bluuebunny/crossref_metadata_2025 huggingface dataset:
Transient electric birefringence of agarose gels. I. Unidirectional electric fields
Authors: Stellwagen John , Stellwagen Nancy C.
Published: December 2004

The orientation of agarose gels in pulsed electric fields has been studied by the technique of transient electric birefringence. The unidirectional electric fields ranged from 2 to 20 V/cm in amplitude and 1 to 100 s in duration, values within the range typically used for pulsed field gel electrophoresis (PFGE). Agarose gels varying in concentration from 0.3 to 2.0% agarose were studied. The sign of the birefringence varied randomly from one gel to another, as described previously [J. Stellwagen & N. C. Stellwagen (1989), Nucleic Acids Research, Vol. 17, 1537–1548]. The sign and amplitude of the birefringence also varied randomly at different locations within each gel, indicating that agarose gels contain multiple subdomains that orient independently in the electric field. Three or four relaxation times of alternating sign were observed during the decay of the birefringence. The various relaxation times, which range from 1 to ∼ 120 s, can be attributed to hierarchies of aggregates that orient in different directions in the applied electric field. The orienting domains range up to ∼ 22 μm in size, depending on the pulsing conditions.

The absolute amplitude of the birefringence of the agarose gels increased approximately as the square of the electric field strength. The measured Ker constants are ∼ 5 orders of magnitude larger than those observed when short, high‐voltage pulses are applied to agarose gels. The increase in the Kerr constants in the low‐voltage regime parallels the increase in the relaxation times in low‐voltage electric fields. Birefringence saturation saturation curves in both the low‐ and high‐voltage regimes can be fitted by theoretical curves for permanent dipole orientation. The apparent permanent dipole moment increase approximately as the 1.6 power of fiber length, consistent with the presence of overlapping agarose helices in the large fiber bundles orienting in low‐voltage electric fields, the optical factor is approximately independent of fiber length. Therefore, the marked increase in the Kerr constants observed in the low‐voltage regime is due to the large increase in the electrical orientation factor, which is due in turn to the increased length of the fiber bundles and domains orienting in low‐voltage electric fields. Since the size of the fiber bundles and domains approximates the size of the DNA molecules being separated by PFGE, the orientation of the agarose matrix in the applied electric field may facilitate the migration of large DNA molecules during PFGE. © 1994 John Wiley & Sons, Inc.
Conformational analysis of chitobiose and chitosan
Authors: Yui Toshifumi , Kobayashi Hisayoshi , Kitamura Shinichi , Imada Kiyohisa
Published: December 2004

The relaxed potential energy surfaces of chitobiose were calculated based on the MM3‐force field by optimizing dimer structures on a 10° grid spacing of the torsional angles about the glycosidic bonds (Φ,Ψ). The 36 conformations; the four combinations of the hydroxymethyl group orientations coupled with the nine of the secondary group ones— were assumed for each Φ,Ψ conformation. The four conformations, each differing in the hydroxymethyl group orientations, were considered for the whole Φ,Ψ space, and all the 36 conformations, for the restricted space of low energy. While the resulting energy map and the structures of the energy minima were similar to those proposed for cellobiose in many respects, more restricted energy profile was suggested for the relaxed map of chitobiose where differences in the energy level between the global minimum and the local minima were within 5.4 kcal/mol, compared with the equivalent value of 3.6 kcal/mol for cellobiose. Further depression of the global minimum occurred when the acidic residue was used. The Monte Carlo samples of the chitosan chain were generated based on the relaxed map to predict the unperturbed coil dimension in solution. The chitosan chains showed Gaussian behavior at x = 500 (x, degree of polymerization) and gave the characteristic ratio Cx, of about 70, which was much larger than the experimental values observed for the chitosan and cellulosic chains. © 1994 John Wiley & Sons, Inc.
Specificity of trypsin digestion and conformational flexibility at different sites of unfolded lysozyme
Authors: Noda Yasuo , Fujiwara Keiro , Yamamoto Koji , Fukuno Takuji , Segawa Shin‐Ichi
Published: December 2004

Fourteen tryptic peptides and nine intermediates were identified as products of trypsin digestion of reduced and S‐3‐(trimethylated amino) propylated lysozyme. Kinetics of the appearance and disappearance of these products were observed by monitoring the peak areas on the chromatogram. In spite of the complicated reaction pathways, kinetics of the digestion of proteins and several intermediate products show simple decay curves with a single rate constant. In this paper, the trypsin susceptibility of the individual cleavage site is defined as a hydrolytic rate constant of the susceptible peptide bond in the presence of 10 nM trypsin. The cleavage sites of unfolded lysozyme are classified into two groups in terms of the trypsin susceptibility: one has a high susceptibility (10–20 h−1) and the other a low susceptibility (1.0–2.0 h−1). In the unfolded state of lysozyme, in conclusion, the region from residues 15 to 61 has a strong resistance to trypsin digestion; on the other hand, the C‐terminal half of the polypeptide chain is flexible enough to fit into the active site of trypsin.

In addition, six kinds of pentapeptides were synthesized as analogues of lysozyme fragments including Arg 14, Arg 21, Lys 33, Arg 45, Arg 61, and Arg 73. Kinetics of typtic digestion of them were observed. Both kcat and KM were determined for these synthetic pentapeptides. The susceptibility of each cleavage site in pentapeptides is determined and compared with that corresponding in proteins. The susceptibility is usually higher when the susceptible peptide chain is flexible. However, susceptibilities of a few sites in proteins are lower than those in pentapeptides. This means that the peptapeptides, this means that the peptide chains tend to fold locally to prevent trypsin from binding to the sites. It was found that the sites of Arg 21 and Arg 45 are indeed resistant to trypsin, but the site of Lys 33 is not so much, although the hydrolytic rate at Lys 33 itself is extremely slow. © 1994 John Wiley & Sons, Inc.
Electrophoretic mobility of DNA in gels. II. Systematic experimental study in agarose gels
Authors: Heller C. , Duke T. , Viovy J. L.
Published: December 2004

A systematic study has been undertaken to prove or disprove the predictions of a revised reptation model, biased reptation with fluctuations (BRF). Our data, which scan about two orders of magnitude of DNA sizes and of electric fields, and a fourfold range of gel concentrations, are in qualitative and quantitative agreement with the model and support the applicability of this theory to DNA gel electrophoresis. In particular, we show that the mobility in the compression zone scales as the first power of the electric field, and that the limit of separation scales as the inverse first power of the electric field, for low enough fields. © 1994 John Wiley & Sons, Inc.
Thermodynamic strategies for stabilizing intermediate states of proteins
Authors: Haynie Donald T. , Freire Ernesto
Published: December 2004

This paper presents three theorems pertaining to thermodynamic properties of the intermediate (e.g., molten globule) state of proteins exhibiting such a conformation in the presence of GuHCl or urea. The theorems are proved for the three‐state case using the denaturant binding model and the linear extrapolation model; their utility is illustrated via applications to examples in the literature. Theorem One states that the denaturant activity that maximizes the population of a partly folded conformation is at any temperature independent of the Gibbs free energy difference between the intermediate and native states. This result holds for both models of protein–denaturant interaction. The second theorem claims that the population maximum is independent, of the denaturant association constant for the denaturant binding model. Theorem Three, which also applies to both models considered here, states that at the temperatures corresponding to the extrema in the population of the intermediate, the enthalpy change of the intermediate is equal to the excess enthalpy function, an experimentally accessible quantity. In the absence of denaturant, the enthalpy change of the intermediate state at the population extrema can be written as a function of the thermodynamic parameters of the unfolded state alone. These results, which can be applied to systems of any number of states under certain conditions, should aid in the optimization of conditions employed for experimental studies of partly organized states of proteins. © 1994 John Wiley & Sons, Inc.
Measuring the geometry of DNA grooves
Authors: Stofer E. , Lavery R.
Published: December 2004

We present a new method for measuring the widths and depths of the grooves formed within DNA helices. This method overcomes the limitations of simply measuring interstrand phosphate–phosphate distances and has the advantage of yielding continuous values for groove geometry along a DNA fragment. In the case of oligonucleotides, it also clearly indicates the zones in which grooves exist, bounded by two phosphodiester backbones. The methodology has been developed within the Curves algorithm for studying irregular DNA geometries and is based on the optimal, and generally curved, helical axis obtained by this analysis. © 1994 John Wiley & Sons, Inc.
Folding polypeptide α‐carbon backbones by distance geometry methods
Authors: Aszóadi A. , Taylor W. R.
Published: December 2004

Polypeptide α‐carbon backbones were modeled as freely rotating chains made up of spherical monomers. The monomers were assigned an abstract binary “hydrophobicity” property that could be either present or absent. Under the assumption that “hydrophobic” residues tend to cluster together, away from the polar solvent, three‐dimensional conformations of random copolymers of “hydrophobic” and “hydrophilic” monomers were calculated by a novel algorithm based on distance geometry techniques. The simulated molecules were globular and compact, in shape, and possessed distinct hydrophobic cores, indicating that our method was capable of reproducing some of the important global features of real polypeptides. © 1994 John Wiley & Sons, Inc.
On higher buckling transitions in supercoiled DNA
Authors: Schlick Tamar , Olson Wilma K. , Westcott Timothy , Greenberg Jerry P.
Published: December 2004

A combination of detailed energy minimization and molecular dynamics studies of closed circular DNA offers here new information that may be relevant to the dynamics of short DNA chains and/or low superhelical densities. We find a complex dependence of supercoiled DNA energies and geometries on the linking number difference ΔLk as physiological superhelieal densities (|σ| ∼ 0.06) are approached. The energy minimization results confirm and extend predictions of classical elasticity theory for the equilibria of elastic rods. The molecular dynamics results suggest how these findings may affect the dynamics of super‐coiled DNA.

The minimization reveals sudden higher order configurational transitions in addition to the well‐known catastrophic buckling from the circle to the figure‐8. The competition among the bending, twisting, and self‐contact forces leads to different families of supercoiled forms. Some of those families begin with configurations of near‐zero twist. This offers the intriguing possibility that nicked DNA may relax to low‐twist forms other than the circle, as generally assumed. Furthermore, for certain values of ΔL𝓀, more than one interwound DNA minimum exists. The writhing number as a function of ΔL𝓀 is discontinuous in some ranges; it exhibits pronounced jumps as ΔL𝓀 is increased from zero, and it appears to level a characteristic slope only at higher values of ΔL𝓀. These findings suggest that supercoiled DNA may undergo systematic rapid interconversions between different minima e both close in energy and geometry.

Our molecular dynamics simulations reveal such transitional behavior. We observe the macroscopic bending and twisting fluctuations of interwound forms about the global helix axis as well as the end‐over‐end tumbling of the DNA as a rigid body. The overall mobility related to |σ| and to the bending, twisting, and van der Waals energy fluctuations. The general character of molecular motions is thus determined by the types of energy minima found at a given ΔL𝓀. Different time scales may be attributed to each type of motion: The overall chain folding occurs on a time scale almost an order of magnitude faster than the end‐over‐end tumbling. The local bending and twisting of individual chain residues occur at an even faster rate, which in turn correspond to several cycles of local variations for each large‐scale bending and straightening motion of the DNA. © 1994 John Wiley & Sons, Inc.
Relaxed‐residue conformational mapping of the three linkage bonds of isomaltose and gentiobiose with MM3(92)
Authors: Dowd Michael K. , Reilly Peter J. , French Alfred D.
Published: December 2004

Isoenergy surfaces were calculated for the α‐ and β‐anomers of isomaltose and gentiobiose, based on 46,656 conformers for each disaccharide. Low‐energy regions exist for each of the three staggered positions about the C‐5′  C‐6′ bonds, and known crystal structures lie in two of these regions. As expected, the molecular partition function showed greater flexibility for these three‐bond‐linked disaccharides than for comparable two‐bond‐linked structures. A model miniature crystal of gentiobiose accounts for most of the remaining structural differences between the modeled isolated molecule and the crystal structure. Based on models of isolated molecules of isomaltose and gentiobiose, the predicted Boltzmann‐weighted nmr coupling constants were satisfactory, as were predicted optical rotations for gentiobiose. © 1994 John Wiley & Sons, Inc.
Conformation of the flexible bent helix of Leu1‐zervamicin in crystal C and a possible gating action for ion passage
Authors: Karle Isabella L. , Flippen‐Anderson Judith L. , Agarwalla S. , Balaram P.
Published: December 2004

The membrane channel‐forming polypeptide, Leu1‐zervamicin, Ac‐Leu‐Ile‐Gln‐Iva‐Ile5‐Thr‐Aib‐Leu‐Aib‐Hyp10‐Gln‐Aib‐Hyp‐Aib‐Pro15‐Phol (Aib: α‐aminoisobutyric acid; Iva: isovaline; Hyp: 4‐hydroxyproline; Phol: phenylalininol) has been analyzed by x‐ray diffraction in a third crystal form. Although the bent helix is quite similar to the conformations found in crystals A and B, the amount of bending is more severe with a bending angle ≈ 47°. The water channel formed by the convex polar faces of neighboring helices is larger at the mouth than in crystals A and B, and the water sites have become disordered. The channel is interrupted in the middle by a hydrogen bond between the OH of Hyp (10) and the NH2 of the Gln (11) of a neighboring molecule. The side chain of Gln (11) is wrapped around the helix backbone in an unusual fashion in order that it can augment the polar side of the helix. In the present crystal C there appears to be an additional conformation for the Gln (11) side chain (with ≈ 20% occupancy) that opens the channel for possible ion passage. Structure parameters for C85H140N18O22 · xH2O · C2H5OH are space group P212121, a = 10.337(2) Å, b = 28.387(7) Å, c = 39.864(11) Å, Z = 4, agreement factor R = 12.99% for 3250 data observed > 3σ(F), resolution = 1.2 Å. © 1994 John Wiley & Sons, Inc.
Conformation and molecular dynamics calculations on uteroglobin fragment 18‐47
Authors: Improta Sabina , Pastore Annalisa , Mammi Stefano , Peggion Evaristo
Published: December 2004

The conformational properties of fragment 18–47 of rabbit uteroglobin in aqueous solution containing SDS micelles were investigated by two‐dimensional nmr spectroscopy and molecular dynamics calculations. The fragment comprises helices II and III and the β‐turn connecting the two helices.

The nmr results and nmr‐restrained molecular dynamics calculations showed that in the isolated fragment the elements of secondary structure present in the intact protein are preserved only in part. Specifically, a well‐defined α‐helix was found in the sequence 33–44, corresponding to helix III of uteroglobin, while the regions of helix II and β‐turn are characterized by high flexibility in the fragment. © 1994 John Wiley & Sons, Inc.
Quadratic nonlinear optical susceptibility of helical polymers
Authors: Lalov I. J. , Atanasov R. D.
Published: December 2004

The quadratic nonlinear optical susceptibility of a solution of helical polymers and of samples with helices oriented parallel to each other is calculated for regions of characteristic vibrations and of their overtones. The important role of electrooptical and of mechanical anharmonicity for exhibition of overtones in nonlinear spectroscopy is shown. The possibility of the appearance of the giant polarizabilities near bound overtone states is analyzed. The overtone spectrum of amide I is modeled numerically. © 1994 John Wiley & Sons, Inc.
Shape complementarity at protein–protein interfaces
Authors: Norel Raquel , Lin Shuo L. , Wolfson Haim J. , Nussinov Ruth
Published: December 2004

A matching algorithm using surface complementarity between receptor and ligand protein molecules is outlined. The molecular surfaces are represented by “critical points,” describing holes and knobs. Holes (maxima of a shape function) are matched with knobs (minima). This simple and appealing surface representation has been previously described by Connolly [(1986) Biopolymers, Vol. 25, pp. 1229–1247]. However, attempts to implement this description in a docking scheme have been unsuccessful (e.g., Connolly, ibid.). In order to decrease the combinatorial complexity, and to make the execution time affordable, four critical hole/knob point matches were sought. This approach failed since some bound interfaces are relatively flat and do not possess four critical point matches. On the other hand, matchings of fewer critical points require a very time‐consuming, full conformational (grid) space search [Wang, (1991) Journal of Computational Chemistry, Vol. 12, pp. 746–750]. Here we show that despite the initial failure of this approach, with a simple and straightforward modification in the matching algorithm, this surface representation works well. Out of the 16 protein‐protein complexes we have tried, 15 were successfully docked, including two immunoglobulins. The entire molecular surfaces were considered, with absolutely no additional information regarding the binding sites. The whole process is completely automated, with no manual intervention, either in the input atomic coordinate data, or in the matching. We have been able to reach this level of performance with the hole/knob surface description by using pairs of critical points along with their surface normals in the calculation of the transformation matrix. The success of this approach suggests that future docking methods should use geometric docking as the first screening filter. As a geometrically based docking methodology predicts correct, along with incorrect, receptor‐ligand bound conformations, all solutions need to undergo energy screening to differentiate between them. © 1994 John Wiley & Sons, Inc.
Solution three‐dimensional structure of surfactin: A cyclic lipopeptide studied by1H‐nmr, distance geometry, and molecular dynamics
Authors: Bonmatin Jean‐Marc , Genest Monique , Labbé Henri , Ptak Marius
Published: December 2004

The solution three‐dimensional structure of the protonated [Leu7]‐surfactin, an hepta‐peptide extracted fromBacillus subtilis, has been determined from two‐dimensional1Hnmr performed in2H6‐dimethylsulfoxide and combined with molecular modeling. Experimental data included 9 coupling constants, 61 nuclear Overhauser effect derived distances, NH temperature coefficients, and13C relaxation times. Two distance geometry (DISMAN) protocols converged toward models of the structure and the best of them were refined by restrained and unrestrained molecular dynamics (GROMOS). Two structures in accord with the set of experimental constraints are presented. Both are characterized by a “horse saddle” topology for ring atoms on which are attached the two polar Glu and Asp side chains showing an orientation clearly opposite to that of the C11–13aliphatic chain. Amphipathic and surface properties of surfactin are certainly related to the existence of such minor polar and a major hydrophobic domains. The particular “claw” configuration of acidic residues observed in surfactin gives important clues for the understanding of its cation binding and transporting ability. © 1994 John Wiley & Sons, Inc.
Thermodynamic basis of site‐specific cooperativity
Authors: Cera Enrico Di
Published: December 2004

Cooperative phenomena in biological macromolecules arise from the interaction of many distinct subsystems, such as structural domains or binding sites. Cooperative properties of the system as a whole, like protein folding or allosteric transitions, are subject to the restrictions imposed by thermodynamic stability. These restrictions, however, do not apply in the case of individual subsystems open to interactions with the rest of the macromolecule. The site‐specific properties of such subsystems can be understood in general thermodynamic terms from those of a multicomponent system under particular conditions. The analogy provides a thermodynamic basis for site‐specific Cooperativity. © 1994 John Wiley & Sons, Inc.
Molecular dynamics studies of the human CD4 protein
Authors: Ptaszek L. M. , Vijayakumar S. , Ravishanker G. , Beveridge D. L.
Published: December 2004

A dynamical model for an N‐terminal fragment of the human CD4 protein has been determined by computer simulation. The protein has been studied both in vacuo and in solution. Data from both simulations agree moderately well with each other and with the crystal structure. All elements of secondary structure were retained during simulation. Point mutation and sequence replacement studies have shown that a loop in CD4, residues 40–52, is involved in binding with gp120, the human immunodeficiency virus surface glycoprotein.1,2 Our results show that the gp120‐binding loop and a few regions which bind to monoclonal antibodies and class II MHC molecules are the most highly motile areas of the protein. These results are consistent with the suggestion that CD4 binds to target molecules by using induced‐fit contacts. © 1994 John Wiley & Sons, Inc.
13C‐labeled oligodeoxyribonucleotides: A solution study of a CCAAT‐containing sequence at the nuclear factor I recognition site of human adenovirus
Authors: Wu Jian , Serianni Anthony S.
Published: December 2004

The solution behavior of the single‐stranded CCAAT‐containing octamer 1, d(AGCCAATA), that comprises part of the nuclear factor I (NF‐I) recognition site at the origin of replication of human adenovirus has been studied by nmr spectroscopy at 500 and 600 MHz. Proton resonance assignments for 1 were aided by selective 13C enrichment at C1′ of A1 or A5. High‐resolution 13C‐1H heteronuclear multiple‐bond coherence spectra of the 13C‐labeled oligomers permitted the selective detection of furanosyl ring protons within each labeled residue due to short‐ and long‐range 13C‐1H couplings to the enriched C1′. The resulting assignments provided firm starting points in the interpretation of double quantum filtered correlated spectra, yielding information supplemented by total correlated spectroscopy (TOCSY) and rotating frame nuclear Overhauser effect spectroscopic data to completely assign the 1H‐nmr spectrum of 1 and extract 3JHH values for furanose con‐formational analysis. Several 13C‐1H spin‐coupling constants within the 13C‐enriched A1 or A5 residues were measured from cross‐peak shifts in TOCSY spectra, and their signs determined by inspection of the relative orientations of these shifts. 1H‐2‐H and 13C‐1H spin‐couplings both indicate a preference (> 75%) for south (C2′‐endo) conformations by the furanosyl rings of 1. © 1994 John Wiley & Sons, Inc.
Theoretical conformational analysis of the opioid δ antagonist H‐Tyr‐Tic‐Phe‐OH and the μ agonist H‐Tyr‐D‐Tic‐Phe‐NH2
Authors: Wilkes Brian C. , Schiller Peter W.
Published: December 2004

A molecular mechanics study (grid search and energy minimization) of the highly δ receptor‐selective δ opioid antagonist H‐Tyr‐Tic‐Phe‐OH (TIP; Tic: tetrahydroisoquinoline‐3‐car‐boxylic acid) resulted in four low energy conformers with energies within 2 kcal/mol of that of the lowest energy structure. These four conformers contain trans peptide bonds only and represent compact structures showing various patterns of aromatic ring stacking. The centrally located Tic residue imposes several conformational constraints on the N‐terminal dipeptide segment; however, the results of molecular dynamics simulations indicated that this tripeptide still shows some structural flexibility, particularly at the Phe3 residue. Analogous studies performed with the structurally related μ receptor‐selective μ agonist H‐Tyr‐D‐Tic‐Phe‐NH2 resulted in low energy structures that were also compact but showed patterns of ring stacking different from those obtained with TIP. Superim‐position of low energy conformers of TIP and H‐Tyr‐D‐Tic‐Phe‐NH2 revealed that the Phe3 residues of the L‐Tic‐ and the D‐Tic peptide were always located on opposite sides of the plane defined by the Tic residue, thus providing an explanation for the distinct activity profiles of the two compounds in structural terms. Attempts to demonstrate spatial overlap between the pharmacophoric moieties of low energy conformers of TIP and the nonpeptide δ antagonist naltrindole were made by superimposing either the Tyr1 and Tic2 aromatic rings and the N‐terminal amino group or the Tyr1 and Phe3 aromatic rings and the N‐terminal amino group of the peptide with the corresponding aromatic rings and nitrogen atom in the alkaloid structure. In each case a low energy structure of TIP was found that showed good spatial overlap of all three specified pharmacophoric groups. These two conformers may represent candidate structures for the δ receptor‐bound conformation of TIP. © 1994 John Wiley & Sons, Inc.
α,β‐Dehydro‐amino acid residues in the design of peptide structures: Synthesis, crystal structure, and molecular conformation of two homologous peptides—N‐Ac‐Dehydro‐Phe‐L‐Leu‐OCH3and N‐Ac‐Dehydro‐Phe‐NorVal‐OCH3
Authors: Sharma Pushkar , Narula Punit , Singh Tej P.
Published: December 2004

The dehydro‐residue containing peptides N‐Ac‐dehydro‐Phe‐L‐Leu‐OCH3(I) and N‐Ac‐dehydro‐Phe‐NorVal‐OCH3(II) were synthesized by the usual workup procedures. The peptides crystallize from their solutions in methanol in space group P65: (I)a=b= 12.528(2) Å,c= 21.653(5) Å; (II)a=b= 12.532(2) Å,c= 21.695(4) Å. The structures were determined by direct methods. Both peptides adopt similar conformations with ϕ,ψ of dehydro‐Phe as follows: (I) −57.0(5)° and −37.0(5)°; (II) −56.0(5),° and −37.5(5)°. The observed data on dehydro‐Phe when placed at the (i+ 1) position show that the ϕ,ψ values of dehydro‐Phe are either −60°, 140° or −60°, −30°. The conformation of −60°, 140° can be accommodated only with a flexible residue at the (i+ 2) position while the ϕ,ψ values of −60°, −30° are obtained with a bulky residue at the (i+ 2) position as in the present structures. The molecules are packed in a helical way along thecaxis. These are held by two strong intermolecular hydrogen bonds involving both NH as donors and acetyl group and dehydro‐Phe oxygen atoms as acceptors. © 1994 John Wiley & Sons, Inc.
Modified chemotactic peptides: Synthesis, conformation, and biological activity of for‐Thp‐Leu‐ΔzPhe‐OMe
Authors: Torrini I. , Zecchini G. Pagani , Paradisi M. Paglialunga , Lucente G. , Gavuzzo E. , Mazza F. , Pochetti G. , Traniello S. , Spisani S. , Cerichelli G.
Published: December 2004

For‐Thp‐Leu‐ΔzPhe‐OMe (2), an analogue of the chemotactic tripeptide For‐Met‐Leu‐Phe‐OMe, containing 4‐aminotetrahydrothiopyran‐4‐carboxylic acid (Thp) and (Z)‐2,3‐didehydrophenylalanine (ΔzPhe) as achiral, conformationally restricted mimics of Met and Phe, respectively, has been synthesized. In the crystal the new formyltripeptide adopts a type I β‐turn conformation stabilized by a weak H bond between the formylic oxygen and the ΔzPhe NH. 1H‐nmr analysis based on NH solvent accessibility and nuclear Overhauser effect experiments suggests that the β‐turn is not preferred in CDCl3 solution where a γ‐turn, centered at the Thp residue, prevails. The biological activity of 2 has been determined on human neutrophils and compared to that of previously studied analogues. The tripeptide 2 is practically unable to elicit superoxide anion production and lysozyme release, while slight, but not statistically significant activity was induced in chemotaxis. The role of the orientation of the aromatic ring with respect to the backbone adjacent atoms is discussed. © 1994 John Wiley & Sons, Inc.
Molecular modeling of the conformational and sodium ion binding properties of the oligosaccharide component of ganglioside GM1
Authors: Rodgers James C. , Portoghese Philip S.
Published: December 2004

The receptor‐like recognition behavior of the GM1 ganglioside has been examined theoretically in terms of conformational and binding properties. Modeling was conducted at two limiting conditions of dielectric constant in order to determine sensitivity to scaling of coulombic interactions. A systematic conformational search of the GM1 oligosaccharide in the absence of explicit solvent molecules indicates that there are many inherently low energy conformational states. Up to 39 conformers were found with energies within 5 kcal/mole of the observed lowest energy conformer. Using a dielectric constant of 80, a systematic search of sodium binding sites on GM1 identified 37 sites where a positively charged group might bind, while at least 12 sites were identified using a dielectric constant of 1. Notably important binding sites include pockets formed by the proximity of glycosidic (O1), sugar ring (O5), and exocyclic methylene hydroxyl (OH6) oxygens on the sugars. The oxygens of acetyl groups attached to sugars also contribute to the binding. Direct coordination with the carboxylate of sialic acid is not a prerequisite for cationic binding. The large number of conformational states and binding sites for the GM1 oligosaccharide are paradoxical to the specific recognition behavior of the molecule. This paradox can be explained in terms of bridging ligands, which are found from molecular dynamics to be capable of stabilizing molecular conformation. © 1994 John Wiley & Sons, Inc.
Effects of DNA charge and length on the electrophoretic mobility of intercalated DNA
Authors: Reese Howard R.
Published: December 2004

DNA molecules ranging in size from 1 to 630 kilobase pair and intercalated with either ethidium bromide (EtBr) or propidium iodide (PI) were electrophoresed in 1% agarose at four different electric field strengths. The extent of intercalation of EtBr under the conditions of our electrophoresis experiments was determined by a spectroscopic technique, whereas the extent of intercalation of PI was inferred from previous studies. The effects of the increase in DNA contour length and the concomitant decrease of linear charge density were separated based on our analysis of the mobility data. We conclude that the main factor responsible for the reduced electrophoretic mobility of intercalated DNA is the diminished linear charge density and not the increased contour length. © 1994 John Wiley & Sons, Inc.
Vibrational analysis of glutathione
Authors: Qian Weili , Krimm Samuel
Published: December 2004

Infrared and Raman spectra have been obtained of crystalline glutathione and its deuterated derivative and interpreted by normal mode analysis. The force field consisted of our empirical force fields for the peptide group and NH and CO end groups, plus our ab initio force fields for the CH2SH and CH2COOH moieties. Observed bands are reproduced with an average error of 5 cm−1, demonstrating that the vibrational spectrum of such a complex molecule can be understood in great depth. © 1994 John Wiley & Sons, Inc.
The potential energy surface of methyl 3‐O‐(α‐D‐mannopyranosyl)‐α‐D‐mannopyranoside in aqueous solution: Conclusions derived from optical rotation
Authors: Stevens Eugene S.
Published: December 2004

The optical rotation of methyl 3‐O ‐(α‐D‐mannopyranosyl)‐α‐D‐mannopyranoside is calculated semiempirically as a function of the linkage dihedral angles ϕ (H1‐C1‐O1‐C3′) and ψ (C1‐O1‐C3′‐H3′). Comparison with the observed optical rotation in aqueous solution indicates the existence of at least two conformers in solution, which implies a degree of linkage flexibility. The result is in agreement with some, but not all, calculated potential energy surfaces, and with recently published nmr data. © 1994 John Wiley & Sons, Inc.
Modeling of arabinofuranose and arabinan, II. Nmr and Conformational analysis of arabinobiose and arabinan
Authors: Cros Soizic , Imberty Anne , Bouchemal Nadia , Du Penhoat Catherine Hervé , Perez Serge
Published: December 2004

The disaccharide arabinobiose (5‐O‐α‐L‐arabinofuranosyl‐α‐L‐arabinofuranose) constitutes the basic repeating structures found in such polysaccharides as arabinan or in the side chains of the hairy regions of pectins. The conformational behavior of aqueous arabinobiose has been investigated by high resolution nmr and computerized molecular modeling. The complete conformational analysis of the, disaccharide has been achieved with the MM3 molecular mechanics methods using the flexible residue method. In this study, both the puckering of the arabinofuranose, rings and the orientations about the glycosidic torsion angles ϕ, ψ, and ω; were considered. Some insights into conformational transitions were obtained through molecular dynamics simulation using the CHARMM force field. In parallel, transient nuclear Overhauser effects at 400.13 MHz and long‐range vicinal homonuclear and heteronuclear coupling constants have been measured. The theoretical nmr data were calculated taking into account all accessible conformations and using averaging methods for both slow and fast internal motions models. The data do not support a single conformational model, and only conformational averaging yields the excellent agreement between the observed and simulated parameters. Within the potential energy surfaces computed for the disaccharide, several low energy conformers can be identified. When these conformations are extrapolated to regular polysaccharide structures, they generate chains of arabinan displaying right‐ and left‐handed chirality and a wide range of repeating units per turn of helix. © 1994 John Wiley & Sons, Inc.
Redox‐active bis‐cysteinyl peptides. I. Synthesis of cyclic cystinyl peptides by conventional methods in solution and on solid supports
Authors: Musiol Hans‐Jürgen , Siedler Frank , Quarzago Daniela , Moroder Luis
Published: December 2004

Cyclic mono‐cystinyl active‐site fragments of thioredoxin and thioredoxin reductase were synthesized as N‐acetyl and C‐amide octapeptides by conventional methods of peptide synthesis in solution and on solid supports. Using a side‐chain protection based on acid‐labile tert‐butanol‐derived groups and on the S‐tert‐butylthio unsymmetric disulfide for the thiol functions, in combination with Nα‐Z‐ or Nα‐Nps derivatives in the chain elongation steps, the synthesis in solution was carried out in straightforward manner yielding the fully protected octapeptides as well characterized compounds. Upon deprotection with trifluoroacetic acid and reduction of the unsymmetrical disulfides with tri‐butylphosphine, the resulting bis‐cysteinyl‐octapeptides were oxidized in dimethylformamide with azodicarboxylic acid di‐tert‐butyl ester to produce the desired cyclic compounds in good overall yields. For the synthesis on solid supports a similar acid‐labile side‐chain protection was applied in combination with the Nα 9‐flourenylmethyoxycarbonyl derivatives in the chain elongation steps. Thereby acylations were performed with the related amino acid N‐car‐boxyanhydrides (UNCAs) or by the O‐(1H‐benzotriazol‐1‐yl)‐N,N,N′,N′‐tetramethyl‐uronium‐tetrafluoroborate/1‐hydroxybenzotriazole (TBTU/HOBt) procedure. The solid phase synthesis of the two octapeptides led to unexpected difficulties in terms of recovery of peptidic material from the resins in the final acidolytic cleavage step as well as of racemization at the level of the cysteine residues by the TBTU/HOBt coupling method. Racemization was efficiently suppressed by employing the related pentafluorophenyl ester and this method led to crude octapeptide products of a degree of purity comparable to those obtained by the synthesis in solution. However, the recovery of the peptides from the resin, i.e., irreversible reattachment of cleaved peptidic material via alkylation of various side‐chain functions, could not be avoided even using the most efficient scavengers or their cocktails. © 1994 John Wiley & Sons, Inc. © 1994 John Wiley & Sons, Inc.
Nmr study of collagen‐water interactions
Authors: Renou J. P. , Bonnet M. , Bielicki G. , Rochdi A. , Gatellier P.
Published: December 2004

A proton magnetic resonance study of different cross‐linked collagens was performed as a function of water content and temperature. Collagens from three connective tissues (calf, steer, and cow) were chosen according to the different number of nonreducible multivalent cross‐links, which increases during the life of animal. Samples were hydrated under five well‐defined water activities (Aw) ranging from 0.44 to 0.85. The transverse and cross‐relaxation times of water protons were studied as a function of temperature from −20 up to 100°C. From the temperature dependence of relaxation rates, the dynamics of water molecules can be described according to different processes: exchange of protons at the higher temperatures and dipole‐dipole interactions that prevail at the lower temperatures. The exchange processes are analyzed as a function of the residence lifetime of water molecules at the protein interface and of the transfer of spin energy from water protons to macromolecule protons. The proton dipole‐dipole interactions are related to the relaxation parameters of protein and water protons. All the relaxation parameters showed specific behavior for the 0.44 water activity for every tissue. The collagen tissue from calf also showed distinct behavior in comparison with other tissues. © 1994 John Wiley & Sons, Inc.
Predicting immunoglobulin‐like hypervariable loops
Authors: Vasmatzis George , Brower Richard , Delisi Charles
Published: December 2004

A two‐stage method is developed to search the conformational space of small protein segments for low energy structures. Central features of the method are efficient procedures for generating small, eight‐backbone atom, local moves in Cartesian coordinates and for introducing geometric constraints in adaptable Monte Carlo procedures. This allows natural implementation of an adaptive simulated annealing algorithm, which achieves an effective trade‐off between speed and acceptance ratio. The method is applied to the calculation of various immunoglobulin loops. We also develop data base derived rules for identifying constraint conditions, and show that the incorporation of an identified side‐chain constraint allows a 1.2 Å all‐backbone atom rms deviation prediction of a 9 residue long L1 loop. © 1994 John Wiley & Sons, Inc.
Characterization of β‐bend ribbon spiral forming peptides using electronic and vibrational CD
Authors: Yoder Gorm , Keiderling Timothy A. , Formaggio Fernando , Crisma Marco , Toniolo Claudio
Published: December 2004

Terminally blocked (L‐Pro‐Aib)n and Aib‐(L‐Pro‐Aib)n sequential oligopeptides are known to form right‐handed β‐bend ribbon spirals under a variety of experimental conditions. Here we describe the results of a complete CD and ir characterization of this subtype of 310‐helical structure. The electronic CD spectra were obtained in solvents of different polarity in the 260‐180 nm region. The vibrational CD and Fourier transform ir (FTIR) spectra were measured in deuterochloroform solution in the amide I and amide II (1750‐1500 cm−1) regions. The critical chain length for full development of the β‐bend ribbon spiral structure is found to be five to six residues. Spectral effects related to concentration‐induced stabilization of the structures of the longer peptides were seen in the resolution‐enhanced FTIR spectra. Comparison to previous studies of (Aib)n and (Pro)n oligomers indicate that the low frequency of the amide I mode is due to the interaction of secondary and tertiary amide bonds and not to a strong difference in conformation from a regular 310‐helix. © 1995 John Wiley & Sons, Inc.
Molecular dynamics simulations of the effects of ring‐saturated thymine lesions on DNA structure
Authors: Miaskiewicz Karol , Miller John , Ornstein Rick , Osman Roman
Published: December 2004

The effect of thymine lesions produced by radiation or oxidative damage on DNA structure was studied by molecular dynamics simulations of native and damaged DNA. Thymine in position 7 of native dodecamer d(CGCGAATTCGCG)2 was replaced by one of the four thymine lesions 5‐hydroxy‐5,6‐dihydrothymine, 6‐hydroxy‐5,6‐dihydrothymine (thymine photohydrate), 5,6‐dihydmxy‐5,6‐dihydro‐thymine (thymine glycol), and 5,6‐dihydmthymine. Simulations were performed with Assisted Model Building with Energy Refinement force field. Solvent was represented by a rectangular box of water with periodic boundary conditions applied. A constant temperature and constant volume protocol was used, the observed level of distortions of DNA structure depends on the specific nature of the lesion. The 5,6‐dihydrothymine does not cause distinguishable perturbations to DNA. Other lesions produce a dramatic increase in the rise parameter between the lesion and the 5′ adjacent adenine. These changes are accompanied by weakening of Watson–Crick hydrogen bonds in the A6‐T19 base pair on the 5′ side of the lesion. The lesioned bases also show negative values of inclination relative to the helical axis. No changes in the pattern of backbone torsional angles are observed with any of the lesions incorporated into DNA. The structural distortions in DNA correlate well with known biological effects of 5,6‐dihydrothymine and thymine glycol on such processes as polymerase action or recognition by repair enzymes. © 1995 John Wiley & Sons, Inc.
Dominant solvation effects from the primary shell of hydration: Approximation for molecular dynamics simulations
Authors: Beglov Dmitrii , Roux Benoît
Published: December 2004

A simple approximation is developed to account for the dominant effects of solvation in molecular dynamics simulations of biopolymers. A small number of water molecules are included explicitly in the primary hydration shell around the biopolymer. A nonspherical confining potential responding dynamically to the conformational changes of the biopolymer is applied to prevent evaporation and to approximate the conditions of constant pressure of a bulk solution. Simulations of a spherical system of 25 water molecules are lined to adjust the empirical restraining potential to yield a uniform density distribution close to that in the bulk liquid. The primary hydration shell approach is tested with molecular dynamics simulations of simple hydrated peptides. The conformational equilibrium of alanine dipeptide and alanine tripeptide is examined using umbrella sampling calculations. The relative free energies of the C7ax (ϕ = 60, ψ = −80) and αL (ϕ = 60, ψ = 60) conformations of the alanine dipeptide and the opened and closed conformations of a reversed β‐turn modeled with the alanine tripeptide were calculated. The results indicate that the primary hydration shell can reproduce the influence of solvent on small peptides that was observed in simulations involving a much larger number of water molecules. © 1995 John Wiley & Sons, Inc.
Gel electrophoresis measurement of counterion condensation on DNA
Authors: Ma Chenglie , Bloomfield Victor A.
Published: December 2004

We used agarose gel electrophoresis to measure the effective charge neutralization of DNA by counterions of different structure and valence, including Na+, Mg2+, Co(NH3), and sperinidine3+, which competed for binding with an excess of Tris acetate buffer. Linear DNA molecules ranged in size from 1 to 5 kilobases, and supercoiled plasmid pUC18 was also measured. In all cases, the results were in good agreement with theoretical predict ions from counterion condensation theory for two‐counterion mixtures. © 1995 John Wiley & Sons, Inc.
Modeling of long‐range electrostatic interactions in DNA
Authors: Vologodskii Alexander , Cozzarelli Nicholas
Published: December 2004

We used a Monte Carlo approach to compute the statistical properties of closed DNA chains with different descriptions of the electrostatic interactions. We compared these computed results with experimentally measured knotting probabilities, which are very sensitive to intersegment interactions. The calculated results based on the Debye‐Hückel approximation of the solution of the Poisson‐Boltzmann equation agreed very well with the published experimental data, while potential based on counterion condensation theory was clearly less satisfactory. We then compared the simpler hard‐core approximation of electrostatic interactions to the Debye‐Hückel potential. The hard‐core approximation, specified in terms of a DNA effective diameter, gives the same conformational properties of random coils as the Debye‐Hückel approximation. We found clear but relatively small differences between the two potentials for the conformational properties of supercoiled DNA. © 1995 John Wiley & Sons, Inc.
1H‐, 13C‐, and 113Cd‐nmr study of the Cd(II) complex of a blocked peptide, Z‐Cys‐Ala‐Pro‐His‐OMe, in organic solvents
Authors: Zaima Hiroaki , Ueyama Norikazu , Adachi Hayamitsu , Nakamura Akira
Published: December 2004

The Cd(II) complex of a peptide, Z‐Cys‐Ala‐Pro‐His‐OMe was prepared and characterized by absorption, CD, 1H‐, 13C‐, and 113Cd‐nmr, and nuclear Overhauser effect spectroscopy (NOESY) spectra to show the coordination of cysteine thiolate and histidine imizazole to Cd(II) ion. The NOESY spectra in dimethyl formamide showed that the cysteine residue was in proximity to the histidine residue. These results reveal the dictation of Z‐Cys‐Ala‐Pro‐His‐OMe to Cd(II) ion in solution. Temperature‐dependent dissociation equilibrium of histidine imidazole in solution was observed in this complex. Structural features of the chelating peptide are discussed. © 1995 John Wiley & Sons, Inc.
The osmotic sensitivity of netropsin analogue binding to DNA
Authors: Sidorova Nina Yu. , Rau Donald C.
Published: December 2004

The binding of a netropsin analogue to random sequence DNA, monitored by CD, is seen dependent on the concentration of neutral solutes. The binding free energy decreases linearly with solute osmolal concentration and the magnitude of the effect is insensitive to the chemical identity of the solute fur betaine, sorbitol, and triethylene glycol. These solutes appear to modulate binding through their effect on water activity and changes in the hydration of the drug and DNA in the complex reaction, not through a direct interaction with the reactants or the product. The dependence of binding constant on solute concentration can be interpreted as an additional binding of some 50–60 extra solute excluding water molecules by the complex. A water sensitivity of drug binding is further seen from the dependence of binding constants on the type of anion in solution. Anions in the Hofmeister series strongly affect bulk water free energies and entropies. The differences in netropsin analogue binding to DNA with Cl−, F−, and CIO are consistent with the effect observed with neutral solutes. The ability to measure changes in water binding associated with a specific DNA interaction is a first step toward correlating changes in hydration with the strength and specificity of binding. © 1995 John Wiley & Sons, Inc.