bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nmr studies on the induced denaturation of lysozyme by guanidine hydrochloride in the presence of the inhibitor (NAG)3
Authors: Sheinblatt M. 
Published: December 2004

AbstractThe stabilization of the folded conformation of lysozyme, arising from the binding of the inhibitor (NAG)3 against induced denaturation, is demonstrated from the 1H‐nmr spectra of the enzyme. The nmr spectra reveal that the binding of the denaturant (GuHCl) to the enzyme is associated with changes in the conformation of the enzyme. The binding site of the inhibitor site C also serves as one of the binding sites of GuHCl. The observation that higher denaturant concentrations are required in the unfolding of Lys–(NAG)3 as compared to free Lys can be explained partly in terms of the existence of a competitive binding to the enzyme involving the (NAG)3 and GuHCl molecules.
Secondary structure of pig skin proteodermatan sulfate: A perspective from Raman spectroscopic studies in aqueous solution
Authors: Renugopalakrishnan V. , Zheng S. , Tu A. T. , Damle S. P. 
Published: December 2004

AbstractRaman spectroscopic studies of pig skin proteodermatan sulfate in H2O are indicative of a well defined secondary structure consisting of α‐helical, β‐turn, and possibly “random” structures. The above conclusion is surprisingly close to the secondary structure of the “core” protein of pig skin proteodermatan sulfate proposed in the previous paper (V. Renugopalakrishnan et al., Biopolymers 28, 1923–1933, 1989) from FT‐IR and CD spectroscopic studies in aqueous solution.
Probe diffusion in cross‐linked actin gels
Authors: Newman Jay , Schick Kenneth L. , Zaner Ken S. 
Published: December 2004

AbstractThe diffusion of monodisperse polystyrene latex spheres (PLS) in column‐purified 0.65 mg/mL actin solutions, polymerized with 100 mM KCl in the absence and presence of a cross‐linker, actin binding protein (ABP), has been studied using dynamic light scattering. Measurements over a wide range of scattering angles from 90° to 8°, corresponding to inverse scattering vector probing distances of about 40–400 nm, respectively, give a measure of both the fraction of PLS mobile over the probing distance (from the normalized time autocorrelation function amplitude) and the average diffusion coefficient of the mobile PLS. Both 100‐ and 500‐nm diameter PLS are fully mobile in polymerized actin solutions over distances of less than 100 nm, as reported previously (Newman, J., Schick, K. S. & Gukelberger, G. Biophys. J. 53, 573a, and Newman, J., Mroczka, N. & Schick, K. L. Biopolymers, 28, 655–666). At increasing probing distances, or when ABP is added at molar ratios of 1 : 750 or 1 : 150, greater fractions of the PLS are immobilized, up to almost 99% at the conditions of a 400‐nm probing distance with 500‐nm probes and at a ratio of 1 : 150 added ABP to actin. The degree of immobilization correlates well with the amount of added ABP, the size of the PLS, and the probing distance. At increasing probe distances, as the degree of immobilization increases, the remaining mobile fraction of PLS has an increasing average diffusion coefficient. These results suggest a range of pore size in the actin gels with a mean size of a few hundred nanometers.
The effects of pH on hyaluronate as observed by light scattering
Authors: Reed Christopher E. , Li Xiao , Reed Wayne F. 
Published: December 2004

AbstractHyaluronate was investigated over a wide pH range, and at near zero and intermediate ionic strength, using dynamic and total intensity light scattering. Commercially obtained rooster comb hyaluronate was purified, and solutions were prepared in pure water by low‐power bath ultrasonication and subsequent filtering. These solutions were of low polydispersity and appeared to contain single molecules of hyaluronate. Despite the absence of added electrolyte, these solutions yielded well‐behaved Zimm plots. Increasing ionic strength and changing pH decreased radii of gyration and increased diffusion constants. Except for what appeared to be slow hydrolysis at either extreme of pH, molecular weights remained constant under all pH and ionic strength conditions. Under all solvent conditions investigated, diffusion coefficients increased with decreasing hyaluronate concentration. Unsonicated, lightly centrifuged solutions without added electrolyte were polydisperse, and their light scattering intensity was dominated by what appeared to be stable hyaluronate aggregates. The results are interpreted in terms of the polyelectrolyte properties of hyaluronate and its tendency to form stable entanglements, especially at low ionic strength. Previous light scattering studies in the literature on hyaluronate have shown widely varying results. The present article briefly reviews this literature and attempts to explain the variation among the previous results, emphasizing the Kuhn statistical segment length as an indicator of whether results are influenced by polydispersity or contaminants causing hyaluronate aggregation.
Fourier transform infrared spectroscopy for the characterization of a model peptide–DNA interaction
Authors: Dev S. B. , Walters Lee 
Published: December 2004

AbstractTo better understand the structural basis of protein–DNA interactions, the conformational changes that accompany these interactions need to be described. In order to develop a methodological approach to this problem, Fourier transform infrared spectroscopy (FTIR) with derivative resolution enhancement has been used to identify conformational changes that occur when a 29‐residue synthetic peptide binds nonspecifically to heterogenous cellular DNA in aqueous solution. The peptide sequence was chosen de novo, in order to rationally design a peptide model that would allow the relationship between DNA binding and the stability of protein secondary structure to be studied. Peptide at a concentration of 100–200 μM produces 50% saturation of heterogenous phage DNA sequences as well as of short synthetic oligonucleotides. FTIR spectra reveal significant changes in peptide and DNA upon binding. Second‐derivative spectra resolve the amide I band of native peptide into components located at 1627 (β‐strand), 1658 (α‐helix), and 1681 (turn or β‐strand) cm−1, with a distinct shoulder at 1647 cm−1 (disordered structure). Assignment of the 1681 cm−1 vibration to a turn conformation is supported by uv CD studies, which indicate significant amounts of turn structure in unbound peptide. Ultraviolet CD also confirms the existence of disordered and β‐strand regions in the free peptide. Upon interacting with DNA the band at 1681 cm−1 (turn) is no longer seen; a new band appears at 1675 cm−1; the 1627 cm−1 band (β‐strand) is considerably reduced in intensity; the position of the α‐helical (1658 cm−1) component remains unchanged; the shoulder at 1647 cm−1 (disorder) disappears. The new vibration at 1675 cm−1 is characteristic of β‐strand structures. The asymmetric stretch (vAS) of the DNA phosphates shifts from 1223 (unbound) to 1229 cm−1 (bound); the relative intensities of νAS and the PO symmetric stretch (vs) are altered upon peptide binding. The data is consistent with the following conclusions: (a)DNA binding changes the secondary structure of the peptide, (b) disordered region(s) are only observed in free peptide, i.e., DNA binding stabilizes and increases order in the peptide secondary structure, (c) turn(s) change into β‐strand and/or α‐helical conformations(s) when peptide binds to DNA, (d) a β‐strand conformation that is characterized bya 1627 cm−1 vibration is present in free and bound peptide, (e) there is a particular β‐strand vibration/conformation that is only present in the bound peptide, (f) an α‐helical region exists in both free and bound peptide, (g) DNA remains in a B‐family conformation upon peptide binding, and (h) DNA phosphates participate in peptide binding and/or subtle changes occur in the DNA conformation upon complex formation.
Range of the influence of the carbohydrate moiety on the conformation of the poly(amino acid) backbone in glycosylated mucins
Authors: Tanpipat Noppawan , Mattice Wayne L. 
Published: December 2004

AbstractThe influence of glycosylation on the conformational properties of porcine submaxillary gland mucin has been investigated using rotational isomeric state theory. The specific objective was to determine the conditions under which the polypeptide has the relatively large mean square unperturbed radius of gyration 〈s2〉0, demanded by the measurements of Shogren et al., while retaining the overall architecture of a random coil. The mean square dimensions were monitored as the dimensionless characteristic ratio defined as C = 〈s2〉0/npl, and the overall architecture was monitored by another dimensionless ratio 〈r2〉0/〈s2〉0, where 〈r2〉0 denotes the mean square unperturbed end‐to‐end distance. The computed values of C cannot reproduce the measured values if the conformational influence of glycosylation is restricted to each Ser or Thr, or if this influence extends only as far as their nearest neighbors. Values of C compatible with experiment can be obtained if the influence extends to next nearest neighbors. The behavior of the computed values of 〈r2〉0/〈s2〉0 permits an assignment of 7 ± 1 as the likely upper limit to the number of consecutive amino acid residues that experience alterations in ϕ and ψ if the sequence contains a glycosylated Ser or Thr.
Electrostatic forces at helix–coil boundaries in DNA
Authors: Blake R. D. , Delcourt Scott G. 
Published: December 2004

AbstractThe Tm of internal loop‐forming (dA · dT)N domains in pBR322 DNA has been measured over a tenfold range of [Na+]. The slopes SN = dTm/d log[Na+] are linear and decrease in magnitude with decreasing loop size N, signaling a reduction in Na+ released during the transition of these domains to the coil state. Values of SN decrese linearly with increasing N−1 in accordance with the expectation of a simple model for the occurrence of a gradient of long‐range electrostatic forces at helix–coil boundaries, and extrapolate almost precisely to the value of S∞ observed for (dA · dT)∞. These results indicate (1) less counterion is released per phosphate residue from the finite loop than from the infinitesized loop, and (2) the difference in binding is constant for each boundary formed and independent of the size of the loop within the range examined: ∼ 350 base pair (bp) > N > 71 bp. The slope of the dependence of SN on N−1 indicates the region of higher charge density at the boundary extends at least 18 Å into the coil and probably 40–50 Å before dropping to a value characteristic of the unperturbed coil. The free energy for excess counterion binding at boundaries can be expressed by

When the loop entropy function in a statistical mechanical algorithm for the dissociation of DNA is weighted by this quantity, calculated Tm are seen to vary by only ±0.09°C from observed.
Assignment of the 13C‐nmr spectra of virgin and reactive‐site modified turkey ovomucoid third domain
Authors: Robertson A. D. , Rhyu G. I. , Westler W. M. , Markley J. L. 
Published: December 2004

AbstractThe virgin (reactive‐site Leu18‐Glu19 peptide bond intact) and modified (reactive‐site Leu18‐Glu19 peptide bond hydrolyzed) forms of turkey ovomucoid third domain (OMTKY3 and OMTKY3*, respectively) have been analyzed by proton‐detected 1H{13C} two‐dimensional single‐bond correlation (1H{13C}SBC) spectroscopy. Previous 1H‐nmr assignments of these proteins [A. D. Robertson, W. M. Westler, and J. L. Markley (1988) Biochemistry, 27, 2519–2529; G. I. Rhyu and J. L. Markley (1988) Biochemistry, 27, 2529–2539] have been extended to directly bonded 13C atoms. Assignments have been made to 52 of the 56 backbone 13Cα‐1H units and numerous side‐chain 13C‐1H groups in both OMTKY3 and OMTKY3*. The largest changes in the 13C chemical shift upon conversion of OMTKY3 to OMTKY3* occur at or near the reactive site, and tend toward values observed in small peptides. Moreover, the side‐chain prochiral methylene protons attached to the Cγ of Glu19 and Cδ of Arg21 show nonequivalent chemical shifts in OMTKY3 but more equivalent chemical shift in OMTKY3*. These results suggest that the reactive site region becomes less ordered upon hydrolysis of the Leu18‐Glu19 peptide bond. Comparison of 13Cα chemical shifts of OMTKY3 and bovine pancreatic trypsin inhibitor [D. Brühuiler and G. Wagner (1986) Biochemistry 25, 5839–5843; N. R. Nirmala and G. Wagner (1988) Journal of the American Chemical Society, 110, 7557–7558] with small peptide values [R. Richarz and K. Wüthrich (1978) Biopolymers, 17, 2133–2141] suggests that 13Cα chemical shifts of residues residing in helices are generally about 2 ppm downfield of resonances from nonhelical residues.
The elastic modulus of fibrin clots and fibrinogen gels: The effect of fibronectin and dithiothreitol
Authors: Procyk R. , King R. G. 
Published: December 2004

AbstractThe elastic modulus (G′) of factor XIIIa induced fibrinogen gels was found to be substantially lower than the G′ of fibrin gels that were formed by clotting fibrinogen with thrombin. The addition of fibronectin and/or the reducing reagent dithiothreitol (DTT) to the factor XIIIa coagulation mixture led to the formation of a weaker gel structure, while the rigidity of thrombin induced clots was not appreciably affected by the inclusion of the DTT but increased somewhat in the presence of fibronectin. The reasons for the differing clot rigidities are discussed in terms of biochemical mechanisms.
Computational analysis of the effects of site‐specific phosphate alkylation in the DNA oligomer {d‐[GGAATTCC]}2
Authors: Broido Michelle S. , Mezei Mihaly 
Published: December 2004

AbstractAlkylation of the sugar–phosphate backbone of DNA can result upon exposure to several potent carcinogens, inducing DNA misfunction. In order to assess the structural and energetic changes in DNA helices induced by such alkylation, we have performed AMBER‐based analyses on phosphotriester containing analogues of {d‐[GGAATTCC]}2. Fourteen analogues of the nonalkylated oligomer were examined, each bearing a single alkylation of known stereochemistry. Results indicate that although there is minimal effect on the aromatic bases, the presence of a phosphotriester disturbs the sugar–phosphate backbone in complex ways. For most analogues, total minimum energies are lower for the Sp‐alkylations than for the Rp‐alkylations which point directly into the major groove of the helix; however, different energetic contributions follow different, or no, trends in dependence on alkylation site and/or stereochemistry. Where data is available, experimental nmr results agree with the calculations reported here.
Free energy calculation on base specificity of drug – DNA interactions: Application to daunomycin and acridine intercalation into DNA
Authors: Cieplak Piotr , Rao Shashidhar N. , Grootenhuis Peter D. J. , Kollman Peter A. 
Published: December 2004

AbstractWe present the results of free energy perturbation/molecular dynamics studies on B‐DNA · daunomycin and B‐DNA · 9‐aminoacridine complexes as well as on B‐DNA itself in order to calculate the free energy differences between complexes having different base pair sequences. The results generally reproduce the trends observed experimentally, i.e., preferences of acridine and daunomycin to bind to a specific base sequence in the DNA. This is encouraging, given the simplicity of the molecular mechanical/dynamical model in which solvent is not explicitly included.
Energetics of intrachain salt‐linkage formation in collagen
Authors: Katz E. P. , David C. W. 
Published: December 2004

AbstractThe energy of formation of salt linkages between Arg or Lys with Asp or Glu in a polypeptide chain having the collagen fold have been estimated using the fully empirical energy minimization scheme AMBER. The polypeptide was considered both in an isolated and a hydrated triple helical state. The collagen fold associated with a one‐bonded triple helical conformation allows intrachain salt linkages having stabilization energies of 60–100 kcal when the reacting residues are separated by no more than two intervening residues. The amino end of one side chain always approaches the carboxyl end of the other side chain, and simultaneously approaches the carbonyl oxygen of the intervening backbone residue. The salt linkage conformation and the backbone conformation of the isolated collagen fold in vacuo are maintained when the molecules are in a hydrated triple helix. These results are compatible with a fold‐forming role for salt linkages, especially in proline poor regions, during collagen polypeptide synthesis, and with the persistence of intrachain salt linkages throughout molecular and fibril assembly.
Synthetic fragments and analogues of elastin. I. The synthesis
Authors: Guantieri V. , Grando S. , Pandolfo L. , Tamburro A. M. 
Published: December 2004

AbstractThe synthesis of some repetitive sequences of elastin and their simplified analogues, all comprising the structural unit Gly‐X‐Gly (X = Val, Leu, Ala), is described. In particular, the following peptides and polypeptides were synthesized and characterized: Boc‐Gly‐Val‐Gly‐Gly‐Leu‐OMe, Boc‐Gly‐Leu‐Gly‐Gly‐Val‐OMe, Boc‐(Gly‐Val‐Gly‐Gly‐Leu)2‐OMe, Boc‐(Gly‐Val‐Gly‐Gly‐Leu)3‐OMe, Boc‐Gly‐Val‐Gly‐Gly‐OEt, Boc‐Leu‐Gly‐Gly‐Leu‐OMe, Boc‐Val‐Gly‐Gly‐Val‐OMe, poly(Ala‐Gly‐Gly), poly(Val‐Gly‐Gly), and poly (Leu‐Gly‐Gly).In every case, the synthesis was accomplished by classical procedures in solution, by using the p‐nitrophenyl ester method for the polycondensation step, and the mixed anhydride or the azide methods for the coupling steps.
Synthetic fragments and analogues of elastin. II. Conformational studies
Authors: Tamburro A. M. , Guantieri V. , Pandolfo L. , Scopa A. 
Published: December 2004

AbstractConformational studies on synthetic repetitive sequences and analogues of elastin are described.CD and nmr measurements gave evidence of flexible β‐turns as the dominant structural feature whose stability was found to decrease by increasing the number of repetitive units. The sequences comprised the structural unit Gly‐X‐Gly (X = Val, Leu, Ala), with X‐Gly or Gly‐Gly located at the corners of the bend.Based on that, it is proposed that these regions of elastin, unlike the proline‐containing sequences, contribute to the elasticity of the protein through a classical mechanism in terms of the rotational isomeric state theory.
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
Authors: McCaskill J. S. 
Published: December 2004

AbstractA novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the sequence length N. The temperature dependence of the partition function gives information about melting behavior for the secondary structure. The pair binding probabilities, the computation of which depends on the partition function, are visually summarized in a “box matrix” display and this provides a useful tool for examining the full ensemble of probable alternative equilibrium structures. The calculation of this ensemble representation allows a proper application and assessment of the predictive power of the secondary structure method, and yields important information on alternatives and intermediates in addition to local information about base pair opening and slippage.The results are illustrated for representative tRNA, 5S RNA, and self‐replicating and self‐splicing RNA molecules, and allow a direct comparison with enzymatic structure probes. The effect of changes in the thermodynamic parameters on the equilibrium ensemble provides a further sensitivity check to the predictions.
Block‐units method for conformational calculations of large nucleic acid chains. II. The two‐hierarchical approach and its application to conformational arrangement of the unusual TψC loop of rabbit tRNAval
Authors: Vorobjev YU. N. 
Published: December 2004

AbstractThe two‐level hierarchical methodology is suggested for conformational calculations of large fragments of nucleic acids. The method of the first level is intended for performing a fast screening of the conformational phase space. The high‐level method may be used to refine structurally important conformations. The method of the first level is the block‐units method, which has been developed specially for these purposes (see part I). It has been shown that the block‐units method allows the satisfactory calculation of the structure parameters of the optimal conformations of polynucleotides. The results of the conformational rerrangement calculations of the TψC loop of the tRNAPhe after modification of its sequence are represented.
Viscoelastic and rheological properties of concentrated solutions of proteoglycan subunit and proteoglycan aggregate
Authors: Soby L. , Jamieson A. M. , Blackwell J. , Choi H. U. , Rosenberg L. C. 
Published: December 2004

AbstractThe oscillatory and steady shear rheological properties of concentrated solutions of proteoglycan subunit (PGS) and aggregate (PGA) from bovine articular cartilage have been studied using a Rheometrics fluids spectrometer. At comparable concentrations in the physiological range tan δ increases from 0.5 to 1.0 for PGA as the oscillation frequency (ω) increases from 10−1 to 102 rads / s, compared to a decrease from 40 to 5 for PGS. Thus PGA solutions exhibit predominantly elastic response whereas those of PGS exhibit primarily viscous behavior. PGA solutions show pronounced shear‐thinning behavior at all shear rates (γ) in the range 10−2 < γ (s−1) < 10 2, whereas PGS solutions exhibit predominantly Newtonian flow. For PGA, the small‐strain complex viscosity η* (ω) is substantially smaller than the steady‐flow viscosity η (γ) at comparable values of ω and γ. These observations indicate that the presence of proteoglycan aggregates leads to formation of a transient or weak‐gel network. Since aggregation leads to a large increase in molecular hydrodynamic volume and hence in the relaxation times for macromolecular rotation, it appears that role of aggregate formation is to shift the linear viscoelastic response from the terminal viscous flow into the plateau elastomeric regime of relaxational behavior. Normal or pathological changes that produce a decrease in aggregation will result in a loss of elastomeric behavior of the proteoglycan matrix.
Distinct gelation mechanism between linear and branched (1 → 3)‐β‐D‐glucans as revealed by high‐resolution solid‐state 13C NMR
Authors: Saitô Hazime , Yoshioka Yûko , Yokoi Motoko , Yamada Junko 
Published: December 2004

AbstractWe have recorded high‐resolution 13C‐NMR spectra of linear (curdlan) and branched (lentinan, HA‐β‐glucan and its polyol and aldehyde derivatives) (1 → 3)‐β‐D‐glucans in hydrate and gel states, in order to gain insight into their gelation mechanism. Network structure of curdlan turned out to be highly heterogeneous from its motional state, from liquid‐like, through intermediate, to solid‐like domains. They are studied by a variety of experiments, conventional high‐resolution NMR by broad‐band decoupling, high‐power decoupling with magic angle spinning (MAS), and cross‐polarization‐magic‐angle‐spinning (CP‐MAS). Nevertheless, we found that conformations of these distinct liquid‐like and solid‐like do‐ mains exhibit an identical single helix conformation with a small proportion of a triple helix form, supporting our previous view as to the gelation mechanism. In contrast, the network structure of branched (1 → 3)‐β‐D‐glucans in the gel state arises mainly from the triple helix conformation. This means that gelation of branched (1 → 3)‐β‐D‐glucan proceeds from partial association of the triple helical chains, previously proposed for gelation of a linear glucan. Furthermore, we found that conversion from the single chain to the single helix was not achieved readily by hydration of over 8h at 96% R. H. for branched glucan but the triple helix form is obtained when these samples are hydrated fully as in gel state.