bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel and simple interpretation of the three‐dimensional structure of globular proteins based on quantum mechanical computations on small model molecules. II. The clusters of myoglobin
Authors: Peters David , Peters Jane 
Published: December 2004

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

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

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

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

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

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

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

AbstractFourier transform ir vibrational circular dichroism (VCD) spectra in the amide I′ region of poly(L‐lysine) in D2O solutions have confirmed the existence of three distinct conformational states and an unordered conformational state in this homopolypeptide. Characteristic VCD spectra are presented for the right‐handed α‐helix, the antiparallel β‐sheet, an extended helix conformation previously referred to as the so‐called “random coil,” and a completely unordered conformation characterized by the absence of any amide I′ VCD. VCD for the antiparallel β‐sheet in solution and the unordered chain conformation are presented for the first time. Each of the four different VCD spectra is unique in appearance and lends weight to the view that VCD has the potential to become a sensitive new probe of the secondary structure of proteins in solution.
Temperature‐correlated force and structure development in elastomeric polypeptides: The Ile1 analog of the polypentapeptide of elastin
Authors: Urry D. W. , Long M. M. , Harris R. D. , Prasad K. U. 
Published: December 2004

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

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

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

Abstract1H‐ and 31P‐nmr spectroscopy have been used to investigate the self‐association of M2(5′‐CMP) [M = Li+, Na+, K+, Rb+, or (CH3)4 N+; 5′‐CMP = cytidine 5′‐monophosphate], the self‐association of Li2(5′‐GMP) (5′‐GMP = guanosine 5′‐monophosphate), and the heteroassociation of 5′‐GMP and 5′‐CMP (1 : 1 mole ratio) in aqueous solution as a function of the nature of the monovalent cation. Proton spectral differences for the different 5′‐CMP salts exhibit a cation‐size dependence and have been ascribed to a change in the stacking geometry. An average stacking association constant of 0.63 ± 0.24M−1 at 1°C, consistent with the weak stacking interactions of the cytosine bases, was determined for the 5′‐CMP salts. Heteroassociation of 5′‐GMP and 5′‐CMP follows the reverse of the cation order for the formation of ordered aggregates of 5′‐GMP. Heteroassociation occurs in the presence of Li+, Na+, and Rb+ ions, but only self‐association occurs for the K+ nucleotides. Li2(5′‐GMP), which does not form ordered species, self‐associates to form disordered base stacks with a stacking constant of 1.63 ± 0.11M−1 at 1°C.
Synthesis, and conformational and biological study of 2‐D‐Ala,5‐des‐Met‐enkephalin hydrazide modified at the carboxylic end by poly‐N‐vinylimidazole
Authors: Vlasov G. , Krasnikova E. , Kozhevnikova N. , Illarionova N. , Denisov I. 
Published: December 2004

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

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

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

AbstractThe possible role of conformational constraints in the posttranslational hydroxylation of lysyl residues in collagen has been investigated by means of conformational energy computations for the N‐acetyl‐N′‐methylamides of the four tetrapeptides Ala‐Xxx‐Gly‐Ser and Gly‐Xxx‐Ala‐Gly, where Xxx = Lys or Ala. When hydration is taken into account, all four peptides are shown to exist as a mixture of conformations, but there is a strong preference for type II bends in the conformational ensembles of two Ala‐Xxx‐Gly‐Ser tetrapeptides and for type I bends in the conformational ensembles of the other two. The results agree with experimental evidence suggesting that a type II bend is an important conformation for Ac‐Ala‐Lys‐Gly‐Ser‐NHCH3, and they support an earlier suggestion that a β‐bend may play a role in the posttranslational hydroxylation of Lys residues in position Y of the Gly‐X‐Y triplet in collagen.