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Conformational changes in the reversed phase liquid chromatography of recombinant human growth hormone as a function of organic solvent: the molten globule state.

As a continuation of a previous paper on the retention behavior of recombinant human growth hormone (rhGH) in reversed phase chromatography at pH 6.5 (Oroszlan, P., et al. Anal. Chem. 1992, 64, 1623-1631) the effect of 1-propanol (1-PrOH) and acetonitrile on the conformation of rhGH at this pH has been investigated by circular dichroism (CD), second-derivative UV spectroscopy, fluorescence anisotropy, fluorescence quenching, and fluorescence lifetime measurements. Addition of 1-PrOH up to a concentration of 10% (v/v) does not cause any significant changes in protein structure. However, above this concentration, a transition from the native to a new state is observed; the transition is completed above 30% (v/v) of 1-PrOH, the composition for completion being dependent on temperature. This change in structure correlates with retention changes observed in reversed phase chromatography. The new rhGH conformation retains much of the alpha-helicity and possesses a slightly expanded hydrodynamic radius relative to native rhGH. Second-derivative UV spectroscopy suggests that the hydrogen bond between Trp 86 and Asp 169, spanning two alpha-helices, remains intact. On the other hand, the near-UV CD intensity changes from positive to negative in the Trp region of the spectrum, signaling an alteration in the Trp environment. In addition, fluorescence quenching measurements with trichloroethanol reveal greater accessibility to solvent of the Trp residue after the conformational transition has occurred. From the results, it is concluded that a molten globule state (compact state retaining much of the secondary structure of the native state but with a disrupted tertiary structure) is produced with the addition of > 30% (v/v) 1-PrOH.(ABSTRACT TRUNCATED AT 250 WORDS)

1-Propanol↗

Conformational analysis of [Cpp1, Sar7, Arg8] vasopressin by 1H-NMR spectroscopy and molecular mechanics calculations.

A combined 1H-NMR and molecular mechanics study of [Cpp1, Sar7]AVP was performed in order to select the most probable conformations in DMSO solutions. The NMR constraints obtained were employed in the selection of starting conformations of the cyclic moiety of the analog. In particular, the diminished accessibility of the Asn5 NH proton to solvent and the close contact between Cpp1 and Cys6 C alpha H protons suggests a beta-turn conformation at the Phe3-Gln4 residues. Energy minimization was carried out both in the ECEPP/2 (rigid-valence geometry) and in the AMBER (flexible-valence geometry) force fields. Comparison of the experimental and calculated values of NMR characteristics has revealed that conformations containing type I, II, and III beta-turns at the Phe3-Gln4 residues are in reasonable agreement with the experimental data, with a dynamic equilibrium between the beta I (beta III) and beta II type structures of the cyclic part being the most probable. All of these conformations prefer the negative chirality of the disulfide bridge (theta 3 approximately -90 degrees). Five representative conformations were chosen for the acyclic tail: one with a beta I, one with a beta II'-turn at the Sar7-Arg8 residues, two extended-type conformations, and a conformation with a gamma-turn at Sar7. Because only high-energy extended conformations were in agreement with NMR data, it was concluded that the acyclic tail has considerable conformational flexibility in solution. The conformations obtained are discussed in terms of the structure-function relationship of the neurohypophyseal hormone analogs.

Amino Acid Sequence↗

Ethidium bromide as a probe of conformational heterogeneity of DNA in chromatin. The role of histone H1.

The accessibility and the tertiary structure of the DNA inside chromatin were studied by using ethidium bromide (EB) as a fluorescent probe. The exclusion model of binding was refined by introductina a parameter alpha (0less than alpha less than 1) which measures the accessibility of the DNA and by taking into account when necessary the existence of two sets of binding sites. We were thus able to fit predicted and experimental isotherms and then to describe completely EB binding to native or partially histone depleted chromatin under various conditions. Itn native chromatin 95% of the DNA (alpha = 0.95) appears to be accessible to EB but two sets of sites are present. The first one corresponds to alpha = 0.13 and is characterized by an affinity constant which is higher by two orders of magnitude than that relative to pure DNA. The second set corresponds to alpha = 0.82 and the corresponding binding constant is only three or four times lower than that of pure DNA. The sites with high affinity are still present after treatment with formaldehyde but disappear after removal of histon H1. By comparison with chromatin treated with deoxycholate of with artifical complexes between H1 and DNA, high affinity sites were found only when all of the histons are bound to DNA. An alpha value around 0.8 is still obtained in 1 M NaC1 treated chromatin, pointing to the fact that histones H3 and H4 are preventing 20% of the DNA to intercalate EB.

Binding Sites↗

Engineering of stable and fast-folding sequences of model proteins.

The statistical mechanics of protein folding implies that the best-folding proteins are those that have the native conformation as a pronounced energy minimum. We show that this can be obtained by proper selection of protein sequences and suggest a simple practical way to find these sequences. The statistical mechanics of these proteins with optimized native structure is discussed. These concepts are tested with a simple lattice model of a protein with full enumeration of compact conformations. Selected sequences are shown to have a native state that is very stable and kinetically accessible.

Kinetics↗

Distribution of cross-links between mRNA analogues and 16 S rRNA in Escherichia coli 70 S ribosomes made under equilibrium conditions and their response to tRNA binding.

The interaction between mRNA and Escherichia coli ribosomes has been studied by photochemical cross-linking using mRNA analogues that contain 4-thiouridine (s4U) or s4U modified with azidophenylacyl bromide (APAB), either two nucleotides upstream or eight nucleotides downstream from the nucleotide sequence ACC, the codon for tRNA(Thr). The sequences of the mRNA analogues were described earlier (Stade, K., Rinke-Appel, J., and Brimacombe, R. (1989) Nucleic Acids Res. 17, 9889-9908; Rinke-Appel, J., Stade, K., and Brimacombe, R. (1991) EMBO J. 10, 2195-2202). Under equilibrium conditions, both of these mRNA analogues bind and cross-link to 70 S ribosomes without the presence of tRNA(Thr); however, there are significant increases both in binding and particularly in cross-linking in the presence of the tRNA(Thr). Four regions contain cross-linking sites that increase in the presence of tRNA, C1395, A532, A1196 (and minor sites around these three positions), and C1533/U1532. Three other cross-linking sites, U723, A845, and U1381, show very little change in extent of cross-linking when tRNA is present. A conformational change in the 30 S subunit allowing additional accessibility to the 16 S rRNA by the mRNA analogues upon tRNA binding best explains the behavior of the tRNA-dependent and tRNA-independent mRNA-16 S rRNA cross-linking sites.

Base Sequence↗

Synthesis, enantiomeric conformations, and stereodynamics of aromatic ortho-substituted disulfones.

[structure in text] Aromatic ortho-disulfone derivatives are readily accessible from diiodide precursors by Cu(I)-mediated reactions with sodium sulfinate salts. The sulfone substituents adopt C(2)-symmetric enantiomeric conformations (lambda and delta) as evidenced by X-ray structural analysis and (1)H and (31)P NMR on chiral bis(sulfonyl)veratrol derivatives and hexacoordinated tris(benzenediolato)phosphate anions. Slow dynamic conformational isomerism (DeltaG(++) > or = 19.8 kcal mol(-1)) was detected in solution.

Journal Article↗

Structural interactions between alpha- and beta-subunits of the gastric H,K-ATPase.

Structural and functional interactions between alpha- and beta-subunits of the H,K-ATPase were explored. The sensitivity to trypsinolysis of alpha-subunit was monitored by SDS-PAGE in control H,K-ATPase-enriched microsomes and in microsomes in which disulfide bonds of the beta-subunit were reduced using 2-mercaptoethanol (2-ME). Reduction of beta-subunit disulfide bonds increased the susceptibility of the alpha-subunit to tryptic digestion. Kinetics of trypsinolysis were also carried out in the presence of ligands known to bind with H,K-ATPase and favor a particular conformer state in the native enzyme. The time-course for release of tryptic peptides was monitored in protein stained gels and Western blots probed with monoclonal antibody alpha-H,K,12.18. In control preparations, where beta-subunit disulfides remained intact, trypsinolysis in the presence of ATP or K+ produced distinctive patterns of tryptic fragments, each characteristic of the conformational states induced by the respective ligand. For 2-ME-treated microsomes the altered alpha-subunit was unable to undergo ligand-induced conformational changes. The increased susceptibility of the alpha-subunit to trypsinization, the change in accessibility of tryptic cleavage sites and the inability of the alpha-subunit to undergo ligand-induced conformational changes after reduction of the beta-subunit disulfides suggest that the interactions between alpha- and beta-subunits are important for the conformational stability of the functional holoenzyme. A model localizing the most susceptible tryptic cleavage sites in control and 2-ME-reduced states is presented.

Animals↗

Activation of deoxycytidine kinase in lymphocytes is calcium dependent and involves a conformational change detectable by native immunostaining.

Deoxycytidine kinase (dCK), the principal deoxynucleoside salvage enzyme, plays a seminal role in the bioactivation of a wide array of cytotoxic nucleoside analogues. Recently, activation of dCK has been considered as a protective cellular response to a number of DNA-damaging agents in lymphocytes. Regarding the molecular mechanism of the enzyme activation, a post-translational modification by protein phosphorylation has been suggested. Here we provide evidence that both the activation process and the maintenance of the activated state require free cytosolic calcium. BAPTA-AM, a cell-permeable calcium chelator selectively inhibited the activation of dCK in a time- and concentration-dependent manner while extracellular calcium depletion had no effect. On the other hand, elevation of cytoplasmic calcium levels by thapsigargin did not potentiate the enzyme, referring to the permissive function of calcium in the activation process. Denaturing Western blots of extracts from lymphocytes incubated with 2-chlorodeoxyadenosine, aphidicolin and/or BAPTA-AM clearly demonstrated that dCK protein levels were unchanged during these treatments. However, a striking correlation was found between enzyme activity and the intensity of dCK-specific signals in native Western blots. Extracts from CdA-treated cells were much better recognized by the antibody raised against the C-terminal peptide of dCK than the BAPTA-AM-treated samples. These results indicate that the calcium-dependent activation of dCK is accompanied by a conformational change that renders the C-terminal epitope more accessible to the antibody.

Calcium↗

The three-dimensional structure of 6-phospho-beta-galactosidase from Lactococcus lactis.

BACKGROUND: The enzyme 6-phospho-beta-galactosidase hydrolyzes phospholactose, the product of a phosphor-enolpyruvate-dependent phosphotransferase system. It belongs to glycosidase family 1 and no structure has yet been published for a member of this family. RESULTS: The crystal structure of 6-phospho-beta-galactosidase was determined at 2.3 A resolution by multiple isomorphous replacement, using the wild-type enzyme and a designed cysteine mutant. A second crystal form, found with the mutant enzyme, was solved by molecular replacement, yielding the conformation of two chain loops that are invisible in the first crystal form. The active center, located through catalytic residues identified in previous studies, cannot be accessed by the substrate if the two loops are in their defined conformation. The enzyme contains a (beta alpha)8 barrel and the relationship of its chain fold to that of other glycosidases has been quantified. As a side issue, we observed that a cysteine point mutant designed for X-ray analysis crystallized mainly as a symmetric dimer around an intermolecular disulfide bridge formed by the newly introduced cysteine. CONCLUSIONS: The presented analysis provides a basis on which to model all other family 1 members and thereby will help in elucidating the catalytic mechanisms of these sequence-related enzymes. Moreover, this enzyme belongs to a superfamily of glycosidases sharing a (beta alpha)8 barrel with catalytic glutamates/aspartates at the ends of the fourth and the seventh strands of the beta barrel.

Binding Sites↗

Mixed conformations of deoxyribonucleic acid in chromatin: a preliminary report.

We have established empirical limits for the circular dichroism spectra appropriate for aqueous solutions of the B, C, and A forms of calf-thymus DNA and have analyzed DNA conformations in biological structures. The circular dichroism spectrum above 250 nm of purified calf-thymus chromatin can be satisfactorily accounted for as a linear combination of contributions of the B and C reference spectra without invoking higher-order structures such as supercoils. The amount of A contribution, if any, is below the limit of detection (</=4%). The fraction of bases in the B conformation depends on the method of isolation of nucleohistone, and ranges from 30-50%. The B content of a given preparation is increased by addition of a chelating agent and decreased by addition of divalent ions. More radical increases ensue upon protein removal. Nuclease treatment results in a dramatic decrease in B content. The fraction of bases melting out in the lower transitions of the complex melting profile of a given chromatin preparation corresponds to its B content. We propose a model for chromatin structure in which part of the DNA duplex is exposed or accessible to the solvent and is in the B conformation. The remainder of the base pairs and ribophosphate backbone are protected from interaction with the solvent by efficient histone coverage and are in the C conformation. Divalent ions modulate the distribution of bases between these two conformations.

Animals↗

Studies on the mechanism of action of A80915A, a semi-naphthoquinone natural product, as an inhibitor of gastric (H(+)-K+)-ATPase.

A semi-naphthoquinone natural product, A80915A, produced by Streptomyces aculeolatus was found to be a potent inhibitor of gastric (H(+)-K+)-ATPase, the enzyme responsible for acid secretion in the stomach. Enzyme activity was measured by potassium-stimulated hydrolysis of ATP or p-nitrophenolphosphate with enzyme prepared from the stomach fundic mucosa of pigs. Concentration-dependent inhibition was observed with an IC50 of about 2-3 microM for both ATPase and p-nitrophenylphosphatase. A Hill plot indicated that the enzyme has two binding sites for A80915A. Inhibition was not affected by the presence of the reducing agent dithiothreitol, indicating a lack of involvement of enzyme sulfhydryl groups. A 30-min incubation of enzyme with increasing drug concentrations followed by a 10-fold dilution did not alter the IC50, indicating that A80915A does not covalently modify the enzyme. Coincubation of enzyme with 3.8 microM A80915A resulted in time-dependent inhibition. The rate of inhibition was slowed significantly by the presence of 20 mM potassium, rubidium and ammonium but not by 20 mM sodium, lithium and choline, or by 40 mM sucrose. The level of inhibition was influenced by the order of addition of potassium and drug to the enzyme. Taken together, these studies indicate that inhibition by A80915A is dependent on the conformation of gastric (H(+)-K+)-ATPase and that potassium slows the rate of inhibition by converting the enzyme to a conformation where the drug binding site is not as accessible. The mode of action of A80915A is distinct from that of two well characterized proton pump inhibitors, omeprazole and SCH 28080.

Adenosine Triphosphatases↗

The activation of ribulose-1,5-bisphosphate carboxylase-oxygenase from spinach by oxygen.

The effect of oxygen on ribulose-1,5-bisphosphate carboxylase-oxygenase from spinach was investigated. Both activities were deactivated by removal of oxygen and reversibly reactivated by oxygenation of the enzyme solution. The change in enzyme activities was accompanied by conformational changes as studied by the use of intrinsic and extrinsic fluorescent probes. The analysis of cysteine sulfhydryl groups accessible to 5,5'-dithiobis-(2-nitrobenzoic acid) revealed that the number of these groups changed with the oxygen concentration. The kinetic of the exposure of eight cysteine residues was similar to the loss of enzyme activities. The modification of these groups with 5,5'-dithiobis-(2-nitrobenzoic acid) caused almost complete loss of both the activities. The enzyme isolated from a photolithotrophic organism, Chromatium vinosum, was not affected by oxygen removal. During air--argon transitions, neither the enzyme conformation nor the number of accessible sulfhydryl groups changed.

Carboxy-Lyases↗

Probing myosin light chain 1 structure with monoclonal antibodies.

Five monoclonal antibodies that react with different regions of myosin light chain 1 from human ventricular myocardial muscle were used to obtain information on interactions between the light chain 1 and heavy chains and generally on the tertiary structure of the light chain 1 within the myosin head. We performed Western blot assays of the five antibodies with myosins from different cardiac and skeletal muscles, with different proteolytic fragments of bovine ventricular myosin light chain 1 (LC1) and to different recombinant fragments of human ventricular LC1 and rat fast skeletal light chain LC1/LC3. The five antibodies were mapped in three different regions of the light chain 1: two antibodies mapped within the first eight amino-terminal residues, two between residues 71 and 74, and one between residues 129 and 134. The apparent dissociation constants of the last three antibodies, determined by antibody-antigen equilibria in solution, were lower than when isolated light chains were used as antigens. It is probable that the corresponding amino acids involved in the antibody epitopes were either involved in interactions between the light and heavy myosin subunits, or somehow hindered by the myosin heavy chain bulk. In contrast, the apparent dissociation constants measured for both other antibodies were higher when myosin, rather than isolated light chains, was used as antigen. Thus LC1 fixation to heavy chains within the myosin molecule induced conformation changes at the amino-terminal end of the light chain 1. No difference in the accessibility of this mobile LC1 segment was detected in the presence of actin. Finally, observed differences in epitope accessibility on the light chain LC1 in myosin, as compared with chymotryptic subfragment 1 (SF1), indicated conformational differences between native myosin and extensively studied SF1 molecules.

Amino Acid Sequence↗

The action of chymotrypsin on nucleosome cores. Histone products and conformational effects of limited digestion.

alpha-Chymotrypsin was used to probe accessible hydrophobic amino acid residues in nucleosome cores. Small amounts of chymotrypsin rapidly and selectively cleaved at leucine 20 of histone H3. Cleavage at this site caused partial unfolding of the nucleosome core at low ionic strengths indicated by a small decrease in sedimentation coefficient and increase in circular dichroism in the 265-285-nm range. Unfolding did not occur at moderate ionic strengths, probably because of more effective electrolyte screening of residual negative charge on the nucleosome core. More extensive treatment with chymotrypsin partially degraded other core histones in nucleosome cores at similar rates. The primary sites of cleavage were assigned to Leu115 of H2a, Val18 or Gln22 of H2b, and Leu10 plus Leu22 of H4. We conclude that these primary sites of chymotrypsin cleavage of the four core histones lie on or near the nucleosome core surface, while the large number of other hydrophobic histone residues located in more central sequences must be inaccessible. Extensive chymotrypsin treatment yielded a set of "limit" products approximately 80-100 residues long that were similar to the limit products of trypsin digestion. Sedimentation coefficients and circular dichroism spectra of nucleosome cores treated to near limits with chymotrypsin or chymotrypsin followed by trypsin were not consistent with significant unfolding of the proteolyzed cores at moderate ionic strength. These results indicate that the amino-terminal 20-30 residues of H2b, H3, and H4 and the amino- and carboxyl-terminal approximately 12 residues of H2a, in toto, interact weakly if at all with DNA of isolated nucleosome cores. These histone termini stabilize less than two turns and perhaps only one turn on each DNA terminus.

Amino Acids↗

Tandem SH2 binding sites mediate the RasGAP-RhoGAP interaction: a conformational mechanism for SH3 domain regulation.

Many cellular signaling proteins contain SH3 (Src homology 3) domains that mediate protein interactions via specific proline-containing peptides. Unlike SH2 domains, whose interactions with tyrosine-containing peptides are promoted by phosphorylation of the SH2 binding site, the regulatory mechanism for SH3 interactions is unclear. p120 RasGAP (GTPase-activating protein), which contains an SH3 domain flanked by two SH2 domains, forms an abundant SH2-mediated complex with p190 RhoGAP in cells expressing activated tyrosine kinases. We have identified two closely linked tyrosine-containing peptides in p190 that bind simultaneously to the RasGAP SH2 domains upon p190 phosphorylation. This interaction is expected to bring the two SH2 domains into close proximity. Consequently, RasGAP undergoes a conformational change that results in a 100-fold increase in the accessibility of the target binding surface of its SH3 domain. These results indicate that the tandem arrangement of SH2 and SH3 domains found in a variety of cellular signaling proteins can provide a conformational mechanism for regulating SH3-dependent interactions through tyrosine phosphorylation. In addition, it appears that the role of p190 in the RasGAP signaling complex is to promote additional protein interactions with RasGAP via its SH3 domain.

Animals↗

Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions.

Sugar-oligoamides have been designed and synthesized as structurally simple carbohydrate-based ligands to study carbohydrate-DNA interactions. The general design of the ligands 1-3 has been done as to favor the bound conformation of Distamycin-type gamma-linked covalent dimers which is a hairpin conformation. Indeed, NMR analysis of the sugar-oligoamides in the free state has indicated the presence of a percentage of a hairpin conformation in aqueous solution. The DNA binding activity of compounds 1-3 was confirmed by calf thymus DNA (ct-DNA) NMR titration. Interestingly, the binding of the different sugar-oligoamides seems to be modulated by the sugar configuration. Semiquantitative structural information about the DNA ligand complexes has been derived from NMR data. A competition experiment with Netropsin suggested that the sugar-oligoamide 3 bind to DNA in the minor groove. The NMR titrations of 1-3 with poly(dA-dT) and poly(dG-dC) suggested preferential binding to the ATAT sequence. TR-NOE NMR experiments for the sugar-oligoamide 3-ct-DNA complex both in D(2)O and H(2)O have confirmed the complex formation and given information on the conformation of the ligand in the bound state. The data confirmed that the sugar-oligoamide ligand is a hairpin in the bound state. Even more relevant to our goal, structural information on the conformation around the N-glycosidic linkage has been accessed. Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized.

Amides↗

Dual solvent cavities and hydrogen-bond networks define the chromophore environment in a far-red/orange-sensing cyanobacteriochrome.

Cyanobacteriochromes (CBCRs) are bilin-binding photoreceptors that exhibit remarkable spectral diversity and mediate light-dependent signaling in cyanobacteria. Far-red/orange-sensing CBCRs (froCBCRs) have attracted interest because of their unusually red-shifted absorption properties, yet structural information for their illuminated states has been lacking. Here, we report the first high-resolution (1.8&#xa0;&#xc5;) crystal structure of the orange-absorbing (Po) state of the froCBCR ToFrO from Tolypothrix sp. PCC 7910. The structure reveals a compact, cyclic bilin configuration and water-mediated hydrogen-bonding networks within two solvent-accessible cavities. Within the GAF domain, the D-ring remains nearly perpendicular to the planar A-to-C ring system through interactions involving a flexible loop region. Comparative analyses of cryogenic synchrotron and room-temperature X-ray free-electron laser (XFEL) structures, together with molecular dynamics (MD) simulations, revealed alternative Met636 conformations associated with dynamic water exchange through the solvent-accessible cavity. Site-directed mutagenesis of cavity-lining and water-interacting residues resulted in modest spectral shifts. By contrast, mutations of two Trp residues, participating in &#x3c0;-&#x3c0; stacking with the D-ring and likely imposing a steric constraint near the A-ring, resulted in substantial blue and red shifts in the dark and illuminated states, respectively. Together with the observed chromophore geometry, these findings indicate that the spectral properties of ToFrO are governed by chromophore conformation and its direct interaction with surrounding residues through hydrogen-bonding, electrostatic, and &#x3c0;-&#x3c0; interactions. These results further suggest that cavity-mediated solvent organization contributes to stabilizing the local structural environment surrounding the chromophore and adjacent protein backbone. Collectively, these findings elucidate the structural basis for photoconversion and spectral tuning in froCBCRs.

Cyanobacteria↗

2.8 A crystal structure of the malachite green aptamer.

Previous in vitro selection experiments identified an RNA aptamer that recognizes the chromophore malachite green (MG) with a high level of affinity, and which undergoes site-specific cleavage following laser irradiation. To understand the mechanism by which this RNA folds to recognize specifically its ligand and the structural basis for chromophore-assisted laser inactivation, we have determined the 2.8 A crystal structure of the aptamer bound to tetramethylrosamine (TMR), a high-affinity MG analog. The ligand-binding site is defined by an asymmetric internal loop, flanked by a pair of helices. A U-turn and several non-canonical base interactions stabilize the folding of loop nucleotides around the TMR. The aptamer utilizes several tiers of stacked nucleotides arranged in pairs, triples, and a novel base quadruple to effectively encapsulate the ligand. Even in the absence of specific stabilizing hydrogen bonds, discrimination between related fluorophores and chromophores is possible due to tight packing in the RNA binding pocket, which severely limits the size and shape of recognized ligands. The site of laser-induced cleavage lies relatively far from the bound TMR ( approximately 15 A). The unusual backbone conformation of the cleavage site nucleotide and its high level of solvent accessibility may combine to allow preferential reaction with freely diffusing hydroxyl radicals generated at the bound ligand. Several observations, however, favor alternative mechanisms for cleavage, such as conformational changes in the aptamer or long-range electron transfer between the bound ligand and the cleavage site nucleotide.

Base Pairing↗