bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel nucleic acid helices with hoogsteen base pairing: Symmetry and structure
Authors: Raghunathan G. , Miles H. Todd , Sasisekharan V. 
Published: December 2004

AbstractMolecular structures for parallel DNA and RNA double helices with Hoogsteen pairing are proposed for the first time. The DNA helices have sugars in the C2′‐endo region and the phosphodiester conformations are (trans, gauche−), and the RNA helices have sugars in the C3′‐endo region and the phosphodiester conformations are (gauche−, gauche−). A pseudorotational symmetry relates the two parallel strands of DNA helices and a screw symmetry relates the two strands of RNA helices, which have an associated tilt of the The conformational space of parallel helices with Hoogsteen base pairing, unlike the Watson‐Crick duplex, is highly restricted due to the unique positioning of the symmetry axis in the former case. The features of the parallel double helix with Hoogsteen pairing are compared with the Watson‐Crick duplex and the corresponding triple helix. © 1994 John Wiley & Sons, Inc.
Mixed conformation in Cα,α‐disubstituted tripeptides: X‐ray crystal structures of Z‐Aib‐Dph‐Gly‐Ome and Bz‐Dph‐Dph‐Gly‐Ome
Authors: Pavone V. , Lombardi A. , Saviano M. , Di Blasio B. , Nastri F. , Fattorusso R. , Zaccaro L. , Maglio O. , Yamada T. , Omote Y. , Kuwata S. 
Published: December 2004

AbstractWe report here the synthesis and molecular structure in the solid state of fully protected tripeptides containing Cα,α‐diphenylglycine (Dph), namely Z‐Aib‐Dph‐Gly‐OMe (Aib: Cα,α‐dimethylgrycine) and Bz‐Dph‐Dph‐Gly‐OMe. The molecular conformation around the Dph residue, containing two bulky substituents, is fully extended, while the Aib residue, containing two smaller groups on the Cα atom, adopts the typical 310/α‐helical conformation. Gly residues, without substituents on the Cα atom, show different conformational preferences. Each residue seems to behave, from a conformational point of view, independently from the presence of the other residues, and thus mixed local conformations (folded and extended) are present in the crystals. The nonconventional peptide synthesis, using the Ugi reaction, is also reported. © 1994 John Wiley & Sons, Inc.
Li+ counterion self‐diffusion in ordered DNA
Authors: Andreasson Bo , Nordenskiöld Lars , Eriksson Per‐Olof , Rupprecht Allan 
Published: December 2004

AbstractThe anisotropic self‐diffusion coefficient of 7Li+ (I = 3/2) counterions has been studied in hydrated, macroscopically oriented Li‐(B)DNA fibers at relatively high water contents, corresponding to approximate DNA‐DNA helix axis distances of 22–35 Å, using the pulsed field gradient hmr spin‐echo method. Self‐diffusion coefficients parallel (D∥) and perpendicular (D⟂) to the DNA helix axis increase with increasing salt content and with increasing DNA‐DNA helix axis distance. The observed anisotropy D∥/D⟂ decreases from 1.6 to 1.2 with the DNA‐DNA separation increasing from 22 to 35 Å in the salt‐free sample. This result can be understood by the obstruction effect caused by the DNA molecules themselves. The values of the Li+ self‐diffusion coefficients in the most water‐rich system with no added salt (corresponding to an approximate distance of 35 Å between the DNA helix axes) were D∥ ∼ 1.15 × 10−10 m2 s−1 and D⟂ ∼ 0.98 × 10−10 m2 s−1, compared to 9.14 × 10−10 m2 s−1 for the diffusion of Li+ in an aqueous solution of LiCl (∼ 2.1M). The possible occurrence of restriction effects in the DNA fibers have also been studied by determining the self‐diffusion coefficient at different effective diffusion times. The self‐diffusion coefficient of Li+ in the sample with the largest DNA‐DNA helix axis distance seems to be independent of the effective diffusion time, which indicates that the lithium ions are not trapped within impermeable barriers. The possibility of diffusion through permeable barriers has also been investigated, and is discussed. © 1994 John Wiley & Sons, Inc.
Crystal structure of guanylyl‐2′,5′‐cytidine dihydrate: An analogue of msDNA‐RNA junction in stigmatella aurantiaca
Authors: Krishnan R. , Seshadri T. P. 
Published: December 2004

AbstractSequence analysis of msDNA from bacterium such as Stigmatella aurantiaca, Myxococcus xanthus and Escherichia coli B revealed that the guanine residue of the single‐stranded RNA is linked to the cytosine residue of the msDNA through a 2′–5′ instead of a conventional 3′–5′ phosphodiester bond. We have now obtained the crystal structure of the self‐complementary dimer guanylyl‐2′,5′‐cytidine (G2′p5′C) that occurs at the msDNA‐RNA junction. G2′p5′C crystallizes in the orthorhombic space group P212121 with a = 8.376(2), b = 16.231(5), c = 18.671(4). CuK ∝ intensity data were collected on a diffractometer in the ω −2θ scan mode. The amount of 1699 out of 2354 reflections having I ≥ 3σ (F) were considered observed. The structure was solved by direct methods and refined by full‐matrix least squares to a R factor of 0.054. The conformation of the guanine base about the glycosyl bond is syn (χ1 = −54°) and that of cytosine is anti (χ2 = 156°). The 5′ and 2′ and ribose moieties show C2′‐endo and C3‐endo mixed puckering just like in A2′p5′A, A2′p5′C, A2′p5U, and dC3′p5′G. Charge neutralization in G2′p5′C is accomplished through protonation of the cytosine base. An important feature of G2′p5′C is the stacking of guanine on ribose 04′ of cytosine similar to that seen in other 2′–5′ dimers. G2′p5′C, unlike its 3′–5′ isomer, does not form a miniature double helix with the Watson‐Crick base‐pairing pattern. Comparison of G2′p5′C with A2′p5′C reveals that they are isostructural. A branched trinucleotide model for the msDNA‐RNA junction has been postulated. © 1994 John Wiley & Sons, Inc.
Thermal unfolding equilibria in homodimeric chicken gizzard tropomyosin coiled coils
Authors: Wrabl James , Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractCD studies are presented on thermal unfolding of coiled‐coil homodimers of two genetic variant chains of chicken gizzard tropomyosin (CG‐Tm). The experiments include the effects of cross‐linking both isoforms and the dependence on protein concentration of unfolding in both reduced isoforms, variables not examined in extant work. The general shapes of the unfolding curves for singly cross‐linked species depend on whether the crosslink is at C190 (its site on one isoform) or at C36 (its site on the other). These curves are compared with extant ones for various cross‐linked species of rabbit tropomyosin. The comparison supports the view that the unfolding behavior of cross‐linked species results from a complex interaction of strain at the cross‐link, local variations in structural stability, and loop entropy. The observed concentration dependence of the transition temperature for the uncross‐linked (reduced) species of CG‐Tm is very small (2.9°C) for one variant homodimer and unobservably small (< 2°C) for the other in the 100‐fold concentration range (∼ 0.01–1.0 mg/mL) accessible here. These experimental values of ΔTm are much smaller than are predicted from extant values of the van't Hoff transition enthalpies, calling the latter into question. © 1994 John Wiley & Sons, Inc.
Structural stability of short subsequences of the tropomyosin chain
Authors: Holtzer Marilyn Emerson , Crimmins Dan L. , Holtzer Alfred 
Published: December 2004

AbstractThe native tropomyosin molecule is a parallel, registered, α‐helical coiled coil made from two 284‐residiic chains. Long excised subsequences (≥ 95 residues) form the same structure with comparable thermal stability. Here, we investigate local stability using shorter subsequences (20‐50 residues) that are chemically synthesized or excised from various regions along the protein chain. Thermal unfolding studies of such shorter peptides by CD in the same solvent medium used in extant studies of the parent protein indicate very low helix content, almost no coiled‐coil formation, and high thermal lability of such secondary structure as does form. This behavior is in stark contrast to extant data on leucine‐zipper peptides and short “designed” synthetic peptides, many of which have high α‐helix content and form highly stable coiled coils. The existence of short coiled coils calls into question the older idea that short subsequences of a protein have little structure. The present study supports the older view, at least in its application to tropomyosin. The intrinsic local α‐helical propensity and helix–helix interaction in this prototypical α‐helical protein is sufficiently weak as to require not only dimerization, but macro‐molecular amplification in order to attain its native conformation in common benign media near neutral pH. © 1995 John Wiley & Sons, Inc.
Impact of moisture on thermally induced denaturation and decomposition of lyophilized bovine somatotropin
Authors: Bell Leonard N. , Hageman Michael J. , Bauer Juliane M. 
Published: December 2004

AbstractThe nonisothermal transitions of lyophilized recombinant bovine somatotropin (rbSt) as seen via differential scanning calorimetry were evaluated with respect to moisture content. The transition peak temperature of rbSt decreased with increasing moisture from 161°C in the dry state to a plateau of 65°C at 28% moisture, which is similar to that of rbSt in solution. Using high performance liquid chromatography, this irreversible endothermic transition consisted primarily of unfolding, hydrophobic aggregation, and some covalent modifications. In the dry state, covalent modifications, including polymerization into compounds of higher molecular weight, were more prominent, while in the presence of moisture, hydrophobic aggregation was most prominent. The irreversibility and scan rate dependence of the endothermic phenomena supports the kinetic nature of the transition rather than a simple equilibrium between globular and unfolded states. The apparent activation energy, for the net transition (i.e., unfolding, hydrophobic aggregation, and covalent modifications) was 57 kcal/mol for rbSt at 9.9% moisture. The observed enthalpy of the transition increased, decreased, then approximately leveled off as a function of increasing moisture content. This can be explained by the increasingly significant contribution of the exothermic aggregation at higher moisture contents. © 1995 John Wiley & Sons, Inc.
Some properties of acid‐reassembled tropomyosin
Authors: Holtzer Marilyn Emerson , Downing Lisa J. , Holtzer Alfred 
Published: December 2004

AbstractThe preference for parallelism of the two chains in tropomyosin coiled coils is thought to result from interchain salt bridges. To examine this idea, studies are presented of tropomyosin molecules reassembled from chaotropic solvents in acid solution, where cross‐links cannot exist. The acid‐reassembled molecules are appreciably less disulfide cross‐linkable in acid than native molecules, a result explainable if some antiparallel dimers indeed form at low pH. Physical studies (backbone‐ and tyrosine‐region CD and intrinsic viscosity) indicate that refolding in acid yields a molecular population demonstrably different in tyrosine‐region CD from native, but having comparable (but not identical) helix content, thermal stability, and dimensions. Moreover, the refolding in acid after either thermal or chaotropic‐solvent denaturation yields the same final state, arguing that it is an equilibrium state. All these results are consistent with, but do not prove, that the acid‐reassembled population includes an appreciable fraction (2/3) of antiparallel coiled‐coil dimers. © 1995 John Wiley & Sons, Inc.
For‐Met‐Lys‐Phe‐ For‐Met‐Lys‐Phe‐: A new cyclic analogue of the chemotactic formylpeptides
Authors: Torrini I. , Zecchini G. Pagani , Paradisi M. Paglialunga , Lucente G. , Gavuzzo E. , Mazza F. , Pochetti G. , Traniello S. , Spisani S. 
Published: December 2004

AbstractAs a continuation of the studies on chemotactic N‐formylpeptides, we report here the synthesis and activity of a new cyclic analogue of the prototypical ligand For‐Met‐Leu‐Phe‐OMe. The new compound contains a 20‐membered cyclic moiety made up of a dimeric‐Lys‐Phe‐sequence in which For‐Met is attached to each Lys α‐NH2‐and hence remains outside the ring. The conformation in the crystal of the cyclic precursor of 4, namely and the activity of the structurally related linear analogue For‐Met‐Lys(Z)‐Phe‐OBzl (6), have also been examined. The new analogues 4 and 6 are active as chemoattractants, secretagogues and superoxide anion generating agents, when tested on human neutrophils. The structure‐activity relationship is discussed and related to that of a previously studied cyclic model. © 1995 John Wiley & Sons, Inc.
Solvent effects on model d(CG·G)7 and d(TA·T)7 DNA triple helices
Authors: Cheng Yuen‐Kit , Pettitt B. Montgomery 
Published: December 2004

AbstractUsing free energy molecular mechanics, we find that the molecular effects of solvent are critical in determining relative stabilities in DNA triple helices or triplexes. The continuum solvent model is unable to differentiate the thermodynamics reflecting the basic solvation differences around the occupied major groove in triplexes. In order to avoid the local minimum problem, which is a major limitation of any modeling study, we started our computations with multiple structures rather than relying on the optimization of a single reference structure. By constructing triplex models with different initial helical twists, helical rises, and sugar‐pucker permutations, we explore the potential surface and the structural preference with respect to these variations. We find that in order to accommodate a third strand in triplex formation, the backbone geometry of the B‐DNA duplex target has to be adjusted into A‐DNA‐like form with a deep major groove. This is achieved by concerted adjustment in torsions β, ε, and ζ around the phosphate groups. However, the sugar pucker displays a more rich variation, resulting in conformations not usually associated with the canonical duplex structures. © 1995 John Wiley & Sons, Inc.
Hydrolysis of β‐lactoglobulin by thermolysin and pepsin under high hydrostatic pressure
Authors: Dufour Eric , Hervé Guy , Haertle Tomasz 
Published: December 2004

AbstractHydrolysis of β‐lactoglobulin with thermolysin and pepsin at pressures ranging between 0.1 and 350 MPa showed a significant increase of cleavage rates. Pressure‐induced changes of susceptibility to hydrolysis of β‐lactoglobulin proteolytic sites were also observed. The pressure, raised to 200 MPa, accelerates the hydrolysis of β‐lactoglobulin by thermolysin and changes obtained peptide profiles. Initially, higher pressure makes the N‐terminal, and to a smaller extent, C‐terminal peptide fragments of β‐lactoglobulin molecule, more susceptible to removal by thermolysin. This indicates combined influence of pressure‐induced thermolysin activation and partial unfolding of β‐lactoglobulin by compression at neutral pHs.The rates of hydrolysis of β‐lactoglobulin by pepsin (negligible at 0.1 MPa) are increased considerably with pressure up to 300 MPa. The Susceptibility of β‐lactoglobulin proteolytic sites to peptic cleavage remains constant over all the studied pressure range. The lack of significant qualitative changes in the peptic peptide profiles produced at different pressures and at clearly pressure‐dependent rates points to negative reaction volume changes as the major factor in peptic hydrolysis of β‐lactoglobulin under high pressure. Thus the β‐lactoglobulin molecule resists pressure‐induced unfolding in acid pHs and yields to it in neutral pHs. © 1995 John Wiley & Sons, Inc.
Conformational properties of the proline region of porcine neuropeptide Y by CD and 1H‐NMR spectroscopy
Authors: Chu Shao Song , Velde David Vander , Shobe David , Balse Preeti , Doughty Michael B. 
Published: December 2004

AbstractWe synthesized porcine neuropeptide Y (pNPY) N‐terminal fragments by solid‐phase synthesis techniques and analyzed them for solution Conformational properties by CD and 1H‐nmr spectroscopy. The analogues pNPY1–9 and pNPY1–14 displayed CD spectra indicative of random structures and showed no evidence for induced α‐helical structures in trifluoroethanol (TFE) up to 50%. However, the CD spectra of pNPY1‐9 suggested a Conformational shift in tetrahydrofuran. Although in aqueous solution the CD spectra of pNPY1–21 indicated random structures with induction of only a small percentage of α‐helix in aqueous TFE, pNPY1‐25 displayed 13% a‐helical structure in aqueous solution that increased to 40 and 41% by the addition of TFE and methanol, respectively. The nmr spectra of pNPY1‐9 and the proline region of pNPY1–25 indicated extended structures with all‐trans conformers at Pro5 and Pro8 for pNPY1–9 and at Pro5, Pro8, and Pro13 for pNPY1–25; in each case the Tyrl‐Pro2 amide bond was in both cis and trans conformations. However, observed nuclear Overhauser effect correlations and UN exchange experiments indicated an α‐helical segment in pNPY1–25 initiated by Pro 13 and extending from residues 14 to 25. Thus, the N‐terminal polyproline region of NPY has no propensity to fold into a regular secondary structure, although Pro 13 is a helix initiator, a result consistent with the proposed role of this amino acid in the NPY structural model. © 1995 John Wiley & Sons, Inc.
The “cratic correction” and related fallacies
Authors: Holtzer Alfred 
Published: December 2004

AbstractThe “cratic correction” for removing the contribution of translational motion from standard free energies and entropies of chemical reactions is examined. Although removal of translational effects is useful in interpreting free energy and entropy changes in molecular terms, this particular correction does not do so. No basis for it is found in thermodynamics or statistical mechanics. The appropriate correction for center‐of‐mass translational motion is derived from classical statistical mechanics. However, the importance of recognizing the proper molecular meaning of the remaining free energy is stressed. In any case, this latter correction, however legitimate, is shown to be futile, since it has long been recognized from classical statistical mechanics that all terms involving momenta (thermal wavelength terms) —be they classified as translational, rotational, vibrational, or whatever—necessarily cancel out informing the standard free energy change of any chemical reaction from the constituent standard chemical potentials. © 1995 John Wiley & Sons, Inc.
The energy of formation of internal loops in triple‐helical collagen polypeptides
Authors: Paterlini M. Germana , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractThe sequence‐dependent local destabilization in the interior of the collagen triple helix has been evaluated by means of conformational energy computations. Using a model poly(Gly‐Pro‐Pro) triple helix as the reference state, a method was developed for generating local loops, i.e., internal deformations, and analyzing their conformations. A seven‐residue Gly‐Pro‐Pro‐Gly‐Pro‐Pro‐Gly fragment was replaced by the Gly‐Pro‐Ala‐Gly‐Ala‐Ala‐Gly sequence in one, two, or all three of the strands of the loop region. A set of loop conformations was generated in which the ends of the loop were initially fixed in the triple‐helical structure. The potential energy of the entire deformed triple helix was then minimized, resulting in a variety of structures that contained deformed loops. The conformations of the triple helices at the two ends of the loops remained essentially unchanged in many of the low‐energy conformations. In numerous high‐energy conformations, however, the triple‐helical segments were also partially or totally disrupted. The minimum‐energy conformations of the whole structures were compared in terms of rms deviations of atomic coordinates with respect to the original triple helix, and of the shapes of the loops (using a distance function derived from differential geometry). Three new geometrical parameters—stretch S, kink K, and unwinding U—were defined to describe the changes in the overall orientation of the triple helices at the two ends of the loop. It is shown that, when the number of Pro residues in a short fragment is reduced, the triple helical structure can accomodate internal loops (i.e., distortions) within a 5 kcal/mol cutoff from the essentially unperturbed triple helical structure. For structures with a Gly‐Pro‐Ala‐Gly‐Ala‐Ala‐Gly sequence in all three strands, the probability of finding conformations with internal loops is small, i.e., 0.06. Internal loops affect the overall orientation of these structures, as measured by the helix‐distortion parameters S, K, and U. © 1995 John Wiley & Sons, Inc.
Packing interactions of aib‐containing helices: Molecular modeling of parallel dimers of simple hydrophobic helices and of alamethicin
Authors: Breed J. , Kerr I. D. , Sankararamakrishnan R. , Sansom M. S. P. 
Published: December 2004

Abstractα‐Aminoisobutyric acid (Aib) is a helicogenic α,α‐dimethyl amino acid found in channel‐forming peptaibols such as alamethicin. Possible effects of Aib on helix–helix packing are analyzed. Simulated annealing via restrained molecular dynamics is used to generate ensembles of approximately parallel helix dimers. Analysis of variations in geometrical and energetic parameters within ensembles defines how tightly a pair of helices interact. Simple hydrophobic helix dimers are compared: Ala20, Leu20, Aib20, and P20, the latter a simple channel‐forming peptide [G. Menestrina, K. P. Voges, G, Jung, and G. Boheim (1986) Journal of Membrane Biology, Vol. 93, pp. 111–132]. Ala20 and Leu20 dimers exhibit well‐defined ridges‐in‐grooves packing with helix crossing angles (Ω) of the order of +20°. Aib20 α‐helix dimers are much more loosely packed, as evidenced by a wide range of Ω values and small helix‐helix interaction energies. However, when in a 310 conformation Aib20 helices pack in three well‐defined parallel modes, with Ω ca. −15°, +5°, and 10°. Comparison of helix–helix interaction energies suggests that dimerization may favor the 310 conformation. P20, with 8 Aib residues, also shows looser packing of α‐helices. The results of these studies of hydrophobic helix dimers are analyzed in the context of the ridges‐in‐grooves packing model. Simulations are extended to dimers of alamethicin, and of an alamethicin derivative in which all Aib residues are replaced by Leu. This substitution has little effect on helix–helix packing. Rather, such interactions appear to be sensitive to interactions between polar side chains. Overall, the results suggest that Aib may modulate the packing of simple hydrophobic helices, in favor of looser interactions. For more complex amphipathic helices, interactions between polar side chains may be more critical. © 1995 John Wiley & Sons, Inc.