bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of the dodecapeptide corresponding to domain III of bovine brain calmodulin: α‐β Shift side reactions during the synthesis by the classical method in solution
Authors: Borin Gianfranco , Calderan Andrea , Ruzza Paolo , Pezzoli Anna , Marchiori Fernando , Peggion Evaristo
Published: December 2004

We report details of the chemical synthesis of the dodecapeptide corresponding to the calcium binding loop III of bovine brain calmodulin (sequence 93–104) and its fragments 96–04, 93–98, and 99–104.

The preparation of the peptides employed classical solution methods and a fragment‐condensation strategy. The major difficulties were encountered during the synthesis of the peptides containing the N‐terminal sequences‐Gly‐Asn‐Gly‐ and ‐Asp‐Lys‐Asp‐Gly‐Ans‐Gly‐, in which α‐β shift side reactions were observed.
Conformational analysis of cyclic peptides in solution
Authors: Kessler Horst , Bats Jan‐Willem , Wagner Klaus , Will Martin
Published: December 2004

The strategy and tactics of conformational analysis of cyclic peptides in solution is demonstrated by the example of cyclo(‐D‐Pro‐Phe‐Thr‐Phe‐Trp‐Phe‐). Spin‐locked experiments like rotating frame nuclear Overhauser enhancement spectroscopy (ROESY), ROTO, and TOCSY are successfully applied to assign all proton signals and to obtain distance information. A crude conformational model was built using the nmr data. This starting model was refined by restrained molecular dynamics (MD) calculations using ROE derived distances and fixed bond angles as determined from homo‐ and heteronuclear coupling constants. To mimic the solvent and to reduce artifacts in an in vacuo calculation the charges of the solvent‐exposed NH protons were gradually reduced according to the temperature gradients. The thus obtained “conformation” (mean of a 40 ps MD trajectory) shows very close similarity to x‐ray structures in an orthorhombic and in two monoclinic crystal modifications of the same compound. The main difference is the breaking of an intermolecular hydrogen bond of the theronine hydroxyl group on dissolution of the crystal and forming an intramolecular hydrogen bond in solution.
Two‐dimensional 1H‐nmr study of synthetic peptides containing the main immunogenic region of the Torpedo acetylcholine receptor
Authors: Cung M. T. , Marraud M. , Hadjidakis I. , Bairaktari E. , Sakarellos C. , Kokla A. , Tzartos S.
Published: December 2004

A comparative 1H‐NMR spectral study of a synthetic decapeptide containing the main immunogenic region of the Torpedo acetylcholine receptor (AChR; WNPADYGGIK, representing the α67–76 fragment of Torpedo AChR) with four analogous peptides (WNP3‐D5YGGIK, WNPAA5YGGIK, WNPADYGGA9K, and WNPD4DYGGV9K) has been carried out in dimethyl sulfoxide.

One‐ and two‐dimensional nmr experiments [correlated spectroscopy (COSY), relayed COSY, and phase‐sensitive nuclear Overhauser enhancement spectroscopy (NOESY)] were performed to obtain complete assignments of the proton resonances. The presence of strong and multiple short‐ and long‐range NOEs, and especially a strong long‐range NOE between the two Asn2‐CαH and Gly7‐CαH protons, argues in favor of a rigid folded structure in all five cases. Temperature dependence measurements indicate the existence of three intramolecular interactions involving the Asp3, Gly8, and Lys10 amide protons.
CD spectra of isoionic DNA solutions
Authors: Davydova O. V. , Kuznetsov I. A. , Florentiev V. L.
Published: December 2004

The ion‐exchange transition of Na‐DNA → H‐DNA in concentrated salt‐free solutions is accompanied by strong variations in CD spectra. The rotational force of the negative band |Δε249| decreases when going to H‐DNA by about 4 times, and the value of Δε279, by 1.2 times. These changes are irreversible to a considerable extent, which is evident because the spectra of Na‐DNA obtained by neutralizing isoionic H‐DNA solutions with NaOH or by the ion‐exchange method significantly differ from those of Na‐DNA taken by dissolving solid Na‐DNA in deionized water. It has been shown that additions of NaCl to an isoionic solution of DNA leads to variations of spectra, typical for deprotonation processes as well as for an increase in DNA hydration.
Harmonic dynamics of a DNA hexamer in the absence and presence of the intercalator ethidium
Authors: Rudolph Barbara R. , Case David A.
Published: December 2004

Vibrational normal mode calculations are presented for a DNA hexanucleoside pentaphosphate, d(CpGpCpGpCpG)2, and for its complex with the cationic interclator ethidium. Two intercalation sites are modeled that differ in DNA backbone torsion angles. Normal mode frequencies for the DNA fragment itself are significantly lower than those reported earlier using different force fields, but an analysis of “effective” frequencies suggests that somewhat higher frequencies are more appropriate. Intercalation leads to significant lowering of mobility for the base pairs adjacent to the drug; in this sequence, the ethidium binding affects the guanosine atoms more strongly than the cytosine atoms. Motions of the bases and the intercalator are analyzed in terms of “twist” about the local helix axis and a “tilt” angle relative to this axis, and the results are compared to fluorescence studies of ethidium‐DNA complexes.
Phonon interpretation of inelastic neutron scattering in DNA crystals
Authors: Schroll W. K. , Prabhu V. V. , Prohofsky E. W. , Van Zandt L. L.
Published: December 2004

The calculated spectrum of longitudinal compressional waves on DNA polymer chains is shown to be in excellent agreement with recently performed inelastic neutron scattering measurements in hydrated, oriented DNA crystals. This opens up a previously unexplored frequency regime of DNA science and establishes the validity of the phonon extended wave description of DNA elementary excitations in this region.
New x‐ray diffraction results from agarose: Extended single helix structures and implications for gelation mechanism
Authors: Foord S. A. , Atkins E. D. Y.
Published: December 2004

A new series of x‐ray fiber diffraction patterns is reported from agarose films dried at temperatures close to 100°C from water or dimethylacetamide solutions, cooled to room temperature, stretched above 40°C, and finally x‐rayed at room temperature. This procedure gives x‐ray patterns showing highly crystalline forms of agarose with projected axial advances (h) per repeating disaccharide in the range of 0.888–0.973 nm, and favoring extended and single agarose chains. Stretching the films below 40°C yields an oriented but fairly diffuse x‐ray pattern, similar to that reported previously for agarose, and that has been interpreted in terms of a model with two semicontracted agarose chains, with a value of h = 0.634 nm, draping around each other to form a double helix.

The new data requires that double‐helix to single‐chain transitions be considered in condensed films as well as in solution. Alternatively, two populations of double‐helix and single‐helix conformations may coexist in the same film, or the original case for the double‐helix model may be flawed, perhaps through misinterpretation of the diffuse x‐ray pattern. The new results have prompted a critical discussion of evidence for the double‐helix model and to indicate that there is potential to improve the data experimentally with a view to gaining a clearer insight into the molecular mechanisms involved in gelation of agarose.
The stabilization of β‐lactoglobulin by glycine and NaCl
Authors: Arakawa Tsutomu
Published: December 2004

Effect of glycine and NaCl on the thermal denaturation of β‐lactoglobulin was examined. The results showed that the transition temperature of β‐lactoglobulin is increased by the addition of glycine and NaCl at 0.5 and 1M. This observed stabilization by glycine and NaCl was interpreted in terms of their favorable interactions with the native state of β‐lactoglobulin and unfavorable interactions with the denatured state.
Free energy of hydration of collagen models and the enthalpy of the transition between the triple‐helical coiled‐coil and single‐stranded conformations
Authors: Némethy George , Scheraga Harold A.
Published: December 2004

Interactions with water make an important contribution to the free energy of stabilization of the collagen triple helix, but they do not alter the structure of the triple helix, i.e., the packing geometry of the three strands. Conformational energy computations have been carried out on poly(tripeptide) analogues of collagen, with the introduction of a newly developed form of a hydration shell model to compute the free energy of hydration. The most stable triple helix formed by poly(Gly‐Pro‐Pro), obtained earlier from conformational energy computations [M. H. Miller & H. A. Scheraga (1976) J. Polym. Sci. Polym. Symp. 54, 171], with a structure that is very closely similar to the observed structure, is strongly favoured over other three‐strand complexes, both in the absence and the presence of hydration. The hydration shell model does not provide an explanation for the increased stability of the poly(Gly‐Pro‐Hyp) triple helix as compared to poly(Gly‐Pro‐Pro). It appears that the difference should be attributed to specific binding of water, an effect that is not yet included in the present version of the hydration shell model. On the other hand, this model accounts for the observed enthalpy of unfolding of a poly(Gly‐Pro‐Pro) triple helix to isolated single chains in solution in terms of intramolecular noncovalent interactions and the free energy of hydration.
CD and small‐angle x‐ray scattering of silk fibroin in solution
Authors: Canetti Maurizio , Seves Alberto , Secundo Francesco , Vecchio Giuseppe
Published: December 2004

We investigated the structure of silk fibroin dissolved in water and in water–organic solvent mixtures by CD and small‐angle x‐ray scattering (SAXS). CD spectra indicated a disordered secondary structure in water and a β‐sheet conformation in aqueous organic solvents, such as methanol, dioxane, and trifluoroethanol (in trifluoroethanol a transient form evolving toward β‐sheet conformation was seen just after dissolution). The SAXS technique indicated the presence of fibroin particles of lamellar shape. The molecular weight was 188,000 daltons in water and 302,000 daltons in aqueous methanol.
Effects of chloroquine on the torsional dynamics and rigidities of linear and supercoiled DNAs at low ionic strength
Authors: Wu Pengguang , Schurr J. Michael
Published: December 2004

The magnitude and uniformity of the torsion elastic constant (α) of linear and supercoiled pBR322 DNAs are measured in 3 mM Tris as a function of added chloroquine/basepair ratio (chl/bp) by studying the fluorescence polarization anisotropy of intercalated ethidium dye. The time‐resolved FPA is measured using a picosecond dye‐laser for excitation and time‐correlated single‐photon counting detction. For both linear and supercoiled DNAs, α remains uniform except at the very highest chl/bp ratio examined. For the linear DNA, α decreases from 5.0 × 10−12 dyne‐cm at chl/bp = 0 to about 3.5 × 10−12 dyne‐cm at chl/bp = 0.5, and remains at that value up to chl/bp = 5, whereupon it increases back up to its original value. For the supercoiled DNA, α remains constant at about 5.2 × 10−12 dyne‐cm from chl/bp = 0 up to chl/bp = 5, whereupon it increases in parallel with the linear DNA. The effect of chloroquine on the secondary structure, torsion constant, and torsional dynamics evidently differs substantially between linear and supercoiled DNAs, even under conditions where the supercoiled DNA is completely relaxed and both DNAs bind the same amount of dye. This strongly contradicts any notion that the local structures of linear and relaxed supercoiled DNA/dye complexes with the same binding ratio are identical. The increase in apparent α at chl/bp = 5 for both DNAs may be due to stacking of the chloroquine in the major groove and consequent stiffening of the filament.
The biased reptation model of DNA gel electrophoresis: Mobility vs molecular size and gel concentration
Authors: Slater Gary W. , Noolandi Jaan
Published: December 2004

The biased reptation model provides a good framework for interpreting the results of continuous field DNA electrophoresis experiments performed in agarose gels. Here we discuss the main features of the mobility–molecular size and mobility–gel concentration diagrams as obtained from new extensive computer simulations of the model. Our aim is to suggest a global and coherent picture of this widely used yet poorly understood experimental technique, and to point out the areas where a systematic experimental study is still needed.
A Monte Carlo simulation study of the influence of internal motions on the molecular conformation deduced from two‐dimensional nmr experiments
Authors: Genest D.
Published: December 2004

Monte Carlo methods have been used to simulate internal motions of aromatic protons of an oligonucleotide at the nanosecond time scale. Each proton is allowed to fluctuate about its equilibrium position. The longitudinal cross‐relaxation rates of such a system of spins have been determined by computing the appropriate correlation functions. Then the interproton distances have been deduced according to the procedure generally used in two‐dimensional nmr techniques (nuclear Overhauser effect spectroscopy—NOESY) and compared to the true values. The influence of the amplitude A and of the internal rotational diffusion constant Dint characterizing the dynamics of the system has been checked for in‐phase and for uncorrelated motions. It is shown that for the investigated models the distances deduced from NOESY experiments may be under or overestimated, depending strongly on the values of A and Dint. Furthermore, the cross‐relaxation rate of a couple of protons is very sensitive to the correlation level of the motions of both protons.
Effects of nucleotide bromination on the stabilities of Z‐RNA and Z‐DNA: A molecular mechanics/thermodynamic perturbation study
Authors: Ross Wilson S. , Hardin Charles C. , Tinoco, Ignacio , Rao Shashidhar N. , Pearlman David A. , Kollman Peter A.
Published: December 2004

The structures of ZI‐ and ZII‐ form RNA and DNA oligonucleotides were energy minimized in vacuum using the AMBER molecular mechanics force field. Alternating C‐G sequences were studied containing either unmodified nucleotides, 8‐bromoguanosine in place of all guanosine residues, 5‐bromocytidine in place of all cytidine residues, or all modified residues. Some molecules were also energy minimized in the presence of H2O and cations. Free energy perturbation calculations were done in which G8 and C5 hydrogen atoms in one or two residues of Z‐form RNAs and DNAs were replaced in a stepwise manner by bromines. Bromination had little effect on the structures of the energy‐minimized molecules. Both the minimized molecular energies and the results of the perturbation calculations indicate that bromination of guanosine at C8 will stabilize the Z forms of RNA and DNA relative to the nonbrominated Z form, while bromination of cytidine at C5 stabilizes Z‐DNA and destabilizes Z‐RNA. These results are in agreement with experimental data. The destabilizing effect of br5C in Z‐RNAs is apparently due to an unfavorable interaction between the negatively charged C5 bromine atom and the guanosine hydroxyl group. The vacuum‐minimized energies of the ZII‐ form oligonucleotides are lower than those of the corresponding ZI‐ form molecules for both RNA and DNA. Previous x‐ray diffraction, nmr, and molecular mechanics studies indicate that hydration effects may favor the ZI‐ conformation over the ZII‐ form in DNA. Molecular mechanics calculations show that the ZII–ZI energy differences for the RNAs are greater than three times those obtained for the DNAs. This is due to structurally reinforcing hydrogen‐bonding interactions involving the hydroxyl groups in the ZII form, especially between the guanosine hydroxyl hydrogen atom and the 3′‐adjacent phosphate oxygen. In addition, the cytidine hydroxyl oxygen forms a hydrogen bond with the 5′‐adjacent guanosine amino group in the ZII‐ form molecule. Both of these interactions are less likely in the ZI‐ form molecule: the former due to the orientation of the GpC phosphate away from the guanosine ribose in the ZI form, and the latter apparently due to competitive hydrogen bonding of the cytidine 2′‐hydroxyl hydrogen with the cytosine carbonyl oxygen in the ZI form. The hydrogen‐bonding interaction between the cytidine hydroxyl oxygen and the 5′‐adjacent guanosine amino group in Z‐RNA twists the amino group out of the plane of the base. This may be responsible for differences in the CD and Raman spectra of Z‐RNA and Z‐DNA.
Ir vibrational CD in model deoxyoligonucleotides: Observation of the B → Z phase transition and extended coupled oscillator intensity calcuations
Authors: Gulotta Miriam , Goss Dixie J. , Diem Max
Published: December 2004

The first observation of ir vibrational CD (VCD) in small model DNA molecules is reported. The VCD signals in the 1550–1750‐cm−1 spectral region, which originate from coupling of carbonyl stretching modes of the nucleic acid bases, are found to be sensitive to the handedness of the polymer helix.

The formalism to calculate VCD intensities of polymers is developed from the exciton model derived earlier by Tinoco [(1963) Radiation Res. 20, 133; (1960) J. Chem. Phys. 33, 1332; (1964) J. Am. Chem. Soc. 86, 297] and Schellman and co‐workers [(1975) Biopolymers 14, 173; (1969) J. Phys. Chem. 73, 28]. The resulting equations, which are a direct extension of the dimeric case known as the “coupled oscillator,” are used in model calculations of the helical polymers.
Cyclic pentapeptides as models for reverse turns: Determination of the equilibrium distribution between type I and type II conformations of Pro‐Asn and Pro‐Ala β‐turns
Authors: Stradley Sarah J. , Rizo Josep , Bruch Martha D. , Stroup Adam N. , Gierasch Lila M.
Published: December 2004

Cyclic pentapeptides are excellent models for reverse turns and have been used extensively in our laboratory to explore the influence of different amino acid sequences on turn preference. This paper is divided into two parts: In the first, we review our previous studies of cyclic pentapeptides. We summarize work that demonstrates the range of conformations possible within the cyclic pentapeptide backbone, the importance of sequence chirality in determining the backbone fold, and the utility of these cyclic pentapeptides as models for various turns. In the second, we present new results on two cyclic pentapeptides that contain β‐turns with Pro‐Ala or Pro‐Asn sequences in the i + 1 and i + 2 positions. By stereochemical criteria, a type I β‐turn is expected to be preferred by such L‐L sequences. On the other hand, in proteins Asn occurs frequently in the i + 2 position of type II turns. We asked whether the same propensity would be manifest in an isolated model peptide, and if so, what the interactions were that influenced the relative stability of the type I and type II turns. To address these questions we have compared the conformational behavior of two peptides: cyclo(Gly‐Pro‐Ala‐D‐Phe‐Pro) and cyclo(D‐Ala‐Pro‐Asn‐Gly‐Pro). From previous studies, we anticipated that both peptides would contain an inverse γ‐turn and a β‐turn which consisted of either Gly‐Pro‐Ala‐D‐Phe or D‐Ala‐Pro‐Asn‐Gly in positions i to i + 3, respectively. Nuclear magnetic resonance analysis confirms this overall backbone conformation. Furthermore, quantitative nuclear Overhauser effect measurements in combination with molecular dynamics simulations and torsionally‐forced energy minimizations have enabled us to determine that both type I and type II β‐turns are present in equilibrium in these peptides. The introduction of Asn in position i + 2 shifts this equilibrium significantly towards type II. We have done preliminary assessment of the possible side‐chain/backbone conformations that contribute to the shift in populations.
Biodegradation of copoly(L‐aspartic acid/L‐glutamic acid) in vitro
Authors: Hayashi Toshio , Iwatsuki Makoto
Published: December 2004

The preparation of copolypeptides consisting of L‐aspartic acid and L‐glutamic acid was performed to determine the effects of copolymer composition and sequential distributions on the rate of degradation by papain in a PECF (pseudoextracellular fluid) at pH 4.75 and 7.40, at 37.0°C, to simulate in vivo polymer degradation. Random copolymers consisting of β‐benzyl L‐aspartate and γ‐benzyl L‐glutamate were synthesized by the N‐carboxyanhydride method. Water‐soluble copolymers were obtained by successive reactions of side chains by anhydrous HBr treatment. All the samples were found to be degraded by random chain scission with papain. Further, the degradation data for the samples followed the Michaelis–Menten rate law, being the first order in papain concentration. The nature of side chains are important to the rate of degradation by papain and it was controlled by the comonomer composition as well as the sequential distribution of comonomers in the copolymer chains.
Solvent effects on protein association and protein folding
Authors: Ben‐Naim A.
Published: December 2004

Solvent effects on the thermodynamics of two processes—folding of proteins and association between proteins—are examined in detail. A complete inventory of the multitude of solvent effects may be obtained by employing the concept of conditional solvation free energy. This theoretical tool allows for the isolation of specific side‐chain effects from the entire protein and for the study of its contribution to the overall free energy change in small model compounds. Some numerical examples are presented, and ways of estimating other cases, for which no relevant experimental data are available, are suggested. Our findings lead to the conclusion that the currently used hydrophobicity scales, based on partition coefficients between water and an organic solvent, are inadequate measures of the contribution of side chains being transferred from water to the interior of the protein. We have also tentatively concluded that correlation between hydrophilic functional groups might be more important than correlations between hydrophobic side chains.
The program FANTOM for energy refinement of polypeptides and proteins using a Newton – Raphson minimizer in torsion angle space
Authors: Schaumann Thomas , Braun Werner , Wüthrich Kurt
Published: December 2004

The program FANTOM (fast Newton–Raphson torsion angle energy minimizer) performs minimizations of the ECEPP/2 energy function for proteins with the Newton–Raphson method. It is implemented for use with conventional computer hardware. The torsion angles are chosen as independent variables. The first and second derivatives are calculated with a previously described rapid algorithm. For the matrix inversion a modified Cholesky factorization is used. A line search adjusts the step length and nonbonded interactions can be calculated with a cutoff. The following tests of the program are described: All local minima of the ECEPP/2 energy function for the amino acids glycine and alanine were determined. An exhaustive search by more than 16,000 independent energy minimizations was used to identify low‐energy structures of Met‐enkephalin, which were then compared with previously published structures of this pentapeptide. To investigate the use of FANTOM with disulfide bonds, it was applied with conotoxin. As an illustration of the intended primary use of the program, an energy refinement of the structure of the basic pancreatic trypsin inhibitor determined by nmr spectroscopy in solution is described.
Theoretical studies of cis‐Pt(II)‐diammine binding to duplex DNA
Authors: McCarthy Sharon L. , Hinde Robert J. , Miller Kenneth J. , Anderson Janet S. , Basch Harold , Krauss Morris
Published: December 2004

The binding of cis‐Pt(II) diammine (cis‐DP) to double‐stranded DNA was studied with several kinked conformations that can accommodate the formation of a square planar complex. Molecular mechanics (MM) calculations were performed to optimize the molecular fit. These results were combined with quantum mechanical (QM) calculations to ascertain the relative energetics of ligand binding through water vs direct binding of the phosphate to the ammine and platinum, and to guide the selection of DNA conformations to model complex formation. Based on QM and MM calculations, models are proposed that may be characterized by several general features. A structure involving hydrogen bonding between each ammine and distinct adjacent phosphate groups, referred to as closed conformation (CC), has already been reported. This is also found in the crystal structure of small dimers. We report alternative conformations that may be important in platination of duplex DNA. They are characterized by an intermediate conformation (IC), involving hydrogen bonding between one ammine and phosphate group, and an open conformation (OC), without ammine phosphate hydrogen bonding. The IC and OC can be stabilized by water bridges in the space between the ammine and the phosphate groups. Sugar puckers alternate from the type C(2′)‐endo or C(1′)‐exo (S), to the type C(3′)‐endo or C(2′)‐exo (N), with intermediate types near O(1′)‐endo (O). In general, the sugar puckers alternate from S to N to S through the platinated region (3′‐TpG*pG*p‐5′), with the complexed strand exhibiting, (3′)‐S*‐N*‐S‐(5′) alternation, while the complementary strand shows either (3′)‐S*‐N*‐S(5′) or (3′)‐S*‐N*‐O‐(5′) alternation. In both the OC and IC, a hydrogen bond is found between the ammine and O4(T) on thymine (T) at the (3′) end, adjacent to the complex site. There is a continuous range of backbone conformations through the platinated region which relate the OC to the IC. The models presented suggest that the dynamics of the binding of the cis‐Pt(II)‐diammines to adjacent N7(G) in double‐stranded DNA may encompass several conformational possibilities, and that water bridges may play a roll in supporting open and intermediate conformations. Proton–proton distances are reported to assist in the experimental determination of conformations.
B to Z transition in poly(dG‐dC) modified with benzo(a)pyrene diol epoxides studied with polarized light spectroscopy
Authors: Eriksson Magdalena , Nordén Bengt , Jernström Bengt , Gräslund Astrid
Published: December 2004

The NaCl‐induced transition from B to Z conformation in poly (dG‐dC), covalently modified with benzo(a)pyrene diol epoxides (BPDE), has been studied by use of flow linear dichroism (LD), CD, and fluorescence spectroscopy. In contrast to unmodified poly (dG‐dC), the BPDE‐modified polynucleotide displays a B to Z conversion that is incomplete in 2.7 M NaCl. This and a number of other observations are found consistent with a locally retained BPDE perturbed B‐like conformation in the vicinity of the BPDE adduct. In 2.7 M NaCl the polynucleotide orientation in flow is strongly reduced, which could indicate flexibility at the junctions between domains of BPDE perturbed B‐like conformation and Z conformation. A virtually stable high‐salt B form is found in 2.25 M NaCl at 0°C; its CD spectrum resembles that of the transient so‐called B* form, which is observed at an early stage of the B to Z transition. Characteristic B to Z transition times were evaluated by taking this B*‐form CD spectrum as the initial state spectrum. The kinetics of the B to Z transition, monitored by the CD signal at 287 nm, shows an increased transition rate with (+)‐anti‐BPDE modification whereas the (−)‐anti‐ and (±)‐syn‐BPDE adducts have retarding effects. The difference is discussed against the background of the different binding geometries of the BPDE isomer adducts.
Secondary‐structure dependent chemical shifts in proteins
Authors: Williamson Michael P.
Published: December 2004

Chemical shift data have been collected on eight proteins that have the same conformation in solution as in their crystal structures. Ring‐current shifts have been calculated and subtracted from the experimentally measured shifts, to leave shifts that depend only on local conformation. Overall, the shifts show an approximately normal distribution with no appreciable skewness, thus confirming that ring‐current shifts have the overall effect of skewing the distribution to high field. In helices, NH and CαH have a highly significant tendency to resonate to high field, whereas they resonate to low field in β‐sheets. Side‐chain protons resonate slightly to high field in γ‐sheets. Chemical shift distributions are narrowest for side‐chain protons, and widest for amide protons. When only slowly exchanging amide protons are considered, the high field shift for amide protons in helices is more pronounced, but there is only a small difference in sheets. CαH signals at the N‐terminal end of helices tend to resonate to higher field than those at the C‐terminal end, whereas for NH signals it is the C‐terminal end that resonates to higher field. There is no significant effect of position within the helix on side‐chain signals, implying that the helix dipole has little effect on shifts within the helix.
Physicochemical studies on tomato bushy stunt virus variants
Authors: Molina‐Garcia Antonio D. , Harding Stephen E. , Fraser Ronald R. S.
Published: December 2004

Tomato bushy stunt virus particles have previously been physically and chemically well characterized. Different strains, however, are known to have different host plants and symptoms, and they can be distinguished serologically. In an attempt to correlate this behaviour with physicochemical properties, we have performed a comparative study on isolates of four of the main variants of this virus (Type strain, petunia asteroid mosaic virus, pelargonium leaf curl virus, and carnation Italian ringspot virus) with regard to sedimentation velocity characteristics, translation diffusivity (from quasi‐elastic light scattering measurements), and molecular weight (from both low‐speed sedimentation equilibrium and the Svedberg equation).

It is demonstrated that there are no clear differences between the four strains, particularly insofar as their sedimentation characteristics (both velocity and low‐speed equilibrium). There is some suggestion from diffusion measurements that the Type strain virus particles may have a higher mass, although the presence of some aggregation phenomena may provide an alternative explanation for the diffusion data.
Adenine and guanine 8CH exchange in nucleic acids: Resolution and measurement by Raman optical multichannel analysis
Authors: Lamba Om P. , Becka Renee , Thomas George J.
Published: December 2004

Deuterium exchange of 8C protons of adenine and guanine in nucleic acids is conveniently monitored by laser Raman spectrophotometry, and the average exchange rate so determined (〈kA + kG〉) can be exploited as a dynamic probe of the secondary structure of DNA or RNA [J. M. Benevides and G. J. Thomas, Jr. (1985) Biopolymers 24, 667–682]. The present work describes a rapid Raman procedure, based upon optical multichannel analysis, which permits discrimination of the different 8CH exchange rates, kA of adenine and kG of guanine, in a single experimental protocol. For this procedure, simultaneous measurements are made of the intensity decay or frequency shift in separately resolved Raman bands of adenine and guanine, each of which is sensitive only to 8C deuteration of its respective purine. Resolution of the rates kA and kG is demonstrated for the mononucleotide mixtures, 5′‐rAMP + 5′‐rGMP and 5′‐dAMP + 5′‐dGMP, for the polynucleotides poly (dA‐dT) . poly (dA‐dT) and poly (dG‐dC)·poly (dG‐dC), for calf thymus DNA, and for the 17 base‐pair operator OR3. We show that the different exchange rates of adenine and guanine, in nucleotide mixtures and in DNA, may also be calculated independently from intensity decay of the composite 1481‐cm−1 band, comprising overlapped adenine and guanine components, over a time domain that encompasses two distinct regimes: (1) a relatively more rapid exchange of guanine, and (2) a concurrent slower exchange of adenine. Both methods developed here yield consistent results. We find, first, that exchange of guanine is approximately twofold more rapid than that of adenine when both purines are present in the same structure and solvent environment, presumably a consequence of the greater basicity of the 7N site of guanine. Second, we find that adenine suffers greater retardation of exchange than guanine when both purines are incorporated into a “classical” B‐DNA secondary structure, such as that of calf thymus DNA. This finding suggests different microenvironments at the 7N‐8C loci of adenine and guanine in aqueous B‐DNA. We also confirm that adenine residues of B‐form poly (dA‐dT)·poly (dA‐dT) exchange much more slowly than those of other B‐DNA sequences, implying a secondary structure for the alternating‐AT sequence with unusual stereochemistry in the major groove. The greater resistance of adenine than guanine to 8CH exchange in the B‐DNA secondary structure is more evident in high molecular weight calf thymus DNA and in the alternating AT and GC copolymer duplexes than in the smaller 17 base‐pair operator OR3. The present results provide direct experimental evidence for structural heterogeneity of B‐DNA in aqueous solution, involving the purine 7N‐8C imidazole network. The methods developed here establish an experimental basis for future study of purine‐specific interactions that may be important in gene regulatory complexes and in nucleic acid condensation and packaging processes.
Depsipeptide analogues of elastin repeating sequences: Conformational analysis
Authors: Arad O. , Goodman M.
Published: December 2004

In this work the effect of elimination of a specific hydrogen bond on the conformation of the repeating peptides of elastin was studied. These repeating sequences are the pentapeptide Val‐Pro‐Gly‐Val‐Gly and the hexapeptide Val‐Ala‐Pro‐Gly‐Val‐Gly. These sequences have been proposed to occur in a β‐turn conformation with a hydrogen bond involving the amide NH of the internal valine residue and the carbonyl oxygen of the residue preceding proline. In the depsipeptide analogues studied in this work, this 4–1 β‐turn hydrogen bond cannot occur. We studied the depsipeptide sequences Val‐Pro‐Gly‐Hiv‐Gly and Val‐Ala‐Pro‐Gly‐Hiv‐Gly (Hiv denotes S‐α‐hydroxyisovaleric acid, the hydroxy acid analogue of valine), as well as the peptide sequences Val‐Pro‐Gly‐Val‐Gly and Val‐Ala‐Pro‐Gly‐Val‐Gly. Compunds studied included sequences with the Boc and benzyl ester protecting groups, derivatives with the acetyl and N‐methylamide end groups and polymers of the above sequences. Our conclusions are based on a comparison of depsipeptides with analogous peptides. Conformational analysis was carried out by nmr, CD, and ir spectroscopy. We propose that in the repeating sequences of elastin an equilibrium exists between a γ‐turn structure and a β‐turn structure in the Pro‐Gly segment resulting in a structure that combines flexibility with strong conformational preferences. The C7 involves the amide NH of the internal glycine and the carbonyl oxygen of the residue preceding proline. In the N‐methylamide derivatives a similar equilibrium exists in the Gly‐Val‐Gly segment. In the depsipeptides the β‐turn cannot occur and only the γ‐turn is seen. In the polydepsipeptides the major conformational feature is a type I β‐turn involving Gly5 NH and Pro CO.
Statistical descriptors for the size and shape of globular proteins
Authors: Abad‐Zapatero C. , Lin C. Thomas
Published: December 2004

The atomic structures of proteins epitomize the ideas of complexity and irregularity in three‐dimensional objects. For such objects, size and shape are difficult to quantify, and therefore the development of unbiased parameters for these properties could facilitate their description. Statistical analysis of the frequency distribution of interatomic distances in protein structures of different classes has revealed two numerical descriptors that correlate with physicochemical properties of these macromolecules. The median (μ) of the distribution correlates (r> .98,n= 45) with variables indicative of size (e.g., molecular weight and radius of gyration). The exponent of the Box–Cox transformation λ, used for converting this distribution into a symmetrical one, correlated (r= .75,n= 43) with a general dimensionless shape parameter defined as the combination of the shape‐related accessible surface (A), molecular volume (V), and radius of gyration (Rg) in the forms= (ARg/V). It is suggested that for globular proteins λ is a function of both the shape parametersand the fractal dimensionDof the protein surface. These objective descriptors of size and shape could be useful to describe other complex objects.
Structural effects of hydration: Studies of lysozyme by 13C solids nmr
Authors: Kennedy Scott D. , Bryant Robert G.
Published: December 2004

13C‐nmr spectra of lysozyme obtained at 50.3 MHz using both static and magic‐angle‐spinning‐cross‐polarization methods are reported at several water contents. The line widths and consequent resolution in the hydrated material is substantially improved over that in the lyophilized protein. The line narrowing is not commensurate with loss of a proton–carbon dipole–dipole coupling or dramatic changes in the relaxation parameters characterizing magnetization transfer from protons to carbon in the Hartmann–Hahn cross‐polarization experiment. We interpret these data in terms of the water inducing a decrease in the conformational reorientations required to account for the data are not necessarily large nor do they imply a major unfolding of the protein on dehydration.
Gel electrophoresis of micron‐sized particles: A problem and a solution
Authors: Griess Gary A. , Serwer Philip
Published: December 2004

The gel electrophoresis of spherical particles with a radius above 0.2 μm has not been reported yet. In the present study, video phase‐contrast light microscopy is used to observe the motion of individual latex spheres, 0.52 μm in radius, during electrophoresis in 0.1% agarose gels. At 2V/cm, the spheres initially migrate in the direction of the electrical field. However, each sphere eventually undergoes a cessation of all motion. Brownian motion is restored when the electrical potential gradient is reduced to zero. Arrest can be prevented by periodically inverting the direction of the electrical field. These observations are explained by electrical field‐ induced steric trapping of the spheres by gel fibers. Inversion of the electrical field should assist the application of agarose gel electrophoresis to micron sized cellular organelles and cells.
Solvent effect on the stability of isomaltose conformers
Authors: Tvaroska Igor , Imberty Anne , Pérez Serge
Published: December 2004

The conformational equilibria of the low‐energy conformers of isomaltose have been studied in different solvents. The structure of each individual conformer was refined from the 18 distinct low‐energy regions determined from potential energy function. Molecular geometry optimization was carried out using the quantum chemical method of perturbative configuration interaction with localized orbitals or PCILO and yielded to 15 distinct minima. Carbon‐proton vicinal coupling constants 3JC‐H have been calculated based on the finite perturbation theory formulation with the intermediate neglect of differential overlap for these minima. For evaluation of the influence of the environment on the conformational structure of isomaltose, the population of the low‐energy conformers was estimated in four solvents by a method in which the total energy is divided into the energy of the isolated molecule and the solvation energy. The calculated abundances of conformers depend strongly on the solvents. Based on the determined abundance of conformers, thermodynamically averaged torsion angles and coupling constants 3JC‐H describing the “average” conformation about glycosidic linkage have been calculated. Results obtained are compared with available experimental data from solution and solid state.
On the physicochemical properties of gellan gum
Authors: Milas M. , Shi X. , Rinaudo M.
Published: December 2004

This paper concerns the behavior in dilute and semidilute solutions of deacetylated gellan. The conformational transition, controlled by temperature and ionic strength, is investigated. It corresponds to a double‐helix single‐chain transition. Large ionic selectivity is observed in the helical conformation that controls the degree of aggregation upon gelation. Potentiometry and conductivity measurements are interpreted in terms of the Manning poly‐electrolyte theory in the sol state.
Conditions for the stability of the alternative structures of duplex poly(dA‐dT)
Authors: Loprete D. M. , Hartman K. A.
Published: December 2004

The alternative structures of the lithium, sodium, potassium, and rubidium salts of poly(dA‐dT) were studied using ir spectra of hydrated, nonoriented gels. Poly (dA‐dT) · Na existed as the B structure at high hydration and as the A structure at moderate hydration. A disordered state occurred at low hydration. No hint of the C, D, or other structures was observed at any hydration for nonoriented gels containing NaCl up to 0.56 moles NaCl/mole of nucleotide residue. Poly (dA‐dT) · Li existed as the B structure at high hydration, made a gradual transition to the C structure at moderate hydration, and became disordered at low hydration. Poly (dA‐dT) · K and poly (dA‐dT) · Rb existed as the B structure at high hydration and as the presumptive D structure at lower hydration. The addition of Zn(II) to poly (dA‐dT) · Na produced a gradual transition from the B to the C structure upon dehydration. The addition of NaNO3 to poly (dA‐dT) · Na gave only the A and B structures, and not the C or Z structures that are promoted by NO3 in other base sequences. The DNA secondary structure stabilized by a given ion is determined by a specific base sequence and not simply by the properties of the ion.
Thermodynamic cycle‐perturbation study of the binding of trifluoroacetyl dipeptide anilide inhibitors with porcine pancreatic elastase
Authors: Lesyng Bogdan , Meyer Edgar F.
Published: December 2004

The variety of results of crystallographic studies of the serine proteases complexed with isocoumnrin inhibitors presents a challenging problem to modeling methods and molecular energetics. Therefore, the thermodynamic cycle‐perturbation technique has been used to study a model system of elastase and two peptidic inhibitors. Using the program AMBER, the technique correctly predicts changes of the binding constants for the trifluoroacetyl dipeptide inhibitors in comparison with available experimental (kinetic and crystallographic) data. However, the absolute values obtained are shown to be sensitive to the specific electrostatic interaction potential parameters used in the simulations. The reader and user are cautioned that thermodynamic cyle‐perturbation results may be too optimistic by underestimating the accuracy of free energy values. This is especially a matter of concern for those cases where a direct comparison with experimental values is not possible, viz., (1) the simulation of binding of novel compounds, (2) structurally uncertain binding sites, or (3) structurally different binding modes. With our best 4‐31G* ESP (electrostatic potential) charges we were able to reproduce experimentally determined free energy differences (ΔΔA) with an accuracy of about 1.5 kcal/mol. Dynamically induced structural changes in the binding site of elastase, and particularly changes in hydrogen‐bond patterns of the binding site, are also reported.
The effect of the L‐azetidine‐2‐carboxylic acid residue on protein conformation. II. Homopolymers and copolymers
Authors: Zagari Adriana , Némethy George , Heraga Harold A.
Published: December 2004

The alteration of polymer conformational properties caused by the replacement of L‐proline by L‐azetidine‐2‐carboxylic acid (Aze) has been studied by means of conformational energy computations. In addition to poly (Aze), two sequential copolymers, poly (Pro‐Aze) and poly(Aze3‐Pro3), have been investigated. All polymers containing Aze are more flexible than poly(Pro). This is a consequence of an increased number of permitted conformational states for the Aze residue, as compared to Pro, when they are incorporated into a polypeptide, as well as of a lessened cooperativity of the trans‐cis transition. The results of the computation can be used to interpret the observed physical properties of poly (Aze) and of its copolymers.
Multiple helix–coil transitions
Authors: Dupré Donald B.
Published: December 2004

Conditions for the occurrence of one, two, and even three helix–coil transitions are summarized and further delineated in terms of thermodynamic parameters in simple modifications of a 2 × 2 matrix of statistical weights for amino acid residues in the coiled and helical conformations. Solvent interaction with segments in both the exposed, coiled and compact, helical conformations is worked into the model. Theoretical expressions for the temperature dependence of helical fractions, maximum attained degrees of helicity, and the compositional dependence of transition temperatures are compared with experimental data for two synthetic polypeptides that exhibit multiple helix–coil transitions.
Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. II. Amide absorption bands of polypeptides and fibrous proteins in α‐, β‐, and random coil conformations
Authors: Venyaminov S. Yu. , Kalnin N. N.
Published: December 2004

Infrared spectra of poly(D,L‐alanine), poly(L‐glutamic acid), poly(L‐lysine), silk fibroin, and tropomyosin have been registered for various conformations of the polypeptide chain. Assuming additivity of the main‐ and side‐chain absorption, spectral parameters of amide I and II absorption bands corresponding to α‐, β‐, and random coil conformations have been derived. The amide I band parameters for H2O and D2O have been compared.
Prediction of the rotational diffusion behavior of biopolymers on the basis of their solution or crystal structure
Authors: Müller Jürgen J.
Published: December 2004

Two low structure‐resolution methods are proposed for prediction of rotational diffusion parameters. The indirect procedure is based on the structure of a molecule in solution or in crystal, and uses the structure parameters of radius of gyration, and low‐resolution molecular surface and volume, determined from measured or theoretically calculated small‐angle x‐ray scattering intensities, to estimate a frictional equivalent ellipsoid of revolution. The direct method starts mainly from the crystallographic structure of a molecule and calculates the triaxial inertia equivalent ellipsoid, experimentally calibrated by translation diffusion data, to simulate the frictional behavior. The predicted harmonic mean of the rotational correlation times of compact globular macromolecules with molar masses of 14,000–65,000 g/mol agree with experimental results within the error limits. The prediction method is recommended for expert systems in structure research and for detection of internal protein flexibility or marker mobility by nmr and electron paramagnetic resonance experiments.
A vibrational spectroscopic study of the self‐association of 5′‐GMP in aqueous solution
Authors: Audet Pierre , Simard Christine , Savoie Rodrigue
Published: December 2004

The Raman spectra of highly concentrated solutions of 5′‐GMP at neutral and acid pH were recorded in order to better characterize the structure of the self‐aggregates formed in these solutions and their melting behavior. Vibrational coupling of the CO stretching vibrations in tetrameric units at neutral pH is shown to yield a characteristic pattern of two Raman bands at ca. 1730 and 1680 cm−1 (1708 and 1664 cm−1 in D2O), and an iractive mode at 1678 cm−1 in D2O. From the intensity of the 1730‐cm−1 band, proportional to tetramer concentration, and that at 1485 cm−1, which reflects the stacking of the bases, the thermal stability of the self‐associates formed at neutral pH is shown to be higher for stacked tetramers. At acid pH, the melting of the helical aggregates responsible for the formation of a gel is preceded by the freeing of the hydrogen‐bonded phosphate groups, accompanied by a change of conformation from C3′‐endo to C2′‐endo in some of the associated ribose units. Previous spectroscopic results suggesting the formation of tetramers as an intermediate step in the melting of the gel were not reproduced in this study.