bluuebunny/crossref_metadata_2025 huggingface dataset:
Lateral and rotational diffusion of EGF–receptor complex: Relationship to receptor‐mediated endocytosis
Authors: Schlessinger Joseph
Published: December 2004

The clustering and internalization of epidermal growth factor (EGF)–receptor complexes on human tumor cells are temperature‐sensitive processes that are completely inhibited at 4°C. The rotational diffusion of EGF–receptor is limited by the viscosity of the lipid matrix, while additional constraints limit the lateral diffusion of the receptor molecule. Although the lateral and rotational diffusion of the occupied receptors are temperature sensitive, they do not provide a rate‐determining factor for the clustering and subsequent internalization of the EGF–receptor. Even at 4°C the occupied receptors move quickly enough to allow the formation of EGF–receptor clusters. The lack of internalization at 4°C must be due to the inhibition of interactions other than a temperature effect on receptor mobility. EGF‐induced receptor clustering involves the formation of microclusters composed of 10–50 receptor molecules.
Excluded volume of an intermediate‐molecular‐weight DNA. A Monte Carlo analysis
Authors: Post Carol Beth
Published: December 2004

A Monte Carlo procedure wasused to determine the effect of excluded volume on the dimensions of an intermediate‐molecular‐weight DNA for different Na+ concentrations. The calculation of α, the parameter for the linear expansion due to excluded volume, was accomplished by generating sets of chains and, for each set, comparing the average radius of gyration for the set of chains that do not overlap to that averaged over the entire set of chains. Each chain was defined by cylinders linked with free rotation and with bend angles generated according to a weighted Gaussian distribution. The chain parameters—contour lenght, cylinder lenght and diameter—were fixed in order to resemble published light‐scattering experiments on Col E1 DNA. Values for α were less than 1.08. for Na+ concentrations between 0.007 and 1.0M. A previously reported analytical calculation of the excluded‐volume correction of intermediate‐sized DNA gave results that are closely similar to those from the Monte Carlo analysis.
Orientational interactions in low‐concentration DNA solutions
Authors: Marion Christian , Roux Bernard , Hanss Maxime
Published: December 2004

The rotational relaxation tiem τ3 of DNA molecules (Mw ≃ 5 × 106) in solution has been determined by the transient electric birefringence method. The analysis of the birefringence decay makes it possible to study only the higher‐molecular‐weight fraction, the molecules being considered as rigid elongated particles in a short time scale. A marked concentration dependence of the relaxation time has been observed for DNA in low ionic strengths. Above a critical concentration c*, τ3 increases with the DNA concentration, c. The value of c* increases with the ionic strength. For 10−3 ionic strength (with NaCl), c* is about 10 μg/mL; then we observe the same strong concentration dependence of rotational relaxation times as recently reported for rodlike M‐13 viruses [Maguire, J. F., McTague, J. P. & Rondelez, F. (1980) Phys. Rev. Lett. 45, 1891–1894]. These results may be discussed in terms of the Doi‐Edwards theory for rotational relaxation time of rigid macromolecules [Doi, M. (1975) J. Phys. 36, 607–611; Doi, M. & Edwards, S. F. (1978) J. Chem. Soc. Faraday Trans. 74, 918–932] and the critical concentration above which the interactions between the molecules begin to appear allows determining the corresponding molecular length. We observe a very good agreement between the DNA lengths obtained from the c* values and by using the infinite dilution value of τ3 and Broersma's equation. Therefore, only highly diluted solutions can be used if intrinsic molecular properties based on the rotational diffusion of high‐molecular‐weight elongated molecules are studied.
Conformation of 2‐aminofluorene‐modified DNA
Authors: Broyde S. , Hingerty B.
Published: December 2004

Minimized potential‐energy calculations were performed to determine the conformation of the 2‐aminofluorene (AF) adduct to dCpdG at guanine C‐8. The AF adduct has many low‐energy conformers in both the anti and the syn domains of the guanine. This is in contrast with the acetylated adduct, (AAF), which greatly prefers the syn domain. Two types of low‐energy guanine anti‐conformations were obtained: (1) conformers that preserve guanine–cytidine stacking and (2) conformers with fluorene–cytidine stacking. Of special importance are conformers with ω′,ω,ψ = g−, g−, g+, characteristic of normal A‐ or B‐helices, which are found in both groups. No conformers of this type were obtained for the acetylated AAF adduct. The guanine–cytidine stacked from with this conformation can be incorporated in the B‐helix without any distortion, with the carcinogen situated at the helix exterior. The fluorene in this model can slide into the helix to yield a fluorene–cytidine stacked minimum‐energy conformation. This requires no denaturation, although one base pair is unstacked and the helix axis is bent. Low‐energy syn‐conformations, similar to those obtained for the AAF adduct, were also computed. These were either guanine‐cytidine stacked or fluorene–cytidine stacked. The syn froms are less likely to be observed in larger DNA polymers of the adduct, since they cause more distortion than the anti‐conformations. However, they might well be observed in crystals of small subunits, and they should contribute significantly to the population in solution.
1H‐Nuclear magnetic resonance study on imidazole–imidazole interaction in L‐histidyl‐L‐histidine and D‐histidyl‐L‐histidine: Analysis including microscopic dissociation series
Authors: Tanokura Masaru
Published: December 2004

The 1H‐nmr titration curves of chemical shifts versus pH were observed for the protons of D,L‐histidyl‐D,L‐histidine as representative of cases with two or more ionizable groups with similar pKa values. The titration curves of L‐histidyl‐L‐histidine and D‐histidyl‐L‐histidine were individually analyzed according to two mathematical models: one of a macroscopic dissociation series and one of a microscopic dissociation series. Most‐probable values and standard deviations were obtained for pKa values and intrinsic chemical shifts. An analysis including the microscopic dissociation series yielded an electrostatic interaction between twoimidazole rings of about 0.3 pH units for L‐histidyl‐L‐histidine and about 0.7 pH units for D‐histidyl‐L‐histidine. The difference of the magnitude of imidazole‐imidazole interactions between L‐histidyl‐L‐histidyne and D‐histidyl‐L‐histidine was interpreted in terms of the spatial arrangement of two imidazole rings in each molecule based on the solution conformation estimated from Gd(III)‐induced relaxation enhancements.
Unwinding kinetics of cooperatively melting regions in DNA
Authors: Suyama Akira , Wada Akiyoshi
Published: December 2004

Unwinding of a single cooperatively melting region of ColE1 DNA is investigated by a slow temperature jump in formamide–neutral buffer mixed solvent. The semilogarithmic plots of unwinding relaxation curves show a marked terminal linear region following the fast decay, which occurred within the temperature rise time (1 ∼ 2 s). This longest relaxation is ascribed to the total unwinding of a single cooperatively melting region. The longest relaxation time, τ1, is uniquely determined by the final equilibrium state and becomes shorter as the final temperature increases. Decrease in ionic strength makes τ1 and its fractional amplitude increase, and the relaxation almost approaches single‐exponential decay. The facts that (1) τ1 of a single cooperatively melting region whose unwinding suffers larger frictional resistance does not always unwind more slowly, as was shown by the observations of τ1's of almost the same cooperatively melting region located at different positions on two linearized ColEl DNAs and of τ1's of two cooperatively melting regions on the same linearized ColEl DNA; (2) τ1 has strong dependence on the equilibrium state after a temperature jump; and (3) the observed τ1 is much longer than the expected time of the frictional barrier all demonstrate that the τ1 is limited by chemical but not hydrodynamic processes. The detailed unwinding process of a single cooperatively melting region, elucidated by evidence of a negative apparent activation energy of the rewinding process and by extensive computer simulation of the equilibrium melting process, suggests that the local heterogeneity of G+C content in a cooperatively melting region, as well as its averaged G+C content, strongly affects its unwinding rate. The present study of a single cooperatively melting region is found to be useful to improve our understanding of the detailed mechanism of complex unwinding of large natural DNAs, in which many cooperatively melting regions unwind.
Alternative pathways in diffusion–collision controlled protein folding
Authors: Weaver D. L.
Published: December 2004

The diffusion–collision model of protein folding has been solved exactly for a three‐microdomain protein subunit. Numerical analysis shows that the exact kinetics may be excellently approximated in all cases studied by a standard chemical kinetics approach with the forward rate constants calculated from the mean folding time formula found previously.
Mechanism of gel formation in κ‐carrageenan
Authors: Rochas C. , Rinaudo M.
Published: December 2004

We present a general view of κ‐carrageenan gelation and some new experimental results concerning their behavior in the presence of Na+, K+, or Rb+ counterions in semidilute concentration. The gelation mechanism is based on the aggregation of helical dimers.
Circular dichroism studies of α‐aminoisobutyric acid‐containing peptides: Chain length and solvent effects in alternating Aib‐L‐Ala and Aib‐L‐Val sequences
Authors: Vijayakumar E. K. S. , Sudha T. S. , Balaram P.
Published: December 2004

The CD spectra of the peptides Boc‐X‐(Aib‐X)n‐OMe (n = 1, 2, 3) and Boc‐(Aib‐X)5‐OMe, where X = L‐Ala or L‐Val have been examined in several solvents. The X = Ala and Val peptides behave similarly in all solvents, suggesting that the Aib residues dominate the folding preferences of these peptides. The decapeptides adopt helical conformations in methanol and trifluoroethanol, with characteristic negative CD bands at 222 and 205 nm. In the heptapeptides, similar spectra with reduced intensities are observed. Comparison with nmr studies suggest that estimates of helical content in oligopeptides by CD methods may lead to erroneous conclusions. The pentapeptides yield solvent‐dependent spectra indicative of conformational perturbations. Peptide association in dioxane results in an unusual spectrum with a single negative band at 210 nm for the decapeptides. Disaggregation is induced by the addition of methanol or water to dioxane solutions. Aggregation of the heptapeptides is less pronounced in dioxane, suggesting that a critical helix length may be necessary to promote association stabilized by helix dipole–dipole interactions.
Vibrational analysis of peptides, polypeptides, and proteins. XVIII. Conformational sensitivity of the α‐helix spectrum: αI‐ and αII‐Poly(L‐alanine)
Authors: Dwivedi Anil M. , Krimm S.
Published: December 2004

The αII‐helix (ϕ = −70.47°, ψ = −35.75°) is a structure having the same n and h as the (standard) αI‐helix (ϕ = −57.37°, ψ = −47.49°). Its conformational angles are commonly found in proteins. Using an improved α‐helix force field, we have compared the vibrational frequencies of these two structures. Despite the small conformational differences, there are significant predicted differences in frequencies, particularly in the amide A, amide I, and amide II bands, and in the conformation‐sensitive region below 900 cm−1. This analysis indicates that αII‐helices are likely to be present in bacteriorhodopsin [Krimm, S. & Dwivedi, A. M. (1982) Science 216, 407–408].
Locally oscillatory motion of RNA helix derived from linear relationships of backbone torsion angles
Authors: Kitamura Kunihiro , Mizuno Hiroshi , Amisaki Takashi , Tomita Ken‐Ichi , Baba Yasumasa
Published: December 2004

A linear relationship in each of the torsion angle pairs, α‐β, β‐ϵ, ϵ‐ζ, and α‐γ, has been found by applying a statistical method based on the concept of circular variates to backbone torsion angle data of helical in yeast tTNAPhe. A series of helical dimer models generated with these relationships have been found to be stereochemically acceptable, and the models also indicate that the backbone unit in the RNA helix is geometrically capable of an oscillatory motion with the distance of about 3.4 Å between adjacent bases. The motion of the backbone unit is analogous to that of a helical spring. The adjacent bases, because of being attached to the backbone, oscillate in a manner similar to the oscillatory dimer model proposed by Davis and Tinoco [Davis, R. C. & Tinoco, I., Jr. (1968) Biopolymers 6, 223–242]. Here, the oscillation of the backbone unit in the RNA helix is discussed in terms of two geometrical quantities: the torsion (τ) and curvature (κ) of the helix. On these lines, a stereochemical model of RNA strand separation is proposed.
Interaction of metal ions with gastrointestinal hormones: Binding studies of Mg++ to biologically active analogs of little gastrin and minigastrin
Authors: Peggion E. , Mammi S. , Palumbo M. , Moroder L. , Wünsch E.
Published: December 2004

The interaction of magnesium ions with Des‐Trp1‐Nle12‐minigastrin I (Nle11‐HG‐13) and Nle115‐little gastrin I (Nle15‐HG‐17) has been studied by CD and spectrophotometric techniques in trifluoroethanol. Spectrophotometric titrations using murexide as a metallochromic indicator showed that there are three binding sites for magnesium ions in Nle11‐HG‐13, with binding constants of the order of (6 ± 2) × 106, (1.7 ± 0.5) × 106, and (5.0 ± 0.5) × 105M−1. These figures have been independently confirmed by CD measurements in the far‐uv in the presence of increasing amounts of magnesium ions. Elongation of the peptide chain from Nle11‐HG‐13 to Nle15‐HG‐17 does not provide any additional binding site for the metal ions. In both hormones, we have observed different responses in the near‐ and fur‐uv CD properties with regard to added magnesium. The intensity of the CD bands in the aromatic region changes cooperatively with the ion/hormone molar ratio. These findings lead us to conclude that at the C‐terminal, the biologically important sequence, ‐Trp‐Nle‐Asp‐Phe‐Nh2, is directly involved in the interaction with magnesium.
Circular dichroic studies on Cu(II) interactions with a protamine, scylliorhinine Z3
Authors: Kozlowski H. , Aubert J. P. , Gusse M. , Chevaillier P. , Loucheux‐Lefebvre M. H.
Published: December 2004

The interaction of Cu(II) with the protamine scylliorhinine Z3 was studied by means of CD measurements. At a 1:1 molar ratio, three complexes are formed. (1) In the pH range 5–6.5, the results suggest the formation of a five‐membered chelate ring through the coordination of two nitrogen atoms, the N‐terminal and the contiguous peptide nitrogen. (2) At pH ≥ 6.4, there is involvement of the lateral NH2 group of Arg; at pH 6.5–8, the formation of a 3N cupric complex is strongly suggested. (3) At pH ≥ 8, results indicate the formation of a 4N complex as a major species in Cu(II)‐Z3 solution. The transformation from a 2N to a 3N complex, and from a 3N to a 4N complex was followed with the help of the σ(αNH2) → Cu(II) charge‐transfer dichroic band transitions. At Cu(II):Z3 molar ratios ≥ 2 and at pH > 8, a new dichroic band appears, indicating the involvement of the tyrosine residue side chain in metal‐ion complexation.
Induced optical activity in the complex of poly(L‐arginine) with azo dyes
Authors: Yamamoto Hiroyuki , Nakazawa Ayako
Published: December 2004

The absorption and CD spectra of the complexes of poly(L‐arginine) (PLA) and azo dyes have been measured in aqueous solution. On complexation, Blue‐shifted additional absorption bands were observed. In the wide pH 4–11 range, induced CD was observed at the visible wavelengths corresponding to the blue‐shifted absorption bands. The induced CD arose from the dimeric dye molecules bound to PLA in the α‐helical structure. When a modified analysis of induced CE is made by the excition chirality method, the origin of the induced CD can be assigned to the dipole coupling. The PLA–dye complexes showed the counterlockwise (negative, S) chirality of the transition dipole moments of dyes.
Conformation of a cyclic tetrapeptide related to an analog of enkephalin
Authors: Hall David , Pavitt Nicola
Published: December 2004

A systematic survey has been made, using molecular mechanics, of the conformation of cyclo(‐Nγ‐Mabu‐Gly‐Ala‐Ala‐), where Mabu is (R)‐α‐methyl‐γ‐aminobutyric acid. This molecule corresponds to the 14‐membered ring of the conformationally restricted, biologically active, Leu‐enkephalin analog, Tyr‐cyclo(N γ‐D‐A2bu‐Gly‐Phe‐Leu‐), reported by DiMaio and Schiller [(1980) Proc. Natl. Acad. Sci. USA 77, 7162–7166]. There is one extensive low‐energy conformational region, in which the two lowest energy minima are separated by a low barrier; other low‐energy conformations exist but are closely restricted. Assuming that enkephalin in its active form shares conformation features with the cyclic molecule, it is deduced that enkephalin contains a Gly3‐Phe4 type II′ bend and that it could be similar to the model proposed by Clarke et al. [(1978) J. Med. Chem. 21, 600–606].
Characterization of intermediate conformational states in the B↔Z transitions of poly(dGdC) · poly(dGdC)
Authors: Goto Sachio
Published: December 2004

Time‐dependent uv absorption and CD spectrum changes in salt‐induced conformational B → Z and Z → B transitions of poly(dGdC) · poly(dGdC) were measured. This polynucleotide does not convert directly from a right‐handed double‐helical B form to a left‐handed double‐helical Z form, but goes through an intermediate, B* form, with the B → B* transition proceeding nearly instantaneously, and then transforms gradually to the Z form. Uv absorption spectra of these B and B* forms are nearly identical, but their CD spectra are quite different. The CD spectrum of the B* form is identical with that obtained for DNA in high salt solutions and is similar to a spectrum which for some time was thought to be a C form. These B and B* forms have the same number of base pairs per turn [Sprecher, C.A., Baase, W.A. & Johnson, Jr., W.C. (1979) Biopolymers 18, 1009–1019]. Kinetic measurements showed that uv absorption and CD intensities at fixed wavelengths do not change in a simple exponential curve. However, both the uv absorption spectrum change in the B → Z transition and the CD spectrum change in the B* → Z transition, respectively, have isosbestic points. In the B → Z transition, no hyperchromicity can be observed. These results suggest that this B* form unfolding or premelting process is a rate‐determining step in the B* → Z transition and makes it easy for the unfolded or premelted polynucleotide to almost immediately fold into the Z form. The double helix does not dissociate into single strands and transforms from the B* form to the Z form point‐by‐point along the chain in a soliton‐like manner of with a small amount of open states in which the bases are unpaired. Also, in the Z → B transition, the polynucleotide does not convert directly from the Z to the B form, but goes through a B*‐like form. In this transition, the uv‐absorption spectra also have an isosbestic point. The reaction velocity in the Z → B transition is much faster than that in the B → Z transition. Possibly, the positive CD band between 265 and 310 nm in the B form comes from a n‐π* transition due to an interaction of the bases with sugarphosphate groups.
Viscoelasticity of rigid macromolecules with irregular shapes in the limit of overwhelming Brownian motion
Authors: Wegener William A.
Published: December 2004

We consider viscoelastic properties of complex rigid macromolecules in fluids undergoing steady or sinusoidal linear shearing. An arbitrary body is hydrodynamically described by six tensors to allow for irregular shapes that couple rotational and translational motions to each other and to the shear field. The viscosity increment ν is obtained for infinitely dilute suspensions in the limit of overwhelming Brownian motion by balancing drag forces and torques with entropic forces and torques. For sinusoidal shearing, ν is a complex number that exhibits five resonances at frequencies matching the j = 2 eigenvalues of the rotational diffusion equation for a stationary fluid. The resonance amplitudes are conveniently expressed in terms of a second‐rank body‐fixed tensor χ that characterizes alignment by the shear field, and special cases of symmetry are considered which reduce the number of contributing terms. Steadyshear methods, which assume a body matches the translational and rotational motions of the fluid element it replaces, are shown to slightly overestimate ν when complex shapes are involved. An algebraic criterion is found to locate the center of viscosity needed in these other methods although our treatment is independent of the choice of position in the body used for calculations. Bead‐model expressions are derived in order to provide numerical treatments of complicated structures. As an example, we examine a long bent rod.
Suppression of the statistical coil state during the α ↔ β transition in homopolypeptides
Authors: Mattice Wayne L. , Scheraga Harold A.
Published: December 2004

A matrix formulation of the conformational partition function has been used to examine helix ↔ sheet transitions in homopolyamino acids. α‐Helices are weighted by Zimm‐Bragg parameters σ and s. Antiparallel β‐sheets with tight bends are weighted by the parameters t, δ, and τ, where t is the propagation parameter. In addition, each bend contributes a factor δ, and each residue in the sheet that does not have a partner in the preceding strand contributes a factor τ. The helix can be the dominant conformation in a long chain only if two conditions are satisfied simultaneously: (i) s > 1, and (ii) either s > t, or σ, δ, and τ are assigned values that inflict a greater penalty on antiparallel sheets than on helices. The maximum amount of coil developed during the helix ↔ sheet transition is strongly influenced by the size of τ, but it is only weakly dependent on the size of δ. Previously reported optical rotatory dispersion, CD, laser Raman, and nmr studies of thermally induced α ↔ β transitions in homopolyamino acids, notably poly(L‐lysine), demonstrate that little random coil is present. If the random coil content is to remain small during the helix ↔ sheet transition, τ must be significantly less than unity. A small value for τ means that there is a significant penalty assessed to lysyl residues in an antiparallel sheet that do not have a partner in a preceding strand.
Molecular‐dynamics simulation of phenylalanine transfer RNA. II. Amplitudes, anisotropies, and anharmonicities of atomic motions
Authors: Prabhakaran M. , Harvey Stephen C. , McCammon J. Andrew
Published: December 2004

The atomic motions from a molecular‐dynamics simulation of yeast tRNAPhe are analyzed and compared with those observed in protein simulations. In general, the tRNA motions are of larger amplitude, they are more anisotropic, and they arise from potentials of mean force that are more anharmonic than in the protein case. In both cases, the amplitudes are largest for atoms on the surface of the molecules. On the other hand, the most anisotropic and anharmonic atomic motions are generally found in the interior of the tRNA, while they are found on the surface of the protein. These differences are discussed in terms of the differences in structure between nucleic acids and proteins.
Effect of anisotropic bending rigidity and finite twisting rigidity on statistical properties of DNA model filaments
Authors: Schurr J. Michael
Published: December 2004

The persistence length and effective long‐range bending rigidity are derived for a discrete model of an anisotropically bending filament and shown to be independent of the torsional rigidity. The twisting persistence length is found to be independent of the anisotropic bending rigidity. Other statistical properties are briefly discussed, including the dependence of tangent vector projections on contour length. The dependence of a tensor contraction on contour length is derived for an isotropically bending filament with no equilibrium twist.
Vibrational circular dichroism of polypeptides. IV. Film studies of L‐alanine homo‐oligopeptides
Authors: Narayanan Usha , Keiderling T. A. , Bonora G. M. , Toniolo C.
Published: December 2004

Vibrational CD (VCD) and ir absorption data are reported for a series of films of Boc‐(L‐Ala)n‐OMe homo‐oligopeptides (n = 3–7) in the amide I and A regions. The data evidenced a sharp change between n = 3 and n = 4, which parallels the onset of β‐structure formation, and another between n = 5 and n = 6, which parallels the full development of β‐structure. This represents the first report of the application of VCD to oligopeptide conformation. The data resembled earlier reported film VCD studies of higher‐molecular‐weight polypeptides of known β‐structure.
Direct evidence for antifreeze glycoprotein adsorption onto an ice surface
Authors: Brown Robert A. , Yeh Yin , Burcham Timothy S. , Feeney Robert E.
Published: December 2004

Aqueous solutions of antifreeze glycoproteins (AFGP) exhibit hysteresis between the freezing and melting temperatures. Several recent studies on the mechanism of function of this protein system suggest that a likely model is for the antifreeze molecules to be adsorbed onto the surface of the crystals. However, direct proof of the presence of adsorbed AFGP has eluded previous researchers. In the present study, enhanced surface second‐harmonic generation (SSHG) was observed in the presence of an active AFGP solution in contact with a pure single crystal of ice. The enhancement of SSHG is a positive indication that active AFGP molecules adsorb to the surface of ice crystals.
Heavy‐atom effects on energy transfer from polynucleotides to terbium (III)
Authors: Burns Victor W.
Published: December 2004

Energy transfer in nucleic acids or polynucleotides at room temperature can be studied by using the fluorescence of complexed terbium (III) as a tool. Complexing the heavy atom thallium (I) enhances energy transfer from poly(G) to terbium (III). Thallium has no effect on transfer from GMP to terbium and a small negative effect on the transfer from single‐stranded DNA to terbium. Use of the Medinger‐Wilkinson model to analyze the poly(G) results provides an estimate of the room‐temperature intersystem crossing constant.
Conformational analysis of polyoxyethylene‐bound homo‐oligo‐L‐glutamates in a weakly interacting medium, CDCl3
Authors: Ribeiro Anthony A. , Saltman Robert , Goodman Murray
Published: December 2004

A detailed conformational analysis of polyoxyethylene‐bound N‐t‐butyloxycarbonyl homo‐oligo‐L‐glutamates up to the heptamer was carried out in CDCl3 solution using high‐resolution 1H‐nmr spectroscopy. Unequivocal assignments of resolved backbone NH and α‐CH resonances were obtained with specifically deuterated oligomers. From nmr measurements, chemical‐shift dependencies with respect to temperature and solvent, and the line‐broadening effects of free radicals allowed the determination of hydrogen‐bonded residues. The nmr data, along with model‐building studies, suggest that seven‐membered rings may exist in the N‐terminal portion of these peptides. Replacement of the N‐t‐butyloxycarbonyl group by an acetyl or pyroglutamyl residue gave aggregated peptides, pointing to a special contribution by the Boc group to hydrogen bonding and solubility in CDCl3.
Fast approximations for accessible surface area and molecular volume of protein segments
Authors: Zehfus Micheal H. , Seltzer Jack P. , Rose George D.
Published: December 2004

Equations are presented that approximate the accessible surface area of a continuous protein segment using the surface area of an inertial ellipsoid and that approximate the molecular volume from the number of non‐hydrogen atoms in the segment. These approximations, which are appropriate for segments of four or more residues in length, are much faster to calculate than the exact solutions, yet suffer only a 3–8% error. Included in an appendix are FORTRAN subroutines that calculate the surface area of an ellipsoid from its three principal moments of inertia.
Temperature dependence of dielectric constant at 10 GHz of Na‐DNA gels
Authors: Bonincontro A. , Di Biasio A. , Pedone F.
Published: December 2004

Permittivity ε′ and dielectric loss ε″ of aqueous Na‐DNA gels have been measured at 10 GHz in the temperature interval −15 to + 45°C. The experimental results are analyzed in terms of a three‐component equation (Na‐DNA, interfacial water, bulk water) and yield a value of 35 water molecules/nucleotide interacting with DNA. According to theoretical and experimental data the presence of strongly bonded and weakly bonded water is considered. The modified water exhibits a mean dielectric relaxation time two‐or threefold greater than that of bulk water.
The properties of calmodulin at physiological temperature
Authors: Steiner Robert F. , Marshall Leda , Needleman Donna
Published: December 2004

Several of the physical properties of calmodulin are changed significantly upon increasing the temperature from 25 to 37°C. Among the observed changes are a minor increase in intrinsic viscosity, a decrease in molecular ellipticity in the peptide region, the development of a difference spectrum in the aromatic region, and an increase in the mobility of extrinsic fluorescent labels. Except for the latter case, the magnitudes of the changes are substantially reduced in the presence of Ca2+. The above observations are consistent with an expanded and less tightly organized structure of calmodulin at the higher temperature.
Vacuum UV CD of the low‐salt Z‐forms of poly(rG‐dC)·poly(rG‐dC), and poly(dG‐m5dC)·poly(dG‐m5dC)
Authors: Behe Michael J.
Published: December 2004

The vacuum CD spectra of poly(rG‐dC)·poly(rG‐dC) and poly(dG‐m5dC)·poly(dG‐m5dC) have been obtained for the low‐salt Z‐conformations of both polymers. The spectra are very similar to those for the high‐salt Z‐forms. This behavior is consistent with the suggestion that the low‐ and high‐salt Z‐forms are comprised of different proportions of ZI‐ and ZII‐conformations.
Effect of NaCl on the association of thrombin with heparin
Authors: Oshima Genichiro , Uchiyama Hideki , Nagasawa Kinzo
Published: December 2004

The association of heparin with thrombin was investigated by fluorometric titration. A maximum of 25% of the fluorescence of fluorescein‐labeled heparin (FTC‐heparin) was quenched at thrombin saturation in the absence of NaCl. FTC‐heparin (H) associated tightly with thrombin (T) and the association constant of the ternary complex, H2T, formed in the absence of NaCl, was calculated to be 1.7 × 108M−1. However, the association was strongly influenced by the NaCl concentration, and the association constant of the equimolar complex, HT, formed in 0.15M NaCl was found to be 1 × 106M−1. The first‐order rate constant, kapp, for inactivation of thrombin by antithrombin III (AT III) and low‐affinity heparin (LA‐heparin) was comparable with that of high‐affinity heparin (HA‐heparin) in the absence of NaCl, but decreased with an increase in the concentration of NaCl. The decreased enhancement of the thrombin‐AT III reaction by LA‐heparin at high NaCl concentration appeared to result from a decreased association of thrombin with LA‐heparin, thus reducing the formation of the ternary complex, thrombin‐LA‐heparin‐AT III.
Models for the subunit arrangement in soluble and aggregated plasma fibronectin
Authors: Hörmann Helmut , Richter Hartmut
Published: December 2004

Fibronectin, consisting of two threadlike subunits connected close to their C‐terminal ends, exists in a soluble and a fibrous form. Models are presented that propose distinct foldings of the rodlike subunits in the soluble dimer and an extended arrangement in the aggregates. The proposed conformations are based on the analysis of electrostatic attractions and noncovalent affinities between domains. Electrofocusing of proteolytic fragments revealed a sequence of four domains with alternating charges in the N‐terminal half of each subunit and two domains with opposite charges close to the C‐terminus. Complementary sites with affinity to each other were localized by radioimmuno‐binding assay in the gelatin‐binding and in the subsequent DNA‐binding domain of the N‐terminal tetra‐domain sequence. Claiming that in soluble fibronectin electrostatic attractions and noncovalent affinities should be neutralized within the molecule resulted in the construction of a conformation with backfolded subunits, each containing an extra loop in which domains with complementary affinity sites are saturated by each other. The model is in accord with hydrodynamic and electronmicroscopic data. There is, however, an alternative folding in which electrostatic and noncovalent affinity sites in the N‐terminal half of each subunit are saturated by an interchain interaction within the molecule. Consequently, a rearrangement of the molecule without significant shape change cannot be excluded. In the aggregated form, the N‐terminal tetra‐domain sequence gives rise to an intermolecular interaction while the C‐terminal domains become available for binding ligands.
Dynamics of molecular organization in agarose sulphate
Authors: Norton I. T. , Goodall D. M. , Austen K. R. J. , Morris E. R. , Rees D. A.
Published: December 2004

Nongelling solutions of structurally regular chain segments of agarose sulphate show disorder–order and order–disorder transitions (as monitored by the temperature dependence of optical rotation) that are closely similar to the conformational changes that accompany the sol–gel and gel–sol transitions of the unsegmented polymer. The transition midpoint temperature (Tm) for formation of the ordered structure on cooling is ∼25 K lower than Tm for melting. Salt‐induced conformational ordering, monitored by polarimetric stopped‐flow, occurs on a millisecond time scale, and follows the dynamics expected for the process 2 coil ⇌ helix. The equilibrium constant for helix growth (s) was calculated as a function of temperature from the calorimetric enthalpy change for helix formation (ΔHcal = −3.0 ± 0.3 kJ per mole of disaccharide pairs in the ordered state), measured by differential scanning calorimetry. The temperature dependence of the nucleation rate constant (knuc), calculated from the observed second‐order rate constant (kobs) by the relationship kobs = knuc(1 − 1/s) gave the following activation parameters for nucleation of the ordered structure of agarose sulphate (1 mg mL−1; 0.5M Me4NCl or KCl): ΔH* = 112 ± 5 kJ mol−1; ΔS* = 262 ± 20 J mol−1 K−1; ΔG*298 = 34 ± 6 kJ mol−1; (knuc)298 = (7.5 ± 0.5) × 106 dm3 mol−1 s−1. The endpoint of the fast relaxation process corresponds to the metastable optical rotation values observed on cooling from the fully disordered form. Subsequent slow relaxation to the true equilibrium values (i.e., coincident with those observed on heating from the fully ordered state) was monitored by conventional optical rotation measurements over several weeks and follows second‐order kinetics, with rate constants of (2.25 ± 0.07) × 10−4 and (3.10 ± 0.10) × 10−4 dm3 mol−1 s−1 at 293.7 and 296.2 K, respectively. This relaxation is attributed to the sequential aggregation processes helix + helix → dimer, helix + dimer → trimer, etc., with depletion of isolated helix driving the much faster coil–helix equilibrium to completion. Light‐scattering measurements above and below the temperature range of the conformational transitions indicate an average aggregate size of 2–3 helices.
The proteoglycans of bovine nasal cartilage and human articular cartilage: A sedimentation equilibrium analysis
Authors: Hinnie J. , Serafini‐Fracassini A.
Published: December 2004

Cartilage proteoglycan was isolated from bovine nasal septum and fractionated according to buoyant density after dissociative CsCl density gradient centrifugation. Gel‐exclusion chromatography showed that hyaluronic acid was present in fractions of density lower than 1.69 g/mL. The molecular weight, assessed by sedimentation equilibrium analysis, of the proteoglycan present in the fractions with density > 1.69 g/mL, which appeared chromatographically homogeneous and constituted 54% of the preparation, ranged from 1.0 to 2.6 × 106 for v = 0.55 cm3 g−1. Carbodiimide‐induced modification of the carboxyl groups by methylamine resulted in a reduction of the molecular weight to 0.74 – 1.25 × 106. An analogous reduction in molecular weight was obtained after equilibration of this proteoglycan fraction with hyaluronic acid oligomers containing five disaccharide units. Since both procedures are known to cause inhibition of the interaction between proteoglycans and hyaluronic acid, it is suggested that this lower molecular‐weight range represents the true degree of polydispersity of the sub‐units of hyaline cartilage proteoglycan constituting this fraction, while the higher values obtained for the intact proteoglycan are the result of the presence of hyaluronic acid in the sample. The molecular‐weight range of the whole proteoglycan subunit preparation, assessed after carboxyl group modification, was 0.5–1.2 × 106. Apparently normal and abnormal cartilage was excised from single human osteoarthrosic femoral heads. Proteoglycans extracted by 4M guanidine hydrochloride were isolated after dissociative density gradient centrifugation and subjected to carboxyl group modification. Preparations from normal tissue exhibited molecular‐weight averages ranging from 5 to 9 × 105. A molecular‐weight reduction was observed with proteoglycans isolated from abnormal areas.
Gel formation by fibrin oligomers without addition of monomers
Authors: Janmey Paul A. , Ferry John D.
Published: December 2004

Soluble fibrin oligomers were formed by reacting fibrinogen with thrombin under fine clotting conditions where the action of thrombin is the rate‐determining step for polymerization, and by inhibiting the reaction shortly before gelation. Oligomeric fibrin was separated from unreacted fibrinogen and small oligomers by gel permeation chromatography. Electron microscopy revealed that the largest soluble fibrin oligomers resemble the protofibrils present in fine clots, but are somewhat shorter and entirely lack the twisted, trifunctional junctions that contribute to the elastic properties of fine clots. When thrombin was added to the soluble fibrin oligomers, polymerization resumed and clots were formed at a more rapid rate than from fibrinogen at the same concentration and resulted in a less‐opaque clot under coarse clotting conditions. The results confirm a prediction of a theory for the polymerization of fibrin and provide additional evidence that the final state of a coarse fibrin clot depends on the mobility of protofibrils during its formation.
A study of apo‐ and holo‐forms of horse liver alcohol dehydrogenase in solution by diffuse X‐ray scattering
Authors: Yu. Pavlov M. , Sinev M. A. , Timchenko A. A. , Ptitsyn O. B.
Published: December 2004

Apo‐ and holo‐forms of horse liver alcohol dehydrogenase (LADH) in solution were studied by diffuse x‐ray scattering. Experimental scattering curves for apo‐ and holo‐forms coincide both with the curves calculated from the crystal structures of apo‐ and holo‐enzymes, and with each other. Thus the “sliding” of catalytical domains in LADH upon substrate binding, which has been shown by x‐ray analysis, cannot be detected by diffuse x‐ray scattering. Sensitivity of the scattering curves to the domain displacements of sliding and “locking” types has been investigated. It has been shown that the scattering curves of LADH are rather sensitive to the domain “unlocking.” However, these curves change only slightly upon sliding of domains, including the sliding of domains observed in LADH by x‐ray analysis.
Molecular structure of the cis‐syn photodimer of d(TpT) (cyanoethyl ester)
Authors: Hruska F. E. , Voituriez L. , Grand A. , Cadet J.
Published: December 2004

The three‐dimensional structure was determined by x‐ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis‐syn cyclobutane (CB) geometry and the S‐configuration at the chiral phosphorus atom. The crystals of C23H30N5O12P · 2H2O belong to the orthorhombic space group P212121 (Z = 4), with cell dimensions a = 11.596 Å, b = 14.834 Å, and c = 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by –29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer–Pople parameters for T[p] and in parentheses [p]T: Q: 0.24 Å (0.31 Å); θ: 123° (120°); ϕ: 141° (86°). These represent half‐chairs designated as 6H1 (T[p]) and 6H5 ([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p] segment has the syn glycosyl conformation, a 2T3 sugar pucker, and gauche− conformation at C4′‐C5′; the [p]T segment is anti, 3T4, trans. The C5′‐O5′ torsion of the [p]T unit is –124.5°, and the C3′‐O3′ torsion of the T[p] unit is –152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P‐O3′ and P‐05′ torsion angles are –138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.
Evolutionary similarity among peptide segments is a basis for prediction of protein folding
Authors: Sweet Robert M.
Published: December 2004

Short segments of polypeptide, from a protein for which the primary sequence but not the three‐dimensional structure is known, are compared to a library of known structures. The basis of comparison is the probability with which residues in the unknown segment might substitute through evolution for residues in segments of known structure. In test cases, segments from known structures that are similar in sequence to those from a protein treated as unknown are often found to be similar in three‐dimensional structure to one another and to the true structure of the “unknown” segment. This provides a basis for prediction of the local configuration (secondary structure) of polypeptides.
The crystal structure of the photosynthetic inhibitors DCMU and DTPU
Authors: Gilon Chaim , Cohen Shmuel , Siderer Yona
Published: December 2004

X‐ray diffraction studies have been carried out on a single crystal of the photosynthetic inhibitors N‐(3,4‐dichlorophenyl)‐N′‐dimethylurea (DCMU) and its newly synthesized spin‐labeled analog N‐(3,4‐dichlorophenyl)‐N′‐(3,3,5,5‐tetramethylpiperidine‐4‐oxyl)‐urea (DTPU). The synthesis of DTPU as well as its crystallographic data are reported. The crystal system of both compounds is monoclinic with a space group P21/c. The cell constants of DCMU are a = 7.759(1), b = 14.737(3), c = 9.233(2) Å, β = 100.99(6)°; of DTPU they are a = 6.976(1), b = 11.998(2), c = 23.585(3) Å, β = 91.38(5)°. Comparison of conformational parameters of DCMU and DTPU reveal differences in the dihedral angle between the aromatic ring and the ureido plane. The measured volumes of DCMU and DTPU are 259.1 and 493.3 Å3, respectively. These figures suggest the size of the binding site of the inhibitors in the photosynthetic membrane.
Stereochemistry of peptides containing 1‐aminocyclopentanecarboxylic acid (Acc5): Solution and solid‐state conformations of Boc‐Acc5‐Acc5‐NHMe
Authors: Bardi R. , Piazzesi A. M. , Toniolo C. , Sukumar M. , Balaram P.
Published: December 2004

The conformational analysis of a protected homodipeptide of 1‐aminocyclopentanecarboxylic acid (Acc5) has been carried out. 1H‐nmr studies establish a β‐turn conformation for Boc‐Acc5‐Acc5‐NHMe in chloroform and dimethylsulfoxide solutions involving the methylamide NH in an intramolecular hydrogen bond. Supportive evidence for the formation of an intramolecular hydrogen bond is obtained from ir studies. X‐ray diffraction studies reveal a type III β‐turn conformation in the solid state stabilized by a 4 → 1 hydrogen bond between the Boc CO and methylamide NH groups. The ϕ,ψ values for both Acc5 residues are close to those expected for an ideal 310‐helical conformation (ϕ≃ ± 60°, ψ∼ ±30°).
Pf1 virus particle dynamics
Authors: Tsang P. , Opella S. J.
Published: December 2004

The overall dynamics of the Pf1 filamentous bacteriophage particle in solution are characterized by nmr experiments. The chemical‐shift anisotropy powder‐pattern lineshapes from both DNA and protein backbone sites of the virus are motionally averaged in the same way, indicating that the entire particle undergoes rapid (< 104 Hz) reorientation about the long axis of the filament when the virus is in solution at high pH. In contrast, the virus particles in samples at low pH are immobile on this time scale.
Comparison between the unfolding rate and structural fluctuations in native lysozyme—effects of denaturants, ligand binding, and intrachain cross‐linking on hydrogen exchange and unfolding kinetics
Authors: Segawa Shin‐Ichi , Kume Katsuya
Published: December 2004

The hydrogen‐exchange reactions of peptide NH groups in lysozyme were studied by the change in the intensity of the amide II band in the ir spectrum. The slowest exchanging hydrogens, which are involved in intramolecular hydrogen bonding, are further divided into two groups at lower temperatures; half of them are exchanged through local unfolding and the other half through major cooperative unfolding. In order to study the correlation of the change in hydrogen‐exchange rates with the change in the unfolding rate constant, we observed the effects of intrachain cross‐linking, the addition of denaturant and ligand binding on the exchange rates through local unfolding. Although the exchange rate through major unfolding is greatly decreased by intrachain cross‐linking between Glu 35 and Trp 108 (1/22000), the exchange rate through local unfolding is only slightly decreased (1/20). Even at higher temperatures, where most intact lysozyme molecules unfold, the folded conformation of cross‐linked lysozyme remains compact, and no intermediate exists in which many side‐chain atoms are packed loosely so that the hydrogen‐exchange reaction occurs rapidly. Neither the addition of 2‐PrOD molecules nor (NAG)3 binding affects the exchange rates through local unfolding. Our experiments confirm that the change in the unfolding rate constant does not correlate with the change in fluctuations in the relatively flexible hydrogen‐bonded structure through which the exchange of peptide hydrogens takes place.
Concentration of protein in fibrin fibers and fibrinogen polymers determined by refractive index matching
Authors: Voter William A. , Lucaveche Carmen , Erickson Harold P.
Published: December 2004

We have used refractive index matching to determine the concentration of protein in the fibers in fibrin clots and of needlelike crystals of native fibrinogen. Our results are in agreement with those of Carr and Hermans [(1978) Macromolecules 11, 46–50], as determined by light scattering—namely, that protein makes up about 20% of the volume of the fiber. However, we have found that the protein concentration is strongly dependent on ionic strength. An increase in ionic strength caused a substantial drop in the protein concentration. In a buffer containing 100 mM NaCl, the protein concentration was 26.6–29.8 g of protein per 100 cm3 of polymer, and at 200 mM NaCl it was reduced to 22.1–23.1 g/100 cm3.