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PubMed2006

The chaperonin TRiC controls polyglutamine aggregation and toxicity through subunit-specific interactions.

Misfolding and aggregation of proteins containing expanded polyglutamine repeats underlie Huntington's disease and other neurodegenerative disorders. Here, we show that the hetero-oligomeric chaperonin TRiC (also known as CCT) physically interacts with polyglutamine-expanded variants of huntingtin (Htt) and effectively inhibits their aggregation. Depletion of TRiC enhances polyglutamine aggregation in yeast and mammalian cells. Conversely, overexpression of a single TRiC subunit, CCT1, is sufficient to remodel Htt-aggregate morphology in vivo and in vitro, and reduces Htt-induced toxicity in neuronal cells. Because TRiC acts during de novo protein biogenesis, this chaperonin may have an early role preventing Htt access to pathogenic conformations. Based on the specificity of the Htt-CCT1 interaction, the CCT1 substrate-binding domain may provide a versatile scaffold for therapeutic inhibitors of neurodegenerative disease.

Animals↗
PubMed2000

Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe.

Arabidopsis thaliana provides a useful model system for functional, evolutionary and ecological studies in plant biology. We have analysed natural genetic variation in A. thaliana in order to infer its biogeographical and historical distribution across Eurasia. We analysed 79 amplified fragment length polymorphism (AFLP) markers in 142 accessions from the species' native range, and found highly significant genetic isolation by distance among A. thaliana accessions from Eurasia and southern Europe. These spatial patterns of genetic variation suggest that A. thaliana colonized central and northern Europe from Asia and from Mediterranean Pleistocene refugia, a trend which has been identified in other species. Statistically significant levels of multilocus linkage disequilibrium suggest intermediate levels of disequilibrium among subsets of loci, and analysis of genetic relationships among accessions reveal a star or bush-like dendrogram with low bootstrap support. Taken together, it appears that there has been sufficient historical recombination in the A. thaliana genome such that accessions do not conform to a tree-like, bifurcating pattern of evolution - there is no 'ecotype phylogeny.' Nonetheless, significant isolation by distance provides a framework upon which studies of natural variation in A. thaliana may be designed and interpreted.

Arabidopsis↗
PubMed2004

Mechanism of diacylglycerol-induced membrane targeting and activation of protein kinase Cdelta.

The regulatory domains of novel protein kinases C (PKC) contain two C1 domains (C1A and C1B), which have been identified as the interaction site for sn-1,2-diacylglycerol (DAG) and phorbol ester, and a C2 domain that may be involved in interaction with lipids and/or proteins. Although recent reports have indicated that C1A and C1B domains of conventional PKCs play different roles in their DAG-mediated membrane binding and activation, the individual roles of C1A and C1B domains in the DAG-mediated activation of novel PKCs have not been fully understood. In this study, we determined the roles of C1A and C1B domains of PKCdelta by means of in vitro lipid binding analyses and cellular protein translocation measurements. Isothermal titration calorimetry and surface plasmon resonance measurements showed that isolated C1A and C1B domains of PKCdelta have opposite affinities for DAG and phorbol ester; i.e. the C1A domain with high affinity for DAG and the C1B domain with high affinity for phorbol ester. Furthermore, in vitro activity and membrane binding analyses of PKCdelta mutants showed that the C1A domain is critical for the DAG-induced membrane binding and activation of PKCdelta. The studies also indicated that an anionic residue, Glu(177), in the C1A domain plays a key role in controlling the DAG accessibility of the conformationally restricted C1A domain in a phosphatidylserine-dependent manner. Cell studies with enhanced green fluorescent protein-tagged PKCdelta and mutants showed that because of its phosphatidylserine specificity PKCdelta preferentially translocated to the plasma membrane under the conditions in which DAG is randomly distributed among intracellular membranes of HEK293 cells. Collectively, these results provide new insight into the differential roles of C1 domains in the DAG-induced membrane activation of PKCdelta and the origin of its specific subcellular localization in response to DAG.

Animals↗
PubMed1998

The conformational change induced by FAD in covalently flavinylated 6-hydroxy-D-nicotine oxidase does not require (8alpha)FAD-(N3)histidyl bond formation.

The contribution of (8alpha)-(N3)histidyl bond formation to the conformation of covalently flavinylated proteins was investigated by trypsin treatment of wild type and mutant versions of a model enzyme, 6-hydroxy-D-nicotine oxidase (6-HDNO) of Arthrobacter nicotinovorans. In the absence of FAD, apo-6-HDNO exhibited a conformation exposing a protease accessible site. Holoenzyme formation through FAD-attachment to His71 induced a conformational change in the protein that shielded the trypsin recognition site. This conformational change, however, did not require FAD-histidyl bond formation since trypsin resistance was also exhibited by a 6-HDNO.Cys71 mutant protein which was unable to bind FAD covalently. Replacement of Arg67, an amino acid residue supposed to be essential in flavinylation, by Ala rendered the protein protease sensitive as did replacement of Pro73 by Ala. These amino acids apparently play an essential role in stabilizing the native protein conformation. The inability to reach the native conformation also prevented FAD attachment, indicating that a specific conformation of the protein is a prerequisite for FAD-histidyl bond formation. Deletion of Phe448 and Arg449 from the 458 amino acid residues-containing enzyme resulted in complete protease sensitivity, demonstrating that flavinylation takes place posttranslationally.

Flavin-Adenine Dinucleotide↗
PubMed2006

Phage display selection of efficient glutamine-donor substrate peptides for transglutaminase 2.

Understanding substrate specificity and identification of natural targets of transglutaminase 2 (TG2), the ubiquitous multifunctional cross-linking enzyme, which forms isopeptide bonds between protein-linked glutamine and lysine residues, is crucial in the elucidation of its physiological role. As a novel means of specificity analysis, we adapted the phage display technique to select glutamine-donor substrates from a random heptapeptide library via binding to recombinant TG2 and elution with a synthetic amine-donor substrate. Twenty-six Gln-containing sequences from the second and third biopanning rounds were susceptible for TG2-mediated incorporation of 5-(biotinamido)penthylamine, and the peptides GQQQTPY, GLQQASV, and WQTPMNS were modified most efficiently. A consensus around glutamines was established as pQX(P,T,S)l, which is consistent with identified substrates listed in the TRANSDAB database. Database searches showed that several proteins contain peptides similar to the phage-selected sequences, and the N-terminal glutamine-rich domain of SWI1/SNF1-related chromatin remodeling proteins was chosen for detailed analysis. MALDI/TOF and tandem mass spectrometry-based studies of a representative part of the domain, SGYGQQGQTPYYNQQSPHPQQQQPPYS (SnQ1), revealed that Q(6), Q(8), and Q(22) are modified by TG2. Kinetic parameters of SnQ1 transamidation (K(M)(app) = 250 microM, k(cat) = 18.3 sec(-1), and k(cat)/K(M)(app) = 73,200) classify it as an efficient TG2 substrate. Circular dichroism spectra indicated that SnQ1 has a random coil conformation, supporting its accessibility in the full-length parental protein. Added together, here we report a novel use of the phage display technology with great potential in transglutaminase research.

Amino Acid Motifs↗
PubMed2001

Characterization of the structure and dynamics of amyloidogenic variants of human lysozyme by NMR spectroscopy.

The structures and dynamics of the native states of two mutational variants of human lysozyme, I56T and D67H, both associated with non-neuropathic systemic amyloidosis, have been investigated by NMR spectroscopy. The (1)H and (15)N main-chain amide chemical shifts of the I56T variant are very similar to those of the wild-type protein, but those of the D67H variant are greatly altered for 28 residues in the beta-domain. This finding is consistent with the X-ray crystallographic analysis, which shows that the structure of this variant is significantly altered from that of the wild-type protein in this region. The (1)H-(15)N heteronuclear NOE values show that, with the exception of V121, every residue in the wild-type and I56T proteins is located in tightly packed structures characteristic of the native states of most proteins. In contrast, D67H has a region of substantially increased mobility as shown by a dramatic decrease in heteronuclear NOE values of residues near the site of mutation. Despite this unusual flexibility, the D67H variant has no greater propensity to form amyloid fibrils in vivo or in vitro than has I56T. This finding indicates that it is the increased ability of the variants to access partially folded conformations, rather than intrinsic changes in their native state properties, that is the origin of their amyloidogenicity.

Amyloid↗
PubMed1985

A novel form of factor VII in plasma from men at risk for cardiovascular disease.

In the Northwick Park Heart Study high activity of the coagulation factor VII was associated with cardiovascular deaths. We confirm here that men at high risk for such disease have increased levels of factor VII activity and demonstrate for the first time that this is due to a phospholipid-factor VII complex in their plasma. This complex increases the specific activity of its factor VII significantly. It is not inhibited by a neutralizing antiserum to thromboplastin and thus does not represent a factor VII-thromboplastin complex. Gel filtration data suggest an apparent Mr of 66-72 000 for the complex. Factor VII in this phospholipid complex is more sensitive than native factor VII to the serine protease inhibitor diisopropyl-fluorophosphate, consistent with a more accessible active site conformation (and a higher specific activity) for factor VII in the complex. The level of phospholipid-factor VII complex showed a significant positive correlation with plasma triglycerides and correlation of borderline significance with cholesterol.

Adult↗
PubMed1995

First-principles calculation of the folding free energy of a three-helix bundle protein.

The folding and unfolding of a three-helix bundle protein were explored with molecular-dynamics simulations, cluster analysis, and weighted-histogram techniques. The folding-unfolding process occurs by means of a "folding funnel," in which a uniform and broad distribution of conformational states is accessible outside of the native manifold. This distribution narrows near a transition region and becomes compact within the native manifold. Key thermodynamic steps in folding include initial interactions around the amino-terminal helix-turn-helix motif, interactions between helices I and II, and, finally, the docking of helix III onto the helix I-II subdomain. A metastable minimum in the calculated free-energy surface is observed at approximately 1.5 times the native volume. Folding-unfolding thermodynamics are dominated by the opposing influences of protein-solvent energy, which favors unfolding, and the overall entropy, which favors folding by means of the hydrophobic effect.

Amino Acid Sequence↗
PubMed1989

Blockade of rabbit atrial sodium channels by lidocaine. Characterization of continuous and frequency-dependent blocking.

Lidocaine block of the cardiac sodium channel is believed to be primarily a function of channel state. For subthreshold potentials, block is limited to the inactivated state, whereas above threshold, block results from the combination of open- and inactivated-state block. Since, in the absence of drug, inactivation develops with time constants that vary from several hundred milliseconds to a few milliseconds as potential is varied from subthreshold to strongly depolarized levels, we would predict a similar voltage dependence of at least a fraction of block. Prior theoretical analyses from our laboratory suggest that there should be a direct parallel between blockade determined with a single pulse and trains of pulses. We tested these predictions by measuring the blockade of sodium current in cultured atrial myocytes during exposure to 80 microM lidocaine. We selected two test potentials for most of our studies, -80 mV, which was clearly in the subthreshold range of potentials, and -20 mV, which was close to the peak of the current-voltage curve. With single pulses of increasing duration, block developed with a single exponential time course and with time constants that decreased from 694 +/- 117 msec at -80 mV to 373 +/- 54 msec at -20 mV. In the absence of drug, inactivation developed with a time constant 176 +/- 17 at -80 mV and 2.9 +/- .5 msec at -20 mV. Despite the much slower onset of inactivation at -80 mV, no second-order delay in block development was observed. This suggests that at -80 mV block is occurring to a channel conformation that is accessed without delay rather than the classical inactivated state. We compared the kinetics of block during a single continuous pulse with trains of pulses at -20 mV. The rate of block onset was faster during the pulse trains, suggesting an element of "activated state" block. We computed shifts in apparent inactivation from observed steady-state blockade. The computed shifts agree well with those observed, indicating that shifts in apparent inactivation result largely from voltage-sensitive equilibrium blockade. The classical states described in the Hodgkin-Huxley formalism may be too restrictive to fully describe the voltage- and time-dependent block of cardiac sodium channels.

Animals↗
PubMedDate not supplied

The Glu-modification of alpha-tubulin in the feeding apparatus of the primitive flagellate Entosiphon sulcatum is only apparent after detergent treatment.

Using specific monoclonal antibodies, we investigated the distribution of post-translational modified Tyr- and Glu-tubulins during interphase of the primitive flagellate Entosiphon sulcatum. Immunofluorescence studies of simultaneously permeabilized and fixed cells revealed that microtubular structures comprising Ca(2+)-labile subpellicular and flagellar MTs and Ca(2+)-stable MTs in the siphon complex (feeding organelle) reacted surprisingly unorthodox with antibodies against Tyr- and Glu-tubulin: Unexpectedly, the siphon complex consisting of Ca(2+)-stable MTs appeared exclusively Tyr-positive, whereas the Ca(2+)-labile subpellicular and flagellar MTs reacted with the Glu- as well as with the Tyr-antibody. That the siphon MTs were indeed Ca(2+)-stable and all other MTs had become solubilized, was verified by EM-observation. This surprising result contrasting considerably with the permanent nature of the siphon complex, was reconsidered after preceding lysis and extraction procedures. Depending on the type of detergent used and on extraction times applied, the MTs of the siphon complex now always showed also Glu-positivity, indicating the presence of detyrosinated alpha-tubulin as a biochemical marker of stabilized MTs. Since saponin, irrespective of subsequent extraction times, always produced a Glu-positive reaction and ultrastructural analysis never gave compelling evidence for a drastic MAP-removal, we conclude that the Glu-epitope became freely accessible due to conformational changes in the tubulin polymeres.

Animals↗
PubMedDate not supplied

Phenanthrene sorption to structurally modified humic acids.

Several studies emphasize the importance of soil organic matter characteristics in hydrophobic contaminant sorption and outline the strong dependence of sorption on organic matter aromaticity. In this study, the role of organic matter aromaticity in phenanthrene sorption was investigated using humic acids (HAs) from compost, peat, and soil that were structurally modified by bleaching, hydrolysis, oximation, and subcritical water extraction. The HAs were characterized with cross polarization magic angle spinning carbon-13 nuclear magnetic resonance (CPMAS 13C NMR) spectroscopy and used in batch equilibrations with phenanthrene. Bleaching substantially reduced the aromaticity of the samples whereas the other treatments increased the relative aromaticity. Phenanthrene sorption increased, even though there was a substantial reduction in sorbent aromaticity with some samples. The HAs that exhibited comparable CPMAS 13C NMR spectra and aromaticity did not behave similarly with respect to phenanthrene sorption. When the sorption data (K(oc) values) were correlated to sample aromaticity, the correlation coefficients (r2) did not exceed 0.39. Comparisons with the atomic H to C ratio provided slightly better r2 values (up to 0.54). This study demonstrates that macroscopic sorbent characteristics could not explain the observed phenanthrene sorption coefficients, aliphatic structural components of HAs can contribute appreciably to phenanthrene sorption, and organic matter physical conformation may regulate access to organic matter structures. Therefore, the use of only macroscopic sorbent properties, such as aromaticity, to predict and rationalize sorption values cannot solely be used to explain the behavior of organic contaminants in soil environments.

Adsorption↗
PubMed1993

Antigenicity and immunogenicity of antigenized antibodies. Studies on B and T cells.

This laboratory has been testing the possibility of using the complementarity-determining region (CDR) loops of the antibody molecule to express oligopeptide epitopes in an immunologically-accessible and conformationally-suitable way. The new process consists in grafting peptides epitopes derived from antigens other than immunoglobulins into antibody CDR loops. This process, "antibody antigenization," utilizes the immunoglobulin fold as a scaffold to immobilize and present oligopeptide epitopes to the immune system as the integral part of the immunoglobulin molecule. Here we describe some of the initial results with antigenized antibodies (AgAbs).

Amino Acid Sequence↗
PubMedDate not supplied

Fluorescence quenching study of melittin-membrane interactions.

The bee venom peptide melittin is a popular object for studying lipid-protein interactions. In this paper we show that binding of melittin to the bilayer is a complex process involving several steps. We were able to resolve those steps by utilizing a new approach in the quantitative analysis of depth-dependent fluorescence quenching in membranes. The "distribution analysis" technique (DA) employed here provides not only the most probable depth of the fluorophore but also allows the estimation of its conformational heterogeneity and accessibility to the lipid phase. A model for melittin interaction with the membranes is suggested.

Iodides↗
PubMed2002

Constitutive DNase I hypersensitivity of p53-regulated promoters.

The ability of p53 to alter, at the transcriptional level, the gene expression of downstream targets is critical for its role as a tumor suppressor. Most models of p53 activation postulate the stepwise recruitment by p53 of coactivators, histone acetyltransferases, and/or chromatin remodeling factors to a promoter region to facilitate the subsequent access of the general transcriptional machinery required for transcriptional induction. We demonstrate here, however, that the promoter regions for the p53 target genes, p21, 14-3-3sigma, and KARP-1, exist in a constitutively open conformation that is readily accessible to DNase I. This conformation was not altered by DNA damage or by whether p53 was present or absent in the cell. In contrast, p53 response elements, which resided outside the immediate promoter regions, existed within DNase I-resistant chromatin domains. Thus, p53 activation of downstream target genes occurs without p53 inducing chromatin alterations detectable by DNase I accessibility at either the promoter or the response element. As such, these data support models of p53 activation that do not require extensive chromatin alterations to support cognate gene expression.

14-3-3 Proteins↗
PubMed1993

An iodoacetamide spin-label selectively labels a cysteine side chain in an occluded site on the sarcoplasmic reticulum Ca(2+)-ATPase.

Sarcoplasmic reticulum vesicles were labeled with [14C]iodoacetamide spin-label (ISL) under conditions where time courses of the reaction predicted that one amino acid residue would be preferentially labeled. Solubilized tryptic peptides were separated by high-performance liquid chromatography following extensive digestion, and amino acid sequences were determined for major and minor radio-labeled peptides. Only one radio-labeled residue, Cys-674 on the Ca(2+)-ATPase, could be identified. Extensive incubation with excess label increased nonspecific labeling, but did not produce detectable amounts of any other reactive side chain residue. Time courses of the iodoacetamide spin-label reaction were compared to those of 6-(iodoacetamido)fluorescein (IAF), and the ISL reaction was found to be more selective, in accordance with previous studies showing that IAF labeled both Cys-674 and Cys-670 [Bishop, J. E., Squire, T. C., Bigelow, D. J., & Inesi, G. (1988) Biochemistry 27, 5233-5240]. Titrations with spin-broadening reagents NiCl2 and Ni-EDTA showed Cys-674 to be in a region with very low solvent accessibility. These titrations also showed the ATPase to be distributed between two alternating conformations based on the accessibility of the label to NiCl2.

Amino Acid Sequence↗
PubMed2004

Latency and substrate binding globally reduce solvent accessibility of plasminogen activator inhibitor type 1 (PAI-1). An adaptation of PAI-1 conformer crystal structures by hydrogen-deuterium exchange.

Plasminogen activator inhibitor type 1 (PAI-1) plays key regulatory roles in fibrinolysis, cell migration, and tissue remodeling. A regulatory protein without known catalytic activity, PAI-1 modulates plasminogen activators through protein-protein interactions. Although global conformational alterations that occur in PAI-1 determine its regulatory activity, comprehensive assessments of concurrent dynamic, structural, and functional alterations of this critical regulatory protein have not yet been clearly defined. X-ray crystallographic studies have described four distinct PAI-1 conformational states: active, latent, reactive center loop peptide-annealed (RCL-PA), and cleaved mutant. In this study, backbone amide hydrogen-deuterium exchange detected by mass spectrometry was used to characterize dynamic and structural alterations of human PAI-1 (hPAI-1) in relation to its function. hPAI-1 conformers were defined by surface mapping the solvent-accessible sites for strategic secondary structural components of the protein. We observed a global protection from solvent for a majority of peptides in the latent conformer relative to the active conformer. Significant differences were observed in the RCL, helix A, helix D, and sheet 1C, and these regions were markedly more dynamic or solvent-exposed in the active conformation. The RCL-PA form adopts an intermediate conformational state between the active and the latent conformers. Our results demonstrate that the most dynamic regions of PAI-1 (the RCL, helices D and A, and sheet 5A) are flexible in the transition toward latency. They also show that the dynamic surface structures of the active, latent, and peptide-annealed conformers of PAI-1 are underestimated by theoretical solvent accessibility calculations derived from crystallographic data.

Amino Acid Sequence↗
PubMed2001

Microsecond exchange of internal water molecules in bacteriorhodopsin.

The proton-conducting pathway of bacteriorhodopsin (BR) contains at least nine internal water molecules that are thought to be key players in the proton translocation mechanism. Here, we report the results of a multinuclear (1H, 2H, 17O) magnetic relaxation dispersion (MRD) study with the primary goal of determining the rate of exchange of these internal water molecules with bulk water. This rate is of interest in current attempts to elucidate the molecular details of the proton translocation mechanism. The relevance of water exchange kinetics is underscored by recent crystallographic findings of substantial variations in the number and locations of internal water molecules during the photocycle. Moreover, internal water exchange is believed to be governed by conformational fluctuations in the protein and can therefore provide information about the thermal accessibility of functionally important conformational substates. The present 2H and 17O MRD data show that at least seven water molecules, or more if they are orientationally disordered, in BR have residence times (inverse exchange rate constant) in the range 0.1-10 micros at 277 K. At least five of these water molecules have residence times in the more restrictive range 0.1-0.5 micros. These results show that most or all of the deeply buried water molecules in BR exchange on a time-scale that is short compared to the rate-limiting step in the photocycle. The MRD measurements were performed on BR solubilized in micelles of octyl glucoside. From the MRD data, the rotational correlation time of detergent-solubilized BR was determined to 35 ns at 300 K, consistent with a monomeric protein in complex with about 150 detergent molecules. The solubilized protein was found to be stable in the dark for at least eight months at 277 K.

Bacteriorhodopsins↗
PubMed1992

[Dependence of anti-acetylcholinesterase effectiveness of phosphoorganic inhibitors on the accessibility of the phosphorus atom].

All equilibrium conformations of 12 anti-acetylcholinesterase organophosphorus inhibitors were calculated by the molecular mechanics method. The accessibility of the phosphorus atom of the inhibitors for interactions with the nucleophilic group at the enzyme active centre was estimated. The conformers with the phosphorus atom sterically accessible from the side opposite to the breaking ester bond were classified as productive. A correlation was revealed between the activity of the inhibitors and the population of their productive conformation.

Acetylcholinesterase↗