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PubMed2005

Geometric diversity through permutation of backbone configuration in cyclic peptide libraries.

Cyclic peptides offer the possibility of varying both scaffold geometry and R-group functionality. For example, parameters such as ring size and the placement of D-amino acid and proline residues can have a dramatic effect on the conformations of cyclic peptides, allowing access to structurally diverse species based on simple modifications in their linear sequences. We synthesized a cyclic peptide library in which ring size, alpha-carbon stereochemistry, and proline placement were varied. Analysis of the products showed that heptapeptides in general cyclized more readily than hexapeptides, and within these groups the scaffolds with a greater number of pralines cyclized with markedly lower yields than scaffolds with fewer pralines. Split-pool libraries based on a sample set of these scaffolds showed that, in general, scaffold geometry outweighed side chains variation in determining cyclization efficiency. These concepts were applied to the synthesis of cyclodimeric variants of an inhibitor of actin assembly in Xenopus egg extracts, yielding side chain variants with improved potency over the original scaffold.

Actins↗
PubMed2000

Regulation of blood coagulation.

The protein C anticoagulant pathway converts the coagulation signal generated by thrombin into an anticoagulant response through the activation of protein C by the thrombin-thrombomodulin (TM) complex. The activated protein C (APC) thus formed interacts with protein S to inactivate two critical coagulation cofactors, factors Va and VIIIa, thereby dampening further thrombin generation. The proposed mechanisms by which TM switches the specificity of thrombin include conformational changes in thrombin, blocking access of normal substrates to thrombin and providing a binding site for protein C. The function of protein S appears to be to alter the cleavage site preferences of APC in factor Va, probably by changing the distance of the active site of APC relative to the membrane surface. The clinical relevance of this pathway is now established through the identification of deficient individuals with severe thrombotic complications and through the analysis of families with partial deficiencies in these components and an increased thrombotic tendency. One possible reason that even partial deficiencies are a thrombotic risk is that the function of the pathway can be down-regulated by inflammatory mediators. For instance, clinical studies have shown that the extent to which protein C levels decrease in patients with septic shock is predictive of a negative outcome. Initial clinical studies suggest that supplementation with protein C may be useful in the treatment of acute inflammatory diseases such as sepsis.

Animals↗
PubMed2000

Optimized representations and maximal information in proteins.

In an effort to quantify loss of information in the processing of protein bioinformatic data, we examine how representations of amino acid sequence and backbone conformation affect the quantity of accessible structural information from local sequence. We propose a method to extract the maximum amount of peptide backbone structural information available in local sequence fragments, given a finite structural data set. Using methods of information theory, we develop an unbiased measure of local structural information that gauges changes in structural distributions when different representations of secondary structure and local sequence are used. We find that the manner in which backbone structure is represented affects the amount and quality of structural information that may be extracted from local sequence. Representations based on virtual bonds capture more structural information from local sequence than a three-state assignment scheme (helix/strand/loop). Furthermore, we find that amino acids show significant kinship with respect to the backbone structural information they carry, so that a collapse of the amino acid alphabet can be accomplished without severely affecting the amount of extractable information. This strategy is critical in optimizing the utility of a limited database of experimentally solved protein structures. Finally, we discuss the similarities within and differences between groups of amino acids in their roles in the local folding code and recognize specific amino acids critical in the formation of local structure.

Amino Acids↗
PubMed1995

Rigor cross-bridges bind to two actin monomers in thin filaments of rabbit psoas muscle.

The mode of binding of myosin subfragment-1 (S1) to actin is known to depend on their molar ratio: when actin is in excess, S1 binds to two actin monomers within the actin filament, and when S1 is in excess or is equimolar with actin, each S1 binds to one actin monomer. Since in vertebrate striated muscle actin is in molar excess over myosin, we expect that in fibers each myosin head binds to two actin monomers. To test this idea, we compared the conformation of the heads in native muscle with the conformation of S1 in fibers that were loaded with either high (S1 equimolar with actin) or low (excess of actin over S1) concentration of extrinsic S1. Conformation was assessed by the accessibility of heads to trypsin (measured by the rate of trypsinolysis) and by their orientation with respect to the muscle axis (measured by a combination of polarization of fluorescence and linear dichroism). In muscle fibers loaded with a high concentration of S1, the region of the heavy chain of the myosin head at the junction of 20 and 50 kDa proteolytic fragments was readily digested by trypsin and its orientation was approximately perpendicular to an axis of a thin filament. In contrast, when muscle fibers were loaded with a low concentration of S1, the 20/50 kDa junction of S1 was protected from trypsinolysis and its orientation was more parallel with a filament axis. Native muscle in rigor behaved like muscle irrigated with a low concentration of S1, i.e. the 20/50 kDa junction of the myosin head was protected from trypsinolysis and the orientation of the heads was parallel to the filament axis. We conclude that in rigor rabbit psoas muscle each myosin head binds to two actin monomers in a thin filament, and that this binding is different from the binding of S1 to actin in equimolar solutions.

Actins↗
PubMed2004

Antibody probe study of Ca2+ channel regulation by interdomain interaction within the ryanodine receptor.

N-terminal and central domains of ryanodine receptor 1 (RyR1), where many reported malignant hyperthermia (MH) mutations are localized, represent putative channel regulatory domains. Recent domain peptide (DP) probe studies led us to the hypothesis that these domains interact to stabilize the closed state of channel (zipping), while weakening of domain-domain interactions (unzipping) by mutation de-stabilizes the channel, making it leaky to Ca2+ or sensitive to the agonists of RyR1. As shown previously, DP1 (N-terminal domain peptide) and DP4 (central domain peptide) produced MH-like channel activation/sensitization effects, presumably by peptide binding to sites critical to stabilizing domain-domain interactions and resultant loss of conformational constraints. Here we report that polyclonal anti-DP1 and anti-DP4 antibodies also produce MH-like channel activation and sensitization effects as evidenced by about 4-fold enhancement of high affinity [3H]ryanodine binding to RyR1 and by a significant left-shift of the concentration-dependence of activation of sarcoplasmic reticulum Ca2+ release by polylysine. Fluorescence quenching experiments demonstrate that the accessibility of a DP4-directed, conformationally sensitive fluorescence probe linked to the RyR1 N-terminal domain is increased in the presence of domain-specific antibodies, consistent with the view that these antibodies produce unzipping of interacting domains that are of hindered accessibility to the surrounding aqueous environment. Our results suggest that domain-specific antibody binding induces a conformational change resulting in channel activation, and are consistent with the hypothesis that interacting N-terminal and central domains are intimately involved in the regulation of RyR1 channel function.

Amino Acid Sequence↗
PubMed1997

Estimation of partitioning parameters of nonionic surfactants using calculated descriptors of molecular size, polarity, and hydrogen bonding.

A study was carried out to verify the capacity of the Abraham's solute descriptors (R2, an excess molar refraction; pi 2H, the dipolarity/polarizability; sigma alpha 2H and sigma beta 2H, the summation hydrogen-bond acidity and basicity; and Vx, the characteristic volume of McGowan) to predict the alkane-water partition coefficient (log Palk) of nonionic surfactants. Log P values were taken from the literature and examined for linear solvation energy-related (LSER) equations with calculated physicochemical descriptors. A stepwise multiple linear regression (MLR) analysis allowed us to derive LSER models which, unlike those previously published for a standard set of solutes, revealed that R2 and sigma beta 2H are the major contributors to log Palk. A minor contribution of Vx was also detected, whereas surprisingly sigma alpha 2H required a positive coefficient. The less relevant size effect seems to indicate that for nonionic surfactants the energy needed for creating a water cavity is largely compensated for by the favorable interactions of ethoxy groups in the polar chain with water, whereas the log P-increasing effect of hydrogen-bond donor groups could be explained by considering the occurrence of folded, more lipophilic conformers, favored by the formation of intramolecular hydrogen bonds in the apolar phase. This hypothesis was substantiated by the calculation of the molecular lipophilicity potential on the water-accessible surface of extended and folded conformers of two representative surfactants, selected by high-temperature molecular dynamics. Besides MLR, a principal component analysis on a larger set of descriptors, comprising three solubility parameters (delta D, based on dispersion forces; delta H, including the contribution of hydrogen bonding; delta O, overall solubility parameter) afforded the so-called principal properties, which were able to characterize nonionic surfactants and to satisfactorily assess their lipophilicity-related properties.

Esters↗
PubMed1995

A comparison of X-ray and NMR structures for human endothelin-1.

Direct comparisons between the recently solved X-ray and NMR structures of human endothelin-1 with respect to secondary structure, RMS deviations, surface accessibilities, and side-chain conformers indicate important differences in conformation, especially in the C-terminus, but also in the central loop region, that are important for defining the specificity of binding. These differences are larger than seen for other X-ray and NMR structures that have been compared. Comparisons between the X-ray structure and the NMR NOE constraints highlight the regions of flexibility and environment-induced diversity in the endothelin structures.

Computer Graphics↗
PubMed2000

Nucleosome dynamics. VI. Histone tail regulation of tetrasome chiral transition. A relaxation study of tetrasomes on DNA minicircles.

We have recently described the relaxation of mononucleosomes on an homologous series of 351-366 bp DNA minicircles, as a tool to study nucleosome structure and dynamics in vitro. Nucleosomes were found to have a tail-regulated access to three distinct DNA conformations, depending on the crossing between the entering and exiting DNAs, and its polarity. This approach was now used to explore tetrasome chiral transition, and the influence of the histone tails. The data confirmed the existence of two states, with linking number differences DeltaLk(t)=-0.74(+/-0.01) and +0.51(+/-0.06). As expected, the particle free energy is higher in the right-handed state (DeltaG(t)=1.9(+/-0.I) kT), but it decreased (to 1.3(+/-0.1) kT) upon histone acetylation and the addition of phosphate, a potent tail destabilizer. Removal of the tails with trypsin further decreased DeltaG(t) (to 0.6 kT), and also induced a loss of supercoiling in both states, to DeltaLk(t)=-0.64(+/-0.03) and +0. 35(+/-0.05). The loop end-conditions, and hence the parameters of the DNA superhelix, were then calculated for both states using the explicit solutions to the equations of the mechanical equilibrium in the theory of elastic rod model for DNA. Whereas the pitch of the DNA superhelix may be approximately equal and opposite in the two conformations, its radius (r) was 20% larger in the right-handed conformation, confirming previous observations by electron microscopy of a tetrasome lateral opening in that conformation. The above supercoiling losses were found to reflect a further 3 % increase in r (to 23 %) upon removal of the tails in the right-handed conformation, and a 14 % increase in the left-handed conformation. The use of composite tetramers with one histone tail intact and the other removed showed these effects to be essentially due to the H3 tails. Altogether, these results show that the H3 tails oppose the tetrasome opening which is expected to be required to relieve the clash between the entering and exiting DNAs in the course of the transition, but which also appears to be intrinsic to the protein reorientation mechanism. We propose that the block against opening results from the H3 tails intercalating into the small groove of the double helix at +/-10 bp from the dyad, and acting as wedges against local DNA straightening. The tails (especially H3) may therefore regulate tetrasome chiral transition in vivo.

Acetylation↗
PubMed1986

Non-enzymatic glycosylation in human diabetic lens crystallins.

Lens crystallins undergo non-enzymatic glycosylation with aging and diabetes mellitus. It is not known, however, whether all crystallins are subject to the same extent of glycosylation. Human diabetic lenses (approximately 80 years of age) were dissected into cortex and nucleus, then fractionated into various crystallins with gel chromatography (Sephacryl S-200, Sephadex G-75 or Bio Gel A-15m). The glycosylated crystallins were then separated from the nonglycosylated crystallins by affinity chromatography on Glyco Gel B boronic acid. The percentage of glycosylated crystallin was about 20-30%, and did not differ much among most crystallins, although gamma-crystallin has significantly less (p less than 0.01) glycosylated protein. The extent of glycosylation in the glycosylated crystallins, however, was found to be greater in the high molecular weight crystallins. The extent of glycosylation in alpha-crystallins is approximately two to four times that observed in beta- or gamma-crystallin. The extent of glycosylation appears to depend not only on the lysine content, which does not vary much among the crystallins, but also on the accessibility of the surface areas where lysine residues are located. This accessibility depends on the protein conformation and appears to correlate with protein unfolding.

Aged↗
PubMed1996

Proliferation of Nonconforming Land Uses in Agricultural Envelope of Urban Hong Kong

Until the late 1960s rural Hong Kong had an attractive rustic landscape and a small but active farming population. The recent widespread agricultural decline provided opportunities for urban-oriented activities to invade, mainly as open storage and workshops unsuitable in city areas. Rapid container-port expansion and cross-border China trade generate demands for cheap and accessible land for non-conforming uses (NCU). Rural development control and land-use planning are inherently weak, and formal provision for such uses is lacking. An unfavorable landmark court judgement allows landowners to degrade the countryside. The activities have caused acute environmental problems, telescoped into a small territory, including visual blight, pollution, drainage blockage, loss of wetland habitats, and increased flooding hazard. The distinction between urban and rural has been blurred in the destruction of the valuable countryside heritage. An interim legislative amendment fails to stop unauthorized conversion of farmland. In the long term, an integrated and comprehensive rural planning strategy to conserve inherent elements, as well as accommodating selected urban spillover in properly located and serviced sites, is needed.

Journal Article↗
PubMed1987

Towards the mapping of the progesterone and androgen receptors.

At a time when the secondary structures of receptor proteins are being predicted from sequence data by modeling techniques, knowledge of the ligand characteristics compatible with high-affinity binding to the receptor and with efficient receptor function is indispensable. We have already compared progesterone receptor (PR) ligands in attempts to map the PR hormone-binding site. In the present study, the relative binding affinities (RBAs) of 33 steroid ligands for the cytosol androgen receptor (AR) of rat prostate, measured in a routine screening system, have been compared. Special emphasis has been given to the effects of modifications (unsaturation, methylation, substitution by halogens) that might influence AR recognition by the ring A carbonyl and also to the consequences of these changes on binding specificity. Nonsteroid antiandrogens are reputed to compete with labelled testosterone (or methyltrienolone) binding to AR. Their RBAs, however, are very low compared to those of steroid antiandrogens. It is feasible that such molecules might occupy and interact with the AR site that binds hormone. The solvent accessible surface of one Anandron conformer is highly similar to that of testosterone and this conformer can be adequately superimposed upon the structure of testosterone and of antiandrogenic Des-A steroid derivatives. The nitro group might assume the role of the ring A carbonyl of steroids; reduction of this group to an amine or a hydroxylamine completely suppresses binding. These observations, however, do not eliminate the hypothesis of interference with AR function, and consequent antiandrogenic activity, by interaction with other (adjacent) sites on AR.

Androgen Antagonists↗
PubMed1987

Protease activation mutants of Sendai virus: sequence analysis of the mRNA of the fusion protein (F) gene and direct identification of the cleavage-activation site.

Trypsin cleaves the fusion protein (F) of wild-type Sendai virus into two disulfide-linked polypeptides, F1 and F2, and thereby activates the membrane fusion activity of the virus. A. Scheid and P.W. Choppin [1976). Virology, 265-277) selected mutant viruses of which the F protein could be activated by different proteases, either elastase, chymotrypsin, or plasmin. Herein, we have further characterized five of these mutants. Sequencing of each mutant mRNA encoding the 60-70 amino acids surrounding the cleavage site revealed one or two amino acid changes near or at the cleavage sites. Virions cleaved in vitro by the appropriate proteases were assayed of their fusion activity by hemolysis, and the cleavage sites were determined by amino acid sequencing. In three cases, the change of protease specificity can be accounted for by changed amino acids right at the cleavage site, whereas several other mutations that potentiate cleavage at new sites by new proteases are somewhat removed from the actual cleavage site. We surmise that such mutations might alter local polypeptide conformation, thereby allowing the proteases access to existing sites. Cleavage at new sites produced fusion proteins with novel F1 NH-termini. We found that a mutant with a charged residue at the third position of this normally hydrophobic NH-terminal sequence retains activity in the hemolysis assay, whereas a mutant with a charged residue at the first position does not.

Amino Acid Sequence↗
PubMed1983

Reversible dissociation of cortisol-transcortin complex by sodium para-chloromercuribenzoate.

Mercurials are considered as sulphydryl group specific reagents and one of them, sodium para-chloromercuribenzoate (PCMB), is currently used for SH titration. It has been shown that cellular steroid receptors are reversibly inactivated by mercurials even when the binding site is occupied by the steroid (Coty, W.A. (1980) J. Biol. Chem. 255, 8035-8037). This is a striking difference with alkylating SH reagents such as iodoacetic acid or N-ethylmaleimide, since these reagents inactivate only steroid-free receptors. In order to explain this discrepancy, we tested, in the present study, the specificity of PCMB on a blood plasma steroid binding protein: human transcortin. This protein presents the advantage, over cellular receptors, of being well characterized and to be available in a pure state. The transcortin-cortisol complex was also reversibly inactivated by PCMB when the reaction was carried out at a high excess of reagent over protein; such conditions are those previously used with steroid receptors. The reversibility was obtained not only with a reducing agent (dithiothreitol) but also with EDTA, which suggests a poor stability of the protein mercurial bond and therefore a nonspecific action. The decrease of activity was the result of a loss of binding sites and Scatchard plot analysis did not reveal any detectable decrease of the affinity constant for cortisol. Transcortin possesses two SH groups per molecule, one of these being buried in native conformation. After blockage of the accessible SH group by aminoethylation, transcortin kept the same activity, but when this aminoethylated transcortin was incubated with PCMB a loss of activity was obtained, although the residual buried SH group was again titrable with Ellman's reagent. Therefore, we can conclude that the action of PCMB on proteins must be interpreted with precaution, since it can induce an inactivation that is SH-independent.

Chloromercuribenzoates↗
PubMed1986

Binding to tubulin of an allocolchicine spin probe: interaction with the essential SH groups and other active sites.

EPR titration of tubulin with an allocolchicine spin probe showed more than one binding site: one high-affinity binding site (Kd = 8 microM), consistent with the Ki found for competition with colchicine, and one or more low-affinity site(s) (Kd higher than 50 microM). No disturbance of the EPR signal of the tubulin-bound allocolchicine spin probe could be observed at room temperature in the presence of other paramagnetic probes: Mn(II) for the binding site of Mg(II), Co(II) for the Zn(II) binding site and Cr(III)GTP for the binding site of the exchangeable GTP. Labelling of tubulin with both the allocolchicine and a SH-group spin probe also showed lack of interaction. The colchicine-binding site is thus sterically isolated from the binding sites for GTP, Mg(II), Zn(II) and the two essential SH-groups. In the tubulin-colchicin complex, all SH-groups could still be labelled with an excess of the SH-reagent, N-ethylmaleimide. Furthermore, colchicine binding was only minimally influenced by the blocking of the two essential SH-groups. However, the rate constant of the reaction of two equivalents of the SH-reagent, a maleimide spin probe, with the tubulin-colchicine complex was only 50% of the rate constant found with uncomplexed tubulin. As direct steric interaction of the essential SH-groups with the colchicine-binding site can be excluded, we can now definitively decide that binding of colchicine to tubulin induces a conformational change, which affects the accessibility of the most reactive SH-groups.

Animals↗
PubMed2006

DNA damaging capability of hematoporphyrin towards DNAs of various accessibilities.

In this work we wanted to verify that photoactivation of DNA-non-binding porphyrin derivative hematoporphyrin IX (Hp) is able to induce damages in DNAs of various accessibilities such as B-conformation and superhelical isolated DNA, nucleoprotein complex and intracellular DNAs. It was found that photodynamic reaction of Hp results significant changes in thermal stability of isolated T7 DNA and induces single strand breaks in supercoiled Bluescript plasmid isolated from Escherichia coli cells. As optical melting measurements revealed, the irradiation of photosensitized T7 nucleoprotein complex leads to a destabilization of the protein capsid. The photodynamic reaction affected both the protein structure and DNA-protein interaction, however, the parameters corresponding to the DNA denaturation are not influenced. The accumulation of Hp in HeLa cells was followed by laser scanning confocal microscopy. The picture received is typical for lipophilic dyes. When Hp loaded cells were irradiated, a reduction of viability could be observed in a concentration and a light dose dependent manner; 12microM porphyrin induced almost complete cell killing after 30min irradiation. After similar treatment, alkaline agarose gel electrophoresis of isolated nuclear DNA did not show the presence of single strand breaks. The alkaline comet assay also failed to demonstrate any DNA damage in HeLa cells. We also considered the possibility of the generation of damages in intracellular SV40 DNA. According to the electropherograms there was no difference between the patterns of DNAs from treated and control samples.

DNA↗
PubMed2000

Secondary structure components and properties of the melibiose permease from Escherichia coli: a fourier transform infrared spectroscopy analysis.

The structure of the melibiose permease from Escherichia coli has been investigated by Fourier transform infrared spectroscopy, using the purified transporter either in the solubilized state or reconstituted in E. coli lipids. In both instances, the spectra suggest that the permease secondary structure is dominated by alpha-helical components (up to 50%) and contains beta-structure (20%) and additional components assigned to turns, 3(10) helix, and nonordered structures (30%). Two distinct and strong absorption bands are recorded at 1660 and 1653 cm(-1), i.e., in the usual range of absorption of helices of membrane proteins. Moreover, conditions that preserve the transporter functionality (reconstitution in liposomes or solubilization with dodecyl maltoside) make possible the detection of two separate alpha-helical bands of comparable intensity. In contrast, a single intense band, centered at approximately 1656 cm(-1), is recorded from the inactive permease in Triton X-100, or a merged and broader signal is recorded after the solubilized protein is heated in dodecyl maltoside. It is suggested that in the functional permease, distinct signals at 1660 and 1653 cm(-1) arise from two different populations of alpha-helical domains. Furthermore, the sodium- and/or melibiose-induced changes in amide I line shape, and in particular, in the relative amplitudes of the 1660 and 1653 cm(-1) bands, indicate that the secondary structure is modified during the early step of sugar transport. Finally, the observation that approximately 80% of the backbone amide protons can be exchanged suggests high conformational flexibility and/or a large accessibility of the membrane domains to the aqueous solvent.

Escherichia coli↗
PubMed2000

Lexical knowledge degradation in schizophrenia.

This study documents a severe picture naming impairment in a series of 22 chronically hospitalised schizophrenics. The pattern and level of naming impairment were comparable in degree and type to that seen neurological patients with left hemisphere lesions. This deficit was further examined to determine whether it conformed to a disorder affecting access to the lexical representations or some degradation of the stored representations themselves. Patient naming was examined twice (18months apart) for evidence of consistency and for word frequency effects. The pattern of individual patient performance on these criteria showed that the majority had storage disorders; access disorders alone occurred in only a small minority of patients. A subset of 11 of the same patients that were tested on three occasions (across 30months) showed the same pattern but further indicated that when access problems are present, they reflect difficulty with deliberate, rather than automatic, access to the lexicon.

Adult↗
PubMed2000

Delineation of the roles of amino acids involved in the catalytic functions of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase.

The roles of particular amino acids in substrate and coenzyme binding and catalysis of glucose-6-phosphate dehydrogenase of Leuconostoc mesenteroides have been investigated by site-directed mutagenesis, kinetic analysis, and determination of binding constants. The enzyme from this species has functional dual NADP(+)/NAD(+) specificity. Previous investigations in our laboratories determined the three-dimensional structure. Kinetic studies showed an ordered mechanism for the NADP-linked reaction while the NAD-linked reaction is random. His-240 was identified as the catalytic base, and Arg-46 was identified as important for NADP(+) but not NAD(+) binding. Mutations have been selected on the basis of the three-dimensional structure. Kinetic studies of 14 mutant enzymes are reported and kinetic mechanisms are reported for 5 mutant enzymes. Fourteen substrate or coenzyme dissociation constants have been measured for 11 mutant enzymes. Roles of particular residues are inferred from k(cat), K(m), k(cat)/K(m), K(d), and changes in kinetic mechanism. Results for enzymes K182R, K182Q, K343R, and K343Q establish Lys-182 and Lys-343 as important in binding substrate both to free enzyme and during catalysis. Studies of mutant enzymes Y415F and Y179F showed no significant contribution for Tyr-415 to substrate binding and only a small contribution for Tyr-179. Changes in kinetics for T14A, Q47E, and R46A enzymes implicate these residues, to differing extents, in coenzyme binding and discrimination between NADP(+) and NAD(+). By the same measure, Lys-343 is also involved in defining coenzyme specificity. Decrease in k(cat) and k(cat)/K(m) for the D374Q mutant enzyme defines the way Asp-374, unique to L. mesenteroides G6PD, modulates stabilization of the enzyme during catalysis by its interaction with Lys-182. The greatly reduced k(cat) values of enzymes P149V and P149G indicate the importance of the cis conformation of Pro-149 in accessing the correct transition state.

Arginine↗