bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature‐correlated force and structure development in elastomeric polypeptides: The Ile1 analog of the polypentapeptide of elastin
Authors: Urry D. W. , Long M. M. , Harris R. D. , Prasad K. U.
Published: December 2004

The Ile1 analog of the polypentapeptide of elastin, (L · Ile1‐L · Pro2‐Gly3‐L · Val4‐Gly5)n, abbreviated as Ile1‐PPP, was synthesized with n > 100 to determine the effect of the increased hydrophobicity of the pentamer resulting from Val1 replacement by Ile1 on the previously characterized inverse temperature transition of the polypentapeptide of elastin (PPP). Ile1‐PPP, dissolved in water at 4°C, was found to aggregate, forming a viscoelastic coacervate on raising the temperature. The onset of aggregation was 8°C for Ile1‐PPP, as compared to 24°C for PPP. Characterization by CD demonstrated an increase in intramolecular order on raising the temperature from 8°C to 25°C, and demonstrated similar conformations for PPP and Ile1‐PPP before and after their respective transitions. The CD‐characterized transition also occurred at a temperature some 15°C lower than that of PPP. By means of 20‐Mrad γ‐irradiation cross‐linking of the Ile1‐PPP coacervate, an elastomeric matrix was formed with an elastic modulus, similar to that of 20‐Mrad cross‐linked PPP. The temperature dependence of elastomeric force of cross‐linked Ile1‐PPP showed an abrupt increase from essentially zero at 8°C to three‐quarters of full force at 10°C and essentially full force by 20–25°C. This development of elastomeric force for the more hydrophobic Ile1‐PPP matrix, which parallels the increase in intramolecular order characterized by the CD studies, also occurs at a temperature some 15°C lower than that for the PPP matrix. Thus, in these elastomeric polypeptides, development of elastomeric force is coupled to an inverse temperature transition, the temperature of which depends inversely on the hydrophobicity of the constituent pentamer. It appears that a series of elastomeric polypeptide biomaterials are possible in which the temperature over which elastomeric force develops can be varied.
D‐Isomeric replacements within the 6–9 core sequence of ac‐[Nle4]‐α‐MSH4–11‐NH2: A topological model for the solution conformation of α‐melanotropin
Authors: Sugg Elizabeth E. , Cody Wayne L. , Abdel‐Malek Zalfa , Hadley Mac E. , Hruby Victor J.
Published: December 2004

Analogs of Ac‐[Nle4]‐α‐MSH4–11‐NH2 and Ac‐[Nle4, D‐Phe7]‐α‐MSH4–11‐NH2 were prepared with D‐isomeric replacements at the His6, Arg8, and Trp9 residues. The requirement for an indole moiety at position 9 also was evaluated by replacement with L‐leucine in both parent fragment analogs. D‐isomeric replacements at positions 6 and 8 in either series were detrimental to biological potency in frog (Rana pipiens) and lizard skin (Anolis carolinensis) in vitro melanotropic assays. However, Ac‐[Nle4, D‐Trp9]‐α‐MSH4–11‐NH2 and Ac‐[Nle4, D‐Phe7, D‐Trp9]‐α‐MSH4–11‐NH2 were equipotent and 10 × more potent than Ac‐[Nle4]‐α‐MSH4–11‐NH2, respectively, in the lizard skin bioassay, and 30 and 1900 times more potent in the frog skin bioassay. Ac‐[Nle4, D‐Phe7, D‐Trp9]‐α‐MSH4–11‐NH2 was 3 × more potent than α‐MSH in the frog skin bioassay. Proton nmr studies in aqueous solution revealed a marked preservation of the backbone conformation of these linear analogs. Chemical‐shift variations due to the through‐space anisotropic influence of the core aromatic amino acid residues permitted evaluation of side‐chain topology. The observed topology was consistent with nonhydrogen‐bonded β‐like structure (ϕ = −139°, ψ = +135° for L‐amino acids; ϕ = +139°, ψ = −135° for D‐amino acids) as the predominant solution conformation. The biological and conformational data suggest that high melanotropic potency requires a close spatial arrangement of the His6, Phe7, and Arg8 side chains.
An analysis of circular intensity differential scattering measurements: Studies on the sperm cell of eledone cirrhosa
Authors: Wells K. Sam , Beach David A. , Keller David , Bustamante Carlos
Published: December 2004

This study represents the first systematic attempt to characterize the possible sources of artifacts that can interfere with the measurement of circular intensity differential scattering (CIDS) as a function of the scattering angle. A theoretical analysis of the effect of imperfect incident circular polarizations in the measurement of baselines from nonchiral scatterers and in the signals from chiral samples is derived. From this analysis the requirements of the tolerance on the quality of the incident circular polarizations to unequivocally measure the CIDS effect are established. The protocol for alignment of the CIDS instrument and the characterization of the incident polarizations utilized in these studies are described in detail. CIDS measurements on suspensions of helical sperm cells are presented. The experimental results are modeled computationally with the use of the current CIDS theory. Good agreement between the data and the computations is obtained. The results clearly indicate the ability of CIDS to provide information on the long‐range chiral organization of samples in solution.
The effect of monovalent cations on the association behavior of guanosine 5′‐monophosphate, cytidine 5′‐monophosphate, and their equimolar mixture in aqueous solution
Authors: Walmsley Judith A. , Sagan Barbara L.
Published: December 2004

1H‐ and 31P‐nmr spectroscopy have been used to investigate the self‐association of M2(5′‐CMP) [M = Li+, Na+, K+, Rb+, or (CH3)4 N+; 5′‐CMP = cytidine 5′‐monophosphate], the self‐association of Li2(5′‐GMP) (5′‐GMP = guanosine 5′‐monophosphate), and the heteroassociation of 5′‐GMP and 5′‐CMP (1 : 1 mole ratio) in aqueous solution as a function of the nature of the monovalent cation. Proton spectral differences for the different 5′‐CMP salts exhibit a cation‐size dependence and have been ascribed to a change in the stacking geometry. An average stacking association constant of 0.63 ± 0.24M−1 at 1°C, consistent with the weak stacking interactions of the cytosine bases, was determined for the 5′‐CMP salts. Heteroassociation of 5′‐GMP and 5′‐CMP follows the reverse of the cation order for the formation of ordered aggregates of 5′‐GMP. Heteroassociation occurs in the presence of Li+, Na+, and Rb+ ions, but only self‐association occurs for the K+ nucleotides. Li2(5′‐GMP), which does not form ordered species, self‐associates to form disordered base stacks with a stacking constant of 1.63 ± 0.11M−1 at 1°C.
Synthesis, and conformational and biological study of 2‐D‐Ala,5‐des‐Met‐enkephalin hydrazide modified at the carboxylic end by poly‐N‐vinylimidazole
Authors: Vlasov G. , Krasnikova E. , Kozhevnikova N. , Illarionova N. , Denisov I.
Published: December 2004

N, N‐bis‐2‐D‐Ala,5‐des‐Met‐enkephalin hydrazide of azo‐isobutyric acid was synthesized. This was used to obtain polyvinylimidazole derivatives of an enkephalin analog, modified at the carboxylic end by poly‐N‐vinylimidazole. The effect of modification of tetrapeptide hydrazide on its conformational properties and biological activity in vivo and in vitro was studied.
A Brillouin scattering study of the hydration of Li‐ and Na‐DNA films
Authors: Lee S. A. , Lindsay S. M. , Powell J. W. , Weidlich T. , Tao N. J. , Lewen G. D. , Rupprecht A.
Published: December 2004

We have used Brillouin spectroscopy to study the velocities and attenuation of acoustic phonons in wet‐spun films of Na‐DNA and Li‐DNA as a function of the degree of hydration at room temperature. Our data for the longitudinal acoustic (LA) phonon velocity vs water content display several interesting features and reveal effects that we can model at the atomic level as interhelical bond softening and relaxation of the hydration shell. The model for interhelical softening makes use of other physical parameters of these films, which we have determined by gravimetric, x‐ray, and optical microscopy studies. We extract intrinsic elastic constants for hydrated Na‐DNA molecules of c11 ≃ 8.0 × 1010 dynes/cm2 and c33 ≃ 5.7 × 1010 dynes/cm2, which corresponds to a Young's modulus, E ≃ 1.1 × 1010 dynes/cm2 (with Poisson's ratio, σ = 0.44). The negative velocity anisotropy of the LA phonons indicates that neighboring DNA molecules are held together by strong interhelical bonds in the solid state. The LA phonon attenuation data can be understood by the relaxational model in which the acoustic phonon is coupled to a relaxation mode of the water molecules. Na‐DNA undergoes the A to B phase transition at a relative humidity (rh) of 92% while Li‐DNA (which remains in the B form in this range) decrystallizes at an rh of 84%. We find that our Brillouin results for Na‐ and Li‐DNA are remarkably similar, indicating that the A to B phase transition does not play an important role in determining the acoustic properties of these two types of DNA.
Theoretical determination of the CD of proteins containing closely packed antiparallel β‐sheets
Authors: Manning Mark C. , Woody Robert W.
Published: December 2004

Proteins containing two closely packed β‐sheets comprise an important class of biopolymers. Rotational and dipole strengths have been determined by the excition coupling model for interacting pairs of two idealized flat β‐sheets and for the double β‐sheets of seven globular proteins: plastocyanin, human prealbumin, immunoglobulin VREI, concanavalin A, Cu,Zn superoxide dismutase, staphylococcal nuclease, and elastase. The effects of various geometrical factors on the CD spectra were investigated. Results for the idealized sheets indicate that two sheets display through‐space interactions that are large at distances of 5–7 Å and remain significant even at distances typical of the intersheet separations in globular proteins (12–15 Å). The CD spectra are sensitive to the angle (Ω) between the strand directions of the two sheets, with maximum intersheet contributions at Ω = ±45°. Both the intrastrand and interstrand twisting were determined in the seven proteins, and their effects on the calculated CD are discussed. This work represents the first theoretical CD study on the interactions of two regular protein secondary structures, including rotational strength calculations on large sections (up to 135 residues) of globular proteins.
Low‐energy conformations of two lysine‐containing tetrapeptides of collagen: Implications for posttranslational lysine hydroxylation
Authors: Takahashi Koichi , Kang Young Kee , Némethy George , Scheraga Harold A. , Ananthanarayanan V. S.
Published: December 2004

The possible role of conformational constraints in the posttranslational hydroxylation of lysyl residues in collagen has been investigated by means of conformational energy computations for the N‐acetyl‐N′‐methylamides of the four tetrapeptides Ala‐Xxx‐Gly‐Ser and Gly‐Xxx‐Ala‐Gly, where Xxx = Lys or Ala. When hydration is taken into account, all four peptides are shown to exist as a mixture of conformations, but there is a strong preference for type II bends in the conformational ensembles of two Ala‐Xxx‐Gly‐Ser tetrapeptides and for type I bends in the conformational ensembles of the other two. The results agree with experimental evidence suggesting that a type II bend is an important conformation for Ac‐Ala‐Lys‐Gly‐Ser‐NHCH3, and they support an earlier suggestion that a β‐bend may play a role in the posttranslational hydroxylation of Lys residues in position Y of the Gly‐X‐Y triplet in collagen.
Conformational unfolding in the N‐terminal region of ribonuclease a detected by nonradiative energy transfer: Distribution of interresidue distances in the native, denatured, and reduced‐denatured states
Authors: Haas E. , McWherter C. A. , Scheraga H. A.
Published: December 2004

Time‐dependent fluorescence measurements have been used to determine the distribution of distances between probes attached to residues 1 and (49 + 53) of bovine pancreatic ribonuclease A in the native, denatured, and reduced‐denatured states. Measurements were made on donor and on doubly labeled (donor + acceptor) protein in 50% aqueous glycerol solutions at −30°C and at room temperature. The fluorescence‐decay curves were used to compute distribution functions for the interprobe distances. The native protein has a narrow distribution of interprobe distances at −30°C (high‐viscosity medium); this distribution is narrower at room temperature (low‐viscosity medium), due primarily to the dynamic flexibility of the probes. Denaturation by 6M guanidine hydrochloride leads to a wider distribution of distances at −30°C, with a shift of the distribution curve to larger distances, because of the increased disorder of the protein. Reduction of the disulfide bonds by dithiothreitol leads to further decreases in transfer efficiency (a unique distribution curve for the reduced protein was not obtained because of the low transfer efficiency). Both the denatured and reduced‐denatured species have average interprobe distances of about 60 Å, compared to 36 Å for the native protein. Reduction of the solvent viscosity leads to nearly monoexponential decay of the donor fluorescence in the doubly labeled derivative. This is interpreted as a manifestation of fast local Brownian motions. It appears that large‐scale segmental motions do not take place in the denatured protein within the excited‐state lifetime of the donor (ca. 8 ns). The above results indicate that reduced‐denatured ribonuclease A has residual structure that limits segmental Brownian motion in the N‐terminal segment.
Identification of regions of potential flexibility in protein structures: Folding units and correlations with intron positions
Authors: Segawa Shin‐Ichi , Richards Frederic M.
Published: December 2004

An algorithm has been developed to estimate flexibility for potential hinge motion at specified residues, that is, the mutual movement of two domains by rotation around a set of main‐chain dihedral angles with torsion angles of neighboring side chains as variables. Such conformational changes must occur without severe atomic collisions. Flexible hinges have been found that satisfy such criteria. Sequence flexibility charts were obtained by plotting the flexibility of each residue against the residue number. Such charts were calculated for 10 proteins (ovomucoid third domain, cytochrome c, lysozyme, hemoglobin β‐chain, α‐chymotrypsin, elastase, carboxypeptidase A, dihydrofolate reductase, triosephosphate isomerase, and alcohol dehydrogenase) taken from the Protein Data Bank. The first step of unfolding is likely to occur at the hinge point with the largest flexibility. Following this idea, the polypeptide chain can be dissected into several folding units according to the sequence flexibility chart. When two domains are separated by conformational changes at such a hinge, the sequence flexibility chart for each domain changes, and it is recalculated and used to indicate subsequent unfolding steps. In this process of iterative estimation of flexibile hinges, some well‐isolated hinges, or the border line between flexible and inflexible regions, were found to be directly at or close to the positions of splice junctions in the eukaryotic genes. Of a total of 45 splice junctions in the 10 proteins examined in this paper, 38 junctions can be identified as flexible hinges between folding units. We suggest that the iterative estimation of flexible hinges may define an array of possible folding/unfolding paths, and that the exon–intron arrangement in the gene may be closely correlated with the folding process of the protein.
Effect of sequence‐specific interactions on the stability of helical conformations in polypeptides
Authors: Vásquez Max , Scheraga Harold A.
Published: December 2004

A modification of the Zimm–Bragg two‐state model for the helix–coil transition in polypeptides, which considers the effect of charge–dipole, charge–charge, and other specific interactions on helix stability, is presented. The new model introduces a series of adjustable parameters whose values are estimated by fitting to recent spectroscopic results on medium‐sized peptides. This formalism, based on traditional two‐state helix–coil transition models, provides a framework in which data on the helix contents of peptides of specific sequence can be rationalized by a statistical mechanical theory.
Translational friction of a particle inside a vesicle studied by an extended shell method
Authors: Allison Stuart A.
Published: December 2004

The translational friction of a particle inside a rigid hollow sphere is determined in this work. This should be important in model studies of solute diffusion in cells or vesicles. An extended shell algorithm is developed and used in which the cell or vesicle is modeled as a large number of beads. In the extended algorithm, the shell is divided into groups of beads and the assumption is made that the force exerted by each bead on the solvent is constant within a group. The algorithm is tested by using it to determine the translational friction constants of spheres and prolate ellipsoids modeled as shells of beads.
Structural versatility of peptides from Cα,α‐dialkylated glycines. I. A conformational energy computation and x‐ray diffraction study of homo‐peptides from Cα,α‐diethylglycine
Authors: Benedetti E. , Barone V. , Bavoso A. , Di Blasio B. , Lelj F. , Pavone V. , Pedone C. , Bonora G. M. , Toniolo C. , Leplawy M. T. , Kaczmarek K. , Redlinski A.
Published: December 2004

Conformational energy computations on a derivative and a homo‐dipeptide of Cα,α‐diethylglycine were performed. In both cases the N‐ and C‐terminal groups are blocked as acetamido and methylamido moieties, respectively. It was found that the Cα,α‐diethylglycine residues are conformationally restricted and that the minimum energy conformation corresponds to the fully extended C5 structure when the NCαC′ bond angle is smaller than 108° (as experimentally observed). The results of the theoretical analysis are in agreement with the crystal‐state structural propensity of the complete series of N‐trifluoroacetylated homo‐peptides of this Cα,α‐dialkylated residue from monomer to pentamer, determined by x‐ray diffraction and also described in this work. Interestingly, for the first time, a crystallographically planar peptide backbone was observed (in the protected tripeptide). A comparison with peptides of Cα,α‐dimethylglycine, Cα‐methyl, Cα‐ethylglycine, and Cα,α‐di‐n‐propylglycine indicates that the fully extended conformation becomes more stable than the helical structures when both amino acid side‐chain Cβ atoms are substituted.
Structural versatility of peptides from Cα,α‐dialkylated glycines. II. An IR absorption and 1H‐nmr study of homo‐oligopeptides from Cα,α‐diethylglycine
Authors: Toniolo C. , Bonora G. M. , Bavoso A. , Benedetti E. , Di Blasio B. , Pavone V. , Pedone C. , Barone V. , Lelj F. , Leplawy M. T. , Kaczmarek K. , Redlinski A.
Published: December 2004

The conformational preferences of the N‐trifluoroacetylated homo‐peptides of Cα,α‐diethylglycine from monomer to pentamer in chloroform solution were determined by using ir absorption and 1H‐nmr. Intramolecular hydrogen bonding was found to be the dominant factor for all NH groups. The likely absence of a conformational transition upon increasing main‐chain length, and the remarkable stability to dilution, heating, and addition of perturbing agents, are additional relevant findings of this study. These results are in agreement with those of the fully extended, C5‐conformation‐forming homo‐peptides from the higher homolog Cα,α‐di‐n‐propylglycine, but contrast dramatically to those of the homo‐peptides from the lower homolog Cα,α‐dimethylglycine, which have been shown to adopt the 310‐helical structure.
Optical activity of saccharides—the vacuum‐uv origin of sodium‐D rotation
Authors: Stevens Eugene S. , Sathyanarayana Bangalore K.
Published: December 2004

A semiempirical theory of saccharide optical activity indicates that the dominant source of NaD rotation is a vacuum‐uv CD band near 150 nm, a band observed experimentally in polysaccharide film CD spectra. The model is a modification of polarizability theory in which high‐energy electronic excitations are coupled by degenerate perturbation theory, giving rise to “molecular excitons.” The existence of an excitation mode well separated in energy from even higher energy modes arises from the local symmetry of tetrahedral carbon atoms in a puckered ring structure. Calculated NaD rotations correlate well with experimental values.
The effect of amino acid substitution on protein‐folding and ‐unfolding transition studied by computer simulation
Authors: Taketomi Hiroshi , Kanô Fumiaki , Gō Nobuhiro
Published: December 2004

Protein‐folding and ‐unfolding transitions were studied by the method of computer simulation. The protein was modeled as a two‐dimensional lattice polymer. Various energy terms were assumed to be operative between units composing the polymer. But hydrophobic interactions were neglected explicitly. Both thermodynamic and kinetic quantities were obtained from the simulation, and from their temperature dependence in the transition zone characteristics of the conformational transition of proteins were discussed. Two amino acid substituted models, differing in the location of substitution, were studied and compared with the original in order to clarify the effect of substitution on conformational transition of proteins. The following conclusions were reached in this study: (1) The relaxation time of the slow mode, which reflects the overall folding and unfolding processes, shows a peak near the transition temperature, while that of the fast mode is almost independent of temperature. The peak of the slow mode occurs at a slightly lower temperature than the transition temperature. (2) The dependence of the logarithm of the rate constants on the inverse of temperature (Arrhenius plot) is linear. Therefore, the plot of the free energy of activation vs temperature is linear. (3) The values of kinetic parameters obtained suggest that in the activated state the intramolecular interactions are half broken, while the state is close to the native state on the entropy axis. (4) The amino acid substitution, which is modeled as having slightly unfavorable short‐range interactions, causes the substituted ones to be slightly unstable. Moreover, it causes the folding transition to slow. From the analysis of the way slowing down is observed in the two substituted models, we conclude that a structure, designed to model a β‐sheet, is formed before it gets assembled with other structures, which are designed to model α‐helices. The process of assembly occurs nearly at the activated state of the folding and unfolding transition. (5) It is suggested from this study that the maximum of folding rate constant in the Arrhenius plot that has been observed experimentally in real proteins is likely due to hydrophobic interactions.
A critical review of the nucleosidic vibration modes appearing in the 800–500‐cm−1 spectral region, based on new harmonic dynamics calculations
Authors: Ghomi M. , Letellier R. , Taillandier E.
Published: December 2004

On the basis of a harmonic dynamics calculation, it is shown that in the 800–500‐cm−1 spectral region of DNA vibrational spectra, the characteristic Raman peaks and ir bands do not arise from the same nucleosidic motions. The Raman spectra involve mainly the ring‐breathing modes of nucleic bases while the ir spectra reveal essentially their out‐of‐plane vibrations. Moreover, the calculated results show the splitting of the guanine‐ and adenine‐residue breathing modes upon their coupling with the sugar‐pucker motions. This fact is in agreement with the poly[d(G‐C)] and poly[d(A‐T)] Raman spectra.
Tanford–Kirkwood theory for concentric dielectric continua: Application to dimethylphosphate
Authors: Jayaram B. , Beveridge D. L.
Published: December 2004

The Tanford–Kirkwood theory for evaluating the electrostatic free energy of a discrete charge distribution in the presence of ion atmosphere is extended to concentric dielectric continua. The theory is applied to study the conformational preferences with respect to phosphodiester torsion angles in the dimethylphosphate anion (DMP−) and the sodium dimethylphosphate ion pair (Na+DMP−), in the absence and presence of ion atmosphere and at varying local dielectric constants. Results indicate that phosphodiester torsion angles in DMP− prefer the gauche‐gauche conformation in aqueous solutions.
Hydrogen exchange of the tryptophan residues in bovine α‐lactalbumin studied by uv spectroscopy
Authors: Harushima Yoshiaki , Kuwajima Kunihiro , Sugai Shintaro
Published: December 2004

The effect of Ca2+ ion on structural fluctuation of a milk Ca2+‐binding protein, α‐lactalbumin, under native conditions was investigated by comparing hydrogen‐exchange reactions of tryptophan residues in the apo‐form without Ca2+ and in the holo‐form at 1 mM CaCl2 at pH 7.0 in the presence of 0.1M Na+. The reactions were followed by measuring time‐dependent absorption changes at 298–300 nm due to the 2H‐1H exchange of the tryptophan imino protons and were found to be biphasic under all the conditions examined. Two of the four tryptophan protons are insensitive to Ca2+ concentration and show a relatively fast exchange rate. The other two protons are much more extensively protected (a protection degree of 103–105) and are markedly affected by the presence of Ca2+. Examinations of the temperature dependence and pH dependence of the individual exchange rates have been utilized for elucidating the exchange mechanism. The fast protons show a low activation energy reaction with so‐called EX2 kinetics. The exchange reaction of the slow protons is accompanied by a high activation energy, and the exchange mechanism of the protons depended on the presence or absence of stabilizing Ca2+ ions—the EX1 kinetics for the apo‐protein and the EX2 kinetics for the holo‐protein at 1 mM Ca2+. The exchange reaction in the thermally unfolded state was also found to be biphasic, but the fast phase, which has an exchange rate in the fully exposed state, becomes predominant with decreasing temperature. By taking this fact and using a structural unfolding model of hydrogen exchange, the present results are fully consistent with thermodynamic parameters of the thermal transition and kinetic parameters of refolding reactions induced by concentration jumps of guanidine hydrochloride obtained in previous studies. It is demonstrated that the reaction of the slow protons in the native state is mediated by a transient global unfolding equivalent to the “thermal” unfolding under a native condition and that switching of the exchange mechanism from the EX1 to EX2 kinetics results from acceleration of the refolding rate with an increase in Ca2+ concentration. The transient global unfolding takes place even under a strongly native condition, e.g., at a temperature 20° below the beginning of the thermal transition.
Moments for DNA topoisomers: The helical wormlike chain
Authors: Shimada Jiro , Yamakawa Hiromi
Published: December 2004

The mean‐square radius 〈S2〉N of gyration of the DNA topoisomer with the linking number N is evaluated as a function of N and chain length L on the basis of a (circular) twisted wormlike chain, i.e., a special case of the helical wormlike chain. Evaluation of 〈S2〉N and also of the moment 〈Wr2〉 of the writhe Wr is carried out over a wide range of L, following the Monte Carlo procedure of Frank‐Kamenetskii et al. It is found that the present Monte Carlo values of 〈Wr2〉 for large L are appreciably larger than the known Monte Carlo values for freely jointed chains. Thus, the empirical interpolation formula for 〈Wr2〉 previously constructed on the basis of the theoretical values for small L along with the latter Monte Carlo values for large L is revised with the present Monte Carlo values. By the use of the revised formula, a reanalysis of the experimental data for the distribution of topoisomers is made, and it is found that the present estimates of the torsional constant and the stiffness parameter are equal to and somewhat larger than the previous ones, respectively. It is shown that 〈S2〉N decreases with increasing |ΔN|, where ΔN = N − N, with N the number of helix turns in the linear DNA chain in its undeformed state. The mean‐square radii of gyration 〈S2〉Wr and 〈S2〉 of the original circular Kratky–Porod wormlike chain with and without Wr fixed are also evaluated.
Ligation of fibrinogen by factor XIIIa with dithiothreitol: Mechanical properties of ligated fibrinogen gels
Authors: Shimizu Akira , Ferry John D.
Published: December 2004

Human fibrinogen (concentration 8.4 mg/mL) was ligated (cross‐linked) with factor XIIIa and dithiothreitol (DTT) at pH 8.5, ionic strength 0.45. With 7.5 μg/mL of factor XIIIa alone, there was almost no γ‐γ ligation, but with 2 mM DTT added, oligomers appeared, and γ‐γ and Aα‐Aα ligation was nearly complete after 3 days. At 38 μg/mL of factor XIIIa, some γ‐γ and Aα‐Aα ligation occurred even without DTT. For fibrinogen concentrations of 4.0 and 8.4 mg/mL, 38 μ/mL factor XIIIa, 2.0 mM DTT, clot‐like gels formed and the shear modulus of elasticity increased slowly over several days to a constant value. The final modulus was similar in magnitude to those of ligated clots of α‐fibrin (clotted by thrombin) and α‐fibrin (clotted by batroxobin) under the same conditions. However, the opacity was somewhat higher; whereas in fine fibrin clots there is minimal lateral association of the protofibrils, in fibrinogen gels at the same pH and ionic strength the protofibrils (which are presumably single chains of fibrinogen monomers joined end to end at their D domains) are evidently associated in bundles (although not to the degree seen in coarse fibrin clots). Creep and creep recovery measurements showed almost perfect elastic behavior, with essentially no creep under stress and complete recovery after removal of stress. The modulus was scarcely affected by introduction of lithium bromide by diffusion to a concentration of 0.6M, which in unligated fibrin clots causes substantial softening. Whereas in fine fibrin clots (both αβ‐fibrin and α‐fibrin) factor XIIIa causes only γ‐γ ligation, addition of 2 mM DTT produced some α‐α ligation in these also.
Interaction of the fibrinogen‐binding tetrapeptide gly‐pro‐arg‐pro with fine clots and oligomers of α‐fibrin; comparison with αβ‐fibrin
Authors: Shimizu Akira , Schindlauer Günther , Ferry John D.
Published: December 2004

The tetrapeptide Gly‐Pro‐Arg‐Pro(GPRP) was introduced by diffusion into fine unligated clots formed from human fibrinogen at pH 8.5 and ionic strength 0.45 by batroxobin (αβ‐fibrin) and by thrombin (α‐fibrin). The α‐fibrin clots were essentially liquefied at GPRP concentrations above 1 mM and αβ‐fibrin clots above 15 mM, and the degree of polymerization of the resulting oligomers decreased progressively with increasing GPRP concentration as shown by γ‐γ ligation with factor XIIIa and subsequent gel electrophoresis. Much smaller concentrations of GPRP, when introduced into unligated clots by diffusion, were sufficient to modify their mechanical properties profoundly. The shear modulus of elasticity G25 measured 25 s after imposition of stress fell, for example, by a factor of 0.4 at 0.1 mM GPRP in α‐fibrin and at 1.1 mM in αβ‐fibrin. The rate of shear creep under constant stress and the proportion of irrecoverable deformation also increased enormously. This behavior, and the corresponding decrease in steady flow viscosity, may be interpreted in terms of competition of GPRP with A sites on the E domains of fibrin monomers for bidning to “a” sites on the D domains, resulting in a moderate increase with increasing GPRP concentration of the average proportion of severed network strands and an enormous increase in the rate at which all strands dissociate and reassociate. Reassociation of severed strands in new configurations is a necessary corollary since the differential modulus or compliance remains constant during creep and creep recovery. The greater susceptibility of α‐fibrin clots to interaction with GPRP is attributed to stabilization of contacts between monomer units by Bb associations in αβ‐fibrin. Ligated clots, with or without GPRP, exhibited essentially no time‐dependent creep and no irrecoverable deformation, corresponding to an absence of any severance of network strands.
1H‐nmr studies of the 20–31 fragment of calmodulin and of its cyclic analogue
Authors: Motta Andrea , Tancredi Teodorico , Borin Gianfranco , Marchiori Ferdinando , Peggion Evaristo , Temussi Pierandrea
Published: December 2004

High‐resolution 1H‐nmr spectroscopy at 500 MHz has been used to study the Ca2+ binding domain I of bovine brain calmodulin in aqueous solution. All the resonances of the linear dodecapeptide Asp‐Lys‐Asp‐Gly‐Asn‐Gly‐Thr‐Ile‐Thr‐Thr‐Lys‐Glu and of its cyclic analogue, synthesized by classical solution methods, have been completely assigned using a combination of several one‐ and two‐dimensional nmr experiments, including the zero quantum correlation. Chemical shift values and 3JCHNH coupling constants indicate that, on the nmr time scale, both peptides are flexible and assume multiple conformations in rapid equilibrium, with no relevant contribution of structured features. Addition of Ca2+ causes only minor spectral changes in aqueous solution of both peptides, while larger effects are observed in more hydrophobic mixtures such as water/trifluoroethanol. The linear analogue shows nonspecific interactions, while only Asp3 and Asn5 are significantly perturbed in the cyclic peptide. This evidence, together with identical findings in La3+ titration studies of the cyclic analogue in pure water, suggest that loop I of calmodulin is endowed with an intrinsic binding ability.
Crystalline structure and packing of mannan I
Authors: Atkins E. D. T. , Farnell Sheila , Burden C. , Mackie W. , Sheldrick B.
Published: December 2004

The x‐ray fiber diffraction pattern of the mannan I polymorph has been reexamined using the linked atom least squares (LALS) model‐building program. The chain conformation and packing were refined using atomic coordinates derived from the x‐ray crystallographic structure of mannotriose. The study confirmed the conclusions of previous investigations and showed that, in mannan I, the chains are antiparallel. Mannan polymorphism is compared with other related polysaccharides and the biological significance of this result in relation to the biosynthesis of mannan is discussed.
Evidence for similar function of transmembrane segments in receptor and membrane‐anchored proteins
Authors: Brandl Christopher J. , Deber Raisa B. , Hsu Lynn C. , Woolley G. Andrew , Young Xenia K. , Deber Charles M.
Published: December 2004

Transmembrane (TM) regions of receptor proteins should have unique structural and/or chemical characteristics if these regions contain residues functional in TM signal transduction. However, in a survey of the membrane‐occurring residues in 37 integral membrane proteins, we found that amino acid compositions of TM regions of receptor proteins (n = 11) could not be distinguished statistically from corresponding regions of membrane‐anchored proteins (e.g., recognition molecules) with a functional external domain attached to a single hydrophobic membrane‐spanning anchor segment (n = 16). TM regions in both categories of proteins differed from the compositions of TM regions in membrane‐transport proteins (n = 10). The analysis implies that TM regions in receptor proteins may function mainly to anchor (and position) receptors in their cellular membranes, and therefore residues in receptors that participate in signal transduction need not be restricted to these regions. In addition to mechanisms involving receptor aggregation, ligand‐activated conformational perturbation of a receptor external aqueous domain, resulting in membrane penetration of hydrophobic segment(s) of this domain to produce intramembranous contact with its cytoplasmic domain, is hypothesized as a further possible mode of signal transduction.
Counterion exchange reactions on DNA: Monte Carlo and Poisson–Boltzmann analysis
Authors: Paulsen Mark D. , Anderson Charles F. , Record M. Thomas
Published: December 2004

In solutions containing DNA and cations of more than one type, the competitive interactions of these cations with DNA can be modeled as an ion exchange process that can be described quantitatively by means of the theoretical approach reported in this paper. Under conditions of experimental interest the radial distribution function of each type of counterion is calculated from the results of canonical Monte Carlo (MC) simulations using the primitive model for DNA (having a helical charge distribution) and for the electrolyte ions. These ions consist of monovalent coions, monovalent counterions intended to represent Na+, and counterions of a second type designated Mz+, having variable size and charge (z ≥ 1). The competitive association of these counterions with DNA is described in terms of D, a parameter analogous to an ion exchange equilibrium quotient. Values of D are calculated from the results of our MC simulations and compared with corresponding predictions of the Poisson–Boltzmann (PB) cell model and with results inferred from analyses of previously published nmr measurements. Over typical experimental concentration ranges (0.02M < [Na+] < 0.20M, 0.001 < [Mz+] < 0.160M), DMC and DPB both are predicted to be relatively independent of the bulk ion concentrations. For various specifications of the size and charge of the competing cation (Mz+), DMC and DPB exhibit similar trends, although the MC simulations consistently predict that the cations bearing a higher charge density than that of Na+ are somewhat stronger competitors than indicated by the PB calculations. For monovalent and divalent competitors of varying radii, theoretical predictions of D are compared with values obtained by fitting nmr measurements. If the hard‐sphere radii specified in the simulations are the (hydrated) ionic radii determined from conductance measurements, then the MC predictions and the corresponding nmr results are in reasonable agreement for various monovalent competitors and for a divalent polyamine, but not for Ca2+ and Mg2+.
Metal‐Induced sequential transitions among DNA conformations
Authors: Shin Yong A. , Butzow James J. , Sinsel Lisa D. , Clark Patricia , Pillai Rajasekharan P. , Johnson W. Curtis , Eichhorn Gunther L.
Published: December 2004

The action of [Co(NH3)6]Cl3 on poly(dGdC) · poly(dGdC) can lead to a series of consecutive reactions, in which B‐DNA is first converted to Z‐DNA [M. Behe and G. Felsenfeld (1981) Proc. Natl. Acad. Sci USA 78, 1619–1623], which in turn is transformed into an unidentified conformer that we tentatively call “U”, and finally the highly associated anisotropic ψ‐DNA is produced. Conditions are given under which the sequence B ⇄ Z ⇄ “U” ψ(+) can be stopped at any point in the direction from left to right. The reverse processes, from right to left, occur when ψ(+) or “U”‐DNA are treated with various amounts of salt concentrations and lowering temperature. Thus it is demonstrated that four conformers of poly(dGdC) · poly(dGdC) are readily interconvertible, and that Z‐DNA and “U” conformers are intermediates in the reversible transformations of B‐ and ψ‐DNA.
The interaction of multiply charged intercalating heterocycles with DNA
Authors: Fairley Terri , Molock Frank , Boykin David W. , Wilson W. David
Published: December 2004

The interaction with DNA of two aromatic nitrogen heterocycles, 1 and 2, which at pH 6 have two positive charges on their ring systems and two cationic side chains, have been determined. A third similar compound, 3, with a single side chain and reduced ring charge, was analyzed as a control. Viscometric titrations with sonicated DNA indicated that all three compounds bind to DNA by intercalation. Spectrophotometric binding studies as a function of ionic strength indicated that both 1 and 2 bind to DNA as tetracations at pH 6. These are the first examples of intercalators with two charges directly on the intercalating ring system. Dissociation kinetics experiments as a function of ionic strength confirmed that 1 and 2 bind to DNA as tetracations. Compound 1 has a G · C base‐pair binding preference, 2 seems to prefer binding to alternating pyrimidine–purine sequences regardless of the composition, and 3 has no significant binding specificity.
Statistical mechanical theory of melting transition in supercoiled DNA
Authors: Sen Srikanta , Majumdar Rabi
Published: December 2004

The melting curve for a covalently closed circular DNA has been analyzed on the basis of an expression for the supercoiling energy derived in terms of the elastic parameters of the macromolecule, treated as a homopolymer. The result obtained by applying the usual methods of statistical mechanics indicate close agreement with the available experimental data. It is found that the elevation of the melting temperature, as compared to that of the nicked circular or linear DNA, is a natural consequence of the fact that the supercoiled molecule is constrained by an invariant linking number. The flattening of the melting curve, on the other hand, arises as the closed circular duplex melts into a loose helix rather than random coils.
Binding of nogalamycin to model tetranucleotides
Authors: Trinquier Georges , Chen Kai‐Xian , Gresh Nohad
Published: December 2004

Intercalated complexes of the antitumor antibiotic nogalamycin (NGM) with the double‐stranded oligonucleotides d(GCGC)2, d(ATAT)2, and d(ACAC) · d(GTGT) are investigated with the theoretical method SIBFA. The amino sugar part of the drug locates preferentially in the minor groove. An intrinsic preference for the d(ATAT)2 sequence over the d(ACAC) · d(GTGT) and d(GCGC)2 sequences is obtained, corresponding to relative energies 0, 11, and 15 kcal/mole, respectively. A mixed sugar‐puckering pattern is preferred in the d(ATAT)2 complex while a uniform sugar‐puckering pattern is preferred for the other sequences. No direct specific interaction involves the N+—H part of protonated NGM. The location of the amino sugar as well as the sequence selectivity is due to the global electrostatic interaction of the dimethylammonium group with the given groove. The two hydroxyl groups of the amino sugar and the carbonyl of the carbomethoxy group encounter partners for hydrogen bonding at the intercalation site, but these interactions do not appear to govern the base sequence selectivity. The nogalose part is not found to be directly involved in the binding or in the selectivity. The conformations of isolated and intercalated NGM are discussed.
Ions around DNA: Monte Carlo estimates of distribution with improved electrostatic potentials
Authors: Conrad Joan , Troll Mark , Zimm Bruno H.
Published: December 2004

Coulomb's law for the electrostatic interactions between ions is modified when discontinuities in dielectric constant (relative permittivity) occur. In a DNA solution such a discontinuity occurs at the interface between the DNA molecular helix and the surrounding water. We take the modified interaction potentials from a previous report [Macromolecules (1986) 19, 1186–1194] and use them with the Monte Carlo method to find the distribution of univalent and bivalent counterions around the DNA helix in the absence of coions (i.e., no added salt). In comparing the ion distribution with the modified potential to the distribution without, we find that the effects of the modifications to the potentials are considerable. The modifications tend to drive the ions out of the grooves of the helix, especially out of the major groove. This result comes partly from the repulsion exerted on the ions by the low‐permittivity helix and partly from the concentration of the field of the phosphates at the surface of the helix, a concentration that is also caused by the discontinuity in permittivity.
Conformational behavior of cyclic CCK‐related peptides determined by 400‐MHz 1H‐nmr: Relationships with affinity and selectivity for brain receptors
Authors: Roy P. , Charpentier B. , Durieux C. , Dor A. , Roques B. P.
Published: December 2004

The conformational study of a homogenous series of cyclic analogues of CCK8, selective for central receptors, such as Boc‐ X‐Tyr(SO3H)‐Nle‐D‐Lys‐Trp‐Nle‐Asp‐Phe‐NH2, where X = L‐Glu, D‐Glu, or γ‐D‐Glu, was performed by 400‐MHz 1H‐nmr. The regular increase in affinity for central receptors when going from [L‐Glu] to [γ‐D‐Glu] is correlated to (a) an enhancement in internal flexibility of the cyclic moiety, (b) an external orientation of the tyrosine side chain, and (c) a restructuring of the C‐terminal part of the peptide. All these results could permit a modeling of biologically active conformation of CCK8 for both receptors types to be performed.
Conformational properties of 2,3‐methanopyroglutamic acid in peptides: Nmr and X‐ray diffraction studies
Authors: Mapelli C. , Elrod L. F. , Switzer F. L. , Stammer C. H. , Holt E. M.
Published: December 2004

The effects of replacing L‐pyroglutamic acid with the cyclopropane analogue 2,3‐methanopyroglutamic acid (2,3‐MeGlp) on conformation and enzymatic stability have been investigated in 2,3‐MeGlp‐NHMe and the novel thyrotropin releasing hormone (TRH) analogue [2,3‐MeGlp1]‐TRH by x‐ray diffraction and nmr. While 2,3‐MeGlp‐NHMe adopts a folded conformation (small ψ angle) in the solid state, several conformations are available to the molecule in solution. 1H‐nmr of the diastereomeric mixture [(±)‐2,3‐MeGlp1]‐TRH indicates a close orientation of the pyrrolidone and imidazole rings. The 2,3‐MeGlp‐His amide bond is considerably more stable to pyroglutamate aminopeptidase than the Glp‐His bond in TRH.
Conformationally constrained D,L‐alternating oligopeptides
Authors: Fenude Emma , Tomasic Lera , Lorenzi Gian Paolo
Published: December 2004

The possibility of selectively reducing the number of β‐helical structures theoretically possible for a D,L‐alternating peptide by using a N‐methyl group as conformational constraint is considered. Some 1H‐nmr data regarding Boc(L‐Nle‐D‐Nle)3‐L‐Nle‐D‐MeNle‐L‐Nle‐D‐Nle‐L‐Nle‐OMe (I), its formyl analogue (II), and the pentadecapeptide Boc(D‐Leu‐L‐Leu)5‐D‐MeLeu‐(L‐Leu‐D‐Leu)2‐OMe (III) are presented. It is shown that these alternating stereocooligopeptides with a N‐methyl group in the (n − 3) (I and II) or (n − 4) position (III) differ drastically in their behavior from the corresponding nonmethylated compounds. In chloroform, I and II form predominantly ↑↓ β7.2‐helices and III forms almost exclusively ↑↓ β5.6 or ↑↓ β7.2‐helices. The helices are in every case those having the maximum possible number of interchain H bonds.
Stereoselective electron transfer between chiral substrates and metal chelates anchored to polypeptides
Authors: Pispisa B. , Palleschi A. , Paradossi G.
Published: December 2004

Electron transfer from ortho‐dihydroxy substrates, such as L(+)‐ascorbic acid, L‐adrenaline, and L‐dopa, to iron(III) in [Fe(tetpy)(OH)2]+ ions anchored to sodium poly(L‐glutamate) (FeTL) or poly(D‐glutamate) (FeTD) was found to proceed stereoselectively when structurally ordered and partially shielded actives sites prevent easy approach for redox partner. Oxidant‐reductant interactions are then mediated by the polypeptide, whose conformational asymmetry ensures an efficient sterically discriminating environment. Evidence is produced that stereoselectivity chiefly arises from transition state effects, while thermodynamic discrimination is of minor importance. Theoretical models of the diastereomeric electron‐transfer complexes were constructed by conformational energy calculations based on Coulombic, nonbonded, and hydrogen‐bonded energy terms. The molecular parameters of the models enabled “differential” thermodynamic functions of the diastereomeric pairs and stereoselectivity to be evaluated and satisfactorily compared with those experimentally determined. The models give good insight into the observed topochemical phenomena and support the idea that stereoselevtivity is coupled with a remote attack mechanism on the central metal ion where the peripheral tetpy ligand of the active sites acts as an electron‐transfer agent.