Potassium-induced loop conformational transition of a potent anti-HIV oligonucleotide

Spectroscopic, thermal denaturation and kinetic studies have revealed that DNA oligonucleotides 5'-d(GGGTGGGTGGGTGGGT) (T30695) and 5'-d(GTGGTGGGTGGGTGGGT) (T30177) from extremely stable intramolecular G-tetrads via a two-step process that involves the binding of one K+ ion to a central pair of G-quartets and two additional K+ ions, presumably, to the loops (Jing et al., (1997) Biochemistry in press). In that these oligonucleotides are potent HIV-1 inhibitors and among the most active HIV-1 integrase inhibitors yet identified, we have sought to further characterize the K(+)-induced folding process for the purpose of rational chemical modification of these anti-HIV agents. Our NMR investigation demonstrates that in the presence of Li+ ions, T30695 forms an unimolecular tetrad fold, stabilized by a pair of syn-anti-syn-anti G-quartets comprising a central core. The NMR spectrum of T30695 as a function of K+ titration reveals a well-defined transition that saturates upon addition of three K+ ions per oligomer. During this process, the initial Li(+)-dependent G-quartet structure converts into a highly symmetrical, stable form (the NMR detected melting transition temperature is increased by approximately 20 degrees C). The conformation of the G-quartet core remains unchanged, while the loosely structured loop residues become organized in a fashion which is stabilized by K+ ion binding and by interactions with the core. To explain these data, we propose a model wherein K+ binding to the loops induces structural rearrangement, to yield a planar array of loop bases in proximity to the underlying G-quartets. By reference to closely related homologues, which lack activity as an HIV-1 or integrase inhibitor, the possibility is discussed that this ion-coordinated loop structure is crucial to the biological activity of T30695.

Ion selective folding of loop domains in a potent anti-HIV oligonucleotide

Previously, we have described inhibition of HIV-1 infection by T30177, 5'-(GTGGTGGGTGGGTGGGT)-3', an oligonucleotide that is a potent inhibitor of HIV-1 integrase in vitro (Mazumder et al. (1996) Biochemistry 35, 13762). Here a family of oligonucleotides, analogs of T30177, has been studied. On the basis of thermal denaturation, we show that a folded structure of T30177 is much more stable than that of the thrombin binding aptamer, which only differs with T30177 in the loop sequence. Sequence changes reveal that loop interactions are solely responsible for this observed stability difference. In the presence of K+ ion, the fold of T30695, a designed 16mer derivative, is indeed more stable than T30177. Loop folding within T30695 is very ion selective. Quantitative analysis of thermal denaturation suggests that the loops of T30695, 5'-(GGGTGGGTGGGTGGGT)-3', and T30177 confer the ability to coordinate three equivalents of K+ ion (one bound to the core octet and two bound to the loops); however, the thrombin binding aptamer is shown to bind only one K+ equivalent. Folding kinetics and CD titration demonstrate that K+-induced folding of T30695 and T30177 is a two-step process, consistent with a sequential model in which a first equivalent of K+ binds to the octet core, followed by slow K+-induced rearrangement of the loop domains. Comparing structural stability with the capacity of the folded oligomers to inhibit the HIV-1 integrase enzyme in vitro or HIV-1 infection in cell culture, we have found that the folding and activity data are highly correlated, suggesting that formation of an orderly, ion-coordinated loop structure similar to that in T30177 or T30695 may be a prerequisite for both integrase inhibition and anti-HIV-1 activity.

Synthesis and characterization of the human elastin W4 sequence

Following the nomenclature of Sandberg, the W4 sequence of human elastin, [sequence: see text], has been synthesized by solid-phase methods and characterized by carbon-13 nuclear magnetic resonance, amino-acid analysis, mass spectra and elemental analysis. This sequence was then polymerized to greater than 50 kDa as determined by retention in 50 kDa molecular weight cut-off dialysis tubing. It has been successfully cross-linked by gamma-irradiation (20 Mrad) to form an elastomeric matrix, designated as X20-poly(W4). Physical characterizations such as stress/strain, thermolelasticity, acid-base titration and inverse temperature transition studies have been carried out on this elastomer, which is homologous to the striking, poly(VPGVG), W4 sequence of bovine and porcine elastins. These results are compared with previous results on the polypentapeptide of elastin, (VPGVG)n, and it has been demonstrated that X20-poly(W4) also is a dominantly entropic elastomer. Finally, the working model for the structure of this human elastin sequence was derived computationally using molecular mechanics and dynamics calculations. Thus the human W4 sequence appears to be structurally and functionally equivalent to the bovine and porcine W4 sequences in spite of the less regular repeating pentamer sequence.

The determination of binding constants of micellar-packaged gramicidin A by 13C-and 23Na-NMR

Based on the malonyl gramicidin A structure of a single-stranded head-to-head hydrogen bonded right-handed, beta 6.3-helix in dodecyl phosphocholine (DPC) lipid micelles (Jing et al. (1994) Biophys. J. 66, A353), the determination of cation binding sites for gramicidin A (GA) in DPC micelles becomes a significant step in the study of ion transport through the model channel. First, the investigation of cation binding sites in DPC micellar packaged gramicidin A was achieved by 13C-NMR experiments at 30 degrees C using four C-13 labeled GA samples. Then, the analyses based on two different equations, one for single and one for double occupancy, were employed to evaluate the correct occupancy model for GA in DPC micelles. The results clearly indicate double occupancy to be correct for Na+ ion as well as for K+, Rb+, Cs+, and Tl+ ions. Finally, the binding constants for Na+ ion were also estimated by the measurement of the longitudinal relaxation time (T1) using 23Na-NMR of the same sample at the same ffmperature as used for the 13C-NMR study. The binding constants obtained from 23Na-NMR are essentially equivalent to those determined from the 13C-chemical shifts.

Ion pair binding of Ca2+ and Cl- ions in micellar-packaged gramicidin A

The two independent NMR experiments were performed to investigate the interaction between CaCl2 and the gramicidin A (GA) ion transport channel, using 13C-enriched GA and GA molecules incorporated into dodecylphosphocholine (DPC) micelles. The chemical shifts of C-13 labeled carbonyl carbons vs. CaCl2 concentration demonstrate that Ca2+ and Cl- ions interact as an ion pair within the GA structure with the Cl- ion located near the position of the carbonyl group of the Trp11 residue some 5.5 A from the mouth of the GA helix, and the Ca2+ ion bound at the position of the carbonyl group of the Trp15 residue some 2.5 A from the entrance to the helical pore. The measurements of the 35Cl line-widths and transverse relaxation times illustrate that the interaction occurs between Cl- ions and GA in DPC when in CaCl2 solution, that no interaction is detected between Cl- ions and GA in DPC when in NaCl solution, and that the interaction between Cl- ions and GA in DPC when in MgCl2 solution is much weaker than in CaCl2 solution. In short, a Cl- ion can enter the GA when it is paired with a divalent Ca2+ ion; and Ca2+ and Cl- ions as a pair exchange rapidly with sites of the GA dimer.

Electro-chemical transduction in elastic protein-based polymers: a model for an energy conversion step of oxidative phosphorylation

A pair of functional moieties, the carboxyl of an aspartic acid (Asp, D) residue and an N-methyl nicotinamide (NMeN) formed on amide linkage to the epsilon-amino group of the lysine (Lys, K) residue, are coupled to perform energy conversion by means of controlling the transition temperature, Tt, of a common hydrophobic folding and assembly domain within the polytricosapeptide, poly[GDGFP GVGVP GVGVP GFGVP GVGVP GVGK(NMeN)P]. The input of electrochemical energy in the form of the reduction of nicotinamide results in a reduction-induced increase in pKa by 2.5 pH units which represents the performance of the chemical work of picking up a proton. The primary structure and the structures of the oxidized and reduced states are verified by two-dimensional nuclear magnetic resonance. Thus electrochemical transduction, the conversion of electrochemical energy into chemical energy, has been demonstrated for the first time in a designed, synthetic protein-based polymer.

Nanometric design of extraordinary hydrophobic-induced pKa shifts for aspartic acid: relevance to protein mechanisms

Commonly a key element enabling proteins to function is an amino acid residue or residues with functional side chains having shifted pKa values. This article reports the results on a set of protein-based polymers (model proteins) that exhibit hydrophobic folding and assembly transitions, and that have been designed for the purpose of achieving large hydrophobic-induced pKa shifts by selectively replacing Val residues by Phe residues. The high molecular weight polypentapeptides, actually poly(tricosapeptides) with six varied pentamers in fixed sequence, were designed and synthesized to have the same amino acid compositions but different proximities between a single aspartic acid residue and 5 Phe residues per 30 residues. With the 5 Phe residues distal from the Asp residue, the observed pKa shift was 2.9 when compared to the Val-containing reference. With the 5 Phe residues within 1 nm of the Asp residue, the pKa shift was 6.2. This represents a free energy of interaction of 8 kcal/mole. To our knowledge, this is the largest pKa shift documented for an Asp residue in a polypeptide- or protein-water system. Data are reviewed that do not support the usual electrostatic arguments for pKa shifts of charge-charge repulsion and/or unfavorable ion self-energies arising from displacement of water by hydrophobic moieties, but rather the data are interpreted to indicate the presence of an apolar-polar repulsive free energy of hydration, which results from a potentially highly cooperative competition between apolar and polar species for hydration.

Reconstruction of neural tube-like structures in vitro from primary neural precursor cells

Vertebrate central nervous system develops from a neural tube derived from the embryonic ectoderm. In mouse, the neural tube around embryonic day 10 primarily consists of neural precursor cells (NPCs). During the development of embryonic central nervous system, NPCs proliferate and migrate outward; thus later stages show NPCs toward the lumen of the neural tube and neurofilament-positive differentiated cells toward the periphery. In conventional liquid culture, NPCs isolated from mouse on embryonic day 10 proliferate and differentiate into neurofilament-positive neurons. In the present communication, we show that fragments of neural tubes and aggregates of NPCs, when placed into collagen gel matrix, form three-dimensional structures which resemble the neural tube formed in vivo in the developing embryos. Even dissociated NPCs form the three-dimensional structures in the collagen gel matrix. Our results indicate that individual NPCs or fragments of neural tubes carry morphogenetic information which allows them to reconstruct neural tube-like structures in vitro.

Studies on blood substitutes based on hemoglobin and perfluorocarbon

Unmodified, and to a lesser extent, modified stroma-free hemoglobin preparations have been reported to exhibit coronary and renal vasoconstrictor activity in isolated perfused hearts and kidneys. The physiological significance in vivo of such ex vivo demonstrated vasoconstriction has not yet been established. We have conducted a number of in vivo dog experiments designed to elucidate (a) whether free hemoglobin in the plasma phase contributes to diffusive oxygen supply to the tissues and (b) whether excessive vasoconstriction results in functional impairment. Our findings indicate that (a) the infusion of unmodified SFHS does not cause a significant disturbance of central hemodynamics, although it causes an elevation of the arterial blood pressure; the latter is accompanied by vasoconstriction in the skeletal muscle vascular bed and in the renal cortex; (b) there is no significant improvement of diffusive oxygen supply to the tissue at rest; and (c) that glutaraldehyde cross-linked SFHS administered to hypotensive dogs causes a brief further aggravation of hypotension as well as renal vasoconstriction accompanied by renal functional impairment. The findings suggest that coronary autoregulatory mechanisms in vivo can override the vasoconstrictor potency demonstrated in vitro, but the renal effects of SFHS containing unmodified hemoglobin can give rise to significant concern.

Nuclear translocation of fibroblast growth factor during Xenopus mesoderm induction

Mesoderm induction, the earliest inductive cell-cell interaction in vertebrate embryogenesis, is thought to be mediated by polypeptide growth factors including fibroblast growth factor (FGF). Here we present an immunocytochemical analysis of FGF during mesoderm induction in Xenopus laevis. Antibodies to both basic and acidic FGF were immunoreactive with oocytes and early embryos. Immunostaining was predominantly intracellular and was concentrated in the marginal zone and vegetal pole throughout cleavage and blastula stages. In addition, basic FGF (bFGF) antibodies showed intense nuclear staining in these regions, at and following the mid-blastula transition, when embryonic transcription begins. Acidic FGF (aFGF) also appeared in some nuclei at these stages. Taken together the evidence suggests that FGF is prepositioned in mesoderm-forming regions and is actively involved in mesoderm induction in vivo.

Murine tenascin: cDNA cloning, structure and temporal expression of isoforms

Mouse tenascin (TN)-encoding cDNA clones were isolated from a cDNA library of the 2H6GR mammary tumor cell line. Nucleotide (nt) and deduced amino acid (aa) sequences revealed the characteristic primary structure, which begins with a signal peptide and TN unique sequences, follows with 14 1/2 epidermal growth factor (EGF)-like repeats and 13 fibronectin type-III repeats (FN repeat), and concludes with fibrinogen-homologous sequences. Similar to chicken and human TN, the mouse TN cDNA contains five consecutive insertional FN repeats, as well as eight constitutive FN repeats. Three different cDNA clones that may have been generated by alternative splicing of these insertional FN repeats were identified and characterized. Based upon the deduced as sequence, a polyclonal antibody was produced against a synthetic TN peptide. It specifically recognized two TN isoforms of 230 kDNA and 190 kDa in protein extracts of mouse tissues. The tissue distributions of mouse TN mRNAs, revealed by Northern blot analysis, suggest that there is tissue-specific expression of TN isoforms. Two distinct mRNA transcripts (7 kb and 5.5 kg) were detected in brain, skeletal muscle, digestive tract and bladder, but only one was observed in lung, kidney (7 kg) and thymus (5.5 kg). TN mRNA expression was down-regulated 1 month after birth in most tissues. However, the 5.5-kb transcript persisted in cerebellum, thymus, and colon. The spatial and temporal patterns of TN expression seem to be controlled at the level of transcription, because analysis of various tissues by Western blots showed the same pattern as that seen in Northern blots.

Stable perfluorocarbon emulsions using XMO-10 as surfactant: potential oxygen-carrying plasma expanders

XMO-10, a perfluorocarbon surfactant produced emulsions of a perfluorocarbon (Perfluorotripropylamine, FTPA) in vitro which were stable at a range of temperatures for at least 5 days. Most of the emulsion particles were smaller than 1 micron, and all emulsion particles were of these dimensions when the emulsification mixture included 2% lecithin. XMO-10 produced more stable emulsions with smaller particles than did PF68, a widely-used emulsifying agent. XMO-10 was toxic to cells in culture but this toxicity was reduced or abolished when the XMO-10 was emulsified with perfluorocarbon. XMO-10 and lecithin produced relatively stable emulsions of perflurodecalin. Such emulsions, if non-toxic in vivo, might permit excretion of perfluorocarbon through the lungs and thus would permit infusion of sufficient quantities of the preparations to function in oxygen transport in severely anemic animals and man.

Vertex representations of quantum affine algebras

We construct vertex representations of quantum affine algebras of ADE type, which were first introduced in greater generality by Drinfeld and Jimbo. The limiting special case of our construction is the untwisted vertex representation of affine Lie algebras of Frenkel-Kac and Segal. Our representation is given by means of a new type of vertex operator corresponding to the simple roots and satisfying the defining relations. In the case of the quantum affine algebra of type A, we introduce vertex operators corresponding to all the roots and determine their commutation relations. This provides an analogue of a Chevalley basis of the affine Lie algebra [unk](n) in the basic representation.

On the mechanism of channel-length dependence of gramicidin single-channel conductance

Single-channel conductance data on four different gramicidin channel lengths demonstrate that conductance magnitude is neither inversely dependent on the square of the channel length nor on the image force arising from differences in the extent of lipid dimpling (Jordan and Vayl (1985) Biochim. Biophys. Acta 818, 416-420). Rather the conductance differences are consistent with the decreased off-rate constant for the singly occupied state as the ionic radius decreases from that of cesium ion to sodium ion coupled with the decreased probability of the doubly occupied channel due to increased ion-ion repulsion as the channel is shortened (Urry et al. (1984) Biochim. Biophys. Acta 774, 115-119).