bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topological aspects of conformational transformations in proteins
Authors: Chiavarini S. , De Santis P. , Morosetti S. , Palleschi A. 
Published: December 2004

AbstractThe topological aspects of the conformational transformations in proteins are investigated using a new peptide‐ribbon representation of the tertiary structure. The topological parameters evaluated on a set of 49 proteins show striking regularities that extend beyond the secondary structures actually present and are interpreted as a manifestation of the topological invariance of conformational transformations in globular proteins.
Buried surface area, conformational entropy, and protein stability
Authors: Rashin Alexander A. 
Published: December 2004

AbstractIn this paper, how to calculate the loss of conformational entropy owing to protein folding from data on protein stability, the disulfide bonding pattern and the buried surface area is suggested. The average values of the initiation constant and entropy loss per residue for the helix‐coil transition, calculated according to the suggested approach, are in a good agreement with available data. It is shown that the loss of conformational entropy for proteins and protein fragments, thus calculated, can be quite accurately approximated by three straight lines, each representing the loss of conformational entropy in a given range of molecular weights. The first line corresponds to the formation of α helices, the second to proteins with molecular weights below 10,000, and the third to proteins with molecular weights above this value. The standard error varied from 1.3 kcal/mol, for the first region, to between ∼3 and 5 kcal/mol for the third. Use of these approximating linear functions is proposed for the calculation of protein stabilities from x‐ray data. Such calculations, performed for more than 20 proteins and their fragments, have led to at least qualitative agreement between the calculated stabilities and available data for more than 90% of the cases. While quantitative predictions are at the limit of the method's accuracy, predictions of the probabilities of proteins or their fragments to be stable are expected to give a correct answer in ∼95% of the cases.
Large‐amplitude bending motions in phenylalanine transfer RNA
Authors: Tung Chang‐Shung , Harvey Stephen C. , McCammon J. Andrew 
Published: December 2004

AbstractConformational energy calculations on yeast tRNAPhe reveal several likely modes of intramolecular bending, including both hingelike motions (rotations about a discrete point) and distributed flexibility (deformations that bend a double‐helical segment along a smooth curve). By combining these modes of motion, the molecule can be bent from the L‐shaped crystallographic structure to two extremes. It can be straightened into a nearly linear conformation at an energy cost of about 50 kcal/mol, and it can be doubled over to a conformation where the anticodon and the amino acid acceptor terminus are separated by about 40 Å at an energy cost of less than 100 kcal/mol. A bending range of over 100° can be covered for 50 kcal/mol, and we estimate that this value could be cut in half with a minimization algorithm that produced optimum stereochemistry. These energies are comparable to those that would be associated with changes in solvation due to changes in surface area as the molecule bends, indicating that there are no major steric barriers to tRNA flexibility and that variations in solvent conditions and interactions with other molecules may produce large changes in the overall conformation of tRNA.
A high‐resolution 13C‐nmr study of collagenlike polypeptides and collagen fibrils in solid state studied by the cross‐polarization–magic angle‐spinning method. Manifestation of conformation‐dependent 13C chemical shifts and application to conformational characterization
Authors: Saitô Hazime , Tabeta Ryoko , Shoji Akira , Ozaki Takuo , Ando Isao , Miyata Teruo 
Published: December 2004

AbstractWe have recorded high‐resolution 13C‐nmr spectra of collagen fibrils in the solid state by the cross‐polarization–magic‐angle‐spinning(CP–MAS)method and analyzed the spectra with reference to those of collagenlike polypeptides. We used two kinds of model polypeptides to obtain reference 13C chemical shifts of major amino acid residues of collagen (Gly, Pro, Ala, and Hyp): the 31‐helical polypeptides [(Gly)nII, (Pro)nII, (Hyp)n, and (AlaGlyGly)nII], and the triple‐helical polypeptides [(ProGlyPro)n and (ProAlaGly)n]. Examination of the 13C chemical shifts of these polypeptides, together with our previous data, showed that the 13C chemical shifts of individual amino acid residues are the same, within experimental error (±0.5 ppm), among different polypeptides with different primary sequences, if the conformations are the same. We found that the 13C chemical shifts of Ala residues of the 31‐helical (AlaGlyGly)n and triple‐helical (ProAlaGly)n are significantly displaced, compared with those of the α‐helix, β‐sheet, and silk I form, and can be utilized as excellent probes to examine conformational features of collagen‐like polypeptides. Further, the 13C chemical shifts of Gly and Pro residues in the triple‐helical polypeptides are substantially displaced from those found in (Gly)nII and (Pro)nII of the 31‐helix, reflecting further conformational change from the 31‐helix to the supercoiled triple helix. In particular, the 13C chemical shifts of Gly C  O carbons of the triple‐helical polypeptides are substantially displaced upfield (4.1–5.1 ppm), with respect to those of the 31‐helical polypeptides. These displacements are interpreted by that Gly C  O of the former is not involved in NH …︁ O  C hydrogen bonds, while this carbon of the latter is linked by these kinds of hydrogen bonds.On the basis of these 13C chemical shifts, as reference data for the collagenlike structure, we were able to assign the 13C‐nmr peaks of Gly, Ala, Pro, and Hyp residues of collagen fibrils, which are in good agreement with the values expected from the model polypeptides mentioned above. We also discuss a plausible conformational change of collagen fibrils during denaturation.
Stress relaxation in fine fibrin films: Comparison of films prepared with thrombin and ancrod
Authors: Müller Michael F. , Ferry John D. 
Published: December 2004

AbstractMeasurements of stress relaxation in uniaxial extension have been made on fibrin film prepared from fine bovine fibrin clots (i.e., clots in which there is minimal lateral aggregation of protofibrils), both ligated and unligated, and polymerized with both thrombin and ancrod, plasticized with either aqueous buffer or glycerol. The stress 100 s after imposition of strain was approximately proportional to In λ, where λ is the stretch ratio. Ligated thrombin films showed comparatively little relaxation over a period of one day and almost complete recovery after release of stress. In unligated thrombin films, there was substantial relaxation in two stages, as previously observed for coarse films, and substantial irrecoverable deformation. The extent of relaxation and the proportion of strain that was irrecoverable increased with the magnitude of the strain. In ancrod films (unligated), there was much more relaxation (stress decaying by as much as a factor of 10) and much more irrecoverable deformation (about 70% of the initial deformation); these results did not depend on the magnitude of the strain. When an ancrod film was released after relaxation and submitted to a second stretch, the extent of the second relaxation was much less. These observations are discussed in relation to the structure of fine films and possible mechanisms for relaxation and irrecoverable deformation.
Conformational transitions and geometry differences between low‐energy conformers of N‐acetyl‐N′‐methyl alanineamide: An ab initio study at the 4‐21G level with gradient relaxed geometries
Authors: Schäfer Lothar , Klimkowski V. J. , Momany Frank A. , Chuman H. , Van Alsenoy C. 
Published: December 2004

AbstractEnergy pathways between the αR, β′, C, and β‐regions of the conformational energy surface of N‐acetyl‐N′‐methylalanyl amide were obtained by SCF ab initio calculations on the 4‐21G level, with gradient geometry optimization at each point. The calculations indicate that no barrier exists at this computational level between αR and β′. The variation of geometry (bond distances and bond angles) with conformation is analyzed in detail, and the most important geometrical parameters that should be treated as variables in both empirical energy calculations and in the fitting of polypeptide chains in proteins by x‐ray methods are identified. In addition to the ϕ,ψ correlation discussed previously for the helical state, a correlation of these dihedral angles in the β‐region is described.
Polyelectrolyte effects on site‐binding equilibria with application to the intercalation of drugs into DNA
Authors: Friedman Richard A. G. , Manning Gerald S. 
Published: December 2004

AbstractA theory of polyelectrolyte effects on site‐binding equilibria is generalized to multivalent ligands, multivalent supporting salt, intercalation, and multiple‐site exclusion. The theory, which contains no adjustable parameters, except the number of sites excluded by a bound ligand, gives the dependence of the equilibrium constant on the binding fraction and the salt concentration. The theory is compared with prior experimental data for the dissociation of poly(acrylic acid), the binding of magnesium to polyphosphate, and the binding of ethidium and actionomycin D to DNA. The theory predicts the binding fraction dependence of the dissociation constant of poly(acrylic acid) well. The theory predicts the binding fraction dependence of the association constant of the binding of Mg2+ to polyphosphate well, if either one or two phosphates are bound by a magnesium ion. We conclude that polyelectrolyte effects on drug‐DNA equilibria must be substantial. It follows that an incorrect estimate of the number of sites excluded by a bound drug molecule (because of its size or some other nonpolyelectrolyte effect) can be obtained from binding data if polyelectrolyte effects are ignored. The estimate is also within the context of, and subject to the validity of, the model used to describe the nonpolyelectrolyte contribution to binding. Our results suggest that, subject to these conditions, the anticooperativity of the binding of ethidium to DNA might be explained solely in terms of polyelectrolyte effects, and without reference to multiple‐site exclusion, if sequence‐specificity effects can be safely ignored. Our results also suggest that as few as two base pairs might be excluded by an actinomycin molecule. The theory gives fairly good agreement for the salt‐concentration dependence of the association constant of all of the systems studied, including the complex of the neutral drug actinomycin with DNA.
Magnetic circular dichroism of adenine, hypoxanthine, and guanosine 5′‐diphosphate to 180 nm
Authors: Sutherland John Clark , Griffin Kathleen 
Published: December 2004

AbstractThe magnetic circular dichroism (MCD) of adenine, hypoxanthine, and guanosine 5′‐diphosphate reveals that, for each species, the uv‐absorption band near 200 nm is composed of at least two electronic transitions. The theory of MCD shows that the dipoles of these transitions are not parallel to one another. The transitions are assigned within the framework of current theories of the electronic structure of the purines. Knowledge of the presence of more than one transition within an absorption envelope is important in interpreting the corresponding natural CD of DNA and RNA.
On the precipitation of proteins by polymers: The hemoglobin—polyethylene glycol system
Authors: Haire Robert N. , Tisel William A. , White James G. , Rosenberg Andreas 
Published: December 2004

AbstractThe addition of polyethylene glycol (PEG) of MW 6000 to solutions of oxy‐ and deoxyhemoglobins results in an increase in the thermodynamic activity of these proteins. This in turn results, when PEG concentration is high enough, in phase separation into two phases; a protein‐rich, PEG‐poor phase and a PEG‐rich, protein‐poor phase. With increasing PEG concentration, the protein‐rich amorphous phase becomes metastable and is converted into a well‐defined crystalline or polymer phase. The logarithm of protein solubility is a linear function of PEG content up to a protein concentration of 150 g/L because the expression for the activity coefficient can, up to this concentration range, be approximated by a logarithmic function. Curvature appears at higher protein concentrations. Activities obtained by extrapolation from linear portions of the function, showing an unchanged, well‐defined crystalline state, yield an activity coefficient for the saturated PEG‐free protein solution in agreement with the appropriate values obtained from hard‐sphere calculations of excluded volume [Ross, P. D. & Minton, A. P. (1977) J. Mol. Biol. 112, 437–452]. Solutions containing two hemoglobin species showed cocrystallization of the hemoglobins with a triple point where two crystal forms can be shown to coexist.
Role of proline …︁ proline interactions in the packing of collagenlike poly(tripeptide) triple helices
Authors: Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractConformational energy computations were carried out on the packing of two identical collagenlike poly(tripeptide) triple helices in order to determine the energetics of favorable packing arrangements as a function of composition and chain length. The triple helices considered were [CH3CO‐(Gly‐Pro‐Pro)nt‐NHCH3]3 and [CH3CO‐(Gly‐Pro‐Ala)nt‐NHCH3]3, with nt = 3, 4, and 5. The packing arrangements were characterized in terms of their intermolecular energies and orientation angles Ω0 of the axes of the two triple helices. For short triple helices (nt = 3 or 4), many low‐energy orientations, with a wide range of values of Ω0, can occur. When the triple helices are longer (nt = 5), the only low‐energy packing arrangements of two poly(Gly‐Pro‐Pro) triple helices are those with a nearly parallel orientation of the two helix axes, with Ω0 ≈ −10°. This result accounts for the observed parallel (rather than antiparallel) arrangement of collagen molecules in microfibril assembly and stands in contrast to the preferred antiparallel arrangement of a pair of α‐helices. Since the preference for a parallel arrangement of these collagenlike triple helices is less pronounced in the case of poly(Gly‐Pro‐Ala), it appears that this preference is a consequence of the frequent presence of imino acids in position Y of the Gly‐X‐Y repeating triplet. In poly(Gly‐Pro‐Ala), most of the low‐energy packing arrangements are parallel, but a few arrangements with low energies and high values of |Ω0| occur. These packing arrangements have a high energy, however, when Pro is substituted for Ala, and thus they are not accessible for collagen with natural amino (imino) acid sequences. The computations reported here account for some of the characteristic features of collagen packing in terms of the local interaction energies of a pair of triple helices.
Absorption and circular dichroism spectra of CuCl2 complexed with poly(S‐carboxymethyl‐L‐cysteine) and poly(S‐carboxyethyl‐L‐cysteine)
Authors: Maeda Hiroshi , Oka Kazuki , Ikeda Shoichi 
Published: December 2004

AbstractThe interaction of CuCl2 with poly(S‐carboxymethyl‐L‐cysteine) (poly[Cys(CH2COOH)]) and poly(S‐carboxyethyl‐L‐cysteine) (poly[Cys(C2H4COOH)]) were studied by absorption spectra and circular dichroism (CD). On mixing CuCl2 with polypeptide solutions, absorption bands appeared at 320–325 nm in both polypeptides, and at 255–260 nm in the case of poly[Cys(CH2COOH)]. A stable bound species was formed in the case of poly[Cys(CH2COOH)], since the apparent molar absorption coefficient of the bound species did not depend on the mixing ratio. From the absorption data, it was inferred that Cu2+ ions were complexed with the side chains, most probably with sulfur atoms and carboxyl groups. Induced optical activities were observed for the two polypeptides. The CD spectra of poly[Cys(CH2COOH)] + CuCl2 gave simpler aspects than those of poly[Cys(C2H4COOH)] + CuCl2.
Determination of NOE “silent” dipolar interactions between magnetically equivalent nuclei: Application to poly(dA) · poly(dT)
Authors: Behling Ronald W. , Kearns David R. 
Published: December 2004

AbstractThe ratio of the spin–spin relaxation rate, R2, to the selective spin–lattice relaxation rate, R, can be used to detect and determine the magnitude of dipolar interactions between magnetically equivalent unclei in macromolecules. We use this method to show that there is strong interaction between adjacent AH2 protons in poly(dA) · poly(dT). The largest possible AH2–AH2 distance that will account for the observed magnitude of the interaction is ∼3.5 Å, provided the AH2 protons are located close (within 0.6 Å) to the helix axis. Structures with shorter AH2–AH2 separations could account for the nmr data, but they are rejected because they would reduce the interbase separation to unacceptably small values. A comparison of rates measured at 360 and 500 MHz shows that the chemical‐shift anisotropy makes a negligible contribution to the observed relaxation rates.
Quasielastic laser light scattering and electron microscopy studies of the conformational transitions and condensation of poly(dA‐dT) · poly(dA‐dT)
Authors: Thomas T. J. , Bloomfield V. A. 
Published: December 2004

AbstractPoly(dA‐dT) · poly(dA‐dT) undergoes a reversible conformational transition in the presence of Co(NH3) or spermidine in low salt (10 mM NaCl + 1 mM Na cacodylate). This transition is similar, as judged by changes in the CD spectrum, to the B‐to‐X transition of the polymer provoked by alcohol and Cs+ [Vorlickova et al. (1983) J. Mol. Biol. 166, 85–92; (1982) Nucleic Acids Res. 10, 6969–6979] and by meso‐substituted porphyrin ligands [Carvlin et al. (1983) Nucleic Acids Res. 11, 6141–6154]. Under the salt conditions indicated, the CD transition begins with Co(NH3) at about 70 μM and is complete by 150 μM; with spermidine, it begins at about 300 μM and is complete by 600 μM. Total intensity light scattering shows a marked increase at trivalent cation concentrations somewhat below those at which the CD transition begins. Quasielastic laser light scattering (QLS) measurement of the translational diffusion coefficient, DT, shows that, in the presence of Co(NH3), the hydrodynamic radius, Rh, increases from 260 to 1450 Å over the concentration range of 25 to 200 μM. With spermidine, Rh is 550±50 Å up to 200 μM, then increases rapidly. Values of Rh in this range are generally found for toroidal or other compact condensed forms of DNA. Such forms—toroidal, spheroidal, and rodlike structures—are observed in electron micrographs of poly(dA‐dT) · poly(dA‐dT) when the trivalent cation concentration is in the transition range. Above that range, extensive aggregation of the polymer chains is seen. Taken together, these results suggest a sequenc of related secondary and tertiary structure changes as trivalent cations are added to a low‐salt solution of poly(dA‐dT) · poly(dA‐dT). At very low Co(NH3) or spermidine, condensation of the polymer takes place while it is still in the B‐form. Further additions of trivalent cation provoke a transition from B‐ to X‐form, finally resulting in extensively aggregated polymer. These results are different from those generally observed with native DNA, where condensation with polyamines or Co(NH3) in aqueous solution is not accompanied by secondary structural change. They are also different from those we have seen with poly(dG‐me5dC) · poly(dG‐me5dC), where condensation and the B–Z transition occur at the same ionic conditions. These distinctions are another entry in the growing catalog of sequence‐dependent structural effects that may be important in the regulation of the biological activity of DNA.
Molecular organization of glycophorin A: Implications for membrane interactions
Authors: Welsh E. J. , Thom D. , Morris E. R. , Rees D. A. 
Published: December 2004

AbstractPhysical studies and conformational analysis of human glycophorin A suggest a revised model for its molecular organization, self‐association, and interactions with the erythrocyte membrane. Intrinsic viscosity has been used to study, under more physiological conditions, the monomer–dimer equilibrium demonstrated previously by polyacrylamide–SDS gel electrophoresis. The results show that the equilibrium persists in the absence of detergent and support earlier indications that the dimer is probably the physiologically relevant form and that it is promoted by salt, inhibited by conventional denaturants, and abolished by carboxymethylation.Combined application of CD, fitted to the poly‐(L‐lysine) model spectra of Greenfield and Fasman, and conformational prediction, by the statistical method of Chou and Fasman and the stereochemical approach of Lim, suggests five helical sequences in glycophorin A: Arg‐39 to Tyr‐52 (A); Gln‐63 to Glu‐70 (B); Glu‐72 to Leu‐89 (C); Ile‐95 to Lys‐101 (D); and Leu‐118 to Asn‐125 (E). Sequence A occurs only at low pH and may be stabilized by favorable noncovalent interactions of O‐linked tetrasaccharide side chains. The other four helices all occur in the dimeric form of glycophorin A at physiological pH and ionic strength. Sequence D is destroyed by trypsin, and is also lost on conversion to the monomeric form of the glycoprotein at low ionic strength. Sequence E is denatured by 6M guanidine hydrochloride/4M urea. Sequences B and C, which are separated by a single proline residue, are stable under all these conditions.Dimerization of the major, hydrophobic helical sequence, (C) may be promoted and directed by an adjacent short sequence of intermolecular parallel β‐sheet (Leu‐90 to Tyr‐93). It is proposed that these two structures span the lipid bilayer in vivo, and that helices B and D lie, respectively, along the outer and inner surfaces of the membrane. Molecular organization in the N‐ and C‐terminal regions of the molecule is discussed in terms of evidence from the present work and from other recent investigations.
Sequence‐specific assignment of the backbone 1H‐ and 31P‐nmr lines in a short DNA duplex with homo‐ and heteronuclear correlated spectroscopy
Authors: Frey M. H. , Leupin W. , Sørensen O. W. , Denny W. A. , Ernst R. R. , Wüthrich K. 
Published: December 2004

AbstractWe report the assignment of the backbone 1H‐ and 31P‐nmr lines in the synthetic hexadeoxyribonucleotide pentaphosphate duplex d(GCATGC)2, using double quantum filtered 1H‐1H correlation spectroscopy, 1H observed 1H‐31P heteronuclear correlation spectroscopy, and 31P relayed 1H‐1H correlation spectroscopy. The strategy used enables one to make sequence‐specific resonance assignments without reference to a known or assumed conformation of the DNA fragment.
Rapid estimation of length distributions of microtubule preparations by quasi‐elastic light scattering
Authors: Hallett F. R. , Keates R. 
Published: December 2004

AbstractA new method for determining the length distribution of microtubule preparations, using quasi‐elastic light scattering (QELS) is described. The experimental electric field autocorrelation functions are analyzed using a closed‐form expression recently described by Hallett, Craig, and Nickel [(1985) Biopolymers 24, 947–960], which is incorporated into an exponential sampling procedure. The resulting length distributions are compared with those obtained for the same samples with electron microscopy (EM). If standard grid‐preparation procedures were used, the EM results yielded shorter length distributions than QELS. When grids were prepared at lower microtubule number densities, less grid washing was required. In these cases, excellent agreement between the EM and QELS techniques were achieved.