast to Lys48-linked chains, Lys63-linked chains are elongated molecules with no stable non-covalent intersubunit interfaces and thus adopt a radically different conformation from that of Lys48-linked chains. [source] Structural basis of MHC class I recognition by natural killer cell receptorsIMMUNOLOGICAL REVIEWS, Issue 1 2001Mark W. Sawicki Summary: Natural killer (NK)-cell function is regulated by NK receptors that recognize MHC class I (MHC-I) molecules on target cells. Two structurally distinct families of NK receptors have been identified, the immunoglobulin-like family (killer cell immunoglobulin-like receptors (KIRs), leukocyte immunoglobulin-like receptors (LIRs)) and the C-type lectin-like family (Ly49, CD94/NKG2A, NKG2D, CD69). Recently, the three-dimensional structures of several NK receptors were determined, in free form or bound to MHC-I. These include those of unbound KIRs, NKG2D, CD69, LIR-1 and the CD94 subunit of the CD94/NKG2A heterodimer. Together, these structures define the basic molecular architecture of both the immunoglobulin-like and C-type lectin-like families of NK receptors. In addition, crystal structures have been reported for the complex between Ly49A and H-2Dd, and for KIR2DL2 bound to HLA-Cw3. The complex structures provide a framework for understanding MHC-I recognition by NK receptors from both families and reveal striking differences in the nature of this recognition, despite the receptors' functional similarity. This research was supported, in part, by National Institutes of Health grants R01 AI47900 and R37 36900 (RAM) and a fellowship from the Cancer Research Institute (MWS). We are grateful to DW Wolan and IA Wilson for providing coordinates of NKG2D prior to publication, and to members of our laboratories for encouragement. [source] Crystal structures of thymidylate synthase mutant R166Q: Structural basis for the nearly complete loss of catalytic activity,JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY, Issue 2 2006Rogerio R. Sotelo-Mundo Abstract Thymidylate synthase (TS) catalyzes the folate-dependent methylation of deoxyuridine monophosphate (dUMP) to form thymidine monophosphate (dTMP). We have investigated the role of invariant arginine 166, one of four arginines that contact the dUMP phosphate, using site-directed mutagenesis, X-ray crystallography, and TS from Escherichia coli. The R166Q mutant was crystallized in the presence of dUMP and a structure determined to 2.9 Å resolution, but neither the ligand nor the sulfate from the crystallization buffer was found in the active site. A second structure determined with crystals prepared in the presence of dUMP and the antifolate 10-propargyl-5,8-dideazafolate revealed that the inhibitor was bound in an extended, nonproductive conformation, partially occupying the nucleotide-binding site. A sulfate ion, rather than dUMP, was found in the nucleotide phosphate-binding site. Previous studies have shown that the substitution at three of the four arginines of the dUMP phosphate-binding site is permissive; however; for Arg166, all the mutations lead to a near-inactive mutant. The present structures of TS R166Q reveal that the phosphate-binding site is largely intact, but with a substantially reduced affinity for phosphate, despite the presence of the three remaining arginines. The position of Cys146, which initiates catalysis, is shifted in the mutant and resides in a position that interferes with the binding of the dUMP pyrimidine moiety. © 2006 Wiley Periodicals, Inc. J Biochem Mol Toxicol 20:88,92, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20122 [source] Structural basis for preferential binding of non- ortho -substituted polychlorinated biphenyls by the monoclonal antibody S2B1JOURNAL OF MOLECULAR RECOGNITION, Issue 4 2005Jean-Luc Pellequer Abstract Polychlorinated biphenyls (PCBs) are a family of 209 isomers (congeners) with a wide range of toxic effects. In structural terms, they are of two types: those with and those without chlorines at the ortho positions (2, 2,, 6 and 6,). Only 20 congeners have no ortho chlorines. Three of these are bound by the aryl hydrocarbon receptor and are one to four orders of magnitude more toxic than all others. A monoclonal antibody, S2B1, and its recombinant Fab have high selectivity and nanomolar binding affinities for two of the most toxic non- ortho -chlorinated PCBs, 3,4,3,,4,-tetrachlorobiphenyl and 3,4,3,,4,,5,-pentachlorobiphenyl. To investigate the basis for these properties, we built a three-dimensional structure model of the S2B1 variable fragment (Fv) based on the high-resolution crystallographic structures of antibodies 48G7 and N1G9. Two plausible conformations for the complementarity-determining region (CDR) H3 loop led to two putative PCB-binding pockets with very different shapes (models A and B). Docking studies using molecular mechanics and potentials of mean force (PMF) indicated that model B was most consistent with the selectivity observed for S2B1 in competition ELISAs. The binding site in model B had a deep, narrow pocket between VL and VH, with a slight constriction at the top that opened into a wider pocket between CDRs H1 and H3 on the antibody surface. This binding site resembles those of esterolytic antibodies that bind haptens with phenyl rings. One phenyl ring of the PCB fits into the deep pocket, and the other ring is bound in the shallower one. The bound PCB is surrounded by the side chains of TyrL91, TyrL96 and TrpH98, and it has a ,-cation interaction with ArgL46. The tight fit of the binding pocket around the ortho positions of the bound PCBs indicates that steric hindrance of ortho chlorines in the binding site, rather than induced conformational change of the PCBs, is responsible for the selectivity of S2B1. Copyright © 2005 John Wiley & Sons, Ltd. [source] Structural basis of pheromone binding to mouse major urinary protein (MUP-I)PROTEIN SCIENCE, Issue 5 2001David E. Timm Abstract The mouse major urinary proteins are pheromone-binding proteins that function as carriers of volatile effectors of mouse physiology and behavior. Crystal structures of recombinant mouse major urinary protein-I (MUP-I) complexed with the synthetic pheromones, 2-sec-butyl-4,5-dihydrothiazole and 6-hydroxy-6-methyl-3-heptanone, have been determined at high resolution. The purification of MUP-I from mouse liver and a high-resolution structure of the natural isolate are also reported. These results show the binding of 6-hydroxy-6-methyl-3-heptanone to MUP-I, unambiguously define ligand orientations for two pheromones within the MUP-I binding site, and suggest how different chemical classes of pheromones can be accommodated within the MUP-I ,-barrel. [source] Structural basis for the phase transitions of Cs2HgCl4ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2001Bagautdin Bagautdinov The a0× b0× 2c0 twofold superstructure of dicaesium mercury tetrachloride, Cs2HgCl4, at T = 120,K has been determined by single-crystal X-ray diffraction using synchrotron radiation. Lattice parameters were found as a = 9.7105,(2), b = 7.4691 (1), c = 26.8992 (4) Å, and , = 90.368,(1)° with the supercell space group P21/c. Refinements on 1828 observed unique reflections converged to R = 0.053 (wR = 0.057) using anisotropic temperature factors for all atoms. This phase is the stable phase of Cs2HgCl4 below 163,K. A quantitative comparison is made of the distortions of the 2c0 superstructure with the undistorted phase that is stable at room temperature, and with the 3c0 and 5a0 superstructures that are stable at temperatures between 163,K and room temperature. The principal difference between the 2c0 superstructure and all other phases of Cs2HgCl4 is that the Cs cations are displaced away from the centers of their coordination polyhedra in the 2c0 superstructure. The structural basis for the driving force of the series of phase transitions in this compound is found in the variations of the environments of Cs atoms and in the variations of the distortions of the HgCl4 tetrahedra. [source] Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1,-hydroxyvitamin D3 -26,23-lactoneACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2010Shinji Kakuda TEI-9647 antagonizes vitamin D receptor (VDR) mediated genomic actions of 1,,25(OH)2D3 in human cells but is agonistic in rodent cells. The presence of Cys403, Cys410 or of both residues in the C-terminal region of human VDR (hVDR) results in antagonistic action of this compound. In the complexes of TEI-9647 with wild-type hVDR (hVDRwt) and H397F hVDR, TEI-9647 functions as an antagonist and forms a covalent adduct with hVDR according to MALDI,TOF MS. The crystal structures of complexes of TEI-9647 with rat VDR (rVDR), H305F hVDR and H305F/H397F hVDR showed that the agonistic activity of TEI-9647 is caused by a hydrogen-bond interaction with His397 or Phe397 located in helix 11. Both biological activity assays and the crystal structure of H305F hVDR complexed with TEI-9647 showed that the interaction between His305 and TEI-9647 is crucial for antagonist activity. This study indicates the following stepwise mechanism for TEI-9647 antagonism. Firstly, TEI-9647 forms hydrogen bonds to His305, which promote conformational changes in hVDR and draw Cys403 or Cys410 towards the ligand. This is followed by the formation of a 1,4-Michael addition adduct between the thiol (,SH) group of Cys403 or Cys410 and the exo -methylene group of TEI-9647. [source] Structural basis for the high-affinity binding of pyrrolotriazine inhibitors of p38 MAP kinaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2008John S. Sack The crystal structure of unphosphorylated p38, MAP kinase complexed with a representative pyrrolotriazine-based inhibitor led to the elucidation of the high-affinity binding mode of this class of compounds at the ATP-binding site. The ligand binds in an extended conformation, with one end interacting with the adenine-pocket hinge region, including a hydrogen bond from the carboxyl O atom of Met109. The other end of the ligand interacts with the hydrophobic pocket of the binding site and with the backbone N atom of Asp168 in the DFG activation loop. Addition of an extended benzylmorpholine group forces the DFG loop to flip out of position and allows the ligand to make additional interactions with the protein. [source] Structural basis for the binding of naproxen to human serum albumin in the presence of fatty acids and the GA moduleACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2008Sara Lejon The previously determined crystal structure of the bacterial albumin-binding GA module in complex with human serum albumin (HSA) suggested the possibility of utilizing the complex in the study of ligand binding to HSA. As a continuation of these studies, the crystal structure of the HSA,GA complex with the drug molecule naproxen and the fatty acid decanoate bound to HSA has been determined to a resolution of 2.5,Å. In terms of drug binding, the structure suggests that the binding of decanoate to the albumin molecule may play a role in making the haemin site in subdomain IB of the albumin molecule available for the binding of naproxen. In addition, structure comparisons with solved structures of HSA and of the HSA,GA complex show that the GA module is capable of binding to different conformations of HSA. The HSA,GA complex therefore emerges as a possible platform for the crystallographic study of specific HSA,drug interactions and of the influence exerted by the presence of fatty acids. [source] Peripheral axotomy induces only very limited sprouting of coarse myelinated afferents into inner lamina II of rat spinal cordEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 2 2002Lan Bao Abstract Peripheral axotomy-induced sprouting of thick myelinated afferents (A-fibers) from laminae III,IV into laminae I,II of the spinal cord is a well-established hypothesis for the structural basis of neuropathic pain. However, we show here that the cholera toxin B subunit (CTB), a neuronal tracer used to demonstrate the sprouting of A-fibers in several earlier studies, also labels unmyelinated afferents (C-fibers) in lamina II and thin myelinated afferents in lamina I, when applied after peripheral nerve transection. The lamina II afferents also contained vasoactive intestinal polypeptide and galanin, two neuropeptides mainly expressed in small dorsal root ganglion (DRG) neurons and C-fibers. In an attempt to label large DRG neurons and A-fibers selectively, CTB was applied four days before axotomy (pre-injury-labelling), and sprouting was monitored after axotomy. We found that only a small number of A-fibers sprouted into inner lamina II, a region normally innervated by C-fibers, but not into outer lamina II or lamina I. Such sprouts made synaptic contact with dendrites in inner lamina II. Neuropeptide Y (NPY) was found in these sprouts in inner lamina II, an area very rich in Y1 receptor-positive processes. These results suggest that axotomy-induced sprouting from deeper to superficial layers is much less pronounced than previously assumed, in fact it is only marginal. This limited reorganization involves large NPY immunoreactive DRG neurons sprouting into the Y1 receptor-rich inner lamina II. Even if quantitatively small, it cannot be excluded that this represents a functional circuitry involved in neuropathic pain. [source] Innervation of interneurons immunoreactive for VIP by intrinsically bursting pyramidal cells and fast-spiking interneurons in infragranular layers of juvenile rat neocortexEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 1 2002Jochen F. Staiger Abstract Cortical columns contain specific neuronal populations with characteristic sets of connections. This wiring forms the structural basis of dynamic information processing. However, at the single-cell level little is known about specific connectivity patterns. We performed experiments in infragranular layers (V and VI) of rat somatosensory cortex, to clarify further the input patterns of inhibitory interneurons immunoreactive (ir) for vasoactive intestinal polypeptide (VIP). Neurons in acute slices were electrophysiologically characterized using whole-cell recordings and filled with biocytin. This allowed us to determine their firing pattern as regular-spiking, intrinsically bursting and fast-spiking, respectively. Biocytin was revealed histochemically and VIP immunohistochemically. Sections were examined for contacts between the axons of the filled neurons and the VIP-ir targets. Twenty pyramidal cells and five nonpyramidal (inter)neurons were recovered and sufficiently stained for further analysis. Regular-spiking pyramidal cells displayed no axonal boutons in contact with VIP-ir targets. In contrast, intrinsically bursting layer V pyramidal cells showed four putative single contacts with a proximal dendrite of VIP neurons. Fast-spiking interneurons formed contacts with two to six VIP neurons, preferentially at their somata. Single as well as multiple contacts on individual target cells were found. Electron microscopic examinations showed that light-microscopically determined contacts represent sites of synaptic interactions. Our results suggest that, within infragranular local cortical circuits, (i) fast-spiking interneurons are more likely to influence VIP cells than are pyramidal cells and (ii) pyramidal cell input probably needs to be highly convergent to fire VIP target cells. [source] In the Search of Glycogen Phosphorylase Inhibitors: Synthesis of C- D -Glycopyranosylbenzo(hydro)quinones , Inhibition of and Binding to Glycogen Phosphorylase in the Crystal,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 4 2007Li He Abstract Penta- O -acetyl-,- D -glycopyranoses and 1,4-dimethoxybenzene led selectively by electrophilic substitution to C-,- D -glycopyranosyl-1,4-dimethoxybenzenes which were converted by simple and efficient reactions (oxidation, reduction and deacetylation) to the corresponding C-glycosylhydro- and C-glycosylbenzoquinones, with either an acetylated or deprotected sugar moiety. C-,- D -Glucosylbenzoquinone 19 and C-,- D -Glucosylhydroquinone 23 were found to be competitive inhibitors of rabbit muscle glycogen phosphorylase b (GPb), with respect to the substrate ,- D -glucose-1-phosphate, with Ki values of 1.3 and 0.9 mM, respectively, whereas C-,- D -glucosylhydroquinone 17 was not effective up to a concentration of 8 mM. In order to elucidate the structural basis of inhibition, we determined the crystal structures of 19 and 23 in complex with GPb at a 2.03,2.05 Å resolution. The complex structures reveal that the inhibitors can be accommodated at the catalytic site at approximately the same position as ,- D -glucose and stabilise the transition state conformation of the 280s loop by making several favourable contacts to Asp283 and Asn284 of this loop. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Conformational stability and multistate unfolding of poly(A)-specific ribonucleaseFEBS JOURNAL, Issue 10 2009Guang-Jun He Poly(A)-specific ribonuclease (PARN) specifically catalyzes the degradation of the poly(A) tails of single-stranded mRNAs in a highly processive mode. PARN participates in diverse and important intracellular processes by acting as a regulator of mRNA stability and translational efficiency. In this article, the equilibrium unfolding of PARN was studied using both guanidine hydrochloride and urea as chemical denaturants. The unfolding of PARN was characterized as a multistate process, but involving dissimilar equilibrium intermediates when denatured by the two denaturants. A comparison of the spectral characteristics of these intermediates indicated that the conformational changes at low concentrations of the chemical denaturants were more likely to be rearrangements of the tertiary and quaternary structures. In particular, an inactive molten globule-like intermediate was identified to exist as soluble non-native oligomers, and the formation of the oligomers was modulated by electrostatic interactions. An active dimeric intermediate unique to urea-induced unfolding was characterized to have increased regular secondary structures and modified tertiary structures, implying that additional regular structures could be induced by environmental stresses. The dissimilarity in the unfolding pathways induced by guanidine hydrochloride and urea suggest that electrostatic interactions play an important role in PARN stability and regulation. The appearance of multiple intermediates with distinct properties provides the structural basis for the multilevel regulation of PARN by conformational changes. [source] Solution structure of the bb, domains of human protein disulfide isomeraseFEBS JOURNAL, Issue 5 2009Alexey Y. Denisov Protein disulfide isomerase is the most abundant and best studied of the disulfide isomerases that catalyze disulfide bond formation in the endoplasmic reticulum, yet the specifics of how it binds substrate have been elusive. Protein disulfide isomerase is composed of four thioredoxin-like domains (abb,a,). Cross-linking studies with radiolabeled peptides and unfolded proteins have shown that it binds incompletely folded proteins primarily via its third domain, b,. Here, we determined the solution structure of the second and third domains of human protein disulfide isomerase (b and b,, respectively) by triple-resonance NMR spectroscopy and molecular modeling. NMR titrations identified a large hydrophobic surface within the b, domain that binds unfolded ribonuclease A and the peptides mastoparan and somatostatin. Protein disulfide isomerase-catalyzed refolding of reduced ribonuclease A in vitro was inhibited by these peptides at concentrations equal to their affinity to the bb, fragment. Our findings provide a structural basis for previous kinetic and cross-linking studies which have shown that protein disulfide isomerase exhibits a saturable, substrate-binding site. [source] A unique binding epitope for salvinorin A, a non-nitrogenous kappa opioid receptor agonistFEBS JOURNAL, Issue 9 2006Brian E. Kane Salvinorin A is a potent kappa opioid receptor (KOP) agonist with unique structural and pharmacological properties. This non-nitrogenous ligand lacks nearly all the structural features commonly associated with opioid ligand binding and selectivity. This study explores the structural basis to salvinorin A binding and selectivity using a combination of chimeric and single-point mutant opioid receptors. The experiments were designed based on previous models of salvinorin A that locate the ligand within a pocket formed by transmembrane (TM) II, VI, and VII. More traditional sites of opioid recognition were also explored, including the highly conserved aspartate in TM III (D138) and the KOP selectivity site E297, to determine the role, if any, that these residues play in binding and selectivity. The results indicate that salvinorin A recognizes a cluster of residues in TM II and VII, including Q115, Y119, Y312, Y313, and Y320. Based on the position of these residues within the receptor, and prior study on salvinorin A, a model is proposed that aligns the ligand vertically, between TM II and VII. In this orientation, the ligand spans residues that are spaced one to two turns down the face of the helices within the receptor cavity. The ligand is also in close proximity to EL-2 which, based on chimeric data, is proposed to play an indirect role in salvinorin A binding and selectivity. [source] Conformational properties of bacterial DnaK and yeast mitochondrial Hsp70FEBS JOURNAL, Issue 12 2005-helical subdomain, Role of the divergent C-terminal Among the eukaryotic members of the Hsp70 family, mitochondrial Hsp70 shows the highest degree of sequence identity with bacterial DnaK. Although they share a functional mechanism and homologous co-chaperones, they are highly specific and cannot be exchanged between Escherichia coli and yeast mitochondria. To provide a structural basis for this finding, we characterized both proteins, as well as two DnaK/mtHsp70 chimeras constructed by domain swapping, using biochemical and biophysical methods. Here, we show that DnaK and mtHsp70 display different conformational and biochemical properties. Replacing different regions of the DnaK peptide-binding domain with those of mtHsp70 results in chimeric proteins that: (a) are not able to support growth of an E. coli DnaK deletion strain at stress temperatures (e.g. 42 °C); (b) show increased accessibility and decreased thermal stability of the peptide-binding pocket; and (c) have reduced activation by bacterial, but not mitochondrial co-chaperones, as compared with DnaK. Importantly, swapping the C-terminal ,-helical subdomain promotes a conformational change in the chimeras to an mtHsp70-like conformation. Thus, interaction with bacterial co-chaperones correlates well with the conformation that natural and chimeric Hsp70s adopt in solution. Our results support the hypothesis that a specific protein structure might regulate the interaction of Hsp70s with particular components of the cellular machinery, such as Tim44, so that they perform specific functions. [source] Thermodynamic analysis of binding of p -substituted benzamidines to trypsinFEBS JOURNAL, Issue 6 2001Reinskje Talhout Understanding the structural basis of inhibitor,enzyme interactions, important for the design of new drugs, requires a complete thermodynamic characterization of the binding process as well as a description of the structure of the complex. In this paper, the binding of p -substituted benzamidinium derivatives to the structurally well-characterized serine proteinase bovine pancreatic trypsin has been studied using isothermal titration calorimetry. These experiments have permitted a complete characterization of the temperature dependence of the inhibitor-binding thermodynamics. At 25 °C, both the enthalpy and entropy of binding are favourable for all studied derivatives, but this is only true for a relatively narrow temperature range. As binding is characterized by a negative change in heat capacity, the process is characterized by enthalpy,entropy compensation, resulting in a change of the net thermodynamic driving force for association from entropic to enthalpic with increasing temperature. These phenomena are not unusual when hydrophobic forces play an important role. The trend in the relative binding potencies can, to a significant extent, be attributed to the electron-donating/withdrawing character of the substituent at the para position, as shown by the Hammett plot for the different inhibitors; the more polar the p -substituted benzamidine, the less potent it will be as a trypsin inhibitor. This behaviour might result from a bulk solvation effect, meaning that the more polar, lower potency inhibitors will be more stabilized in water than the less polar, higher potency inhibitors. [source] The role of exon 5 in fibroblast collagenase (MMP-1) substrate specificity and inhibitor selectivityFEBS JOURNAL, Issue 6 2001Vera Knäuper Interstitial collagen is degraded by members of the matrix metalloproteinase (MMP) family, including MMP-1. Previous work has shown that the region of MMP-1 coded for by exon 5 is implicated both in substrate specificity and inhibitor selectivity. We have constructed a chimeric enzyme, the exon 5 chimera, consisting primarily of MMP-1, with the region coded for by exon 5 replaced with the equivalent region of MMP-3, a noncollagenolytic MMP. Unlike MMP-3, the exon 5 chimera is capable of cleaving type I collagen, but the activity is only 2.2% of trypsin-activated MMP-1. ,Superactivation' of the chimera has no discernible effect, suggesting that the salt bridge formed in ,superactive' MMP-1 is not present. The kinetics for exon 5 chimera cleavage of two synthetic substrates display an MMP-3 phenotype, however, cleavage of gelatin is slightly impaired as compared to the parent enzymes. The Kiapp values for the exon 5 chimera complexed with synthetic inhibitors and N-terminal TIMP-2 also show a more MMP-3-like behaviour. However, the kon values for N-terminal TIMP-1 and N-terminal TIMP-2 are more comparable to those for MMP-1. These data show that the region of MMP-1 coded for by exon 5 is involved in both substrate specificity and inhibitor selectivity and the structural basis for our findings is discussed. [source] Structural basis of target recognition by Atg8/LC3 during selective autophagyGENES TO CELLS, Issue 12 2008Nobuo N. Noda Autophagy is a non-selective bulk degradation process in which isolation membranes enclose a portion of cytoplasm to form double-membrane vesicles, called autophagosomes, and deliver their inner constituents to the lytic compartments. Recent studies have also shed light on another mode of autophagy that selectively degrades various targets. Yeast Atg8 and its mammalian homologue LC3 are ubiquitin-like modifiers that are localized on isolation membranes and play crucial roles in the formation of autophagosomes. These proteins are also involved in selective incorporation of specific cargo molecules into autophagosomes, in which Atg8 and LC3 interact with Atg19 and p62, receptor proteins for vacuolar enzymes and disease-related protein aggregates, respectively. Using X-ray crystallography and NMR, we herein report the structural basis for Atg8,Atg19 and LC3,p62 interactions. Remarkably, Atg8 and LC3 were shown to interact with Atg19 and p62, respectively, in a quite similar manner: they recognized the side-chains of Trp and Leu in a four-amino acid motif, WXXL, in Atg19 and p62 using hydrophobic pockets conserved among Atg8 homologues. Together with mutational analyses, our results show the fundamental mechanism that allows Atg8 homologues, in association with WXXL-containing proteins, to capture specific cargo molecules, thereby endowing isolation membranes and/or their assembly machineries with target selectivity. [source] Retrograde amnesia and the volume of critical brain structuresHIPPOCAMPUS, Issue 8 2003M.D. Kopelman Abstract There are many controversies concerning the structural basis of retrograde amnesia (RA). One view is that memories are held briefly within a medial temporal store ("hippocampal complex") before being "consolidated" or reorganised within temporal neocortex and/or networks more widely distributed within the cerebral cortex. An alternative view is that the medial temporal lobes are always involved in the storage and retrieval (reactivation) of autobiographical memories (multiple trace theory). The present study used quantitative magnetic resonance imaging (MRI) in 40 patients with focal pathology/volume loss in different sites, to examine the correlates of impairment on three different measures of RA. The findings supported the view that widespread neural networks are involved in the storage and retrieval of autobiographical and other remote memories. Brain volume measures in critical structures could account for 60% of variance on autobiographical memory measures (for incidents and facts) in diencephalic patients and for 60,68% of variance in patients with frontal lesions. Significant correlations with medial temporal lobe volume were found only in the diencephalic group, in whom they were thought to reflect thalamic changes, but not in patients with herpes encephalitis or hypoxia in whom the temporal lobes were particularly implicated. The latter finding fails to support one of the main predictions of multiple trace theory, as presently expounded. © 2003 Wiley-Liss, Inc. [source] Experimental determination of the periodicity of incremental features in enamelJOURNAL OF ANATOMY, Issue 1 2006T. M. Smith Abstract Vital labelling of hard tissues was used to examine the periodicity of features of dental enamel microstructure. Fluorescent labels were administered pre- and postnatally to developing macaques (Macaca nemestrina), which were identified histologically in dentine and related to accentuated lines in enamel, allowing for counts of features within known-period intervals. This study demonstrates that cross-striations represent a daily rhythm in enamel secretion, and suggests that intradian lines are the result of a similar 12-h rhythm. Retzius lines were found to have a regular periodicity within individual dentitions, and laminations appear to represent a daily rhythm that also shows 12-h subdivisions. The inclusion of intradian lines and laminations represents the first empirical evidence for their periodicities in primates; these features frequently complicate precise measurements of secretion rate and Retzius line periodicity, which are necessary for determination of crown formation time. The biological basis of incremental feature formation is not completely understood; long-period features may result from interactions between short-period rhythms, although this does not explain the known range of Retzius line periodicities within humans or among primates. Studies of the genetic, neurological and hormonal basis of incremental feature formation are needed to provide more insight into their physiological and structural basis. [source] Construction of the Femoral Neck During Growth Determines Its Strength in Old Age,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 7 2007Roger M D Zebaze Abstract Study of the design of the FN in vivo in 697 women and in vitro in 200 cross-sections of different sizes and shapes along each of 13 FN specimens revealed that strength in old age was largely achieved during growth by differences in the distribution rather than the amount of bone material in a given FN cross-section from individual to individual. Introduction: We studied the design of the femoral neck (FN) to gain insight into the structural basis of FN strength in adulthood and FN fragility in old age. Materials and Methods: Studies in vivo were performed using densitometry in 697 women and in vitro using high-resolution ,CT and direct measurements in 13 pairs of postmortem specimens. Results: The contradictory needs of strength for loading yet lightness for mobility were met by varying FN size, shape, spatial distribution, and proportions of its trabecular and cortical bone in a cross-section, not its mass. Wider and narrower FNs were constructed with similar amounts of bone material. Wider FNs were relatively lighter: a 1 SD higher FN volume had a 0.67 (95% CI, 0.61,0.72) SD lower volumetric BMD (vBMD). A 1 SD increment in height was achieved by increasing FN volume by 0.32 (95% CI, 0.25,0.39) SD with only 0.15 (95% CI, 0.08,0.22) SD more bone, so taller individuals had a relatively lighter FN (vBMD was 0.13 [95% CI, 0.05,0.20 SD] SD lower). Greater periosteal apposition constructing a wider FN was offset by even greater endocortical resorption so that the same net amount of bone was distributed as a thinner cortex further from the neutral axis, increasing resistance to bending and lowering vBMD. This was recapitulated at each point along the FN; varying absolute and relative degrees of periosteal apposition and endocortical resorption focally used the same amount of material to fashion an elliptical FN of mainly cortical bone near the femoral shaft to offset bending but a more circular FN of proportionally more trabecular and less cortical bone to accommodate compressive loads adjacent to the pelvis. This structural heterogeneity was largely achieved by adaptive modeling and remodeling during growth,most of the variance in FN volume, BMC, and vBMD was growth related. Conclusions: Altering structural design while minimizing mass achieves FN strength and lightness. Bone fragility may be the result of failure to adapt bone's architecture to loading, not just low bone mass. [source] WATGEN: An algorithm for modeling water networks at protein,protein interfacesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2007Huynh-Hoa Bui Abstract Water molecules at protein,protein interfaces contribute to the close packing of atoms and ensure complementarity between the protein surfaces, as well as mediating polar interactions. Therefore, modeling of interface water is of importance in understanding the structural basis of biomolecular association. We present an algorithm, WATGEN, which predicts locations for water molecules at a protein,protein or protein,peptide interface, given the atomic coordinates of the protein and peptide. A key element of the WATGEN algorithm is the prediction of water sites that can form multiple hydrogen bonds that bridge the binding interface. Trial calculations were performed on water networks predicted by WATGEN at 126 protein,peptide interfaces (X-ray resolutions , 2.0 Å), using different criteria for water placement. The energies of the predicted water networks were evaluated in AMBER8 and used in the choice of parameters for WATGEN. The 126 interfaces include 1264 experimentally determined bridging water sites, and the WATGEN algorithm predicts 72 and 88% of these sites within 1.5 and 2.0 Å, respectively. The predicted number of water molecules at each interface was much higher than the number of water molecules identified experimentally. Therefore, random placement of the same number of water molecules as that predicted at each interface was performed as a control, and resulted in only 22 and 40% of water sites placed within 1.5 and 2.0 Å of experimental sites, respectively. Based on these data, we conclude that WATGEN can accurately predict the location of water molecules at a protein,peptide interface, and this may be of value for understanding the energetics and specificity of biomolecular association. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Synthesis of high specific activity 35S-labelled N-methanesulfonyl farnesylcysteine and a photoactive analogJOURNAL OF LABELLED COMPOUNDS AND RADIOPHARMACEUTICALS, Issue 1 2003Tamara A. Kale Abstract Prenylated cysteine analogs, which mimic the prenylated cysteine residue of prenylated GTP-binding proteins (G-proteins), have been used in a variety of contexts for the study of prenylated G-protein behavior. In earlier work in this area, we prepared the photoactive analog [35S]4 and showed that it labelled RhoGDI upon photolysis; those results were consistent with the idea that GDI contains an isoprenoid binding site. Here, we describe the preparation of [35S]N -methanesulfonyl labelled analogs (1a and 2a) of N -acetyl farnesylcysteine and its methyl ester together with an improved synthetic procedure for photoactive analogs 3 and 4; specific activities of ,1100 Ci/mmol were achieved. Compounds 1a and 2a in unlabelled form were used as competitors in photolysis reactions to show that the methanesulfonamido group is a reasonable acetamide substitution. Additional experiments show that the photoactive ester [35S]3 can cross-link GDI in both purified form and crude bacterial extract. However, the extent of cross-linking obtained with the ester ([35S]3) is significantly less than that observed with the free acid ([35S]4) despite the fact that the esterified form probably more closely reflects the structure of the C-terminus of a prenylated protein; using the GDI·Cdc42 co-crystal structure, the structural basis for these results is discussed. Copyright © 2002 John Wiley & Sons, Ltd. [source] Limited tendency of ,-helical residues to form disulfide bridges: a structural explanationJOURNAL OF PEPTIDE SCIENCE, Issue 12 2006Alfonso De Simone Abstract Disulfide bridges have an enormous impact on the structure of a large number of proteins and polypeptides. Understanding the structural basis that regulates their formation may be important for the design of novel peptide-based molecules with a specific fold and stability. Here we report a statistical analysis of the relationships between secondary structure and disulfide bond formation, carried out using a large database of protein structures. Our analyses confirm the observation sporadically reported in previous investigations that cysteine residues located in ,-helices display a limited tendency to form disulfide bridges. The very low occurrence of the disulfide bond in all ,-chains compared to all ,-chains indicates that this property is also evident when proteins with different topologies are investigated. Taking advantage of the large database that endorsed the analysis on relatively rare motifs, we demonstrate that cysteine residues embedded in 310 helices present a good tendency to form disulfide bonds. This result is somewhat surprising since 310 helices are commonly assimilated into ,-helices. A plausible structural explanation for the observed data has been derived combining analyses of disulfide bond sequence separation and of the length of the different secondary structure elements. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd. [source] | ||||||||||||||||||||||||||||||||||