bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pair distribution functions in small systems: Implications for protein structure analysis
Authors: Edelman Jay 
Published: December 2004

AbstractA general formula is derived for the relation between the pair correlation function and the histogram of interparticle distances in small nonuniform systems. The formula is applied to random packings of spheres in a spherical container, which are generated by a Monte Carlo method. When measured properly, the resultant correlation functions are very similar to ones in bulk systems with the same volume fraction of particles. In contrast, the density is very nonuniform as a function of distance from the center of the container. The variation is an order of magnitude for the number density of particle centers, or several fold for the occupied volume fraction. It is described how these results can be used to analyze the forces that determine protein structure.
Fourier transform IR attenuated total reflectance study on the secondary structure of poly(γ ‐methyl L‐glutamate) surfaces treated with formic acid
Authors: Kugo Kohei , Okuno Masaki , Kitayama Koji , Kitaura Tatsuro , Nishino Jun , Ikuta Nobuo , Nishio Etsuo , Iwatsuki Makoto 
Published: December 2004

AbstractFourier transform ir attenuated total reflectance (FTIR ATR) spectra have been obtained to investigate the secondary structure of poly(γ ‐methyl L‐glutamate) (PMLG) surfaces untreated and treated with formic acid in a quantitative manner. Curve analysis including Fourier self‐deconvolution and the band fitting was applied to the ir spectra in the amide II region, revealing that the amide II band of those surfaces consists of five components. The essentially α‐helical form in the PMLG surface layer transformed readily into the β‐structure by the formic acid treatment, and the β‐structure content increased with increasing time of the treatment. The content of random coil structure of treated PMLG was generally very little and/or negligible. The depth profile obtained by considering the depth of ir beam penetration indicated that the β‐structure content also increased with approaching the outermost surface.
High osmotic stress behavior of hyaluronate and heparin
Authors: Peitzsch Robert M. , Reed Wayne F. 
Published: December 2004

AbstractUsing polyethylene glycol and dextran as osmotic stressing agents, the concentrations of hyaluronate and heparin were measured as a function of osmotic pressure II over the range of 0.03 to nearly 50 atmospheres. The experimental results were analyzed in terms of the Donnan osmotic pressure, the virial expansion, and Flory's first neighbor interaction parameter. In addition, II was looked at as a function of the reciprocal cube root of the concentration, which represents an average intermonomer spacing at high concentrations. The decay lengths in the so‐called hydration region were found to be around 2.6 Å and negligibly salt dependent. In the electrostatically dominated region the decay lengths were found to be dependent on the ionic strength, but not simply so. The osmotic compressibilities were also calculated, and were compared to compressibility data of corneal stroma and articular cartilage. These latter compressibilities were close to those for the pure hyaluronate and heparin, strengthening the evidence that glycosaminoglycans (GAGs) are largely responsible for connective tissue compressibility. Higher compressibilities for previously reported GAG data is thought to be related to the protein content of those samples.
Stereochemical studies on nucleic acid analogues. I. Conformations of α‐nucleosides and α‐nucleotides: Interconversion of sugar puckers via O4′‐exo
Authors: Latha Y. Swarna , Yathindra N. 
Published: December 2004

AbstractThe preferred conformations of ribo and deoxyribo α‐nucleosides and β‐nucleotides, the stereoisomers of the naturally occurring β‐isomers, are worked out by minimizing the conformational energy as a function of all the major parameters including the sugar ring conformations along the pseudorotation path. The results of the studies bring out certain distinct conformational features that are at variance with their β counterparts. The range of glycosyl conformations are found to be not only quite restricted here but favor predominantly the anti conformation. The syn glycosyl conformation for the entire region of α values are found to be energetically less favorable, with the barrier to anti ⇆ syn interconversion being higher especially in α‐ribonucleosides. The energetically preferred range of pseudorotation phase angles (P) is also considerably restricted and P values corresponding to the C1′‐exo range of sugars are highly unfavorable for α‐nucleosides, in sharp contrast to the broad range of sugar ring conformations favored by β‐isomers. While both trans ≃ 180° and skew ≃ 270° conformations around the C3′‐O3′ (ϕ′) bond are favored for β‐3′‐nucleotides with deoxyribose sugars, ribose sugars seem to favor only the skew values of ϕ′. Most interestingly and in sharp contrast to β‐stereoisomers, an energy barrier is encountered at P values corresponding to O4′‐endo sugars. This suggests that the possible sugar pucker interconversion between C2′‐endo/C3′‐exo and C3′‐endo/C2′‐exo in a‐anomers could take place only through the O4′‐exo region. Likewise the possible path of anti ⇆ syn interconversion in α‐nucleosides is not via high anti, in sharp contrast to α‐nucleosides. These observations should be borne in mind while assigning the sugar ring conformers in α‐nucleosides and those containing them from nmr investigations. Comparison of the results with α‐anomers seem to suggest on the whole a lack of conformational variability or the restricted nature of α‐stereoisomers. This could be one of the reasons for its nonselection in the naturally occurring nucleic acids.
Normal mode refinement: Crystallographic refinement of protein dynamic structure applied to human lysozyme
Authors: Kidera Akinori , Inaka Koji , Matsushima Masaaki , Gō Nobuhiro 
Published: December 2004

AbstractA new method of dynamic structure refinement of protein x‐ray crystallography, normal mode refinement; is developed. In this method the Debye–Waller factor is expanded in terms of the low‐frequency normal modes and external normal modes, whose amplitudes and couplings are optimized in the process of crystallographic refinement. By this method, internal and external contributions to the atomic fluctuations can be separated. Also, anisotropic atomic fluctuations and their interatomic correlations can be determined experimentally even with a relatively small number of adjustable parameters. The method is applied to the analysis of experimental data of human lysozyme to reveal its dynamic structure.
Identification of structured peptide segments in folding proteins
Authors: Pincus Matthew R. 
Published: December 2004

AbstractPrediction of the structures of long polypeptides and small proteins has been carried out using conformational energy calculations. These calculations can be applied to large proteins if structured regions of their sequences can be identified. Three different approaches to identifying such sequences are presented. First, sequences of five or more contiguous hydrophobic residues tend to nucleate α‐helices. Second, peptide sequences from parent proteins that have the same biological activities as the parent proteins are highly structured. Third, structured synthetic peptide segments from proteins inhibit the folding of the parent proteins by competing with the corresponding segment of the protein chain for associating with complementary regions. Examples of each of these approaches are presented.
Perturbation of peptide conformations induced in anisotropic environments
Authors: Büttner K. , Blondelle S. E. , Ostresh J. M. , Houghten R. A. 
Published: December 2004

AbstractReversed‐phase high performance liquid chromatography (RP HPLC) has been found to be a convenient and powerful tool for the study of the secondary structure of peptides. Here, the ability of proline to perturb the secondary structures of peptides induced at aqueous‐lipid interfaces and the induced conformation of polyproline peptides were investigated by means of RP HPLC. For these studies, four different complete sets of substitution analogues of model peptides expected to have specific induced conformations were used. In the first two studies, a single lysine was “walked” through two 18‐residue polyproline sequences (one N‐acetylated, the other not). In the remaining two studies, a proline was “walked” through two different sequences that had been found earlier to be induced into an α‐helical conformation during RP HPLC (an 18‐residue polyalanine sequence and the amphipathic 14‐residue sequence Ac‐LLKLLKKLLKKLKK‐NH2). Sixty‐eight individual analogues were synthesized for this study and the effect of the respective substitutions on retention times was determined. The results are consistent with the concept that, upon interaction with the C‐18 of the stationary phase during RP HPLC, polyproline is induced into a type II helical conformation, polyalanine into an α‐helical conformation, and Ac‐LLKLLKKLLKKLKK‐NH2 into an amphipathic α‐helical array. In an extension of this study, the antimicrobial activities of Ac‐LLKLLKKLLKKLKK‐NH2 and its 18 proline substitution analogues were found to be inversely correlated with their RP HPLC retention times.
Protein: Nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes
Authors: Ilich P. , Prendergast F. G. 
Published: December 2004

AbstractLow singlet transition energies and line strengths were calculated for the cytosine : in‐dole : guanine complex by the INDO/1S‐CI method. The chromophores were arranged in three sets of 270 intercalating geometries. Calculations were executed in the supermolecule model with single excited configurations. Errors due to basis set extension and incomplete configuration representation were assessed, for all chromophore pairs, by full BSSE correction calculations and inclusion of double‐excited configurations. The intercalation‐induced perturbations of the principal transitions are characterized by but not limited to (a) a decrease in strength of {π*,π} transitions, (b) increase in strength in {π*,n} transitions, (c) splitting of {π*,π} transitions into components of unequal strength, and (d) energy and strength dependence in mixed transitions on rise and shift movements of the nucleic acid bases. These predictions are in accord with absorption, fluorescence emission, and scattering, and resonance Raman spectroscopic data on oligonucleotides and analogous aromatic complexes. The calculations suggest that major differences in intercalating coordinations are discernible in the near‐uv spectroscopic domain of proteins and nucleic acids.
Electrostatic forces in two lysozymes: Calculations and measurements of histidine pKa values
Authors: Takahashi Takuya , Nakamura Haruki , Wada Akiyoshi 
Published: December 2004

AbstractIn order to examine the electrostatic forces in globular proteins, pKa values and their ionic strength dependence of His residues of hen egg white lysozyme (HEWL) and human ly−sozyme (HUML) were measured, and they were compared with those calculated numerically.pKa values of His 30 residues in HEWL, HUML, and short oligopeptides were determined from chemical shift changes of His side chains by 1H−nmr measurements. The associated changes in pKa values in HEWL and HUML were calculated by solving the Poisson‐Boltzmann equations numerically for macroscopic dielectric models. The calculated pKa changes and their ionic strength dependence agreed fairly well with the observed ones.The contribution from each residue and each α‐helix dipole to the pKa values and their ionic strength dependence was analyzed using Green's reciprocity theorem. The results indicate that (1) the pKa of His residues are largely affected by surrounding ionized and polar groups; (2) the ionic strength dependence of the pKa values is determined by the overall charge distributions and their accessibilities to solvent; and (3) α‐helix dipoles make a significant contribution to the pKa when the His residue is close to the helix terminus and not fully exposed to the solvent.
Morphiceptin and β‐casomorphin‐5 analogues containing a reduced peptide bond: Selective μ‐receptor agonists and a novel μ antagonist, H‐Tyr‐Proψ(CH2‐NH)Phe‐Pro‐Gly‐OH
Authors: Delaet Nancy G. J. , Verheyden Patricia M. F. , Tourwe Dirk , Van Binst G. , Davis Peg , Burks Thomas F. 
Published: December 2004

AbstractIn order to prevent enzymatic degradation of β‐casomorphin‐5 (1) and morphiceptin, reduced peptide bonds were incorporated at the 2–3 and 3–4 bonds, respectively. The analogues were synthesized by a combination of solid phase methodology and reductive alkylation of resin‐bound peptide amines with Boc‐amino acid aldehydes (Boc: tert‐butyloxycarbonyl) in the presence of NaBH3CN. During reversed phase high pressure liquid chromatography purification, peak shape distortions could be observed. Epimerization was excluded, based on gas chromatography/mass spectroscopy analysis, which indicated acceptable levels of racemization (<3%) in the crude product. Instead, the phenomena could be attributed to slow cis/ trans isomerizations originating from the Xxx‐Pro bonds in the sequence. The presence of different conformational isomers was also established by 1H‐nmr spectroscopy in DMSO‐d6. All analogues showed high stability in blood plasma, enhanced binding affinity for the μ receptor, and very low binding to the δ receptor. While the Phe3Ψ(CH2‐N) Pro4 analogues (3) and (5) displayed agonist activity, the Pro2Ψ(CH2‐NH) Phe3 modified analogue (2) showed antagonist activity comparable to D‐Phe‐Cys‐Tyr‐D ‐Trp‐Arg‐Thr‐Pen‐Thr‐NH2.
A molecular dynamics study of conformational changes and hydration of left‐handed d (CGCGCGCGCGCG)2 in a nonsalt solution
Authors: Eriksson Mats A. L , Laaksonen Aatto 
Published: December 2004

AbstractTwelve dinucleotides (one complete turn) of left‐handed, flexible, double‐helix poly(dG‐ dC) Z‐DNA have been simulated in aqueous solution with K+ counterions for 70 ps. Most of the d(GpC) phosphates have rotated in accordance with a ZI → ZII transition. The ZII conformation was probably partly stabilized by counterions, which coordinate one of the anionic oxygens and the guanine‐N7 of the next (5′ → 3′ direction) base. The presence of base‐coordinating ions close to the helical axis rotated and pulled about half of the d (CpG) phosphates further into the groove. These ions also gave rise to rather large deviations from the crystal structure (ZI) with their tendency of pulling the bases closer toward the helical axis. A flipping of the orientation about the glycosyl bond from the +sc to the −sc region was observed for one guanosine, also leading to deviations from the crystal structure. Many bridges containing one or two water molecules were found, with a dominance for the latter. They essentially formed a network of intra‐ and interstrand bridges between anionic and esterified phosphate oxygens. A “spine” of water molecules could be distinguished as a dark zig‐zag pattern in the water density map. The lifetime of a bridge containing one water was about twice as long as that of a two‐water bridge and it lasted 5–15 times longer than a hydrogen bond in water. The lifetimes were also calculated for a selection of bridge types, in order of decreasing stability: O1P/O2P…︁ W…︁O′4 ≫ O1P/O2P…︁ W…︁ guanine‐N2 > O1P/O2P…︁ W…︁O1P/O2P. The reorientational motion of water molecules in the first hydration shell around selected groups was slowed down considerably compared to bulk water and the decreasing order of correlation times was guanine‐N2 > O′4 > O′3/ O′5 > O1P/O2P. © 1992 John Wiley & Sons, Inc.
Differential hydration of homopurine sequences relative to alternating purine/pyrimidine sequences
Authors: Rentzeperis Dionisios , Kupke Donald W. , Marky Luis A. 
Published: December 2004

AbstractThe minor groove ligand distamycin A has been used to probe the relative hydration of the minor groove of eight synthetic polynucleotides of known sequence and composition. A combination of densimetric, calorimetric, and temperature‐dependent spectroscopic techniques have been used to obtain complete thermodynamic profiles (ΔG°, ΔH°, ΔS°, and ΔV°) for the association of distamycin A to all polymer duplexes. In 10 m M phosphate buffer, pH 7, binding of the drug to each of the polymeric duplexes resulted in characteristic negative changes in both the volume and enthalpy. Although the binding constants were found to be identical for pairs of isomer polynucleotides having identical compositions but different sequences, the values of ΔH°, ΔS°, and ΔV° of each such pair were remarkably different. The entropy changes were found to roughly parallel the volume changes; no such trend was seen between ΔH° and ΔV°.The data support the hypothesis that the volume changes observed for these systems reflect the coulombic‐hydration contribution to the entropy. The heteropolymer duplexes generated much larger exothermic contributions, less favorable entropies and larger volume contractions than did the corresponding homopolymer duplexes of identical composition, and strongly suggest that polynucleotides with homopurine sequences are more hydrated than polynucleotides with alternating purine‐pyrimidine sequences. In addition, it was found that duplexes containing guanine sharply reduced the affinity for the drug, also lowering the exothermicity but raising the entropy. This may be explained by the presence of an amino group in the minor groove that prevents hydrogen bonding. Substitution of the guanine with inosine reversed this trend in the thermodynamic properties. Furthermore, substitution of poly(dA) for poly(rA) in a duplex produced a similar reduction in the affinity, while raising the exothermic contribution and greatly reducing the favorable entropy effect in agreement with an apparent increase in the hydration state. © 1992 John Wiley & Sons, Inc.
DNA flexibility as a function of allomorphic conformation and of base sequence
Authors: Poncin Marc , Piazzola Daniel , Lavery Richard 
Published: December 2004

AbstractSystematic theoretical modeling of symmetric DNA oligomers, carried out earlier for the B conformation, is now extended to A‐DNA. In contrast to the previous results, it is found that A‐DNA shows no multiplicity of low‐energy substate conformations. The possibilities of the Jumna algorithm are subsequently applied to studying deformations of the oligomers. Controlled winding and stretching deformations are used to study how the two allomorphs and different base sequences absorb such external stress. The results help explain the internal mechanics of the DNA double helix and the extent to which fine structure influences this behavior. The results point to some differences between the A and B double helices, but also to many similarities. Sequence effects on flexibility are relatively limited compared to their impact on optimal energy conformations. It is also shown that the conformational substates detected for B‐DNA oligomers are preserved under deformation, but have little influence on its energetics. © 1992 John Wiley & Sons, Inc.
IR (vibrational) CD of peptide β‐turns: A theoretical and experimental study of cyclo‐(‐Gly‐Pro‐Gly‐D‐Ala‐Pro‐)
Authors: Wyssbrod Herman R. , Diem Max 
Published: December 2004

AbstractIR vibrational CD (VCD) has been observed for the cyclic pentapeptide cyclo‐(‐Gly‐Pro‐Gly‐D ‐Ala‐Pro‐) in solution in CDBr3. The observed VCD spectra do not resemble the VCD features of any of the previously reported peptide secondary structures, such as α‐helical, “random coil,” or sheet structures, and might be due to the β‐turn contained in this molecule. To shed light onto the origin of the observed spectra, VCD intensity calculations, based on the solution and solid‐state structures of cyclo‐(‐Gly‐Pro‐Gly‐D‐Ala‐Pro‐), have been carried out. In addition, calculated VCD data for pure β‐turns are discussed. © 1992 John Wiley & Sons, Inc.
Analyzing the normal mode dynamics of macromolecules by the component synthesis method
Authors: Hao Ming‐Hong , Harvey Stephen C. 
Published: December 2004

AbstractThis paper presents a general method for studying the harmonic dynamics of large biomolecules and molecular complexes. The performance and accuracy of the method applied to a number of molecules are also reported. The basic approach of the method is to divide a macromolecule into a number of smaller components. The local normal modes of the components are first calculated by treating individual components and the interactions between nearest neighboring components. The physical displacements of all atoms are then represented in the local normal mode space, in which a selected range of high‐frequency local modes is neglected. The equation of motion of the molecule in the local normal mode space will then have a smaller dimension, and consequently the normal modes of the whole structure, particularly for large molecules, can be solved much more easily. The normal modes of two polypeptides–(Ala)6 and (Ala)12−and a double‐helical DNA– d(ATATA) · d(TATAT)–are analyzed with this method. Reductions on the dimensions of harmonic dynamic equations for these molecules have been made, with the fraction of the deleted high‐frequency modes ranging from ½ to ⅚. The calculated low‐frequency normal modes are found to be very accurate as compared to the exact solutions by standard procedure. The major advantage of the present approach on macromolecule harmonic dynamics is that the reduction on the dimensionality of the eigenvalue problems can be varied according to the size of molecules, so the method can be easily applied to large macromolecules with controlled accuracy. © 1992 John Wiley & Sons, Inc.
Conformation dependence of the SH and CS stretch frequencies of the cysteine residue
Authors: Qian Weili , Krimm Samuel 
Published: December 2004

AbstractIn order to relate the observed SH and CS stretch frequencies of the cysteine residue in proteins more closely to its conformation, we have done normal mode calculations on a model for this structure, viz., (CCONH)(CNHCO)CHCH2SH. A range of ✗1 and ✗2 were studied, combined with the ϕ,Ψ of the α‐helix, β‐sheet, glutathione, and extended‐helix conformations. The force field was a combination of a scaled ab initio force field of the ‐CH2SH group, obtained from ethanethiol and tested on 1‐propanethiol and 3‐thiol‐N‐methylpropionamide, and our empirical force field for the peptide group. The results provide more detailed structure–spectra correlations than are possible from experimental studies of model compounds. © 1992 John Wiley & Sons, Inc.
Amino acid side‐chain populations in aqueous and saline solution: Bis‐penicillamine enkephalin
Authors: Smith Paul E. , Pettitt B. Montgomery 
Published: December 2004

AbstractThe potentials of mean force (pmfs) for rotation around the X1 aromatic side‐chain dihedrals of the zwitterionic bis‐penicillamine enkephalin pentapeptide have been determined in both aqueous and saline solution. These side chains are known to be associated with the pharmacophore and their conformational populations are thought to be critical for activity. It is found that the association between chloride ions and the peptide in saline solution simulations has profound effects on the relative energies of the g−, g+, and t conformations, and also the barriers between them. Using the pmfs we have also calculated the respective Boltzmann‐weighted 3Jαβ vicinal coupling constants. The agreement between the calculated and experimentally determined coupling constants is poor for the pmf in pure water, but substantially improved for the pmf determined in saline solution. Reasons for these differences appear to be related to the experimental conditions. © 1992 John Wiley & Sons, Inc.