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PubMed1997

Effects of nitric oxide synthase inhibitors on bone formation in rats.

NO is synthesized from L-arginine by at least three isoforms of nitric oxide synthase (NOS) and is known to function as a vasodilator and neurotransmitter. NO is produced by bone cells but its function in bone biology is, as yet, unclear. We hypothesized that NOS mediates bone formation in remodeling regions of the skeleton. We studied the effects of two NOS inhibitors: N(G)-nitro-L-arginine methyl ester (L-NAME), which is a general inhibitor of NOS activity and is known to inhibit the vasodilatory effects of the endothelial NOS (eNOS) isoform; and aminoguanidine, which is a selective inhibitor of the inducible NOS (iNOS) isoform. Our hypothesis was tested by treating rats with NOS inhibitors and measuring bone formation rates in the tibial epiphysis and diaphysis. Bone formation indices were measured using standard bone histomorphometry. L-NAME treatment significantly raised mean arterial blood pressure (MAP). This effect was partially reversed by addition of L-arginine. Aminoguanidine had no significant effect on MAP, indicating that it did not block eNOS. The treatments also had substantial effects on bone formation in remodeling trabecular bone. L-NAME did not significantly change trabecular bone formation rate, whereas aminoguanidine reduced bone formation rate in the tibial epiphysis by 79% compared with control. This reduction was completely reversed by L-arginine, suggesting that bone formation during remodeling is, in part, mediated through L-arginine metabolism. No effect of aminoguanidine on bone formation was seen in the tibial diaphysis, a site that undergoes minimal bone remodeling. This finding suggests that the L-arginine-NO pathway is important in bone remodeling.

Animals↗

PubMed1998

Antiangiogenic agent (TNP-470) inhibition of ectopic bone formation induced by bone morphogenetic protein-2.

Bone morphogenetic protein (BMP) is a potent inducer of ectopic bone formation, and TNP-470, a synthetic analog of fumagillin, is an antiangiogenic agent that strongly inhibits neovascular formation in vivo. We investigated the effects of TNP-470 on BMP-induced ectopic bone formation to clarify the role of angiogenesis in bone formation. Collagen pellets containing recombinant human BMP-2 (rhBMP-2) were implanted beneath the fasciae of dorsal muscles in mice. By daily subcutaneous administration of TNP-470, ectopic new bone formation was inhibited in a dose-dependent manner. Histological examination revealed that TNP-470 prevented proliferation of mesenchymal cells and chondrogenesis at the initial step of endochondral bone formation. Immunohistochemical staining with a specific antibody against bone morphogenetic protein type IA receptor showed that TNP-470 reduced the number of receptor-positive cells surrounding the BMP pellets. The inhibitory effect of TNP-470 on bone formation continued during the period of its administration, and discontinuation of treatment was followed by the resumption of the whole process of endochondral bone formation. This study showed that TNP-470 reversibly inhibits the biological activity of rhBMP-2 in the early stage of bone induction, suggesting that angiogenesis may play an essential role in the recruitment of BMP-receptor-positive cells that can respond to rhBMP-2 and differentiate into chondrocytes and/or osteoblasts.

Animals↗

PubMed1993

Thermodynamic and kinetic studies of DNA triplex formation of an oligohomopyrimidine and a matched duplex by filter binding assay.

The filter binding method was found to be a powerful method for studying the formation of triplexes composed of a single-stranded homopyrimidine and a duplex with a matched purine-pyrimidine tract. With this technique, we were able to determine thermodynamic and kinetic parameters for triplex formation between a homopyrimidine 19-mer (5'-TCCTCTTCTTTTCTTTCTT-3') and a duplex with sequence 5'-GCAGGAGAAGAAAAGAAAGAACG-3' for the purine strand. The experiments were performed over a wide pH range (3.8-7.4) and a temperature range of 0-35 degrees C. pH and temperature dependencies of the thermodynamic parameters were best explained in terms of a three-state model for triplex formation at low temperatures relative to the melting point. The main results were as follows: (1) pH dependence of the dissociation constants of the triplex is a result of the rapid acid-base equilibrium of pyrimidine single strands; (2) the association rate for triplex formation decreases with increasing pH in accordance with the dissociation constants; (3) the dissociation constant is virtually temperature-independent at low pH, while it becomes strongly temperature-dependent with increasing pH (these results can be explained in terms of a negative, non-zero delta Cp for triplex formation at low pH); (4) the association rate decreases with increasing temperature, and the resulting negative activation energy indicates that the triplex formation process involves a quasi-stable intermediate; (5) the triplex formation is a second-order reaction at low pH, whereas it can be interpreted as a third-order reaction at neutral pH, suggesting that different triplex formation pathways are observed depending on the pH.

Base Sequence↗

PubMed1991

Proton linkage of complex formation between cytochrome c and cytochrome b5: electrostatic consequences of protein-protein interactions.

Two potentiometric methods have been used to study the pH-dependent changes in proton binding that accompany complex formation between cytochrome c and cytochrome b5. With one method, the number of protons bound or released upon addition of one cytochrome to the other has been measured as a function of pH. The results from these studies are correlated with the complexation-induced difference titration curve calculated from the titration curves of the preformed complex and of the individual proteins. Both methods demonstrate that complex formation at acid pH is accompanied by proton release, that complex formation at basic pH is accompanied by proton uptake, and that the change in proton binding at neutral pH, where stability of complex formation is maximal, is relatively small. Under all conditions studied, the stoichiometry of cytochrome c-cytochrome b5 complex formation is 1:1 with no evidence of higher order complex formation. Although the dependence of complex formation on pH for interaction between different species of cytochrome c and cytochrome b5 are qualitatively similar, they are quantitatively different. In particular, complex formation between yeast iso-1-cytochrome c and lipase-solubilized bovine cytochrome b5 occurs with a stability constant that is 10-fold greater than observed for the other two pairs of proteins under all conditions studied. Interaction between these two proteins is also significantly less dependent on ionic strength than observed for complexes formed by horse heart cytochrome c with either form of cytochrome b5.(ABSTRACT TRUNCATED AT 250 WORDS)

Cytochrome c Group↗

PubMed2000

Formation of the "peroxy" intermediate in cytochrome c oxidase is associated with internal proton/hydrogen transfer.

When dioxygen is reduced to water by cytochrome c oxidase a sequence of oxygen intermediates are formed at the reaction site. One of these intermediates is called the "peroxy" (P) intermediate. It can be formed by reacting the two-electron reduced (mixed-valence) cytochrome c oxidase with dioxygen (called P(m)), but it is also formed transiently during the reaction of the fully reduced enzyme with oxygen (called P(r)). In recent years, evidence has accumulated to suggest that the O-O bond is cleaved in the P intermediate and that the heme a(3) iron is in the oxo-ferryl state. In this study, we have investigated the kinetic and thermodynamic parameters for formation of P(m) and P(r), respectively, in the Rhodobacter sphaeroides enzyme. The rate constants and activation energies for the formation of the P(r) and P(m) intermediates were 1.4 x 10(4) s(-1) ( approximately 20 kJ/mol) and 3 x 10(3) s(-1) ( approximately 24 kJ/mol), respectively. The formation rates of both P intermediates were independent of pH in the range 6.5-9, and there was no proton uptake from solution during P formation. Nevertheless, formation of both P(m) and P(r) were slowed by a factor of 1.4-1.9 in D(2)O, which suggests that transfer of an internal proton or hydrogen atom is involved in the rate-limiting step of P formation. We discuss the origin of the difference in the formation rates of the P(m) and P(r) intermediates, the formation mechanisms of P(m)/P(r), and the involvement of these intermediates in proton pumping.

Carbon Monoxide↗

PubMed2000

Interaction of a mitochondrial presequence with lipid membranes: role of helix formation for membrane binding and perturbation.

The binding of a peptide to a biological membrane is often accompanied by a transition from a random coil structure to an amphipathic alpha-helix. Recently, we have presented a new approach which allows the determination of the thermodynamic parameters of membrane-induced helix formation [Wieprecht et al. (1999) J. Mol Biol. 294, 785]. It involves a systematic variation of the helix content of a given peptide by double D-substitution and a correlation of the binding parameters with the helicity. Here we have used this method to study membrane-induced helix formation for the presequence of rat mitochondrial rhodanese (RHD). The thermodynamic parameters of binding of the peptide RHD and of four of its double D-isomers were determined for 30 nm (SUVs) and 100 nm (LUVs) unilamellar vesicles composed of phosphatidylcholine/phosphatidylglycerol (3:1) using circular dichroism spectroscopy, fluorescence spectroscopy, and isothermal titration calorimetry. The incremental changes of the thermodynamic parameters of helix formation were found to be very similar for SUVs and LUVs. Membrane-induced helix formation of RHD entailed a negative enthalpy of Delta H(helix) = -0.5 to -0.6 kcal/mol/residue and was opposed by an entropy of about Delta S(helix) = -1 to -1.4 cal/mol K/residue. The free energy of helix formation, Delta G(helix), was about -0.2 kcal/mol, and helix formation accounted for 50-60% of the total free energy of membrane binding. Dye-release experiments were used to assess the role of helix formation for the membrane perturbation potential of the peptides. While helix formation plays a major role for membrane binding, it appears to have little importance for inducing membrane leakiness.

Animals↗

PubMed1983

Inhibition of nitrogenase-catalyzed NH3 formation by H2.

We have investigated the inhibition by H2 (D2) of NH3 formation by nitrogenase from Klebsiella pneumoniae and have confirmed that the inhibition is competitive vs. N2. D2 inhibits NH3 formation by diverting nitrogenase from production of NH3 to production of HD (one electron per HD). By careful exclusion of N2 from the reaction mixture, we have been able to place an upper limit on N2-independent HD formation by nitrogenase, under 1 atm of D2, at 1% of the total electron flux. Formation of NH3 and formation of HD were inhibited identically by CO. We observed that as the ratio of dinitrogenase to dinitrogenase reductase is increased, the ratio of HD formed to NH3 formed rises, and D2 becomes a stronger inhibitor of N2 reduction. This may be caused in part by an accompanying increase that is observed in the Km of nitrogenase for N2. We propose a model for D2 inhibition of NH3 formation in which D2 and N2 complete for the same form of nitrogenase. According to our proposal, when N2 reacts with nitrogenase, either N2 reduction proceeds to completion if H2 (D2) is absent or, if D2 already is bound to nitrogenase, N2 reduction is aborted and two molecules of HD are produced at the net expense of one electron per HD. Key consequences of the model are that it predicts that H2 (D2) is a competitive inhibitor of NH3 formation and that the apparent Km (N2) for formation of HD and NH3 may differ.

Ammonia↗

PubMed1975

Formation of transient complexes in the glutamate dehydrogenase catalyzed reaction.

The reaction of glutamate dehydrogenase and glutamate (gl) with NAD+ and NADP+ has been studied with stopped-flow techniques. The enzyme was in all experiments present in excess of the coenzyme. The results indicate that the ternary complex (E-NAD(P)H-kg) is present as an intermediate in the formation of the stable complex (E-NAD(P)H-gl). The identification of the complexes is based on their absorption spectra. The binding of the coenzyme to (E-gl) is the rate-limiting step in the formation of (E-NAD(P)H-kg) while the dissociation of alpha-ketoglutarate (kg) from this complex is the rate-limiting step in the formation of (E-NAD(P)H-gl). The Km for glutamate was 20-25 mM in the first reaction and 3 mM in the formation of the stable complex. The Km values were independent of the coenzyme. The reaction rates with NAD+ were approximately 50% greater than those with NADP+. Furthermore, high glutamate concentration inhibited the formation of (E-NADH-kg) while no substrate inhibition was found with NADP+ as coenzyme. ADP enhanced while GTP reduced the rate of (E-NAD(P)H-gl) formation. The rate of formation of (E-NAD(P)H-kg) was inhibited by ADP, while it increased at high glutamate concentration when small amounts of GTP were added. The results show that the higher activity found with NAD+ compared to NADP+ under steady-state assay conditions do not necessarily involve binding of NAD+ to the ADP activating site of the enzyme. Moreover, the substrate inhibition found at high glutamate concentration under steady-state assay condition is not due to the formation of (E-NAD(P)H-gl) as this complex is formed with Km of 3 mM glutamate, and the substrate inhibition is only significant at 20-30 times this concentration.

Adenosine Diphosphate↗

PubMed2002

Identification of N- and C-terminal amino acids of Lhca1 and Lhca4 required for formation of the heterodimeric peripheral photosystem I antenna LHCI-730.

Apoproteins of higher plant light-harvesting complexes (LHC) share considerable amino acid sequence identity/similarity. Despite this fact, they occur in different oligomeric states (i.e., monomeric, dimeric, and trimeric). As a step toward understanding the underlying structure requirements for different oligomerization behavior, we analyzed whether amino acids at the N- and C-termini of Lhca1 and Lhca4 are involved in the formation of the heterodimeric LHCI-730. Using altered proteins produced by deletion or site-directed mutagenesis for reconstitution, we were able to identify amino acids required for the assembly of LHCI-730. At the N-terminus of Lhca1, W4 is involved in heterodimerization. This interaction probably depends on aromatic properties because only replacement of W4 by F resulted in dimer formation. Also, at the C-terminus of Lhca1, W seems to play a crucial role for interaction with Lhca4. A detailed analysis by point mutants revealed the importance of an aromatic residue at position 185. One or more other amino acid(s) located downstream of position 188 may exert additional stabilizing effects, presumably in a cooperative way. The scenario for Lhca4 is different. Dimerization broke down only after the deletion of the entire extrinsic N- or C-terminal region, demonstrating that the termini of Lhca4 are not involved in strong interactions with Lhca1 decisive for dimerization. At the N-terminus, dimerization was abolished after the removal of the same number of amino acids at which monomer formation failed. Site-specific mutagenesis of the amino acid decisive for LHC-formation in a deletion study demonstrated that its character is of no importance for dimerization and, therefore, that abolition of dimer formation may be the consequence of a loss in monomer formation. At the C-terminus of Lhca4, an even higher number of amino acids than required for monomer formation could be removed without the loss of dimerization. The decisive position is I168, located in the third transmembrane region. Because all point mutants of I168 in the full-length protein yielded dimers, failure of dimerization may be caused by either falling below a critical length of the polypeptide chain, resulting in the loss of too many weak interactions, or by too strong an impairment of Lhca4-folding. Interestingly, N- and C-terminal mutants of Lhca4 not able to form stable monomers formed stable dimers, indicating stabilization of labile monomeric complexes by the Lhca1 subunit in dimerization. Finally, the significance for dimer formation of amino acids in other parts of Lhca1 and Lhca4 which may be involved, besides the amino acids identified here in the specific assembly of the heterodimeric LHCI-730, is discussed. Their identification will result in a better understanding of structure characteristics determining the different oligomerization behavior of LHCs.

Amino Acids↗

PubMed2003

Core formation in Escherichia coli bacterioferritin requires a functional ferroxidase center.

Bacterioferritin from Escherichia coli is able to accumulate large quantities of iron in the form of an inorganic iron(III) mineral core. Core formation in the wild-type protein and a number of ferroxidase center variants was studied to determine key features of the core formation process and, in particular, the role played by the ferroxidase center. Core formation rates were found to be iron(II)-dependent and also depended on the amount of iron already present in the core, indicating the importance of the core surface in the mineralization reaction. Core formation was also found to be pH-dependent in terms of both rate and iron-loading characteristics, occurring with maximum efficiency at pH 6.5. Even at this optimum pH, however, the effective iron capacity was approximately 2700 per molecule, i.e., well below the theoretical limit of approximately 4500, suggesting that competing oxidation/precipitation processes have a major influence on the amount of iron accumulated. Disruption of the ferroxidase center, by site-directed mutagenesis or by chemical inhibition with zinc(II), had a profound effect on core formation. Effective iron capacities were found to be linked to iron(II) oxidation rates, and in zinc(II)-inhibited wild-type and E18A bacterioferritins core formation was severely restricted. Zinc(II) was also able, even at low stoichiometries (12-60 ions/protein), to significantly inhibit further core formation in protein already containing a substantial core, indicating the importance of the ferroxidase center throughout the core formation process. A mechanism is proposed that incorporates essential roles for the core surface and the ferroxidase center. A central feature of this mechanism is that dioxygen cannot readily gain access to the core, perhaps because the channels through the bacterioferritin coat are hydrophilic and dioxygen is nonpolar.

Alanine↗

PubMed2004

Inhibition of islet amyloid polypeptide fibril formation: a potential role for heteroaromatic interactions.

The formation of amyloid fibril is associated with major human diseases, including Alzheimer's disease, prion diseases, and type 2 diabetes. Methods for efficient inhibition of amyloid fibril formation are therefore highly clinically important. A principal approach for the inhibition of amyloid formation is based on the use of modified molecular recognition elements. Here, we demonstrate efficient inhibition of amyloid formation of the type 2 diabetes-related human islet amyloid polypeptide (hIAPP) by a modified aromatic peptide fragment and a small aromatic polyphenol molecule. A molecular recognition assay using peptide array analysis suggested that molecular recognition between hIAPP and its core amyloidogenic module is mediated by aromatic rather than hydrophobic interactions. To study the possible effect of aromatic interactions on inhibition of hIAPP fibril formation, we have used peptide and small molecule inhibitors. The addition of a nonamyloidogenic peptide analogue of the core module NFGAILSS, in which phenylalanine was substituted with tyrosine (NYGAILSS), resulted in substantial inhibition of fibril formation by hIAPP. The inhibition was significantly stronger than the one achieved using a beta-sheet breaker-conjugated peptide NFGAILPP. On the basis of the molecular arrangement of the tyrosine-phenylalanine interaction, we suggest that the inhibition stems from the geometrical constrains of the heteroaromatic benzene-phenol interaction. In line with this notion, we demonstrate remarkable inhibition of hIAPP fibril formation and cytotoxicity toward pancreatic beta-cells by a small polyphenol molecule, the nontoxic phenol red compound. Taken together, our results provide further experimental support for the potential role of aromatic interactions in amyloid formation and establish a novel approach for its inhibition.

Amino Acid Substitution↗

PubMed2001

Ligand preorganization in metal ion complexation: molecular mechanics/dynamics, kinetics, and laser-excited luminescence studies of trivalent lanthanide complex formation with macrocyclic ligands TETA and DOTA.

The molecular mechanics and dynamics calculations, kinetics, and laser-excited luminescence studies were carried out for trivalent lanthanide (Ln(3+)) complexes of macrocyclic polyaminopolycarboxylate ligands TETA and DOTA (where TETA is 1,4,8,11-tetraazacyclotetradecane-1,4,8,11-tetraacetic acid and DOTA is 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) to further understand the observed thermodynamic, kinetic, and structural properties and to examine how ligand preorganization affects metal ion complexation. Excitation spectroscopy (emission monitored at 614.0 nm) of the (7)F(0) --> (5)D(0) transition of Eu(3+) was used to study the aqueous properties of the Eu(3+)-TETA system. A stopped-flow spectrophotometric method was used to study the formation kinetics of the aqueous Ce(3+)-TETA/DOTA systems in the pH range 6.1-6.7. Molecular mechanics calculation results are consistent with the proposed mechanism of Ln(DOTA)(-) formation, i.e., formation of a carboxylate O-bonded precursor, followed by metal ion moving into the preformed macrocyclic cavity. For Ln(TETA)(-) formation, at least two carboxylate O-bonded intermediates have been predicted and Ln(3+) ion assisted reorganization of the TETA ligand is present. The calculated bond distances and overall structures of Ln(DOTA)(-) and Ln(TETA)(-) were in agreement with the single-crystal and solution NMR structural data. The origin of the difference in thermodynamic stability of Ln(DOTA)(-) and Ln(TETA)(-) complexes and the corresponding formation intermediates is mainly due to the differences in water-occupancy energy (i.e., whether there is an apical coordinated water molecule), the ligand strain energy, and the cation-ligand interaction energy. Kinetic studies revealed that the formation rates of the Ce(TETA)(-) complex are smaller at lower pH and temperature but become greater at higher pH and temperature, as compared to those of the Ce(DOTA)(-) complex. This is attributed to the lanthanide ion and both mono- and di-hydroxide ion assisted TETA conformational reorganization and higher kinetic activation parameters. The presence of a di-hydroxide ion assisted intermediate rearrangement pathway could make the Ce(TETA)(-) complex formation rate faster at higher pH, and the higher activation barrier makes Ce(TETA)(-) complex formation rate slower at lower pH, as compared to those of the Ce(DOTA)(-) complex.

Journal Article↗

PubMed2000

Kinetics and mechanism of copper(II) complex formation with tripodal aminopolythiaether and aminopolypyridyl ligands in aqueous solution.

The complex formation kinetics of aquated copper(II) ion reacting with 12 related tripodal ligands have been studied in aqueous solution at 25 degrees C, mu = 0.10 M (NaClO4). For most of the ligands studied, specific formation rate constants have been resolved for both the unprotonated and monoprotonated ligand species. All of the tripodal ligands included in this study contain a bridgehead amine nitrogen with the three legs consisting of 2-methylthioethyl or 2-ethylthioethyl and/or 2-pyridylethyl or 2-pyridylmethyl. Since the bridgehead nitrogen is too sterically hindered to participate in initial coordinate bond formation, the first bond must involve a thiaether sulfur or a pyridine nitrogen on one of the pendant legs followed by coordination to the bridgehead nitrogen to complete the first chelate ring. All kinetic data are interpreted in terms of this presumed sequence in the bond formation steps. For the two ligands in which all three pendant legs contain thiaether sulfur donor atoms, the rate-determining step appears to be at the point of second bond formation (chelate ring closure), although the distinction is not well defined. For all other unprotonated ligands, the kinetic behavior is consistent with the first-bond formation being rate-determining. Upon protonation, the rate-determining step appears to shift to the point of proton loss associated with second-bond formation in several cases. A particularly interesting observation is that the tripodal ligand tris(ethylthioethyl)amine (TEMEA) exhibits specific Cu(II) complex formation rate constants that are virtually identical to those for a closely related macrocyclic ligand, 1,4,8-trithia-11-azacyclotetradecane ([14]aneNS3), but the calculated CuIIL dissociation rate constants differ by a factor of 1000. A further comparison of the calculated dissociation rate constants for Cu(II)-tripodal ligand complexes indicates that a Cu(II)-N(pyridine) bond is approximately 10(4) times stronger than a Cu(II)-SR2 bond. This leads to the conclusion that a 1:1 Cu(II)-SR2 complex would have a predicted stability constant of about 0.04 M-1 in aqueous solution--the first estimate obtained for the strength of a single Cu(II)-S(thiaether) bond.

Journal Article↗

PubMed1994

Kinetic and mechanistic analysis of dinucleotide and oligonucleotide formation from the 5'-phosphorimidazolide of adenosine on Na(+)-montmorillonite.

The rate constants for the condensation reaction of the 5'-phosphorimidazolide of adenosine (ImpA) to form dinucleotides and oligonucleotides have been measured in the presence of Na(+)-volclay (a Na(+)-montmorillonite) in pH 8 aqueous solution at 25 degrees C. The rates of the reaction of ImpA with an excess of adenosine 5'-monophosphoramidate (NH2pA), P1,P2-diadenosine 5',5'-pyrophosphate (A5'ppA), or adenosine 5'-monophosphate (5'-AMP or pA) in the presence of the montmorillonite to form NH2pA3'pA, A5'ppA3'pA, and pA3'pA, respectively, were measured. Only 3',5'-linked products were observed. The magnitude of the rate constants decrease in the order NH2pA3'pA > A5'-ppA3'pA > pA3'pA. The binding of ImpA to montmorillonite was measured, and the adsorption isotherm was determined. The binding of ImpA to montmorillonite and the formation of higher oligonucleotides is not observed in the absence of salts. Mg2+ enhances binding and oligonucleotide formation more than Ca2+ and Na+. The rate constants for the oligonucleotide formation were determined from the reaction products formed from 10 to 40 mM ImpA in the presence of Na(+)-montmorillonite using the computer program SIMFIT. The magnitudes of the rate constants for the formation of oligonucleotides increased in the order 2-mer < 3-mer < 4-mer ... 7-mer. The rate constants for dinucleotide and trinucleotide formation are more than 1000 times larger than those measured in the absence of montmorillonite. The rate constants for the formation of dinucleotide, trinucleotide, and tetranucleotide are 41,2.6, and 3.7 times larger than those for the formation of oligo(G)s with a poly(C) template. The hydrolysis of ImpA was accelerated 35 times in the presence of the montmorillonite. The catalytic ability of montmorillonite to form dinucleotides and oligonucleotides is quantitatively evaluated and possible pathways for oligo(A) formation are proposed.

Absorption↗

PubMed2005

Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains.

Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding. We investigated their effect on the dynamics of intrachain loop formation in various unstructured polypeptide chains. Loop formation is significantly slower around trans prolyl peptide bonds and faster around glycine residues compared to any other amino acid. However, short loops are formed fastest around cis prolyl bonds with a time constant of 6 ns for end-to-end contact formation in a four-residue loop. Formation of short loops encounters activation energies in the range of 15 to 30 kJ/mol. The altered dynamics around glycine and trans prolyl bonds can be mainly ascribed to their effects on the activation energy. The fast dynamics around cis prolyl bonds, in contrast, originate in a higher Arrhenius pre-exponential factor, which compensates for an increased activation energy for loop formation compared to trans isomers. All-atom simulations of proline-containing peptides indicate that the conformational space for cis prolyl isomers is largely restricted compared to trans isomers. This leads to decreased average end-to-end distances and to a smaller loss in conformational entropy upon loop formation in cis isomers. The results further show that glycine and proline residues only influence formation of short loops containing between 2 and 10 residues, which is the typical loop size in native proteins. Formation of larger loops is not affected by the presence of a single glycine or proline residue.

Computer Simulation↗

PubMed2006

Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions.

The effect of molecular crowding on the structure and stability of biomolecules has become a subject of increasing interest because it can clarify how biomolecules behave under cell-mimicking conditions. Here, we quantitatively analyzed the effects of molecular crowding on the thermodynamics of antiparallel G-quadruplex formation via Hoogsteen base pairs and of antiparallel hairpin-looped duplex (HP duplex) formation via Watson-Crick base pairs. The free energy change at 25 degrees C for G-quadruplex formation decreased from -3.5 to -5.5 kcal mol(-1) when the concentration of poly(ethylene glycol) 200 was increased from 0 to 40 wt %, whereas that of duplex formation increased from -9.8 to -6.9 kcal mol(-1). These results showed that the antiparallel G-quadruplex is stabilized under molecular crowding conditions, but that the HP duplex is destabilized. Moreover, plots of stability (ln K(obs)) of the DNA structures versus water activity (ln a(w)) demonstrated that the ln K(obs) for G-quadruplex formation decreased linearly as the ln a(w) increased, whereas that for duplex formation increased linearly with the increase in ln a(w), suggesting that the slope approximately equals the number of water molecules released or taken up during the formation of these structures. Thus, molecular crowding affects the thermodynamics of DNA structure formation by altering the hydration of the DNA. The stabilization of the DNA structures with Hoogsteen base pairs and destabilization of DNA structures with Watson-Crick base pairs under molecular crowding conditions lead to structural polymorphism of DNA sequences regulated by the state of hydration.

Base Pairing↗

PubMed2003

Ionizing radiation induces formation of malondialdehyde, formaldehyde, and acetaldehyde from carbohydrates and organic acid.

A study was conducted to investigate irradiation-induced formation of malondialdehyde (MDA), formaldehyde (FA), and acetaldehyde (ACT) from fructose, sucrose, glucose, and malic acid solutions. MDA and FA were generated from the carbohydrate solutions upon irradiation while little was formed from malic acid solution. On the other hand, a much higher amount of ACT was formed from malic acid than from the carbohydrate solutions. The G values (number of molecules formed per 100 eV radiation) for MDA were 0.042, 0.0066, and 0.0026 from 0.9 mg mL(-1) fructose, sucrose, and glucose solutions at pH 3.5, respectively. The G values for FA formation were 0.134, 0.233, and 0.0081 from the fructose, sucrose, and glucose solutions, respectively. As concentration of sugars in solutions increased from 0 to 90 mg mL(-1), the formation of these compounds increased rapidly. A further increase in sugar concentration from 90 to 900 mg mL(-1) resulted in a lower rate of increase in MDA and FA formation. pH had a profound effect on the irradiation-induced formation of these compounds from carbohydrates, especially on MDA formation. The minimum amount of MDA from fructose and glucose solutions was observed at pH 5 while formation of MDA from sucrose solution decreased as pH decreased from 7 to 2. The results can be used by the food industry to optimize food formulation in order to minimize formation of these compounds.

Acetaldehyde↗

PubMed2005

Inhibitory effect of yuzu essential oil on the formation of N-nitrosodimethylamine in vegetables.

The inhibitory effect of yuzu (Citrus junos Tanaka) essential oil on the formation of N-nitrosodimethylamine (NDMA) in the presence of vegetables (31 species) or saliva was investigated by HPLC. Most vegetable extracts enhanced the formation of NDMA. However, the formation ratio of NDMA in vegetable extracts was decreased by yuzu oil in the range of 59 to 22%. In the presence of yuzu oil and saliva, its ratio ranged between 62 and 24%. These results indicated that yuzu oil inhibited the formation of NDMA even in vegetables and saliva. The contents of ascorbic acid, nitrate, and nitrite in the 31 vegetable species were 0.3-65 mg/100 g, 3-581 mg/100 g, and 10-750 microg/100 g, respectively. Ascorbic acid and nitrite had little effect on the inhibition or formation of NDMA at their intact levels. Nitrate accelerated the formation of NDMA, and the addition of saliva further enhanced it. The mechanism of inhibition of NDMA formation by alpha-terpinene was studied. It was assumed from the results of LC-MS that a new compound formed by the reaction of alpha-terpinene with nitrite would be a derivative of alpha-terpinene with dinitroso groups. The molecular weight of this compound was 194. It is suggested that terpene hydrocarbons in citrus essential oils would contribute to the decrease of NDMA formation.

Ascorbic Acid↗