Hydration of peptides. I. Calculation of accessible surface areas for several conformations of a cyclic dipeptide.
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Dipeptides↗
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A study of the effect of chemical inactivants on the epitopes of Rift Valley fever virus glycoproteins using monoclonal antibodies.
A panel of 23 monoclonal antibodies (mAbs) was used to study the effect of formalin, beta propriolactone (BPL) and binary ethylenimine (BEI) on the epitopes of the Rift Valley fever virus glycoproteins. After the initial inactivation period BEI had very little adverse affect on the epitopes whereas BPL significantly altered seven and formalin partially changed the conformation or accessibility of most of the epitopes. The epitopes of all of the inactivated antigens showed a reduced activity against the specific mAbs over a six month storage period.
Animals↗
Structural and functional aspects of RGD-containing protein antagonists of glycoprotein IIb-IIIa.
In the past few years, knowledge of the structure and function of RGD-containing protein antagonists of the platelet fibrinogen receptor glycoprotein IIb-IIIa has advanced rapidly. The RGD sequence is found at the apex of extended, solvent accessible, and conformationally flexible loops in proteins of vastly different structural frameworks. Conformation of the RGD epitope and the immediate surrounding sequence are critical factors affecting potency and selectivity as integrin antagonists. The RGD sequence has recently been introduced into a number of protein and peptide scaffolds.
Amino Acid Sequence↗
Evidence for structural plasticity of heavy chain complementarity-determining region 3 in antibody-ssDNA recognition.
Anti-DNA antibodies play important roles in the pathogenesis of autoimmune diseases. They also represent a unique and relatively unexplored class of DNA-binding protein. Here, we present a study of conformational changes induced by DNA binding to an anti-ssDNA Fab known as DNA-1. Three crystal structures are reported: a complex of DNA-1 bound to dT3, and two structures of the ligand-free Fab. One of the ligand-free structures was determined from crystals exhibiting perfect hemihedral twinning, and the details of structure determination are provided. Unexpectedly, five residues (H97-H100A) in the apex of heavy chain complementarity-determining region 3 (HCDR3) are disordered in both ligand-free structures. Ligand binding also caused a 2-4A shift of the backbone of Tyr L92 and ordering of the L92 side-chain. In contrast, these residues are highly ordered in the Fab/dT3 complex, where Tyr H100 and Tyr H100A form intimate stacking interactions with DNA bases, and L92 forms the 5' end of the binding site. The structures suggest that HCDR3 is very flexible and adopts multiple conformations in the ligand-free state. These results are discussed in terms of induced fit and pre-existing equilibrium theories of ligand binding. Our results allow new interpretations of existing thermodynamic and mutagenesis data in terms of conformational entropy and the volume of conformational space accessible to HCDR3 in the ligand-free state. In the context of autoimmune disease, plasticity of the ligand-free antibody could provide a mechanism by which anti-DNA antibodies bind diverse host ligands, and thereby contribute to pathogenicity.
Antibodies, Antinuclear↗
A model of hydrogen bond formation in phosphatidylethanolamine bilayers.
We have modelled hydrogen bond formation in phospholipid bilayers formed, in excess water, from lipids with phosphatidylethanolamine (PE) headgroups. The hydrogen bonds are formed between the NH3+ group and either of the PO2- or the (sn2 chain) C=O groups. We used a model that represented the conformational states accessible to a PE headgroup by 17 states and modelled lipid dipole-dipole interactions using a non-local electrostatics theory to include the effects of hydrogen bonding in the aqueous medium. We used Monte-Carlo simulation to calculate equilibrium thermodynamic properties of bilayers in the fluid (T = 340 K) or gel (T = 300 K) phases of the bilayer. We defined Eh to be the difference in free energy between a hydrogen bond formed between a pair of lipid groups, and the energy of hydrogen bonds formed between water and those two groups, and we required its average value, [Eh], to be approximately -0.3kcal/mol (approximately -0.2 X 10(-13) erg) as reported by T.-B. Shin, R. Leventis, J.R. Silvius, Biochemistry 30 (1991) 7491. We found: (i) Eh = -0.9 X 10(-13) erg gave [Eh] = -0.21 X 10(-13) erg (gel phase) and [Eh] = -0.19 X 10(-13) erg (fluid phase). (ii) The relative number of C=O groups on the sn2 chain calculated to take part in interlipid hydrogen bonding in the fluid phase compared to the gel is 1.06 which compares well with the experimental ratio of approximately 1.25 (R.N.A.H. Lewis, R.N. McElhaney, Biophys. J. 64 (1993) 1081). The ratio of such groups taking part in interlipid hydrogen bonding compared to water hydrogen bonding in each phase was calculated to lie between 0.16 and 0.17. (iii) We calculated the distribution of positions of the headgroup moieties, P, O, CH2(alpha), CH2(beta) and N, and found that, in both phases, the O lay furthest from the hydrocarbon chain layer (average approximately 5.3A) with the PO2 and NH3 groups lying at approximately 5A. This results in the P-N dipole lying nearly parallel to the bilayer plane in both phases. The thickness of the headgroup layer underwent essentially no change on going from the gel to the fluid phase. The 2H NMR quadrupole splittings for the alpha and beta CH2 groups were 4.9 and 5.7kHz (fluid phase) and 7.1 and 7.3 kHz (gel phase), respectively, on the assumption of sufficiently rapid rotation around the z-axis. (iv) In both phases, the location of the NH3+ group exhibited a strong peak around 5.2 A into the aqueous medium, with much smaller peaks around 2.6 and 7.8 A, the two CH2 groups exhibited narrower, double-peaked distributions and the O and the PO2 each exhibited a narrow single peak. (v) PE headgroups, in a homogeneous gel phase, exhibited dipolar orientational long-range order in the plane of the bilayer. The distribution of orientation angles exhibited a full width at half height of between approximately 40 degrees and approximately 50 degrees. In a fluid phase no such order was observed. (vi) The number of hydrogen bonds did not differ substantially between the fluid and gel phases. This model is unlikely to display any significant effect of hydrogen bonding upon the "main" hydrocarbon chain melting phase transition at Tm, except, possibly, a broadening of any hysteresis, compared to the case of PC bilayers where interlipid hydrogen bonding is absent.
Computer Simulation↗
Free energy landscapes of encounter complexes in protein-protein association.
We report the computer generation of a high-density map of the thermodynamic properties of the diffusion-accessible encounter conformations of four receptor-ligand protein pairs, and use it to study the electrostatic and desolvation components of the free energy of association. Encounter complex conformations are generated by sampling the translational/rotational space of the ligand around the receptor, both at 5-A and zero surface-to-surface separations. We find that partial desolvation is always an important effect, and it becomes dominant for complexes in which one of the reactants is neutral or weakly charged. The interaction provides a slowly varying attractive force over a small but significant region of the molecular surface. In complexes with no strong charge complementarity this region surrounds the binding site, and the orientation of the ligand in the encounter conformation with the lowest desolvation free energy is similar to the one observed in the fully formed complex. Complexes with strong opposite charges exhibit two types of behavior. In the first group, represented by barnase/barstar, electrostatics exerts strong orientational steering toward the binding site, and desolvation provides some added adhesion within the local region of low electrostatic energy. In the second group, represented by the complex of kallikrein and pancreatic trypsin inhibitor, the overall stability results from the rather nonspecific electrostatic attraction, whereas the affinity toward the binding region is determined by desolvation interactions.
Animals↗
Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state.
The human SWI/SNF complex remodels nucleosome structure in an ATP-dependent manner, although the nature of this change has not been determined. Here we show that hSWI/SNF and ATP generate an altered nucleosomal structure that is stable in the absence of SWI/SNF. This product has an altered sensitivity to digestion by DNAse, restriction enzymes, and micrococcal nuclease, and an increased affinity for GAL4. It has the same protein composition but is approximately twice the size of a normal nucleosome. Incubation of the altered nucleosome with hSWI/SNF converts this structure back to a standard nucleosome in an ATP-dependent process. These results suggest that hSWI/ SNF acts by facilitating an exchange between normal and altered, more accessible, nucleosome conformations.
Adenosine Triphosphate↗
Influence of the structure of the lipid-water interface on the activity of hepatic lipase.
Factors affecting the hydrolytic activity of purified rat hepatic lipase have been examined in mixed-monolayer systems. When nonsubstrate lipids [either egg sphingomyelin or beta-O-hexadecyl-gamma-O-(1-ocadec-9-enyl)-DL-phosphatidylcholine (OPPC-ether)] were used as inert matrices, hydrolytic activity for both triolein and dioleoylphosphatidylethanolamine was shown to decrease with increasing surface pressure (pi); negligible activity occurred at pi greater than or equal to 30 mN/m. Examination of the effect of introduction of cholesterol into either matrix containing 2 mol % triolein indicated that the mean molecular area decreased with increasing cholesterol and that, at pi = 24 mN/m, triolein was fully miscible in the sphingomyelin matrix at cholesterol concentrations less than or equal to 32.5 mol % and in the OPPC-ether matrix at cholesterol concentrations less than or equal to 49 mol %. Above these critical concentrations of cholesterol, the phase diagrams indicate transitions that suggest that triolein is forced out of the monolayer. Introduction of increasing amounts of cholesterol into either inert matrix increased the rate of hydrolysis of triolein by hepatic lipase, although by different degrees. There are at least two factors contributing to these effects: (1) condensation of the monolayer by cholesterol, thus increasing the total surface concentration of triolein at pi = 24 mN/m in the constant area surface balance, and (2) some change in triolein conformation and/or accessibility since at identical surface concentrations of triolein (8.7 +/- 0.1 pmol/cm2) and pi (24 mN/m) the rate of hydrolysis of triolein by hepatic lipase is 1.5-fold higher in the OPPC-ether matrix than in the egg sphingomyelin matrix.(ABSTRACT TRUNCATED AT 250 WORDS)
Animals↗
Macromolecule encapsulation in diazoresin-based hollow polyelectrolyte microcapsules.
A stable enzyme encapsulation technique based on the conversion of weak interactions between diazo resin/poly(styrene sulfonate) to covalent bonds was explored. Photosensitive diazoresin-based polyelectrolyte microcapsules were prepared via layer-by-layer electrostatic self-assembly of poly(styrene sulfonate) and diazoresin on MnCO(3) templates. UV-vis and zeta-potential measurements confirmed the alternate deposition of {PSS/DAR} multilayers on the micrometer-sized dissolvable templates. The DAR-based microcapsules were demonstrated to be permeable to enzymes prior to UV irradiation, while the permeability of the multilayer wall was changed substantially after photo-cross-linking. Encapsulated molecules were stably entrapped after UV irradiation, as shown by confocal microscopy and atomic force microscopy images. Activity assays revealed that encapsulated glucose oxidase possessed 52.8% of the catalytic activity exhibited by the same amount of free enzyme, proving the preservation of native conformation and accessibility of substrate. This encapsulation technique is promising for many biomedical and biotechnological applications, particularly enzyme biosensors, which require stable immobilization of functional components while allowing sufficient transport rates for substrate molecules.
Azo Compounds↗
Relaxation dynamics of a polymer in a 2D confinement.
The molecular dynamics of oligomeric poly(propylene glycol) (PPG) liquids (MW=1000, 2000, and 4000 g/mol) confined in a two-dimensional layer-structured Na-vermiculite clay has been studied by broadband dielectric spectroscopy. The alpha-relaxation and the normal mode relaxation processes were studied for all samples in bulk and confinement. The most prominent experimental observation was that for the normal mode process: the relaxation rate in the clay is drastically shifted to lower frequencies compared to that of the bulk material. This slowing down is probably caused by the strongly reduced number of accessible chain conformations in two dimensions. Also the temperature dependence of the relaxation time for the normal mode process is strongly affected by the confinement. In contrast, for the alpha-relaxation of the confined polymers we observed only a slight increase of the relaxation rate at high temperatures compared to the corresponding bulk samples, and a decrease of its relaxation strength relative to the beta relaxation. Thus, the glass transition is unaffected by the 2D confinement, suggesting that the underlying phenomena responsible for the glass transition is the same as in bulk. Moreover, in the clay the intensity of the normal mode is stronger than that of the alpha-process, in contrast to the bulk samples where the opposite behavior is observed.
Journal Article↗
Differential role of hepatocyte nuclear factor-1 in the regulation of glucose-6-phosphatase catalytic subunit gene transcription by cAMP in liver- and kidney-derived cell lines.
In liver and kidney, the terminal step in gluconeogenesis is catalyzed by glucose-6-phosphatase. To examine the effect of the cAMP signal transduction pathway on transcription of the gene encoding the catalytic subunit of glucose-6-phosphatase (G6Pase), G6Pase-chloramphenicol acetyltransferase (CAT) fusion genes were transiently transfected into either the liver-derived HepG2 or kidney-derived LLC-PK cell line. Co-transfection of an expression vector encoding the catalytic subunit of cAMP-dependent protein kinase (PKA) markedly stimulated G6Pase-CAT fusion gene expression, and mutational analysis of the G6Pase promoter revealed that multiple regions are required for this PKA response in both the HepG2 and LLC-PK cell lines. A sequence in the G6Pase promoter that resembles a cAMP response element is required for the full PKA response in both HepG2 and LLC-PK cells. However, in LLC-PK cells, but not in HepG2 cells, a hepatocyte nuclear factor-1 (HNF-1) binding site was critical for the full induction of G6Pase-CAT expression by PKA. Changing this HNF-1 motif to that for the yeast transcription factor GAL4 reduces the PKA response in LLC-PK cells to the same degree as deleting the HNF-1 site. However, co-transfection of this mutated construct with chimeric proteins comprising the GAL4-DNA binding domain ligated to the coding sequence for HNF-1alpha, HNF-1beta, HNF-3, or HNF-4 completely restored the PKA response. Thus, we hypothesize that, in LLC-PK cells, HNF-1 is acting as an accessory factor to enhance PKA signaling through the cAMP response element by altering G6Pase promoter conformation or accessibility rather than specifically affecting some component of the PKA signal transduction pathway.
Animals↗
Multifaceted consequences of anti-gp41 monoclonal antibody 2F5 binding to HIV type 1 virions.
A human monoclonal antibody (MAb) (2F5) neutralizing a variety of laboratory strains and clinical isolates of the human immunodeficiency virus type 1 (HIV-1) and binding to an epitope of the envelope glycoprotein gp41 encompassing the amino acid sequence ELDKWA has been described (Muster T et al., J Virol 1993;67:6642-6647). It was suggested that an immunogen eliciting virus-neutralizing antibodies having a specificity similar to that of MAb 2F5 should be considered as a component of HIV-1 vaccines. Efforts in this direction would benefit from understanding the mechanism whereby MAb 2F5 neutralizes the infectivity of HIV-1. The segment of gp41 encompassing residues ELDKWA has so far not been directly implicated in initiation of infection by HIV-1, suggesting that MAb 2F5 might affect other sites on HIV-1 envelope glycoproteins playing a role in virus entry into target cells. We provide here evidence that MAb 2F5 binding to HIV-1 virus particles decreases the accessibility or conformation of the gp41 fusion domain and of gp120 domains, including the binding site for the CD4 cell receptor. These apparently indirect consequences of MAb 2F5 binding to HIV-1 are likely to account for or contribute to the virus-neutralizing activity of this MAb.
Amino Acid Sequence↗
Preferential binding of the carcinogen benzo[a]pyrene to DNA in active chromatin and the nuclear matrix.
Rat liver nuclei or hepatocytes were incubated with the proximate carcinogen, benzo[a]pyrene (BP) and its ultimate carcinogen, anti-benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE). Following carcinogen exposure, nuclei were fractionated by micrococcal nuclease digestion and stepwise extraction to yield an active chromatin fraction enriched in transcribed versus non-transcribed genes, a bulk chromatin fraction, a high-salt-extracted chromatin fraction and a nuclear matrix fraction containing elevated concentrations of transcribed and nontranscribed genes. BP binds more readily to DNA of active chromatin and nuclear matrix than to bulk chromatin. Since low concentrations of BPDE also selectively damage active chromatin and matrix DNA, selectivity is not due to the subnuclear location of enzymes which activate BP to BPDE. Higher BPDE concentrations cause more uniform DNA damage. Selective carcinogen attack may result from an accessible DNA conformation in active chromatin and matrix or from partitioning of carcinogen in the nuclear membrane.
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
In vivo stage- and tissue-specific DNA-protein interactions at the D. melanogaster alcohol dehydrogenase distal promoter and adult enhancer.
We performed a high resolution analysis of the chromatin structure within the regions required for distal transcription of the Drosophila melanogaster alcohol dehydrogenase gene (Adh). Using dimethyl sulfate, DNase I, and micrococcal nuclease as structural probes, and comparing chromatin structure in tissues isolated from several developmental stages, we have identified several sites of stage- and tissue-specific DNA-protein interactions that correlate with distal transcription initiation. Most were within previously identified cis-acting elements and/or in vitro protein binding sites of the adult enhancer (AAE) and distal promoter, including the TATA box. We also detected a novel stage-specific DNA-protein interaction at the Adf-2a binding site where a non-histone protein was bound to the DNA on the surface of a positioned nucleosome previously identified between the distal promoter and adult enhancer. In addition to footprints, we have also revealed stage- and tissue-specific DNA helix deformations between many of the non-histone protein binding sites. These helix distortions suggest there are interactions among the adjacently bound proteins that result in bending or kinking of the intervening DNA. The distal promoter and AAE have an accessible chromatin conformation in fat body prior to the third larval instar and many of the regulatory proteins that bind in these regions are also available before distal transcription begins. Nevertheless, the timing of DNA-protein interactions in the distal promoter and AAE suggest these proteins do not bind individually or assemble progressively as they and their binding sites become available. Instead, there appears to be a coordinated assembly of a large cooperative complex of proteins interacting with the distal promoter, the positioned nucleosome, the enhancer of the distal promoter (the AAE), and each other.
Alcohol Dehydrogenase↗
Regulated processive transcription of chromatin by T7 RNA polymerase in Trypanosoma brucei.
Inability of T7 RNA polymerase to processively transcribe higher eukaryotic chromatin is interpreted as a correlate of its reported inhibition by nucleosomes on reconstituted templates in vitro . We used chromosomally integrated reporter cassettes to examine features of T7 transcription in a lower eukaryotic system. Luciferase reporters were targeted to rDNA in transgenic Trypanosoma brucei stably expressing the phage polymerase. Because trypanosome mRNAs are capped by RNA splicing in trans , T7 transcription could be gauged by luciferase activity. In contrast to findings from higher eukaryotes, T7 transcription is vigorous and processive on chromatin templates in T.brucei , surpassing levels achieved with endogenous promoters, including those recruiting RNA polymerase I. This may be a reflection of intrinsic differences in chromatin structure between differently evolved eukaryotes or of an integration site that is exceptionally permissive for T7 transcription due to a local accessible chromatin conformation. T7 transcription could be manipulated to achieve different levels of constitutive expression, through the use of promoter mutations. Moreover, T7 initiation could be regulated by the prokaryotic Tet repressor and elongation halted by T7 terminator sequences. We have exploited these features to construct a robust inducible expression system, whose utility potentially extends to other trans -splicing organisms.
Animals↗
Calcium-binding properties of osteopontin derived from non-osteogenic sources.
Osteopontin (OP), purified from rat bone, binds Ca2+ but whether different molecular forms of OPs derived from non-osteogenic sources and non-phosphorylated OP also possess this property remains to be determined. Furthermore, it is not known which specific site or sites of the molecule bind Ca2+. In the present study, following an established procedure, total proteins in the conditioned media from OP-synthesizing cell cultures were separated by SDS-PAGE, transferred to Immobilon-P membranes, and incubated with 45CaCl2, then Ca2+ ions bound to protein bands were analyzed by autoradiography. Purified OPs, and synthetic oligopeptides representing specific domains of the OP molecule were adsorbed on the membrane and processed as described above. Our results show that OPs synthesized by normal rat kidney cells, oncogenically transformed Rat-1 cells, OP purified from human milk, and non-phosphorylated OP secreted by 1 alpha, 25-dihydroxyvitamin D3-treated mouse epidermal JB6 cells all bind detectable levels of Ca2+ with specificity. We also show that a synthetic peptide representing the domain of OP which contains nine consecutive aspartic acid residues binds Ca2+ with specificity. It is probable, therefore, that a Ca(2+)-binding site resides in this region of the OP molecule. We conclude that Ca(2+)-binding is a general property of OP, irrespective of its molecular mass and origin, and the phosphate moieties of OP may not influence the conformation or accessibility of the Ca2+ affinity sites of the molecule.
Amino Acid Sequence↗
Differential involvement of intracellular domains of the rat NTS1 neurotensin receptor in coupling to G proteins: a molecular basis for agonist-directed trafficking of receptor stimulus.
In this work, we evidenced characteristic features of agonist-induced trafficking of receptor stimulus for the rat neurotensin receptor 1 (NTS1). Thus, reverse potency orders between two agonists, EISAI-1 and neuromedin N, were observed in inositol 1,4,5-trisphosphate and cAMP assays in Chinese hamster ovary cells transfected with this receptor. Indeed, compared with other agonists, EISAI-1 presented lower relative potency toward inositol 1,4,5-trisphosphate production than toward cAMP accumulation, guanosine 5'-O -(3-[35 S]thio)triphosphate binding, and [3H]arachidonic acid production. These results indicated pathway-dependent differences in EISAI-1 intrinsic efficacies, favoring activations of Gs- and Gi/o-related pathways over the Gq/11-related pathway. Moreover, although coupling to Gq/11 and Gi/o involved the third intracellular loop and the C-terminal domain of the NTS1 receptor, respectively, we demonstrated that deletion of the latter domain suppressed agonist-induced cAMP accumulation, suggesting that this domain also mediated coupling to Gs. Together, these results indicated that, unlike other agonists, EISAI-1 discriminated between the pathways involving the receptor C-terminal domain and that involving the third intracellular loop. These properties of EISAI-1 were also observed in cortical neurons endogenously expressing the NTS1 receptor. They were further attributed to the functionalization of its COOH end by an ethyl group, because the unesterified analog EISAI-2 presented normal behavior on inositol 1,4,5-trisphosphate production. These findings support the hypothesis of agonist-selective receptor states with distinct conformations or accessibilities of intracellular domains. They also suggest that the differential involvement of these domains in coupling to G proteins might represent a molecular basis for agonist-selective responses through G protein-coupled receptors.
Animals↗
Structure of the vesicular stomatitis virus nucleoprotein-RNA complex.
Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and assembly. We have determined a 2.9 angstrom structure of a complex containing 10 molecules of the N protein and 90 bases of RNA. The RNA is tightly sequestered in a cavity at the interface between two lobes of the N protein. This serves to protect the RNA in the absence of polynucleotide synthesis. For the RNA to be accessed, some conformational change in the N protein should be necessary.
Amino Acid Sequence↗