bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrostatic interactions between α‐helix dipoles in crystals of an uncharged helical undecapeptide
Authors: Hol Wim G. J. , De Maeyer Marc C. H. 
Published: December 2004

AbstractThe electrostatic interactions between α‐helix dipoles in the crystals of an uncharged helical undecapeptide have been studied in detail. The electrostatic interaction energy between one helix dipole and its 26 nearest neighbors is approximately −23 kcal mol−1. A very similar result is obtained when calculating the interactions between one helix dipole and all 988 helix dipoles occurring within a distance of 75 Å. It therefore appears that in these crystals of completely uncharged molecules large, favorable electrostatic interactions occur.
Physical binding of pyrene and phenanthrene to native and denatured DNA: Measurements by spectral and coupled‐column liquid chromatography methods
Authors: Nelson Henry P. , Devoe Howard 
Published: December 2004

AbstractThe physical (noncovalent) binding of pyrene and phenanthrene to calf‐thymus DNA in aqueous NaCl solutions was measured by a spectral method (analysis of absorption spectra by Benesi‐Hildebrand plots) and a coupled‐column liquid chromatography method (equilibration of DNA solutions with solid hydrocarbon in a generator column and analysis of dissolved hydrocarbon by liquid chromatography). The measurements yielded values of an affinity constant K′ = nK, where n is the apparent number of binding sites per nucleotide and K is the apparent binding constant. The affinity of native DNA for pyrene decreases monotonically with increasing NaCl concentration, whereas the affinity of heat‐denatured DNA exhibits a maximum at 0.10M NaCl.K′ for the binding of phenanthrene to native DNA is an order of magnitude lower than K′ for pyrene. The molar enthalpy for the binding of pyrene to native DNA in 10 mM NaCl is (−34.0 ± 1.0) kJ mol−1. The spectral method data indicate that 50 is an upper limit for the average number of base pairs between intercalation sites for pyrene along the DNA helix and that only a fraction of these sites are bound at the highest binding ratios.
Interaction of poly(I)·poly(C) with trans‐dichloro‐diammine‐platinum (II)
Authors: Hermann Dominique , Fazakerley G. Victor , Houssier Claude , Guschlbauer Wilhelm 
Published: December 2004

AbstractThe covalent binding of trans‐Pt (NH3)2Cl2 to the double‐stranded poly(I)·poly(C) follows three types of reactions, depending on rb and the concentration of polynucleotide in the reaction mixture. At rb ⩽ 0.1, the principal reaction is coordination to poly(I), giving rise to some destabilization of the double strand, as shown by uv and CD spectra, and a decrease in Tm values, giving rise to free loops of poly(C). At higher rb and low polynucleotide concentration, the free cytidine bases react with platinum bound on the complementary strand to form intramolecular (interstrand) crosslinks that restabilize the double‐stranded structure. At high rb and high polynucleotide concentration, while the above reaction still occurs, the predominant one is the formation of intermolecular crosslinks. Under no conditions has strand separation been observed.
Ionic and structural effects on the thermal helix‐coil transition of DNA complexed with natural and synthetic polyamines
Authors: Thomas T. J. , Bloomfield V. A. 
Published: December 2004

AbstractPolyamines are ubiquitous cellular components that interacts strongly with nucleic acids. Although many of the interactions of oligocations with DNA can be rationalized with polyelectrolyte theories that treat counterions as point charges, some structural effects are evident. We have explored the effects of polyamine structure on one important aspect of DNA behavior, its thermal melting transition, by using a series of spermidine analogs NH3(CH2)3NH2(CH2)nNH, where n varies from 2 to 8 [Jorstad et al. (1980) J. Bacteriol. 141, 456–463]. For spermidine itself, n = 4. Tm for calf‐thymus DNA in the presence of each of these analogs, and the other naturally occurring polyamines putrescine2+ and spermine4+, was measured over a wide range of NaCl concentrations and polyamine:DNA phosphate ratios. There are modest, but significant structural effects. particularly with the shorter n = 2 and 3 derivatives, whose geometry my not allow full electrostatic interaction with DNA. Longer analogs, on the other hand, are not much different than spermidine in their effects on Tm, though a moderate maximum occurs at n = 5. Since polyamines are important in the cellular condensation and packaging of DNA, we have also delineated the critical polyamine and salt concentrations that are required to cause DNA aggregation. Here again, there are significant structural effects, which are not easily rationalized by any simple considerations.
pH‐jump titration of the tyrosyl groups of bovine plasma albumin
Authors: Kuwnajima Kunihiro , Matsushima Tadashi , Nitta Katsutoshi , Sugai Shintaro 
Published: December 2004

AbstractIonization properties of the tyrosyl groups of bovine plasma albumin in various conformational states—the native state (N), the two acid states (F and E), and the state (B) stable at slightly alkaline pH—were studied by means of a stopped‐flow‐pH‐jump technique. The technique allows us to obtain the tyrosyl titration curve in a conformational state that is unstable in the pH region of the titration. The pH jumps from the N and B states to various alkaline pH's, where the tyrosines ionize to bring about a time‐dependent increase in absorption at 296 nm, indicating that a number of the tyrosines buried initially become susceptible to ionization as a result of the alkaline transition occurring above pH 10.8. Extrapolation of the observed absorption change to zero time gives a spectrophotometric titration curve in the initial conformational state. Only 30–401% of the 19 tyrosines of the protein can ionize both in the N and the B state at pH 12. The pH jumps from the F and E states, on the other hand, give a decrease in absorption between pH 9 and 11.7, indicating that the tyrosyl groups initially exposed are remarked by refolding after the pH jumps, and the zero‐time titration curves show that essentially all the tyrosyl groups ionize normally in these acid states. The results are discussed in relation to the known results of the tyrosyl exposure of the protein measured by other techniques, and the consistency among them demonstrates the effectiveness of the pH‐jump titration method. Hydrogen bonding between the abnormal tyrosyl and carboxylate groups as a mechanism to stabilize native albumin is suggested from characteristics of the alkaline transition, which also involves the exposure of the tyrosyl groups, and from the tyrosyl titration curves in the native and acid states.
Solvation effects on the 31P‐nmr chemical shifts and infrared spectra of phosphate diesters
Authors: Lerner D. B. , Becktel W. J. , Everett R. , Goodman M. , Kearns D. R. 
Published: December 2004

AbstractThe effects of organic solvents on the 31P‐mr chemical shifts of various phosphate diesters have been investigated in water and mixed‐organic solvent systems. The addition of organic solvents to cyclic phosphates and to diethyl phosphate causes large upfield shifts of the phosphorus resonance which are attributed to solvent‐induced changes in the local hydration of the phosphodiester group. This is consistent with the fact that there is an inverse correlation between the hydrogen‐bond‐donating ability of the solvents and the magnitude of the shifts they induce. Other possible interpretations, such as solvent‐induced ion pairing and solvent‐induced conformational changes, appear to be eliminated. Fourier‐transform ir study of the cyclic nucletides reveals that there are also large solvent‐induced shifts in the frequency of the antisymmetric OPO stretching frequency, and a comparison of the two types of measurements indicates that there is a linear correlation between shifts observed in the ir and in the 31P‐nmr spectra. With UpU, the solvent‐induced 31P‐nmr shifts are ∼3 times smaller than those observed with the cyclic phosphates and the solvent‐induced shift of the OPO band is reduced (factor of ∼1.7) as compared with the cyclic phosphates. With the single‐stranded polynuclotides, poly(C) and poly(U), the solvent‐induced shifts in both the nmr and ir are quite small (∼0.1 ppm and ∼1 cm−1). The very small solvent effects observed with poly(U) and poly(C) are attributed to a combination of steric effects and a polyelectrolyte effect which maintains a high density of counterions with waters of hydration in the vicinity of the charged backbone and makes the phosphates much less susceptible to solvent‐induced changes in hydration.
Analysis of the electrophoretic properties of double‐stranded DNA and RNA in agarose gels at a finite voltage gradient
Authors: Edmondson Stephen P. , Gray Donald M. 
Published: December 2004

AbstractThe electrophoretic mobilities of double‐stranded (ds) DNAs and ds RNAs of various lenths, L, were measured in gels of 0.4–1.8% (w/v) agarose at a voltage gradient of 1.0 V/cm. Differences in the electrophoresis of ds DNA and ds RNA are presented and discussed. A general expression is derived that describes the electrophoretic mobility, M, of either type of ds nucleic acid as a function of the gel concentration and the nucleic acid length: M = M′1(L/L0)−x − M2, where M′1 and L0 are constants, and x and M2 depend on the agarose gel concentration. The results obtained by fitting our data with this equation are consistent with the mobilities of nucleic acids in a wide range of gel concentrations, including free electrophoresis in solution and electrophoresis in gles of high agarose concentration in which nuleic acids are expected to reptate through the gel matrix. Finally, various methods of plotting agarose gel electrophoresis data are discussed.
Molecular‐mechanical studies of hormone–protein interactions: The interaction of T4 and T3 with prealbumin
Authors: Oatley Stuart J. , Blaney Jeffrey M. , Langridge Robert , Kollman Peter A. 
Published: December 2004

AbstractWe present molecular‐mechanical calculations on the interactions of L‐thyroxine (T4) and 3,5,3′‐triiodo‐L‐thyronine (T3) with the binding site of human serum prealbumin. Energy refinement with restraints on the movement of the iodine atoms leads to reasonably low‐energy structures with the iodines within 0.2 Å of their x‐ray determined positions; removal of these restraints leads to larger (∼1.0 Å) deviations from these positions. However the relative energies of T3 and T4 complexation are similar in both cases, and the relative calculated energies for these complexes, when corrected by a simple empirical method for the solvation energy differences of the hormones, are in reasonable qualitative agreement with experiment.
Energetics of multihelix interactions in protein folding: Application to myoglobin
Authors: Gerritsen Mirjam , Chou Kuo‐Chen , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractConformational‐energy calculations have been carried out in order to determine favorable packing arrangements within a group of α‐helices. The influence of side chains and of the number of interacting α‐helices on the mode of packing was analyzed. In this work, our earlier methods for computing the packing energy of a pair of α‐helices [Chou, K.‐C., Némethy, G. & Scheraga, H. A. (1984) J. Am. Chem. Soc. 106, 3161–3170] have been extended to treat the interactions among several helices. Also, new algorithms allow the matching of standard peptide geometry to x‐ray coordinates of helical complexes and the analysis of interrelations between several helices. As a specific test case, the packing of three neighboring α‐helices, viz., the A, G, and H helices of sperm whale myoglobin, was considered. Minimum‐energy arrangements were computed for the separate A‐H and the G‐H α‐helix pairs as well as for the A‐G‐H three‐helix complex. For the packing of the nearly antiparallel G and H α‐helices, the same optimal structure was obtained in two‐ and three‐helix complexes, indicating that a single packing arrangement is specifically favored by interhelix interactions. For the pair of nearly perpendicular A and H α‐helices, interactions are less specific, so that there is no unique optimal structure in the two‐helix complex; in the three‐helix complex, however, a specific mode of packing is favored even for the A‐H pair. This result indicates that the presence of other nearby α‐helices can influence the packing of a given α‐helix pair. The computed arrangement of the A‐G‐H complex is very close to that of the crystallographically determined structure. These results can be used to make deductions about the likely sequence of events in protein folding, where, in this particular case, it appears that the G‐H helix pair may form first and then induce proper orientation of the A helix.
Carcinogen–base stacking and base–base stacking in dCpdG modified by (+) and (−) anti‐BPDE
Authors: Hingerty Brian E. , Broyde Suse 
Published: December 2004

AbstractThe low‐energy conformations accessible to dCpdG modified at guanine N2 via trans epoxide opening by (+) and (−) 7β,8α‐dihydroxy‐9α,10α‐epoxy‐7,8,9,10‐tetrahydrobenzo(a)pyrene (anti‐BPDE) have been delineated by minimized semiempirical potential‐energy calculations with all torsion angles flexible. Nearly 4000 trials were made, representing a fairly thorough investigation of the conformation space of the adducts. Carcinogen–base stacked states and base–base stacked conformers were found in the low‐energy regions of both enantiomers. Many ω′, ω, ψ domains accommodate the two types of conformations, with B‐like backbones among the most preferred states in each case. The conformational differences between the two enantiomers on the dimer level reside in subtle distinctions in orientation of the carcinogen–base linkage.
The effect of solvent viscosity and temperature on DNA viscoelastic behavior
Authors: Ostashevsky J. Y. , Lange C. S. 
Published: December 2004

AbstractThe effect of solvent viscosity (ηs) and temperature (T) on the shape of the concentration dependence of the principal and total recoils in creep‐recovery viscoelastometry experiments has been studied for T4 DNA solutions. The range of DNA concentration (c) was 2 – 40 μg/ml; glycerol, 70–80% v/v, sucrose, 60% v/v; NaCl, 5 mM – 1M; and T, 275 – 323 K. A linear proportionality between recoil and c was obtained at high ηs/T. At low ηs/T, the c‐dependence was nonlinear, approaching saturation at higher c. At low c, the slope of both curves was the same. Transition between “linear” and “nonlinear” values occurred over a narrow range of ηs/T (a width of 1–5 K if ηs/T was changed by varying T). (ηs/T)tr, the midpoint of the transition, was independent of solvent properties other than viscosity. Also, (ηs/T)tr increased with c. For a given c, ηs/T values above this transitional value yield linear behavior; below this, nonlinear behavior. The ratio of linear to nonlinear recoil values is a linear function of c with Kc, the slope of this dependence, independent of ηs and T. A kinetic model for the observed nonlinearity of recoil with c is presented. It explains the independence of Kc on ηs and T. An attempt has been made to explain the linear–nonlinear transitions by comparison of τ1 and TR, the lifetime of the contact points of the polymer network in the de Gennes theory. The nonlinear values are consistent with a pseudogel that exists when τ1 < TR. At τ1 > TR, the DNA behavior is similar to that in dilute solutions (linear values). Thus, the condition for transition is τ1 = TR. However, some unsolved problems remain.
The growth of large single crystals of lysozyme
Authors: Ataka Mitsuo , Tanaka Shoji 
Published: December 2004

AbstractIf protein single crystals larger than those suitable for x‐ray analysis are obtained, various spectroscopic, thermal, mechanical, and electrical measurements become possible. To understand the factors governing the crystal size, tetragonal lysozyme crystals were grown in batches at 15°C from solutions of different protein and salt concentrations between pH 4–7. The number and size of the crystals, and the protein concentration remaining in the supernatant, varied markedly with the initial salt amount, pH, and cation species, but large crystals always grew when the initial protein concentration (P) was in a narrow range of 2.5–3 times the crystal solubility (S). It was also shown (1) that the period before the first crystals appeared (D) varied as D ∝ (P/S)−n, where n ≃ 5, and (2) that many previous experiments used more supersaturated solutions than the optimal ones thus determined. The reason why large crystals grow only from moderately supersaturated solutions is discussed. The crystal size of the orthorhombic form grown at 40°C was less sensitive to pH and P than the tetragonal form. An effort to measure D and the solubility at 40°C revealed many differences between the two crystal forms, which we ascribe to different interactions to promote crystallization.
Effective diffusion rate through a polymer network: Influence of nonspecific binding and intersegment transfer
Authors: Berg Otto G. 
Published: December 2004

AbstractThe effective diffusion rate of a tracer molecule through a polymer network can be influenced by nonspecific binding. If such binding occurs, the local density fluctuations (segmental diffusion) of the network molecules will contribute to the net displacements of tracer molecules. If the network is strongly interconnected by entanglement or cross‐linking, these local motions will only carry the tracer molecules over a small region, and effective transport would require dissociation and reassociation of the tracer molecule to another part of the network. Alternatively, tracer molecules could be transferred directly (intersegment transfer) between different parts of the network whenever they are brought sufficiently close by the density fluctuations. A wormlike‐chain model for the segmental diffusion of a polymer is used to describe the network motions and to derive the effective diffusion rate for a tracer molecule as a function of network density and binding constant with or without intersegment transfer contributing. It is found that the density dependence for the effective diffusion of ethidium bromide through dense DNA solutions studied by photobleaching recovery [R. D. Icenogle and E. L. Elson (1983) Biopolymers 22, 1949–1966] agrees with an intersegment‐transfer mechanism limited by the segmental DNA motions. The calculations are also applied to a model for the intracellular diffusion of molecules loosely bound to the cytomatrix. If intersegment transfer dominates it can account for the observed size independence for the intracellular diffusion rates of various injected macromolecules.
Influence of different tripeptides on the stability of the collagen triple helix. II. An experimental approach with appropriate variations of a trimer model oligotripeptide
Authors: Thakur S. , Vadolas D. , Germann H.‐P. , Heidemann E. 
Published: December 2004

AbstractA collagen model peptide comprising three covalently cross‐linked chains (Ala‐Gly‐Pro)8 with a stable triple‐helix conformation was utilized as the constant part of elongated model peptides of different composition. The tripeptides Gly‐Pro‐Hyp, Gly‐Pro‐Ala, Gly‐Pro‐Pro, Gly‐Pro‐Ser, Gly‐Ala‐Hyp, Gly‐Phe‐Hyp, Gly‐Glu‐Hyp, Gly‐Ala‐Lys, and Gly‐Pro‐Phe were coupled at the N‐terminal to the cross‐linked peptide. The transition temperatures determined by CD measurements are higher for the peptides containing the Gly‐X‐Hyp sequences followed by those with the Gly‐Pro‐Y sequences. In experiments with combinations of two different tripeptides coupled to the constant part of the cross‐linked model peptides higher transition temperatures were observed if the sequence of helix‐promoting tripeptides was not interrupted.
SANS studies of concentrated protein solutions. I. Bovine serum albumin
Authors: Nossal R. , Glinka C. J. , Chen S.‐H. 
Published: December 2004

AbstractSmall‐angle neutron scattering (SANS) was used to examine concentrated bovine serum albumin solutions of up to 20% protein w/v. At higher protein concentrations, scattering data show distinct features that can be ascribed to strong intermolecular interactions. Differential scattering cross‐sections are fitted to a theoretical model of interparticle potential consisting of a hard core plus an exponentially decaying “tail.” For moderate ionic strength (0.03M K Acetate, pH 5.9), the intermolecular interaction agrees with the double‐layer repulsive part of the well‐known DLVO (Derjaguin, Landau, Verwey, Overbeek) theory for interacting colloidal particles. We thus demonstrate that it is possible to determine size parameters and the surface charge of protein molecules in dense solutions. At high salt concentrations (≥0.2M NaCl) data can be fitted by the same potential model, although interpretation in terms of DLVO theory is not possible. Even in this case, however, “effective” molecular size and potential parameters can be determined.
Collagen fibrillogenesis in vitro: An investigation of the thermal memory effect and of the early events occurring during fibril assembly using dynamic light scattering
Authors: Payne K. J. , King T. A. , Holmes D. F. 
Published: December 2004

AbstractDynamic light scattering has been used to characterize a variety of lathyritic rat skin collagen solutions. The technique was used to monitor the onset of fibril assembly in vitro and to investigate the thermal memory effect. Although the incorporation of thermal memory was demonstrated by reheating the sample and subsequently observing a shortened turbidimetric lag phase, no significant differences between naive solutions and ones exhibiting thermal memory could be detected using photon correlation spectroscopy. This suggests that subtle changes in the state of the collagen molecules rather than extensive changes in the degree of aggregation are responsible for the thermal memory effect. During fibrillogenesis, no large‐scale changes in the distribution of monomers or aggregates occur until near the end of the lag phase.
The interaction of Ca2+‐binding proteins with the carbocyanine dye stains‐all
Authors: Caday Cornelio G. , Lambooy Peter K. , Steiner Robert F. 
Published: December 2004

AbstractThe interaction of the carbocyanine dye Stains‐all with the Ca2+‐binding proteins calmodulin, troponin C, and parvalbumin has been monitored by means of absorption spectra and CD. In the absence of Ca2+, complexes with Stains‐all of all three proteins exhibit at high dye: protein mole ratios an intense J absorption band at 600–650 nm, which is associated with a characteristic CD spectrum. In the cases of calmodulin and troponin C, the J‐band is progressively lost as the dye: protein ratio decreases and is replaced by bands of the γ and β types at 450–550 nm, which likewise give rise to characteristic CD spectra. For parvalbumin, only the J‐band is observed; its intensity is undiminished at the lowest dye: protein ratios examined. In the presence of excess Ca2+ the J‐band is lost for all three proteins. For calmodulin and troponin C it is replaced by σ‐ and β‐bands; in the case of parvalbumin the bound dye is released. A tentative model has been proposed to account for these observations.