bluuebunny/crossref_metadata_2025 huggingface dataset:
Ferric complexes of acetoacetyl derivatives of poly(L‐lysine), poly(L‐ornithine), and poly(L‐diaminobutyric acid). I. Preparation and absorption properties in solution
Authors: Palumbo M. , Cosani A. , Terbojevich M. , Bacchion G. , Peggion E.
Published: December 2004

Poly(Nε‐acetoacetyl‐L‐lysine), poly(Nδ‐acetoacetyl‐L‐ornithine) and poly(Nγ‐acetoacetyl‐L‐diaminobutyric acid) form colored complexes with ferric ions in water/dioxane solutions. These complexes are soluble at pH values lower than 2.8 and show their maximum absorption at 257 nm in the uv and at 478 nm in the visible region; whereas the ferric complex of the model compound n‐hexylacetoacetamide exhibits absorptions centered at 258 and 536 nm, respectively. It is shown that in the complex of the model compound one metal ion is bound per acetoacetamide group, while in the complexes of the three polymers two β‐ketoamides side chains are bound per ferric ion under the same solvent, pH, concentration, and ionic strength conditions. The binding constants of ferric ions to the three polymers, and the formation constant of the ferric complex of the model compound are also evaluated.
Intensity fluctuation spectroscopy of deoxyribonucleic acid (DNA). I. Temperature profile of bacteriophage N1‐DNA
Authors: Schmidt R. L. , Boyle J. A. , Mayo John A.
Published: December 2004

Intensity‐fluctuation laser‐light‐scattering spectroscopy has been used to characterize the temperature dependence of the translational diffusion coefficient through the helix–coil region for the DNA isolated from bacteriophage N1. The diffusion coefficient does not change smoothly, but exhibits fine structure detail similar to that seen in the uv absorption hyperchromicity. These changes are related to the heterogeneous distribution of bases along the N1‐DNA chain.
Theory of protein molecule self‐organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments
Authors: Finkelstein A. V. , Ptitsyn O. B. , Kozitsyn S. A.
Published: December 2004

Constants of the helix–coil transition for all natural amino acid residues are evaluated on the basis of thermodynamic parameters obtained in paper I of this series. The specific effects at the termini of the helices are also considered as well as the parameters controlling the formation of β‐bends in the unfolded protein chain. Evaluated s constants of the helix–coil transition agree with the experimental data on helix–coil transitions of synthetic polypeptides in water. Only a very qualitative correlation exists between s constants (both experimental and theoretical) and the occurrence of corresponding residues in internal turns of α‐helices in globular proteins: residues with s > 1 occur in helices as a rule more often than residues with s < 1. At the same time a direct correlation is demonstrated between theoretical parameters of residue incorporation into α‐helical termini and β‐bends in an unfolded polypeptide chain and the occurrence of residues in corresponding positions of the globular protein secondary structures.
Transient electric birefringence of T‐even bacteriophages. III. T2L and T6 with retracted fibers compared with T4B
Authors: Boontje W. , Greve J. , Blok Joh.
Published: December 2004

Measurements of birefringence are used to study electro‐optical and hydrodynamical properties of the bacteriophages T2 and T6 under conditions in which the fibers are folded back along the tail.

The rotational diffusion coefficients corrected to 25°C and water viscosity (D25,w) are 325 ± 12 sec−1 and 322 ± 12 sec−1, respectively. These values differ significantly from those reported for T4(D25,w = 280 ± 9 sec−1). This might be due to a difference in configuration. It could be shown that the orientation of T‐even bacteriophage particles in the electric field is largely due to a permanent dipole moment. This dipole moment can be calculated from the measurements and appeared to be dependent on ionic strength. At low ionic strength (pH 6) the dipole moments of T2 and T6 approach the values 4.1 × 10−25 C·m (1.24 × 105 D) and 6.6 × 10−25 C·m (2.0 × 105 D), respectively, which is much larger than the value of 0.8 × 10−25 C·m (0.24 × 105 D) found for T4. An increase in ionic strength decreases the permanent dipole moment. This effect can be described by a Debye–Hückel model of the screening of surface charges by counterions in the case of T4 and T6. For T2 the picture is more complicated, as an increase in buffer concentration causes a change in configuration.
Cyclic peptides. XVIII. 13C spin‐lattice relaxation times of (X‐pro‐Y)2 cyclic hexapeptides
Authors: Niu C.‐H. , Pease L. G. , Blout E. R.
Published: December 2004

13C spin‐lattice relaxation times (T1's) of four cyclic hexapeptides of sequence, (X‐L‐Pro‐Y)2, are reported. The T1's of the protonated carbons, which undergo dipolar relaxation, are interpreted qualitatively in terms of the overall tumbling motion of the molecule and in terms of internal motion. It is found that three of the cyclic hexapeptides, those which adopt all‐trans β‐conformers, tumble isotropically and appear to lack internal motion in the peptide backbone. The method of Torchia and Lyerla was applied to these compounds in order to compare the mobility of the proline rings. The results show that the sequence and particular type of β‐turn present affect the internal motion of the Pro ring. Data on a fourth cyclic hexapeptide, which occurs in a conformation with two‐cis X‐Pro bonds, suggests that internal motion of the backbone contributes an additional frequency component to the motion of the Y residue α‐carbons. A consideration of the mobility of the proline rings in the conformer with two‐cis peptide bonds revealed that they are significantly more rigid in the two‐cis structure than in the all‐trans.
Differences in circular dichroism and fluorescence between the DNA complexes formed with 3‐amino‐ and 3,8‐ diaminophenanthridinium derivatives
Authors: Kindelis Antonis , Aktipis Stelios
Published: December 2004

The conformation of DNA complexes formed with various 3‐amino‐ and 3,8‐diamino‐phenanthridinium derivatives were examined by CD and fluorescence methods. The CD of these complexes is characterized by major bands in the 300–350‐nm and the 400–550‐nm regions. The CD properties of the complexes formed with diaminophenanthridinium derivatives suggest that the structure of such complexes is well represented by the intercalation complex formed between DNA and ethidium bromide. The substantial and regular increases in ellipticities near 308 nm that occur with increasing DNA‐bound diaminophenanthridinium to DNA phosphate ratios (r) may result from direct interactions between molecules intercalated in neighbouring binding sites. In contrast, the changes in the shape of the CD of DNA complexes of monoaminophenanthridinium derivatives with r and the much lower maximum ellipticities attained suggest that near‐neighbor interactions among intercalated monoaminophenanthridinium derivatives occur much less efficiently than in the corresponding diamino complexes, if at all. Although alternative explanations for the differences in the optical properties between the mono‐ and diaminophenanthridinium complexes of DNA may be offered, such results seem to indicate that complexes formed with monoaminophenanthridinium derivatives are characterized by a conformation which is quite distinct and different from that of the DNA–diaminophenanthridinium complexes. This conclusion is further supported by the considerable increase in fluorescence that accompanies the binding of the diaminophenanthridinium derivatives to DNA as compared to the minor increases, which occur upon the binding of the monoaminophenanthridinium compounds. The importance of conformation as a factor influencing template, function, especially with respect to the RNA polymerase‐catalyzed synthesis of RNA, is now well appreciated. Therefore, methods which could provide information readily about changes in the conformation of a template, i.e., as a result of dye intercalation, are expected to facilitate our understanding of the effects of conformational change on the function and activity of templates.
Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNAPhe
Authors: Sturgill Thomas W.
Published: December 2004

A self‐consistent thermodynamic characterization of the binding of ethidium to yeast phenylalanine‐specific tRNA at 25°C, pH 7.0, in 11 nM MgCl2, 375 nM NaCl, and 25 mM sodium phosphate has been obtained. Two ethidium molecules bind per tRNA under these conditions. The stronger site has a dissociation constant equal to 1.9 ± 0.5 μM and ΔHdis°′ = 12 ± 1 Kcal/mol, and the weaker sites has a dissociation constant equal to 24 ± 9 μM and ΔHdis°′ = 8.9 ± 1.5 Kcal/mol. The average calorimetric ΔHdis°′ for the to sites 10.6 ± 0.4 kcal/mol. The thermodynamics of binding to the stranger sites are most probably the thermodynamics of interaction between A·U (6) and A·U (7), the unique site identified by Jones and Kearns. The binding is enthalpically driven and classical hydrophobic interactions do not appear to be important in the binding reaction.
Influence of local interactions on protein structure. III. Conformational energy studies of N‐acety‐N′‐methylamides of Gly‐X and X‐Gly dipeptides
Authors: Zimmerman S. Scott , Scheraga Harold A.
Published: December 2004

Conformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 20 N‐acetyl‐ N′‐methylamides of Gly‐X and X‐Gly depeptides, where X = Ala, Asn, Asp, Gly, Phe, Ser, Thr, Tyr, Val, and Pro, and also of Leu‐Gly. Each depeptde was found to have 25 or more low‐energy minima, except Gly‐Thr, which had only 11 low‐energy minima because of the stable side chian‐backbone hydrogen present in all low‐energy conformation. As a group, the stble chain‐backbone hydrogen bonds present in all low‐energy conformations. As a group, the Gly‐containing dipeptides were calculated in all low‐energy prpensity for formation of bends than the Ala‐containing depeptides. The X‐ Gly dipeptides were calculated to favor bends more than the Gly‐X dipeptides, primarlly because of the high stability of the type II bend in X‐Gly dipeptides. These results are in agreement with obseved occurrences of bends in the x‐ray structures of globular proteins. The calculated conformation properties were found to be in good agreement with experimental results.
Concentration‐dependent isomerization of bacteriophage T2L
Authors: Welch John B. , Bloomfield Victor A.
Published: December 2004

We have studied the concentration and ionic strength dependence of the fiber‐reorientation transition in T2L bacteriophage, using sedimentation velocity and quasielastic light scattering diffusion measurements. High‐salt and low‐phage concentration favor the form with fibers extended. The equilibrium between the two forms is dependent on the phage Concentration. This behavior is unexpected for a reaction that is apparently unimolecular with respect to phage, and attests to the strong increase in excluded volume and other interactions accompanying fiber extension. The fiber‐extended form has anomalously high diffusion coefficient and low molecular weight according to the Svedberg equation.
Conformation of poly(L‐arginine). II. Complexes with polyanions
Authors: Mita Kazuei , Ichimura Sachiko , Zama Mitsuo
Published: December 2004

Conformaitons of poly(L‐arginine)/polyanion complexes were studies by CD measurements. The polyanions were the homoplolypeptides poly(L‐glutamic acid) and poly(L‐aspartic acid); the synthetic polyelectrolytes and polyethylenesulfonate; and the polynucleotides were native DNA, denatured DNA, and poly(U). It was found that poly(L‐arginine) forms the α‐helical conformation by interacting with the acidic homopolypeptides and the synthetic anionic polyelectrolytes. In each complex, poly(L‐glutamic acid) is in the α‐helical conformation, whereas poly(L‐aspartic acid) is mostly in the random structure. The poly(L‐glutamic acid) complex changed into the β‐sheet structure at the transition temperature about 65°C in 0.01M cacodylate buffer (pH 7). Even in the presence of 5M urea, this complex remained in the α‐helical conformation at room temperature. The existence of the stable complex of α‐helical poly(L‐arginine) and α‐helical poly(L‐glutamic acid) was successfully supported by the model building study of the complex. The α‐helix of poly(L‐arginine) induced by binding with polyacrylate was the most stable of the poly(L‐arginine)‐polyanion complexes examined as evidenced by thermal and urea effects. The lower helical content of the polyethylenesulfonate‐complexed poly(L‐aginine) was explained in terms of the higher charge density of the polyanion. On the other hand, native DNA, denatured DNA, and poly(U) were not effective in stabilizing the helical structure of poly(L‐arginine). This may be due to the rigidity of polyanions and to the steric hindrance of bases. Furthermore, the distinitive structual behavior of poly(L‐arginine) and poly(L‐lysine) regarding polyanion interaction has been noticed throughout the study.
Fluorescence anisotropy decay studies upon hemoglobin A and its subunits
Authors: Bucci E. , Fronticelli C. , Flanigan K. , Perlman J. , Steiner R. F.
Published: December 2004

Fluorescent conjugates of hemoglobin A, its isolated β‐chain, and the apo‐derivative of the β‐chain have been prepared in which the β‐93 sulfhydryl was conjugated with 1,5‐AEDANS. Radiationless enery transfer to the heme group results in a major decrease in fluorescence intensity and decay time. Measurements of the time decay of fluorescence anisotropy, employing single‐photon counting, indicate that the apparent rotational correlation time is, in each case, substantially reduced from the value expected for a rigid molecule of the same molecular weight. This observation raises the possibility that internal degrees of rotational freedom exist.
Solvent accessibility study on tRNAPhe
Authors: Thiyagarajan P. , Ponnuswamy P. K.
Published: December 2004

In order to assess the solvent–solute association in the tRNAPhe molecule, solvent accessibility calculations were carried out for its crystalline and completely extended states following the method of Lee and Richards. To do this, results from the calculations on model trinucleotide systems pApXpA with different bases at position X were used. In the folded form of the molecule, it was found that the oxygen atoms O(I) and O(II) of almost all the phosphate groups and the O(2′) atoms of the sugar rings situated throughout the backbone were highly exposed to the solvent. The amount of reduction found in the solvent accessibilities of the various atoms in going from the extended state to the folded state of the molecule indicates the kind of compactness of the tertiary structure in tRNAPhe. The results give quantitative support to many characteristics of the tRNA molecule, such as loop sections, buried/exposed residues, hydrophobic interactions, etc., which were thought to be due to other factors.
Formation of ternary complexes involving zinc or copper ions, polynucleotides, and polypeptides containing glutamic acid and tyrosine residues
Authors: Bere Augustin , Helene Claude
Published: December 2004

Metal ions such as Zn2+ and Cu2+ can mediate interactions between copolypeptides (Glux, Tyry)n and polynucleotides. CD data show that these ternary complexes are characterized by an unstacking of nucleic acid bases, while the polypeptide adopts an α‐helical conformation as observed in the two binary complexes polynucleotide–cation and polypeptide–cation. Fluorescence studies demonstrate that tyrosyl side chains interact with nucleic acid bases in the ternary complexes, leading to a quenching of tyrosine fluorescence.
Characterization of molecular motions in 13C‐labeled aortic elastin by 13C‐1H magnetic double resonance
Authors: Fleming W. W. , Sullivan C. E. , Torchia D. A.
Published: December 2004

Purified insoluble elastin samples labeled with [1‐13C]valine, [1‐13C]alanine, and [1‐13C]‐lysine were prepared from chick aorta in culture. The molecular mobility at the labeled sites was investigated using 13C‐1H magnetic double‐resonance spectroscopy. Linewidths, T1, and nuclear Overhauser effect (NOE) values of the labeled carbons alone were obtained from dipolar decoupled difference spectra. Analysis of these parameters together with signal intensity measurements showed that essentially all the valyl residues, ca. 75% of the alanyl residues, and ca. 60% of the lysyl residues were characterized by rapid backbone motions having τ = 65 nsec. Resonances due to the remaining alanyl and lysyl residues were detected in cross‐polarization experiments, which enhance the signals of motionally restricted carbons. Since lysyl and alanyl residues are found in the crosslink regions of elastin, whereas valyl residues are not, we conclude that crosslinks rather than secondary structures in the extensible region of the protein are the main source of motional restrictions in the protein. Elastin chain mobility was monitored by linewidth measurements over the range −90 to +70°C. When the swelling solvent (0.15M NaCl) was fixed at 0.6 g/g of elastin, a rapid monotonic reduction in chain mobility was observed as the temperature was lowered from 50 to 5°C. Liquidlike mobility was completely lost at 5°C. In contrast, the same sample in contact with excess solvent retained its liquidlike molecular mobility until −13°C, where it abruptly became rigid. The molecular mobility of this sample was temperature insensitive in the physiologically interesting range, 20–40°C, as a consequence of the opposing influences of temperature and swelling. Taken together these nmr data indicate that under physiological conditions, elastin is a network of mobile chains whose motions are strongly influenced by protein–solvent interactions.
Neutron‐scattering studies of the structure of chromatin core particles in solution
Authors: Braddock Gordon W. , Baldwin John P. , Bradbury E. Morton
Published: December 2004

The structure of the nucleosome core particle in solution has been studied by neutron scattering using the full‐contrast variation technique, which reduces the experimental spectra to three fundamental scatter functions holding information on shape and structure. Systematic calculations of the fundamental scatter functions expected from proposed core‐particle models have been compared with the observed functions and show that the neutron‐scattering criteria severely restrict the number of models which can be valid for the structure in solution. The best model for the core particle in solution has a hydrophobic histone core about which 1.7 ± 0.1 turns of DNA are wrapped at a pitch between 3.0 and 3.5 nm. This core contains most of the histone and has an average thickness of 4 nm and diameter 6.4–7.5 nm. While solution scattering is not able to specify uniquely the actual shape of the core to high resolution, all models which are possible for the shape of the core to a resolution justified by the data have been considered. It is clear that cylindrical or wedge shapes compatible with the above dimensions are valid structures. A hole probably penetrates the histone core, but the data do not allow a diameter greater than 1 nm. Available evidence suggests that about a quarter of the total histone is outside the core.
Interactions between polyelectrolytes. DEAE‐sephadex–polymethacrylic acid
Authors: Feitelson J. , Josephs R.
Published: December 2004

The interaction between a highly swollen polyelectrolyte and a polymer coil‐of low charge density was investigated. Diethylaminoethyl dextran (DEAE) and polymethacrylic acid (PMA) at low pH served as a model system. Distribution measurements of PMA between a DEAE resin and ambient solution showed that the interaction increased with pH (number of charges per PMA molecule), temperature, and molecular weight of PMA. Since the absorption of PMA in the polyelectrolyte phase is an endothermic process it must be accompanied by a large positive entropy increase. The latter was sought in the structural changes of water which occur in the vicinity of the interacting polymers. The magnitude of the enthalpy changes for two PMA fractions indicate that not only interactions between ionized groups but also nonpolar and even purely polymer effects should be considered in this system.
Model connective tissue systems. A physical study of gelatin gels containing proteoglycans
Authors: Meyer F. A. , Comper W. D. , Prestox B. N.
Published: December 2004

The swelling behavior of gelatin gels containing proteoglycans (sulphated proteoglycans from bovine intervertebral discs and a hyaluronate proteoglycan from bovine synovial fluid) when immersed in osmotically active solutions of dextran have been measured. The presence of the proteoglycans markedly affects the internal osmotic contribution to the swelling pressure of the gel. These internal osmotic pressures are considerably in excess of the sum of the osmotic activities of the individual components. This behavior is understood in terms of an entropic interaction between the gelatin and the proteoglycan molecules. By use of the “dilute solution” treatment of Flory, the osmotic pressure excesses are related to the volumes and hence dimensions of the interact acting species. A comparison of these values with those calculated by other means shows good agreement. The osmotic behavior of the complex gels can be understood on a mechanistic basis, if we regard the gelatin and sulphated proteoglycans as spheres and the hyaluronate proteoglycan as a rod.
Comprehensive conformational analysis of (Gly‐Pro‐Pro)n and (Gly‐Pro‐Hyp)n related to collagen
Authors: Tumanyan Vladimir G. , Esipova Natalia G.
Published: December 2004

A complete analysis of all possible conformations with correct hydrogen bonds of the collagen II type was performed on the basis of developed simultaneous equations. Using a unimodal search (by varying Ψ3), the energetically favorable structure was obtained. No other energetically satisfactory structural solutions are possible. The next aim was to obtain a precise model of the molecule. The program used includes a subroutine for continual deformation of the pyrrolidine rings. The set of parameters determining the structure consists of 14 independent variables (8 dihedral and 6 bond angles). As starting points for the energy optimization, conformations produced by scanning and some structures from previous work were used. The final structures (practically the same for both polymers) have helix parameters h = 0.285 nm and t = 52°, which are in excellent agreement with the 7/2 symmetry of diffraction data. The conformations of the pyrrolidine rings are of the B type, i.e., C2‐Cβ‐exo‐Cγ‐endo. For both polypeptides, the conformations of imino acids in position 3 of the triplet are the same; in position 2, however, they are slightly different. The difference in diffraction patterns for the 7/2 and 10/3 helices is discussed.
Sequence‐dependent conformations of DNA duplexes: The TATA segment of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex in aqueous solution
Authors: Patel Dinshaw J. , Shapiro Lawrence , Hare Dennis
Published: December 2004

The base and sugar protons of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex have been assigned from two‐dimensional correlated (COSY) and nuclear Overhauser effect (NOESY) measurements in D2O solution at 25°C. The nucleic acid protons have been assigned from NOEs between protons on adjacent bases on the same and partner strands, as well as from NOEs between the base protons and their own and 5′‐flanking H1′, H2′, H2″, H3′, and H4′ sugar protons. These assignments are confirmed from coupling constant and NOE connectivities within the sugar protons of a given residue. Several of these NOEs exhibit directionality and demonstrate that the d(G‐G‐T‐A‐T‐A‐C‐C) duplex is a right‐handed helix. The relative magnitude of the NOEs between the base protons and the sugar H2′ protons of its own and 5′‐flanking sugar demonstrate that the TATA segment of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex adopts a B‐DNA type helix geometry in solution, in contrast to the previous observation of a A‐type helix for the same octanucleotide duplex in the crystalline state.
Structural investigation of poly‐L,D‐proline, a synthetic ion channel across bilayer membranes: Crystal structure and molecular conformation of two tetra‐D,L‐proline derivatives
Authors: Colapietro M. , De Santis P. , Palleschi A. , Spagna R.
Published: December 2004

The crystal structures and molecular conformations of two tetraproline derivatives with alternating configurations Boc(D‐Pro,L‐Pro)2OH and Boc(D‐Pro,L‐Pro)2OCH3 are investigated in connection with the ability of the homologous polymer to selectively increase (as an ion channel) the ion permeability across bilayer membranes. Both tetramers are characterized by the cis‐trans alternating conformation of the peptide bonds, which formally transforms in a turn of the poly‐D,L‐proline channel after a cis‐trans change of the central peptide residue.
Base tilt of B‐form poly[d(G)]‐poly[d(C)] and the B‐ and Z‐conformations of poly[d(GC)]‐poly[d(GC)] in solution
Authors: Edmondson Stephen P. , Johnson W. Curtis
Published: December 2004

We have measured the CD, isotropic absorption, and linear dichroism (LD) in the vacuum‐uv spectral region for the B‐conformations of poly[d(G)]‐poly[d(C)] and poly[d(GC)]‐poly[d(GC)], and for the Z‐conformation of poly[d(GC)]‐poly[d(GC)] formed in 70% trifluoroethanol. The reduced dichroism (LD divided by isotropic absorption) for all conformations varied with wavelength, indicating that the bases are not perpendicular to the helix axis. Since the directions of the transition dipoles are known, the inclinations and axes of inclination of each base can be determined from the wavelength dependence of the reduced dichroism spectra. The results indicate that the base normals of the (G + C) polymers in the B‐ and Z‐conformations are tilted at angles greater than 19° with respect to the helix axis. The guanine and cytosine bases have different inclinations, and the tilt axes are not parallel. Therefore, the bases for all the (G + C) polymer conformations studied are buckled and propeller twisted.
CD of the li‐salt of DNA in ethanol/water mixtures: Evidence for the B‐ to C‐form transition in solution
Authors: Bokma Jos T. , Curtis W. Johnson , Blok Johan
Published: December 2004

The conformational change of Li‐DNA in water/ethanol mixtures is followed by the change in the CD spectrum in solutions containing various percentages of ethanol in the range from 0 to 95%. Two main transitions can be distinguished. The first occurs in the range from 0 to 70% and is represented by a large reduction of the intensity of the positive CD band around 275 nm, which is apparently related to a small change in the number of base pairs per turn. Secondly, at higher percentages of ethanol (> 80%) a conformational change is detected, which is expressed as a reduction of the 245‐nm negative CD intensity. According to x‐ray diffraction experiments of fibers of Li‐DNA, the C‐form is attained in 95% ethanol, while at 70% ethanol a B‐like structure is observed. The CD experiments reported here also show that for DNA in solution the dependence on percentage of ethanol is composed of two main transition regions. The C‐form would then be adopted at high (∼ 95%) ethanol percentage. The 0–70% transition, although strongly expressed in optical CD experiments, has to be related to relatively small structural changes within the B‐family of DNA structures, which probably induce an enhanced contribution of n → π* transitions to the CD spectrum.
Vibrational spectroscopy of L‐valyl‐glycyl‐glycine, a parallel‐chain β‐structure
Authors: Bandekar Jagdeesh , Krimm S.
Published: December 2004

Bands in the ir and Raman spectra of L‐valyl‐glycyl‐glycine (VGG) and VGG‐ND have been assigned on the basis of a normal mode analysis of the known parallel‐chain β‐structure of this tripeptide. Amide I, II, III, and V mode shifts are obtained by the interactions of dipole derivatives in symmetry coordinates, referred to as dipole derivative coupling. These derivatives, obtained from ab initio studies, are also used to calculate ir intensities of amide I, II, and V modes. The agreement between predicted and observed frequencies and intensities is very good, providing confidence in the application of our force fields to the calculation of the vibrational modes of the general parallel‐chain β‐sheet structure (following paper).
Collective motion in DNA and its role in drug intercalation
Authors: Chou Kuo‐Chen , Mao Boryeu
Published: December 2004

The effects of collective motion in DNA as reflected by resonance coupling among its intact segments have been discussed for both linear and circular DNA molecules. The results indicate that due to the effects of this kind of internal collective motion, the energy will be at times highly concentrated at some spots. As a result of the overfocus of energy, the stress built up along the direction of hydrogen bonds between complementary base pairs will be dramatically increased, rupturing a series of consecutive hydrogen bonds simultaneously and resulting in a suddenly free jerk, such that the DNA molecule will undergo a local “quake.” The “hole” formed by this kind of quake‐like motion will be large enough for bulky drugs to gain entrance and intercalate into DNA. Even for smaller drugs, this local quake‐like motion can also provide a significant mode of entry for intercalation. Energy minimizations carried out for DNA–drug complexes indicate that, for most drugs, a distortion or disruption of 2 to 4 base pairs occurs at the intercalation site in DNA molecules.
On the interaction of daunomycin with synthetic alternating DNAs: Sequence specificity and polyelectrolyte effects on the intercalation equilibrium
Authors: Xodo Luigi Emilio , Manzini Giorgio , Ruggiero João , Quadrifoglio Franco
Published: December 2004

The interaction of daunomycin with ctDNA and six purine–pyrimidine alternating poly‐deoxynucleotides has been studied using fluorometric and uv‐visible absorption methods. In the explored binding range of r > 0.05, the intercalation of the drug into the DNAs proved to be anticooperative, as indicated by the pronounced upward curvature of all the Scatchard plots obtained. The experimental data have been analyzed according to the recent theory of Friedman and Manning, which describes the polyelectrolyte effects on the site binding equilibria, drug intercalation included. We found that, accounting for the polyelectrolyte effects in the neighbor site exclusion model, the experimental data were nearly equally well described, in a wide range of binding ratios, by assuming the presence of sequence specificity effects (site size = 2 base pairs, exclusion parameter n = 1) or its absence (site size = 1 base pair, n = 1.7). The relevant results are as follows: (a) Daunomycin binds to all the DNAs considered with a stoichiometry of approximately 1 drug for every two base pairs. (b) The anticooperative nature of the interaction is essentially polyelectrolytic in origin. (c) The binding affinity shown by the drug for the different sites considered decreases in the order of Gm5C > AT > AC‐GT > IC > GC > AU, indicating a stabilizing effect of the —CH3 group in position 5 of the pyrimidines. (d) The extent of quenching of the intrinsic fluorescence of daunomycin in the presence of DNA is bound to the presence, at the intercalation site, of a guanine residue, since GC, Gm5C, and AC‐GT sites induce a nearly total quenching, whereas AT, AU, and IC sites act only partially in this respect. The structural results obtained from the daunomycin‐d[(CGTACG)]2 crystal suggest that the 2‐NH2 group of guanine might be responsible for such a phenomenon. The influence of both the temperature and the ionic strength on the free energy of drug intercalation into ctDNA, poly[d(G‐C)] : poly[d(G‐C)], and poly[d(A‐C)] : poly[d(G‐T)] is examined and discussed.
CD studies of double‐stranded polydeoxynucleotides composed of repeating units of contiguous homopurine residues
Authors: Gudibande Satyanarayana R. , Jayasena Sumedha D. , Behe Michael J.
Published: December 2004

Double‐stranded synthetic polydeoxynucleotides of the general form poly[d(GnCn)] · poly[d(GnCn)], poly[d(GnC)] · poly[d(GCn)], and poly[d(AnTn)] · poly[d(AnTn)] have been synthesized. When n = 4 or larger, the CD spectra of polymers of the form poly[d(GnCn)] · poly[d(GnCn)] or poly[d(GnC)] · poly[d(GCn)] closely resemble the spectrum of poly[dG] · poly[dC], suggesting that a string of four continguous guanosine residues is sufficient to induce a conformation resembling that of the polypurine · polypyrimidine. With polymers of the form poly[d(AnTn)] · poly[d(AnTn)], however, the CD spectrum only gradually approaches that of poly[dA] · poly[dT].
DNA gel electrophoresis: Effect of field intensity and agarose concentration on band inversion
Authors: Slater Gary W. , Turmel Chantal , Lalande Marc , Noolandi Jaan
Published: December 2004

We study the effect of electric field intensity and agarose gel concentration on the anomalous electrophoretic mobility recently predicted by the biased reptation model and experimentally observed for linear DNA fragments electrophoresed in continuous electric fields. We show that high fields and low agarose concentrations eliminate the physical mechanism responsible for anomalous DNA mobility and band inversion, in good agreement with theory, thus restoring the monotonic mobility–size relationship necessary for unambiguous interpretation of the results of DNA gel electrophoresis.
Modeling cation‐driven (proto)fibrin coagulation
Authors: Marx Gerard
Published: December 2004

The coagulation mechanism of thrombin‐ and reptilase‐activated fibrinogen is the focus of this report. Three types of gels were evaluated for their sensitivity to physiologic levels of Ca(II) and Zn(II): Fibrin gel formed directly by adding thrombin or reptilase to fibrinogen, protofibrin gel generated by adding Ca(II) and Zn(II) to soluble fibrin oligomers (protofibrills), and gels induced by sudden pH increase of fibrin monomer (pH 4.9–7.4). The turbidity and viscoelasticity of reptilase‐ and thrombin‐activated fibrin are similarly sensitive to Ca(II) and Zn(II) scanning electron micrographs (SEM) of fibrin gels from pH jump experiments show that their constituent fibers are relatively homogeneous and only mildly affected by divalent cations. This contrasts with the cation sensitivity of normally formed fibrin and protofibrin gels. Based on these and previously published experiments, a graphic shorthand is developed to describe the directionality of linear and lateral polymerization modes that result in cation‐driven (proto)fibrin gelation.
Analysis of dihedral angles distribution: The doublets distribution determines polypeptides conformations
Authors: Unger Ron , Harel David , Wherland Scot , Sussman Joel L.
Published: December 2004

It is possible to construct fragments of protein structures by using the known values for the fixed bond lengths, bond angles, and torsion angles, and “dialing” in the dihedral angles ϕ and ψ. By choosing these angles in different ways, it is possible to create different populations of fragments and to investigate their properties. We analyzed the following populations: Real fragments taken randomly from known structures. Reconstructed fragments, which are constructed, using the “fixed geometry” assumption, from a set of consecutive pairs of dihedral angles drawn from known structures. Random fragments that are constructed from a random set of dihedral angles from known structures, and doublet‐preserving fragments, which are constructed from a set of dihedral angles drawn at random from known structures in a way such that the distribution of two consecutive pairs of dihedral angles in this population is similar to that distribution in the known structures. We examine the fixed geometry assumption and demonstrate that even reconstructed fragments contain many atomic collisions. We show that random fragments have only slightly more interatomic collisions than the reconstructed fragments. Nevertheless, the population of random fragments is structurally different from the population of reconstructed fragments. On the other hand, we show that the doublet‐preserving fragments exhibit properties that are similar to the real population. Thus the doublet preserving random population can be used to simulate the structure of short polypeptides.
Solution structure of human growth hormone‐releasing factor fragment (1–29) by CD: Characteristic conformational change on phospholipid membrane
Authors: Honda Shinya , Ohashi Shinichi , Morii Hisayuki , Uedaira Hatsuho
Published: December 2004

The conformations of synthetic human growth hormone‐releasing factor fragment (1‐29) in the presence and the absence of l, 2‐dimyristoyl‐sn‐glycero‐3‐phosphorylglycerol liposome as well as in aqueous 2, 2, 2‐trifluoroethanol solution were investigated by CD spectroscopy. The secondary structure of the peptide in each solution was analyzed by two methods. Both results show that the peptide has an unordered structure in the aqueous solution. whereas it folds into helical structure in the aqueous alcohol and in the phospholipid solution. In addition, although the peptide exists as almost complete helix in the 50 vol % aqueous alcohol (80–90% helicity), it does not reach full helicity even in the solution containing excess amount of phospholipid liposome (maximum 65–70% helicity). The conformational difference is explained by the characteristic amphipathy of the peptide, i.e., the necessity to twist the separated amphipathic helical parts in the interaction with the phospholipid membrane probably makes the helicity of the peptide decrease.
Vibrational studies of the disulfide group in proteins. Part V. Correlation of SS stretch frequencies with the CCSS dihedral angle in known protein disulfide bridges
Authors: Qian Weili , Krimm Samuel
Published: December 2004

Normal mode calculations have been done on 92 disulfide bridges in 25 known protein structures in order to correlate the SS stretch frequency with the CCSS dihedral angle. It is possible to classify the frequencies into four major categories, which provide a more detailed classification scheme than previously proposed from dialkyl disulfide correlations.
Computer modeling of polysaccharide–polysaccharide interactions: An approach to the κ‐carrageenan–mannan case
Authors: Tvaroska Igor , Rochas Cyrille , Taravel François‐R. , Turquois Tristan
Published: December 2004

A computer program SAINT has been developed for the investigation of the structure and for the prediction of minimum‐energy structure of polysaccharide–polysaccharide complexes. The energy minimization is carried out on internal geometrical parameters—namely bond angles, torsional angles, and five parameters describing the mutual orientations of polysaccharide chains. For this purpose, the nonderivative method of conjugated directions is used. This procedure was applied to computer modeling of an idealized model of the binary gelling κ‐carrageenan and galactomannan system. It is shown that the interaction between two chains influences the structure of the individual polysaccharide molecule and that in the minimum‐energy structures of the complex, the conformation of the chains does not correspond to the lowest energy.
Molecular dynamics simulation of poly(spiropyran‐L‐glutamate): Influence of chromophore isomerization
Authors: Pachter Ruth , Cooper Thomas M. , Natarajan L. V. , Obermeier Keith A. , Crane Robert L. , Adams W. Wade
Published: December 2004

A study of the influence of the spiropyran to merocyanine ring opening on a model of poly(spiropyran‐L‐glutamate) as implied by the experimental data (T. M. Cooper, K. A. Obermeier, L. V. Natarajan, and R. L. Crane (1992) Photochemistry and Photobiology, 55, 1–7) is presented. The individual chromophore is studied by the AM1 semiempirical approach, while molecular mechanics and dynamics calculations are employed in the analysis of the poly(spiropyran‐L‐glutamate) model. It is shown that the α‐helical secondary structure is less conserved in the polypeptide substituted with the merocyanine form of the chromophore. In particular, larger side‐chain flexibility, increased backbone hydrogen‐bond lengths, as well as a larger helix bending are calculated. Furthermore, a random conformational minimization calculation finds the intrinsic behavior of the spiropyran molecular system as being more of a helix “maker” than its merocyanine analogue. The interactions of the chromophore substituent with other side chains prove, in part, that an early event in the decay of the α‐helical structure is the formation of hydrogen bonds between the carboxylic acid groups and the merocyanine oxygens. The results lend support to the experimental observation that the merocyanine group destabilizes the α‐helical framework of the polypeptide, thus possibly allowing the entry of solvent molecules into the α‐helical core, while spiropyran in its closed form shields it from the solvent. © 1992 John Wiley & Sons, Inc.
Solution conformation of maltose from optical rotation: A procedure for evaluating carbohydrate force fields
Authors: Stevens Eugene S.
Published: December 2004

As one means of evaluating the various force fields that are being developed for the molecular modeling of carbohydrate structures, the statistically averaged optical rotation of β‐maltose can be calculated using the energy surface to be tested in combination with the detailed conformation dependence of β‐maltose optical rotation presented here. Comparison with the observed rotation will indicate the quality of the force field, especially with respect to the parameterization of solvent effects. © 1992 John Wiley & Sons, Inc.
Hydrodynamic modes of arbitrarily shaped flexible macromolecules: Influence on dynamic light scattering
Authors: Goldstein Robert F.
Published: December 2004

The diffusional motions of flexible macromolecules are analyzed with an increasingly realistic Rouse–Zimm model, i.e., by modeling the molecule as an arbitrary set of spheres connected by nearly harmonic springs. New features include (1) nearly arbitrary arrangements of spheres, (2) arbitrary arrangements of translational and torsional springs, (3) significant anharmonic corrections to the elastic potential surface, and (4) inclusion of torsional damping and various hydrodynamic cross‐coupling effects (including two types of translational‐rotational coupling) with no additional fitted parameters.

The hydrodynamic interactions [R. F. Goldstein (1985) Journal of Chemical Physics, Vol. 83, pp. 2390–2397] contain no adjustable parameters other than temperature, viscosity, and the radii and positions of the spheres. These hydrodynamic interactions allow accurate calculations of rigid body diffusion as well as flexible motions.

Given the positions, radii, and spring constant matrix, one can calculate a full set of three‐dimensional diffusional modes. Because one uses an off‐diagonal hydrodynamic resistance matrix instead of a diagonal mass matrix, the diffusional modes are different in structure from vacuum normal modes, and give rise to different rms motions in the laboratory frame. These hydrodynamic modes include the effects of vibrational‐translational cross‐coupling (i.e., motion along a vibrational coordinate may give rise to a translational force, and vice versa).

The diffusional modes are used to simulate dynamic light scattering (DLS). I examine various molecules with different shapes, flexibilities, and with different scattering vectors. Radial and angular motions influence DLS decays differently. These effects are dependent upon the molecular shape (straight, bent, or curved) and type of flexibility (stretching or bending). Furthermore, small cubic corrections to the potential surface can be significant for DLS of certain geometries such as straight rods and semicircles. © 1993 John Wiley & Sons, Inc.
Rayleigh scattering of Mössbauer radiation in hydrated oriented DNA fibers
Authors: Albanese G. , Deriu A. , Cavatorta F. , Rupprecht A.
Published: December 2004

The Rayleigh scattering of Mössbauer radiation has been measured on oriented hydrated fibres of A‐NaDNA. The elastic and inelastic scattering intensities have been determined at different temperatures from 275 to 310 K in the Q range 0.7–3.3 Å−1. The elastic intensity has a main maximum at Q = 1.92 Å−1 due to an ordered structure of water along the DNA double helices. From the temperature dependence of the elastic intensity under the water peak maximum, the mean square displacement of water oxygens in the direction parallel to the DNA axis has been deduced. It varies from 0.110 Å2 at 275 K up to 0.345 Å2 at 310 K. The thermal diffuse scattering intensity is also peaked at the same Q value of the elastic intensity, indicating the presence of coherent vibrational excitations propagating along the ordered water filaments. © 1993 John Wiley & Sons, Inc.
Characterization of the bioactive form and molecular determinants of recognition of cyclic enkephalin peptides at the δ‐opioid receptor
Authors: Chew Clifford , Villar Hugo O. , Loew Gilda H.
Published: December 2004

An extensive and systematic search strategy to determine the conformational profile of 12 cyclic disulfide‐bridged opioid peptides with varying affinities at the δ receptor has been carried out to identify the structure that is recognized by the δ receptor for each analogue. The methods and procedures used here for the conformational search have already been validated for [D‐Pen2, D‐Pen5] enkephalin (DPDPE), one member of this family. Use of these methods led to a low‐energy solution conformation of DPDPE in excellent agreement with all the geometric properties deduced from its solution nmr spectra. Each of the analogue was subjected to the same procedure, involving a combination of molecular dynamics simulations at high and low temperature. The study was repeated in two environmental conditions, an apolar environment, simulated by using a distance‐dependent dielectric constant, and a polar environment by embedding the peptides in a high constant dielectric ( ε = 80). An automated comparison of the different conformers based on their backbone rms and average distance between the key aromatic moieties was followed by graphic analysis using maximum structural overlap. The cross‐comparison of the conformations for each analogue revealed a unique conformer that may be recognized by the δ receptor for each high‐affinity analogue that permitted maintaining the critical elements required for recognition in a simple spatial orientation, while maximizing similarity in other regions. © 1993 John Wiley & Sons, Inc.