bluuebunny/crossref_metadata_2025 huggingface dataset:
Multistep brownian dynamics: Application to short wormlike chains
Authors: Allison S. A. , McCammon J. A.
Published: December 2004

Brownian dynamics simulations of short wormlike chains are carried out using the method of Ermak and McCammon [(1978) J. Chem. Phys. 69, 1352–1360]. Following Hagerman and Zimm [(1981) Biopolymers 20, 1481–1502], the wormlike chain is modeled as a string of beads. In each simulation, the dynamic evolution of an ensemble of 100 randomly generated chains is calculated for a period of from 3 to 200 ns. Two different “experiments,” fluorescence depolarization and dynamic light scattering, were performed in these simulations. Since we are primarily interested in the bending motions and not the torsional motions in this work, we have placed the transition moments along the local symmetry axis of the wormlike chain in the fluorescence depolarization “experiment.” As predicted by the Barkley and Zimm theory [(1979) J. Chem. Phys. 70, 2991–3008], a considerable amount of rapid bending motion was detected by fluorescence depolarization, though not as much as predicted by theory. We conclude that these differences are primarily due to differences between the model used in the theory and the simulations. The light‐scattering experiment was found to be insensitive to internal motion in the low scattering angle limit.
Intercalation of cationic dyes in the DNA double helix: Introductory theory
Authors: Bustamante Carlos , Stigter Dirk
Published: December 2004

The effect of salt on the intercalation of acridine dyes and DNA is rather well explained by the Gouy‐Chapman double‐layer theory as applied to a cylinder model of the DNA–dye complex. The free energy of transfer of a dye ion from the bulk solution to the complex is divided into several parts, one of which, ΔF0, accounts for the short‐range, nonelectrostatic interactions. The assumption that ΔF0 should not depend on the amount of dye in the complex leads to an internal dielectric constant of the cylinder of about Di = 7. The scatter in ΔF0 values, as calculated from individual experimental points, is of order 0.5 kT per dye ion. This scatter is large enough to mask possible effects of heterogeneity in DNA sequences. The calculations are made for a long cylinder with radius 10 Å, with the DNA phosphate charges smeared uniformly at the surface, a uniform spacing of dye charges at the cylinder axis, and a length of b = 3.37 Å per base pair. Each intercalated dye ion also adds a length b to the total length of the cylinder. The salt‐dependent part of the electric free energy of intercalation, ΔF1, is tabulated for complexes with r = 0–0.24 dye ions per DNA phosphate in 0.002–0.2M monovalent salt and dye solutions.
Most‐probable distribution at enzyme depolymerization of polysaccharides
Authors: Mazur A. K.
Published: December 2004

Several research groups have studied depolymerizing processes by enzyme cleavage using product distribution. Although only the shortest chain products can be measured experimentally, interpretation of much evidence requires an assumption of the nature of high polymer distribution. The present work analyzes the high polymer distribution of products on the basis of mathematical models suggested for the two most widespread α‐amylase action‐mechanisms. The most‐probable distribution was found to be distorted by hydrolysis only for the shortest chain products. The size of the distorted region is directly dependent on the characteristics of a specific enzyme. We studied the distribution of products for substrates of varying composition to show that it approaches the most‐probable distribution at depolymerization.
Molecular conformations and 8‐CH exchange rates of purine ribo‐ and deoxyribonucleotides: Investigation by Raman spectroscopy
Authors: Benevides James M. , Lemeur Danielle , Thomas George J.
Published: December 2004

The rate of deuterium exchange of the 8‐CH group in a purine deoxyribonucleotide, is the same as the 8‐CH exchange rate in the corresponding purine ribonucleotide, with the exception of 5′‐nucleotides of guanine. The observed 20% slower rate of 8‐CH exchange in 5′‐dGMP versus 5′‐rGMP, over the temperature range 50–80°C, are attributable to differences in molecular conformation, including differences in ring puckering of the furanose substituents. Minor differences in 8‐CH exhange rates are observed between 5′‐and cyclic (3′:5′)‐deoxyribonucleotides of a given purine, which are similar to those observed previously between corresponding 5′‐ and cyclic ribonucleotides that have been attributed to the charge difference of their respective phosphate groups [Ferreira, S. A. & Thomas, G. J., Jr. (1981) J. Raman Spectrosc. 11, 508–514]. The coupling of guanine and furanose ring structures in the 5′‐nucleotides is also evident from the vibrational frequencies of the guanine ring, which are strongly dependent on the pucker of the attached furanose moiety. Raman difference spectroscopy clearly reveals the dependence of purine nucleotide spectra on sugar‐ring pucker. In the case of GMP, the guanine characteristic ring breathing mode near 600–700 cm−1 depends for its exact position and intensity on the proportion of C3′‐endo (668 cm−1) and C2′‐endo (682 cm−1) conformers in equilibrium with one another. The Raman intensity ratio I(668)/I(682) is proposed as a measure of the conformer ratio C3′‐endo/C2′‐endo in 5′‐dGMP with possible application also to nucleic acids. Among cyclic nucleotides, differences in spectra of deoxyribo‐ and ribo‐ forms also appear to be related to differences of molecular conformation.
Study of polysaccharides by the fluorescence method. III. Chain length dependence of the micro‐Brownian motion of amylose in an aqueous solution
Authors: Kitamura Sinichi , Tanahashi Hiroshi , Kuge Takashi
Published: December 2004

The fluorescence polarization method was applied to the investigation of the micro‐Brownian motion of amylose chains having a wide range of degree of polymerization (DP). We prepared two types of fluorescent conjugates of amylose: amylose conjugated with fluorescein randomly throughout the chain (F‐amylose) and amylose conjugated locally on a terminal segment (t‐F‐amylose). The degree of fluorescence polarization of these conjugates was measured by changing the solvent viscosity at a constant temperature (25°C). The data obtained were analyzed by a Perrin‐type equation to calculate the mean rotational relaxation time, 〈ρ〉. By examination of the plots of 〈ρ〉 vs DP, and by comparison of 〈ρ〉 with the theoretical rotational relaxation time of the whole molecule at a given DP, it was found that 〈ρ〉 mainly reflects the segmental motion of the amylose chain in the high‐DP range. Thus, the fact that 〈ρ〉 for t‐F‐amylose is much smaller than that for F‐amylose at a sufficiently high DP shows that a terminal segment undergoes a more rapid micro‐Brownian motion than interior segments. In the low‐DP range, we felt that the rotational diffusion of the whole molecule contributes significantly to the relaxation process. We also examined, for comparison, the segmental motion of dextran and pullulan in a similar manner and found that these segmental motions are more rapid than those of amylose. Based on the results obtained, the segmental mobility and conformation of the amylose molecule are discussed in relation to its chain length.
Quasi‐harmonic method for studying very low frequency modes in proteins
Authors: Levy R. M. , Srinivasan A. R. , Olson W. K. , McCammon J. A.
Published: December 2004

A quasi‐harmonic approximation is described for studying very low frequency vibrations and flexible paths in proteins. The force constants of the empirical potential function are quadratic approximations to the potentials of mean force; they are evaluated from a molecular dynamics simulation of a protein based on a detailed anharmonic potential. The method is used to identify very low frequency (∼1 cm−1) normal modes for the protein pancreatic trypsin inhibitor. A simplified model for the protein is used, for which each residue is represented by a single interaction center. The quasi‐harmonic force constants of the virtual internal coordinates are evaluated and the normal‐mode frequencies and eigenvectors are obtained. Conformations corresponding to distortions along selected low‐frequency modes are analyzed.
Dynamic light scattering as a probe of superhelical DNA–intercalating agent interaction
Authors: Newman Jay
Published: December 2004

Polarized dynamic light‐scattering measurements on superhelical pBR322‐plasmid DNA solutions in 0.2M NaCl, 2 mM NaPi, pH 7.0, 2 mM EDTA result in a translational diffusion coefficient D = (3.77 ± 0.10) × 10−8 cm2/s for the native molecule. Modeling the DNA, in the simplest approximation, as a 10 × 440‐nm effective hydrodynamic rigid rod yields a good fit to the apparent diffusion coefficient angular‐dependence data up to 70°; the model fails at higher angles, probably due to the effects of flexibility or branching of the rod. Diffusion coefficient titration experiments with a platinum complex intercalating agent (PtTS) result in a titratable superhelix density of σ = −0.079 ± 0.008 under our experimental conditions, corresponding to about 34 superhelical turns in the native DNA. The DNA contour length predicted by our two independent results, the rod dimensions and the number of superhelical turns, is in excellent agreement with the contour length calculated from the number of base pairs, supporting the hydrodynamic approximation of an effective rodlike structure for this small DNA molecule in solution.
Analysis of the high‐ and low‐spin soret bands of horse‐heart metmyoglobin complexes
Authors: Anusiem A. C. I. , Kelleher M.
Published: December 2004

Interest in the thermodynamics of the iron‐binding site in hemoproteins has increased in recent years due to refinements in x‐ray crystallographic studies of hemoproteins [see Deathage, J. F., Lee, R. S., Anderson, C. M. & Moffat, K. (1976) J. Mol. Biol. 104, 687–706; Heidner, E. J., Ladner, R. C. & Perutz, M. F. (1976) J. Mol. Biol. 104, 707–722; Deathage, J. F., Lee, R. S. & Moffat, K. (1976) J. Mol. Biol. 104, 723–728; Ladner, R. C., Heidner, E. J. & Perutz, M. F. (1976) J. Mol. Biol. 114, 385–414; Fermi, G. & Perutz, M. F. (1977) J. Mol. Biol. 114, 421–431; Takano, T. (1977) J. Mol. Biol. 110, 537–568 and 569–589], the synthesis and x‐ray analysis of model heme compounds [see Scheidt, W. R. (1977) Acc. Chem. Res. 10, 339–345; Kastner, M. E., Scheidt, W. R., Mashino, T. & Reed, C. A. (1978) J. Am. Chem. Soc. 100, 666–667; Mashiko, T., Kastner, M. E., Spartalian, K., Scheidt, W. R. & Reed, C. A. (1978) J. Am. Chem. Soc. 100, 6354–6362; Hill, H. A. O., Skite, P. P., Buchler, J. W., Luchr, H., Tonn, M., Gregson, A. K. & Pellizer, G. (1979) Chem. Commun. 4, 151–152; and Scheidt, W. R., Cohen, I. A. & Kastner, M. E. (1979) Biochemistry 18, 3546–3556], and the numerous data on heme–protein interactions that account for the differences observed in ligand binding between the various species of animals. Numerous probes have been used and provide information about the structure and thermodynamics of the binding site, but no single probe can provide the complete picture [see Iizuka, T. & Yonetani, T. (1970) Adv. Biophys. 1, 157–182; Smith, D. W. & Williams, R. J. P. (1970) Struct. Bond. 7, 1–45; and Spiro, T. G. (1975) Biochim. Biophys. Acta 416, 169–189].
The speed of sound in DNA
Authors: Hakim M. B. , Lindsay S. M. , Powell J.
Published: December 2004

We have used Brillouin scattering to determine the speed of sound in (and hence longitudinal modulus of) A‐ and B‐DNA fibers. The speed of sound is very sensitive to the degree of hydration of the fibers, and measurements have to be made at laser powers below 5 mW to avoid local heating and dehydration. Under those conditions, we obtain sound speed perpendicular to the fiber axis of about 2.2 and 1.9 km/s in A‐ and B‐DNA fibers, respectively. A‐DNA fibers show a small anisotropy with sound speeds along the fiber axis higher by up to 10% B‐DNA fibers appear to be isotropic.
Conformation of P‐form DNA
Authors: Zehfus Micheal H. , Johnson W. Curtis
Published: December 2004

The P‐Form of DNA has been studied by use of ir spectroscopy and electron microscopy (EM). The ir data show that the P‐form has little or no hydrogen bonding, while the data from EM show that the P‐form has a condensed tertiary structure. In earlier work, we demonstrated that the P‐form is devoid of base stacking. When that information is combined with the new ir data, we conclude that the P‐Form is denatured because it lacks any of the interactions associated with a normal secondary structure. This is in apparent contradiction to earlier work that showed that the P‐form may be easily transformed back to a native state by adding water. However, the lack of secondary structure can be overcome by the presence of a collapsed tertiary state that does not allow non‐hydrogen‐bonded strands to separate. Thus, the complementary strands can renature quickly on addition of water. The collapse to a condensed tertiary structure occurs when roughly 90% of the charge on the DNA molecule is neutralized by counterion condensation, as calculated by the Manning polyelectrolyte theory, and is consistent with other collapsed DNA states in this respect. This structure explains all physical properties of the P‐form that have been observed.
Conformational analysis of polytripeptides (Gly‐Pro‐Ala)n, (Gly‐Ala‐Hyp)n, and (Gly‐Ala‐Ala)n in connection with the problem of collagen structure
Authors: Tumanyan V. G. , Abagyan R. A. , Esipova N. G.
Published: December 2004

Conformational analysis of triple helics of a type of collagen was performed with typical collagen tripeptide sequences based on Gly‐Pro‐Ala, Gly‐Ala‐Hyp, and Gly‐Ala‐Ala. During energy minimization, the possibility of continual deformation of the pyrrolidine cycle was taken into account in order to achieve better accuracy in the resulting structure. The (Gly‐Pro‐Ala)n structure is almost isomorphic to the (Gly‐Pro‐Hyp)n structure obtained in the previous work [Tumanyan, V. G. & Esipova, N.G. (1982) Biopolymers 21, 475–497]. For a collagen‐type structure, the optimal conformation of (Gly‐Ala‐Hyp)n tends to have a decreased unit twist (t = 15°), although the energy advantage with respect to the conformation with t = 45° is not so significant. A similar situation is observed for (Gly‐Ala‐Ala)n. In this case, the energy decrease during unwinding to t = 15° from t = 45° is quite small. The conformations of (Gly‐Ala‐Hyp)n and (Gly‐Ala‐Ala)n with t = 15° exhibit a similarity with a triple complex of polyproline II helices—a noncoiled coil such as (Gly‐Pro‐Hyp)n and (Gly‐Pro‐Ala)n. A similar structure may be postulated for subcomponent cq1 of the first component of a human complement containing substantial Gly‐X‐Pro and Gly‐X‐Y tripeptide derivatives in the primary structure (X, Y = any amino acid). The results suggest that the observed helical symmetry of collagen (t = 36°) is a consequence of superposition of diffraction patterns (for sufficiently long segments) from various helices (t varies from ∼15° for Gly‐X‐Hyp and Gly‐X‐Y to ∼56° for Gly‐Pro‐Ala). For short alternating segments, some unification of different helical structures is possible.
Vibrational circular dichroism of polypeptides. III. Film studies of several α‐helical and β‐sheet polypeptides
Authors: Sen A. C. , Keiderling T. A.
Published: December 2004

Vibrational CD (VCD) of amides A, I, and II vibrations of a variety of polypeptide films have been measured. VCD of films of α‐helical and β‐sheet structures are compared in the three regions. Reproducible spectra could only be obtained for thin films free of orientation dependence. The sign and band shape of the VCD of films are not always the same as that in solution. However, the magnitude of the observed VCD seems to correlate with the secondary structure such that α‐helical molecules typically have much larger Δε/ε values than do β‐sheet molecules. The possibility of interference by artifacts owing to light‐scattering effects is discussed.
Vibrational analysis of peptides, polypeptides, and proteins. XXI. β‐Calcium‐poly(L‐glutamate)
Authors: Sengupta Pradeep K. , Krimm S. , Hsu S. L.
Published: December 2004

The observed Raman and ir spectra of Ca‐poly(L‐glutamate) in the β conformation have been analyzed by means of a normal mode calculation. The force field for the main chain was transferred without refinement from β‐poly(L‐alanine), yet it provides a good prediction of the observed bands and, in particular, explains subtle differences in the spectra of these two β‐sheet structures. Main‐ and side‐chain modes are well characterized, and the dependence of the amide III frequency on side‐chain composition is again demonstrated.
Differential electrostatic stabilization of A‐, B‐, and Z‐forms of DNA
Authors: Matthew James B. , Richards Frederic M.
Published: December 2004

The static accessibility discrete charge algorithm for protein charge interactions is extended to the case of linear polyelectrolytes. In this model, the effective dielectric value between surface charge sites depends predominantly on the solvent ionic strength and the solvent accessibilities of the charge sites. This treatment accounts for the phenomena of specific ion binding in the context of a general electrostatic effect [Matthew and Richards (1982) Biochemistry 21, 4989]. Specific ion sites are determined by locating areas of high electrostatic potential at the solvent interface of the macromolecule. At a given ionic strength the calculated potential at a site is taken to describe a binding constant and therefore the ion site occupancy. For a 20‐base‐pair fragment of B‐DNA, net charge of −40, 16 ion sites are indicated in the minor groove. The partial occupancy of each site increases from 0.2 to 0.5 as the ionic strength is increased from 0.01 to 0.50. Over the same range of ionic strength, the electrostatic free energy of this charge array is calculated to change from +0.6 to −0.05 kcal/bp. Parallel behavior is predicted for A‐ and Z‐DNA charge geometries. The most stable configuration, based on electrostatic criteria, at high ionic strength (I = 0.1–0.5) is that of Z‐DNA. In this range, the ratio of “bound” sodium to phosphate is predicted to be less than 0.4.
The conformational transition of κ‐carrageenan using microcalorimetry
Authors: Rochas Cyrille , Mazet Jean
Published: December 2004

The interactions between inorganic cations and κ‐carrageenan in aqueous solutions have been studied using microcalorimetry. The enthalpy of dilution and the enthalpy of mixing of κ‐carrageenan in the coil conformation with an alkaline metal chloride have been investigated and are in agreement with theoretical predictions. The formation of helical dimer in a K+ salt form in the absence of a gel formation is confirmed.
Interactions of molecules with nucleic acids. XI. Generalization of techniques to generate nucleic acid structures with applications to intercalation sites and kinked structures
Authors: Taylor Eric R. , Miller Kenneth J.
Published: December 2004

A generalized procedure to generate nucleic acid structures is presented. In this procedure, the bases of a base pair are oriented first for characterization of particular DNA receptor sites. The resultant sites are then used in the study of specific molecule–DNA interactions. For example, intercalation sites, kinked DNA, and twisted and tilted bases are envisioned. Alterations of structures via anti → syn orientations of bases, as well as crankshaft motion about collinear bonds, provide additional conformations without disrupting the overall backbone structure. These approaches to the generation of nucleic acid structures are envisioned as required in studies of the intercalation phenomenon, minor adjustments of DNA to accommodate denaturation, binding of carcinogens to DNA, complex formation of transition metals with DNA, and antitumor agents as ligands. For these base‐pair and base orientations, backbone orientations are calculated by the AGNAS technique to yield physically meaningful conformations, namely, those conformations for which nonbonded contacts are favourable. A procedure is presented to generate dimer duplex units that are physically meaningful and to assemble these units into a polynucleotide duplex. Double helices that begin with B‐DNA, undergo a transition to one of the above‐mentioned receptor sites, and return to B‐DNA can be assembled from a catalog of dimer duplexes. Stereographic projections of the various receptor sites already being used to model binding to DNA are presented.
Molecular‐dynamics simulation of phenylalanine transfer RNA. I. Methods and general results
Authors: Harvey Stephen C. , Prabhakaran M. , McCammon J. Andrew
Published: December 2004

A 24‐ps molecular‐dynamics simulation of motions in yeast tRNAPhe has been completed. The overall structure of the molecule is well preserved, for the motions represent fluctuations about an average structure that is very much like the crystallographic structure. The four helical stems remain intact, the structures of the loop regions do not deteriorate, and even the base stacking in the single‐stranded amino acid acceptor terminus is maintained. With two exceptions, none of the sugar puckers is significantly changed. The unconstrained floppy motions of base A76 are responsible for the repuckering of ribose 76. The other sugar that repuckers is ribose, 46, and this is the result of a very small structural change in the center of the molecule that is also responsible for the breakage of one tertiary hydrogen bond. This change in local structure does not seriously distort the base‐stacking and intercalation patterns where the variable loop and the D‐stem interact.
Solvent accessibility studies of β‐bends and application to cyclic hexapeptides
Authors: Soman K. V. , Ramakrishnan C.
Published: December 2004

The solvent‐accessible surface areas (ASAs), of the atoms in tripeptides around the minimum‐energy conformations of the β‐bend types I, I′, II, and II′ have been computed as a first step in the systematic solvent accessibiity study of secondary structures. The side chains chosen at the two middle positions of the bend are L‐Ala, D‐Ala, and Gly. The ASAs of the hydrogen atoms are reported here and are found useful in determining the type of β‐bends in six examples of cyclic hexapeptides whose crystal structures are known. Comparison with observation showed that all the β‐bends in these cyclic hexapeptides were correctly identified by the present method. This points to a possible use of the method in identifying β‐bend types in solution.
Simulation of the diffusion‐controlled reaction between superoxide and superoxide dismutase. I. Simple models
Authors: Allison S. A. , Ganti G. , McCammon J. A.
Published: December 2004

A Brownian dynamics simulation method is used to study the diffusion‐influenced bimolecular reaction between superoxide and superoxide dismutase (SOD). Using simple models, the details of which are based on the crystallographic structure of SOD, it is found that the electrostatic charge distribution of SOD serves to guide superoxide into the active site and enhance the diffusion‐controlled rate constant by about 40%.
Conformations of blood group H‐active oligosacharides of ovarian cyst mucins
Authors: Rao B. N. Narasinga , Dua Virendra K. , Bush C. Allen
Published: December 2004

Spectroscopic data and conformational energy calculations are reported for eight oligosaccharides from ovarian cyst mucins and from human milk, the nonreducing terminals of which have fucose (α1 → 2)galactose linked either (β1 → 3) (type I) or (β1 → 4)(type II) to N‐acetylglucosamine or in (β1 → 3) linkage to galactosaminitol. The fully assigned proton nmr spectra are reported along with nuclear Overhauser enhancement (NOE) data. Amide proton coupling constants and vacuum‐uv CD spectra provide information on the amide plane orientation and amide environment. Our results imply that the fucosidic dihedral angles are similar for all three cases and that the substantial differences in the chemical shifts of the fucosyl protons of type I, type II, and 3‐ol chains result from different perturbations by the amide group of the residue to which the β‐galactose is linked. Stereopair diagrams of conformational models for both type I and II H chains are presented that are consistent with NOE, coupling constants, conformational energy calculations, and the CD data. While the temperature dependence of the observed NOE of penta‐ and hexasaccharides indicates that their rotational correlation times are strongly temperature dependent, we conclude that the conformations are essentially independent of temperature.
Synthesis and nmr conformational studies of polyoxyethylene‐bound, α‐deuterated glutamate oligopeptides
Authors: Ribeiro Anthony A. , Saltman Robert , Goodman Murray
Published: December 2004

The syntheses of three series of glutamate oligopeptides attached to a macromolecular solubilizing polyoxyethylene (POE) group Boc‐[Glu(OMe)]n‐OPOE, Ac‐[Glu(OMe)]n‐OPOE, pGlu‐[Glu(OMe)]n−1‐OPOE (n − 1–7) and their various analogs specifically deuterated at individual α‐CH positions using the liquid‐phase method of peptide synthesis are described. It was shown that stepwise synthesis using the symmetrical anhydride gave homo‐oligopeptides that are analytically pure. Fragment condensation methods using DCC‐HOBt yield POE‐peptides with POE‐HOBt impurities but the peptide synthesis may be carried stoichiometrically with smaller quantities of amino acid derivatives. 360 MHz 1H‐nmr conformational studies of these homo‐oligopeptides in DMSO‐d6 are presented. The α‐deuterated peptides are shown to allow unequivocal homoligopeptide backbone NH assignments.
Conformational analysis of polyoxyethylene‐bound homo‐oligo‐L‐glutamates in aqueous environment
Authors: Ribeiro Anthony A. , Saltman Robert , Goodman Murray
Published: December 2004

A detailed conformational analysis of homo‐oligo‐L‐glutamates was carried out in aqueous solution using 1H‐nmr spectroscopy. Three series of side‐chain protected (α‐OMe) glutamate oligopeptides, attached to polyoxyethylene (POE) to enhance their solubility, were synthesized. The effect of the N‐terminal blocking groups—Boc, Ac, and pGlu—on the conformations of these peptides in water is discussed. Unequivocal assignments were obtained for all amide NH resonances through use of selectively α‐deuterated oligo‐glutamates. Analysis of vicinal coupling constants, temperature dependence of NH chemical shifts, transfer of saturation experiments, and titration studies with a denaturing solvent (DMSO) were used to investigate the peptide structure. These data suggest that the Glu1 and Glu2 NH protons of each heptamer are solvent exposed, while the NH protons of interior glutamate residues chain are solvent sequestered. The nmr data are consistent with the onset of helical structure at the heptamer of each series in aqueous solution. The POE‐peptides with pGlu at the N‐terminus showed considerably reduced stability of structure than those with the Boc or acetyl blocking groups. Peptide conformations and their stability in water are compared to those in other solvents.
On the reptation theory of gel electrophoresis
Authors: Slater Gary W. , Noolandi Jaan
Published: December 2004

We introduce a new biased reptation theory that allows a qualitative and semiquantitative study of DNA gel electrophoresis. We prove that stretching of the end‐to‐end vector of a very long charged reptating chain in an electric field occurs in a short period of time during a typical electrophoresis experiment, and that this leads to a field‐dependent mobility only weaky dependent upon the size of the chain, in agreement with experiments on DNA. We also propose a practical technique to avoid chain stretching. Finally, many scaling laws are predicted, most of them being verifiable by experiment.
Models of thioredoxin hairpin structures: Conformational properties of β‐turn containing sequences
Authors: Azzena Ugo , Luisi Pier Luigi
Published: December 2004

Sequences 74–91 and 77–91 of E. coli thioredoxin, which according to x‐ray structure contain an irregular β‐turn, a hairpinlike structural element, have been synthesized and their conformational properties in solution have been investigated by means of CD spectroscopy. In addition, analogs of these sequences, containing the regular β‐turn element Gly‐Pro‐(Gly)2, have also been prepared and investigated. These are BOC‐Ile‐Gly‐Pro‐(Gly)2‐Val‐OMe (III) and BOC‐(Ile)3Gly‐Pro‐(Gly)2‐(Val)5‐OMe (IV) that on the basis of probability, should form hairpin structures stabilized by intramolecular interactions. While the natural sequences were shown to be unable to adopt structures characterized by an intrinsic conformational stability, the two analogs showed evidence of intramolecular folding in methanol and trifluoroethanol–water solution. In particular, the CD spectra are indicative of β‐structure. The most interesting case was observed for compound IV, as the highest degree of conformational order was present in solutions containing a large proportion of water. In addition, the formation of this structure took place in a highly cooperative manner. The results are utilized to discuss whether and to what extent conformationally stable folding peptide units of small size can be formed in aqueous solution.
A Raman spectroscopic study on 5′‐rGMP gel and self‐aggregate
Authors: Kim Kang Woo , Kim Sang Kyu , Kim Myung Soo , Suh Se Won
Published: December 2004

In order to analyze the melting behavior of 5′‐rGMP gel at acidic pH and self‐aggregate near neutral pH we have obtained Raman spectra of aqueous solutions of 5′‐rGMP at various temperatures. At low temperature the intensities of Raman peaks at 502, 585, 1083, 1179, 1322, 1366, 1487, and 1578 cm−1 decrease due to the formation of ordered structure (Raman hypochromism). In contrast, the peaks at 671, 725, 813, and 1338 cm−1 become stronger at low temperature (Raman hyperchromism). The Raman hyperchromism of the 671‐ and 813‐cm−1 peaks have been explained in terms of detailed structural models. Recently, the 668‐ and 682‐cm−1 peaks in the Raman spectrum of aqueous 5′‐rGMP solution have been attributed to the guanine ring breathing vibrations in C3′‐ and C2′‐endo conformers [Benevides, J. B., Lemur, D. & Thomas, G. J., Jr. (1984) Biopolymers 23, 1011–1024]. On the basis of this information our Raman data can be interpreted to suggest that the continuous helix model of 5′‐rGMP gel is right‐handed. The 1487‐cm−1 peak intensity has been used to monitor the melting profies at several pHs. Near neutral pH the melting profile shows a single transition, whereas at acidic pH it shows two transitions. From these observations we propose possible pathways for the melting of 5′‐rGMP gel formed at acidic pH and self‐aggregate formed near neutral pH.
Conformation of dioxopiperazines. III. Conformational‐energy calculations and evaluation of specific forces contributing to the intramolecular dioxopiperazine‐phenyl ring‐ring folding in cyclo(glycyl‐phenylalanyl)
Authors: Kołodziejczyk Aleksandra , Ciarkowski Jerzy
Published: December 2004

Conformational energy calculations on cyclo(glycyl‐L‐phenylalanyl), c(Gly‐Phe), were carried out by means of the semiempirical MO CNDO/2 method. They corroborated earlier experimental findings that in c(Gly‐Phe) the conformations with an aromatic side‐chain ring folded over the dioxopiperazine (DOP) ring contribute significantly to the overall equilibrium, provided that the empirical optimization of the DOP ring geometry, extracted from x‐ray data, rather than that of the CNDO/2‐derived data is used throughout the computations. Following these studies, more detailed calculations, based partly on CNDO/2‐derived data and partly on experimental data, were carried out to clarify the question, which are the forces responsible for this ring‐ring stacking? In contrast to early suggestions, it was found that the quadrupole‐quadrupole and dispersion interactions mainly contribute to folded conformations of c(Gly‐Phe). Some implications of this finding on devising force fields for molecular‐mechanics calculations of peptides are briefly outlined.
Molecular cartography of globular proteins with application to antigenic sites
Authors: Fanning David W. , Smith John A. , Rose George D.
Published: December 2004

A method, molecular cartography, is introduced as a way to quantitate the topographic structure of a protein surface. The method is applied to the problem of antigenic determinants, and it is used to examine local and global topography of reported antigenic regions on the surface of myoglobin and lysozyme. In nine antigenic sites taken from the literature and studied in detail, no local property was found in sites that was not also found in remaining regions of the surface. However, a strong correlation was found between antigenic sites and regions of the surface that are globally exposed. This finding suggests that global exposure of the protein surface may play a primary role in determining the antigenic structure of the protein. Molecular cartography may be useful in other instances of protein–protein interactions such as those between proteolytic enzymes and their substrates.
Structural information from electric dichroism measurements of DNA and alternating GC nucleic acids in solution: The question of base tilt
Authors: Charney Elliot , Chen Holly Ho , Henry Eric R. , Rau Donald C.
Published: December 2004

Values of the apparent intrinsic dichroism of the 260‐nm transition of duplex poly(dG‐dC) and poly(dG‐m5dC) in both B‐ and Z‐conformations are determined from electric dichroism (ED) measurements by extrapolation of the data at high field strengths. These values are compared to each other and to values of the intrinsic dichroism calculated for the Z‐ and B‐forms generated respectively from the crystal structure coordinates [(1981) A. H. J. Wang, G. J. Quigley, F. J. Kolpak, G. Van der Marel, T. H. Van Boom & A. Rich, Science 211, 171–176.] of the d(CpGpCpGpCpGp) hexamer and from the coordinates [(1982) A. V. Fratini, M. L. Kopka, H. R. Drew & R. E. Dickerson, J. Biol. Chem. 257, 14686–14707.]. of the terminal CpGpCpGp base pairs of the crystal of straight B‐form dodecamer d(CpGpCpGpApApTpTpCpGpCpGp). Direct association of the dichroism with the orientation of the optical transition moments with respect to the helix axis of poly(dG‐dC) implies that the average tilt of the bases is much different than the values calculated from the structural coordinates. The experimental values for both the B‐ and Z‐forms are, however, almost identical to those observed with fragments of “random” sequence B‐form DNA of the same molecular length. It is argued that this descrepancy and other anomalies reported in the literature are due to the theoretically predicted unusual high field behavior associated with diffuse ion atmosphere polarization. Unlike either permanent dipoles or induced moments based on bond polarizabilities, the orienting dipole energy from the polarization of the counterions surrounding DNA approaches a finite limiting value, dependent on DNA length, at very high field strengths. This can result in extrapolated dichroisms that do not reflect structure at perfect orientation, but rather structure at some limiting orientation. Consequently, we believe, the conclusion drawn from ED measurements on short fragments of DNA that the bases are highly tilted from the perpendicular to the helix axis by propeller twisting or otherwise is suspect.
Influence of different tripeptides on the stability of the collagen triple helix. I. Analysis of the collagen sequence and identification of typical tripeptides
Authors: Dölz R. , Heidemann E.
Published: December 2004

The amino acid sequence of the collagen α1(I) chain (calf) is analyzed. Deviations of random tripeptide distribution leads to the definition of clusters. Inside these regions, collagen‐typical tripeptides are located. Besides Gly‐Pro‐Hyp, Gly‐Pro‐Ala, and Gly‐Ala‐Hyp, the polar sequences Gly‐Glu‐Hyp, Gly‐Ala‐Arg, Gly‐Glu‐Arg, and Gly‐Pro‐Lys form typical sequences. The neighborhood of each tripeptide is analyzed and classified. The proximity to the collagen‐typical tripeptides is registered. Cluster theory: Less‐typical sequences also fold as members of the collagen triple helix and they are as reasonable as well as important for the collagen structure as the cluster tripeptides, but only the latter are important for the nucleation of the triple‐helical folding.
A novel and simple interpretation of the three‐dimensional structure of globular proteins based on quantum mechanical computations on small model molecules. II. The clusters of myoglobin
Authors: Peters David , Peters Jane
Published: December 2004

We show that the bridges and clusters of the kind found earlier in rubredoxin also occur in myoglobin. The familiar acid–base(salt) bridges are at the heart of many of the clusters. The data reported by Takano [(1977) J. Mol. Biol., 110, 537–508] on sperm whale metmyoglobin reveals ten clusters together with the heme structure and some unidentified fragments. The data reported by Hanson and Schoenborn [(1981) J. Mol. Biol. 153, 117–146] on carbonmonoxymyoglobin shows numerous bridges that generally fit into the cluster picture derived from Takano's data. The data reported by S. E. V. Phillips (personal communication) on oxymyoglobin also fits into the same pattern of cluster. All but one of the myoglobin clusters are formed from two pieces of local structure each of which covers up to fifteen consecutive aminoacid residues. A “long‐range” union joins the two pieces of local structure. The clusters are generally involved with the nonhelical structure and with the junctions of the two helices. Two applications of the theory are suggested. First, the clusters offer an explanation for the formation of the α‐helices and second the unfolding of the myoglobin molecule at pH 3.8 to 5.3 is readily interpreted as the protonation at this pH of the carboxylate ions that generate the clusters that in turn support the α‐helices.
Shape complementarity at the hemoglobin α1β1 subunit interface
Authors: Connolly Michael L.
Published: December 2004

A computational method for attempting to predict protein complexes from the coordinates of the individual proteins has been developed. It is based on matching complementary patterns of knobs and holes. The computer algorithm correctly and uniquely predicts the association of the alpha and beta subunits to form the αβ dimer corresponding to the α1β1 interface in the hemoglobin tetramer. It fails to correctly dock trypsin inhibitor onto trypsin. Nevertheless, this lone success is still a significant advance over previous protein‐docking algorithms. The method is also important because it introduces several ways to measure the shape of protein surface regions.
A specific model for the conformation of single‐stranded polynucleotides in complex with the helix‐destabilizing protein GP32 of bacteriophage T4
Authors: Scheerhagen M. A. , Bokma J. T. , Vlaanderen C. A. , Blok Joh. , Van Grondelle R.
Published: December 2004

The CD and absorption (OD) spectra of single‐stranded nucleic acids in complex with the helix‐destabilizing protein of either bacteriophage T4 (GP32) or bacteriophage fd (GP5) show similar and unusual features for all polynucleotides investigated. The change in the CD spectra between 310 and 240 nm is in all cases characterized by a considerable decrease in the positive band, while the negative band (if present) remains relatively intense. These changes are different from those due to temperature or solvent denaturation and, moreover, cannot be induced by the binding of simple oligopeptides. Absorption measurements show that all polynucleotides remain hypochromic in the complex. Both CD and OD spectra point to a specific and probably similar conformation in complex for all polynucleotides with substantial interactions between the bases. The spectral properties are almost temperature independent (0–40°C). Therefore, we conclude that the conformation must be regular and rigid. To investigate the relation between these optical properties and the specific polynucleotide structure, CD and OD spectra were calculated for an adenine hexamer over a wide range of the conformational parameters. It appears that the calculated CD intensity is not very sensitive to an increase in the axial increment and that many different conformations can give rise to more or less similar CD spectra. However, simulation of the very nonconservative experimental CD spectrum of the poly(rA)‐GP32 complex requires that the conformation satisfies two criteria: (1) a considerable tilt of the bases (≲ – 10°) in combination with (2) a small rotation per base (≃20°) and/or a position of the bases close to the helix axis (dx ≃ 0 Å). Such conformations can also explain the observed hyperchromism upon binding of GP32 to poly(rA)/(dA). Very similar structural characteristics also account for the optical properties of the complexes with GP5. These are discussed as an alternative to the structure suggested by Alma‐Zeestraten for poly(dA) in the complex [N. C. M. Alma‐Zeestraten (1982) Doctoral thesis Catholic University, Nijmegen, The Netherlands]. The secondary structure proposed in this work can be reconciled with the overall dimensions of the complex, assuming that the polynucleotide helix is further organized in a superhelix.
CD of nucleic acids: III. Calculated CD of RNAs from new A, U, G, and C transition‐moment parameters
Authors: Moore Dexter S. , Williams Arthur L.
Published: December 2004

New adenine (A) and uracil (U) π → π* transition‐moment parameters have been derived from a recently developed semiempirical procedure. Using conformational energy probabilities based on the Boltzmann equation, the new parameters were assigned by optimizing the calculated CD of cyclic nucleotides against measured CD. The derived A‐and U‐parameters (along with guanine and cytosine parameters derived previously by the same procedure) have been assessed in CD spectral calculations of some polyribonucleic acid sequences, in assumed A‐class geometries. Comparisons have been made between CD spectra calculated from the newly derived parameters and those calculated from parameters obtained from a combination of crystal optical measurements and quantum‐mechanical calculations. Although some spectral differences do occur, for the RNA sequences considered, no major disagreements were found in CD spectral signs and shapes, between measurements and calculations. Overall, the results indicate that the newly derived A‐, U‐, G‐, and C‐parameters show better agreement between theory and experiment than those used in previous nucleic acid CD calculations.
Association of short DNA fragments: Steady state fluorescence polarization study
Authors: Härd Torleif , Kearns David R.
Published: December 2004

We have studied aggregation/association of monodisperse DNA fragments (ranging from 30–90 base pairs) by steady‐state fluorescence polarization of intercalculated ethidium. The method of excitation at different wavelengths in the ethidium absorption spectrum provides information about anisotropic twisting and tumbling mobility of the fragments. We find that end‐over‐end tumbling rather than axial spinning and internal twisting motions are affected by aggregation/association. The critical concentration for observing the effects of intermolecular interactions is approximately 5 mg DNA/mL at room temperature, independent of fragment length. Association is favored by low temperature and high (> 10 mM) concentration of Mg2+. From temperature‐and salt‐dependence experiments we infer that the “aggregates” are similar to those observed in a recently discovered DNA sol–gel transition [M. G. Fried and V. A. Bloomfield (1984) Biopolymers 23, 2141–2155]. We also discuss possible arrangements of the fragments within the aggregates and their possible relation to formation of DNA liquid crystals.
Estimation of the stability of globular proteins
Authors: Ahmad Faizan , Bigelow Charles C.
Published: December 2004

The interpretation of ΔG (the free energy change for the reaction, globular conformation ⇋ randomly coiled conformation, in the absence of denaturant), in terms of the free energies of transfer of various parts of the protein molecule from water to denaturant solution, is unsatisfactory because the latter are assumed to be identical to the transfer‐free energies of similar groups attached to smaller model compounds. We have made empirical adjustments to transfer‐free energy theory that make possible linear extrapolation of the free energy of denaturation of a protein from transition region to zero denaturant concentration. The modified theory, used to analyze the denaturation of proteins by guanidine hydrochloride and urea, allowed us to calculate reasonable values for Δα, the average change in accessibility to solvent of the component groups of protein.
Evidence for heterogeneity in DNA‐associated solvent mobility from acridine phosphorescence spectra
Authors: Milton John G. , Galley William C.
Published: December 2004

The mobility of solvent associated with native DNA in comparison with that of the bulk solvent is monitored from the temperature‐dependent red shift in the phosphorescence spectra of acridines bound to DNA and free in glycol–buffer mixtures. Over the temperature range for which the red shift occurs the phosphorescence decay changes with emission wavelength, indicating the time‐dependent nature of the process. Moreover, at these temperatures, emission anisotropy measurements establish that motions of the dye itself are not involved. Correspondence between perturbations to the solvent that influence the temperature at which the red shift occurs for free acridine with those for the DNA‐bound dye confirm that “bound solvent” is responsible for the spectral changes. For the DNA‐bound acridines the extent of the red shift is smaller and the midpoint T1/2 of the transition is warmer. The reduction in the red shift reveals that the bound dye is less exposed to solvent and varies as 9‐aminoacridine < acridine orange ∼ proflavin, i.e., 9‐amino‐acridine is less exposed to solvent. On the other hand, the warmer T1/2 indicates that DNA‐associated solvent is considerably less mobile than bulk solvent. T1/2 varies for proflavin bound to DNA, poly[d(AT)], poly[d(GC)], and poly(dG): poly(dC), and for proflavin, acridine orange, and 9‐aminoacrine bound to DNA. These observations suggest that there is a heterogeneity in the mobility of DNA‐associated solvent.
Vibrational circular dichroism spectra of three conformationally distinct states and an unordered state of poly(L‐lysine) in deuterated aqueous solution
Authors: Paterlini M. Germana , Freedman Teresa B. , Nafie Laurence A.
Published: December 2004

Fourier transform ir vibrational circular dichroism (VCD) spectra in the amide I′ region of poly(L‐lysine) in D2O solutions have confirmed the existence of three distinct conformational states and an unordered conformational state in this homopolypeptide. Characteristic VCD spectra are presented for the right‐handed α‐helix, the antiparallel β‐sheet, an extended helix conformation previously referred to as the so‐called “random coil,” and a completely unordered conformation characterized by the absence of any amide I′ VCD. VCD for the antiparallel β‐sheet in solution and the unordered chain conformation are presented for the first time. Each of the four different VCD spectra is unique in appearance and lends weight to the view that VCD has the potential to become a sensitive new probe of the secondary structure of proteins in solution.