bluuebunny/crossref_metadata_2025_split huggingface dataset:
A synthetic model of collagen: An experimental investigation of the triple‐helix stability
Authors: Germann H.‐P. , Heidemann E. 
Published: December 2004

AbstractVariations I–XVIII of a trimerlike cross‐linked collagen model peptide were synthesized and used to investigate the cooperation of different neighboring Gly‐X‐Y tripeptides. The carboxy‐terminal decapentapeptide of the tripe‐helical part of collagen type I was chosen as the starting point of sequentially modified elongations. The transition temperatures determined by CD measurements show that the incorporation of the imino acid free tripeptides Gly‐Ala‐Ala and Gly‐Ile‐Ala results in a weakening of the triple‐helical structure. It is demonstrated that the desired thermal stability of the collagen triple helix requires the “clustered” arrangement of helix‐promoting tripeptides, especially of Gly‐Pro‐Hyp.
Effect of discrete distribution of ions on B‐ and Z‐DNA: A theoretical investigation
Authors: Devarajan Sundaram , Pattabiraman Nagarajan , Shafer Richard H. 
Published: December 2004

AbstractUsing an iterative approach, we have placed monovalent (“solvated”) and divalent (both solvated and “unsolvated”) ions around a 20 base pair sequence, (dC‐dG)10, in standard B and ZI conformations. The molecule with its attendant ions in the various conformations is subjected to to energy minimization using the program AMBER. In the presence of solvated cations (both monovalent as well as divalent) the B form is more stable than the Z form. However, direct binding with the unsolvated divalent cations makes the Z form more stable. Groove‐binding provides some insight into the facility with which the B to Z transition occurs with higher charged cations. In the presence of unsolvated divalent cations, the Z form binds more charges at the groove through more ligands, compared to the B form. The orientation around the CpG phosphates in the minor groove of the Z form is found ideal for ion binding. Detailed molecular models for the ion binding have been developed. In general, phosphate groups dominate the ion binding. Large perturbations are seen mostly in the angles that control the phosphate orientation.
Two‐Dimensional NMR studies of [Pro‐10] atrial natriuretic factor [7‐23]
Authors: Gampe Robert T. , Connolly Peter J. , Rockway Todd , Fesik Stephen W. 
Published: December 2004

AbstractThe conformational properties of an analog of atrial naturiuretic factor, [Pro‐10] ANF(7‐23), were examined in H2O, H2O/DMSO‐d6 (2/1), and DMSO‐d6 using two‐dimensional nmr techniques. The sequence differs from the native peptide by the absence of the exocyclic N‐ and C‐terminal residues, and the substitution of a proline for a glycine at position 10—a modification expected to reduce the conformational flexibility of this analog. The backbone proton nmr resonances were assigned from two‐dimensional correlated spectroscopy (2D‐COSY), relayed COSY, and 2D nuclear Overhàuser enhancement (NOE) experiments, and the solution conformation was evaluated from vicinal spin–spin coupling constants and NOE data. Despite the substitution of a proline in the sequence, [Pro‐10] ANF(7‐23) exhibits a considerable amount of flexibility in all of the solvents employed.
The combined use of NMR, distance geometry, and restrained molecular dynamics for the conformational study of a cyclic somatostatin analogue
Authors: Pepermans H. , Tourwé D. , van Binst G. , Boelens R. , Scheek R. M. , van Gunsteren W. F. , Kaptein R. 
Published: December 2004

AbstractA cyclic peptide analogue of somatostatin, including the o‐aminomethylphenylacetic acid spacer, was studied by the combined use of two‐dimensional nmr spectroscopy, distance geometry, and restrained molecular dynamics. Analysis of distances determined from nuclear Overhauser effect (NOE) buildup rates revealed that these were inconsistent with a unique backbone conformation near the spacer. Assuming that the conformational heterogeneity is localized to the spacer, the NOE distances measured for the remaining part of the molecule were used to generate a large number of structures with the distance geometry algorithm, which were then refined by restrained energy minimization. Four classes of structures emerged, which together account for all observed NOEs. A representative structure of each class was further refined with the restrained molecular dynamics technique, and shown to be stable on a 20‐ps time scale. The flexibility of the spacer was examined by simulating interconversions induced by an appropriate restraining potential. As a result, the explanation for the lack of somatostatin activity of the analogue studied was reconsidered.
Molecular and crystal structures of three monothiated analogues of the terminally blocked ala‐aib‐ala sequence of peptaibol antibiotics
Authors: Bardi Renato , Piazzesi Anna Maria , Toniolo Claudio , Jensen Ole E. , Omar Rashad S. , Senning Alexander 
Published: December 2004

AbstractThe molecular and crystal structures of three monothiated analogues of the blocked L‐Ala‐Aib‐L‐Ala sequence of peptaibol antibiotics, t‐Boc‐L‐Ala‐Aib‐ψ(CSNH)‐L‐Ala‐OMe, Ac‐L‐Ala‐Aib‐ψ(CSNH)‐L‐Ala‐OMe, and Ac‐ψ(CSNH)‐L‐Ala‐Aib‐L‐Ala‐OMe, determined by x‐ray diffraction analyses, are reported. In all cases the peptide chain is folded with φ,ψ angles close to or slightly distorted from those expected for a type II β‐bend conformation. However, the 4 → 1 H‐bond distance falls within the accepted limits only for Ac‐L‐Ala‐Aib‐ψ(CSNH)‐L‐Ala‐OMe. The structures are compared with those already published for their two oxygenated analogues.
Mechanism of fibrin coagulation based on selective, cation‐driven, protofibril association
Authors: Marx Gerard 
Published: December 2004

AbstractThe cation sensitivity of linear and lateral assembly processes of thrombin‐ and reptilase‐activated fibrinogen was examined. Analytic ultracentrifugation shows that the linear assembly of fibrin oligomers (protofibrils) is neither cation dependent nor sensitive to chelating agents. Protofibrils generated with thrombin–hirudin gelate with either 1–2 mM Ca(II) or 15–100 μM Zn(II). By contrast, protofibril B, generated with reptilase–diisopropylfluorophosphonate, gelates only with Ca(II) but is insensitive to Zn(II). These results indicate that the release of fibrinopeptides A and B (FPA and FPB) expose two types of lateral binding sites that are sensitive to Ca(II) and Zn(II) respectively. Transmission electron (TEM) micrographs of negatively stained gels indicate that the linear packing of the monomers within the fibrin‐ and cation‐induced protofibrin fibers is essentially identical. Scanning electron (SEM) micrographs show that the Ca(II)‐induced protofibrin B gel is similar to fibrin. In all, it seems that branching and gelation derive from two types of cation‐sensitive, lateral associative processes. Based on these findings, a new paradigm for fibrin coagulation is proposed.
The crystal and molecular structure of the anticancer drug actinomycin D—some explanations for its unusual properties
Authors: Ginell Stephan , Lessinger Leslie , Berman Helen M. 
Published: December 2004

AbstractThe crystal structure of the antitumor antibiotic actinomycin D has been determined by the methods of x‐ray crystallography. There are three independent molecules in the asymmetric unit. Two of the molecules form a hydrogen‐bonded dimer. The peptides within all three molecules have very similar conformations. The greatest conformational variability in the drug molecules occurs in the torsion angles of the bonds connecting the phenoxazone ring to the peptide rings. The results of this analysis has allowed us to explain the unusual physical properties of ActD as well as to provide an explanation for the thermodynamics of its interactions with DNA.
Molecular dynamics of structural transitions and intercalation in DNA
Authors: Prabhakaran M. , Harvey Stephen C. 
Published: December 2004

AbstractThe large‐scale flexibility of DNA and the intercalation of actinomycin D have been studied by computer simulation using molecular dynamics. The stretching and unwinding of B and Z forms of DNA and intercalation in B‐DNA were examined through molecular dynamics simulations, and the energetics of transitions were calculated by the conformational energy minimization method. The principal results of this research are as follows: (1) A dynamic conformational pathway is presented for longitudinal stretching and unwinding of the double helix to open an intercalation site. (2) Large‐scale transitions are possible in both B and Z forms of DNA through a conformationally allowed kinetic pathway. (3) The stretching and untwisting of a 5′(CG)3′ step is energetically more favorable than for a GC step in B‐DNA. (4) The formation of an adjacent second cavity in B‐DNA requires larger energy than the formation of the first cavity, affirming the neighbor‐exclusion principle of intercalation. (5) Docking an intercalated actinomycin D in the stretched structure is shown to be geometrically and energetically feasible.
Cholesteric order in gels and films of regenerated cellulose
Authors: Ritcey Anna M. , Gray Derek G. 
Published: December 2004

AbstractCongo red bound to regenerated cellulose in highly swollen gel films formed by slow precipitation from LiCl/N,N‐dimethylacetamide solution exhibits induced optical activity. The induced CD band of the dye vanishes when these films are dried under uniaxial stress, indicating that the effect is structural in origin and not simply due to association of dye with chiral centers on the cellulose chain. Cellulose was also regenerated from cellulose acetate films, cast both from isotropic and cholesteric solution, by deacetylation in aqueous ammonia. Congo red bound to cellulose regenerated from cholesteric cellulose acetate exhibits an induced CD band similar to that obtained for films precipitated from LiCl/DMAC solution. The CD spectrum of Congo red in cellulose films regenerated from isotropic cellulose acetate is featureless. These observations indicate that cellulose adopts cholesteric order on slow precipitation from solution.
Study of furanose ring flexibility in polynucleotide chains using raman spectra analysis
Authors: Pechenaya V. I. , Serikov A. A. 
Published: December 2004

AbstractThe bands within the range of 800–850 cm−1 of Raman spectra of polynucleotides sensitive to the change in conformation of sugar–phosphate backbone are analyzed theoretically. The bands are interpreted as the appearance of a quasi‐local deoxyribose vibrational mode whose frequency is dependent on the ring puckering. The localization region of the vibrational mode is pointed out. The theory establishes a relationship between the observed spectral intensity and the population of deoxyribose conformational states described in the framework of the pseudorotation concept. The approach developed allowed one to describe the band shapes and their temperature behavior, and to determine the pseudorotation potential of deoxyribose in the helix B‐form of A · T containing polynucleotides. Using the analysis of Raman spectra of DNA fibers in water–ethanol mixture the deoxyribose flexibility during the B‐A transition is investigated in terms of the population of conformers and effective potential. It is shown that N‐ and S‐type deoxyribose conformers are populated in the DNA B‐form (those of the S‐type are preferable), whereas N‐type conformers are primarily populated in the DNA A‐form.
Structural and energetic parameters of Ca2+ binding to peptides and proteins
Authors: Hori Kenzi , Kushick Joseph N. , Weinstein Harel 
Published: December 2004

AbstractThe characteristics of Ca2+‐binding sites and of the structural reorganization induced by Ca2+‐binding in storage proteins and ion carriers are being studied as models for molecular mechanisms in Ca2+ channels and in Ca2+‐dependent modulatory proteins. A first step in the study was the development of energy parameters for Ca2+ compatible with those in the CHARMM package of computer simulation software. Such parameters were obtained from an analytical fit to the potential surface for [(Ca)(OCH2)4]2+ calculated with an ab initio molecular orbital method. The resulting parametrization was tested for the hexapeptide cyclo‐(Pro‐Gly)3, and a 75 residue long calcium binding protein from bovine intestine (ICaBP). The geometrical parameters calculated for the hexapeptide and its 2:1 complex with Ca2+ were in good agreement with experimental data from crystallography and nmr. Similarly, the structure of ICaBP optimized with CHARMM using the new Ca2+ parameters showed good agreement with the x‐ray structure both in the local structures of the calcium‐binding sites and in the overall shape of the protein.
The renin–angiotensin system: An example of the study of linear peptides by x‐ray crystallography
Authors: Precigoux Gilles , Benkoulouche Mohamed , Geoffre Serge 
Published: December 2004

AbstractIn order to get information on the bioactive conformations of the endogenic renin substrate, a few peptide segments of angiotensinogen, along with a pepstatin analogue, were studied in the solid state by x‐ray crystallography. These results are compared with the conformations of acidic proteinase inhibitors observed at the level of the active site. Such a comparison allows us to point out some analogies and differences between the observed conformation for the peptide alone and the conformations on the active sites. The analysis of the results should be a good starting point for making hypotheses on the renin substrate bioactive conformation(s).
Nmr studies of a series of dehydrodermorphins
Authors: Castiglione‐Morelli Maria A. , Saviano Gabriella , Temussi Piero A. , Balboni Gianfranco , Salvadori Severo , Tomatis Roberto 
Published: December 2004

AbstractThe third and fifth aromatic residues of dermorphin, a potent μ‐opioid peptide, and of its N‐terminal fragments, from the pentapeptide to the parent heptapeptide amide, have been systematically substituted with Z‐dehydrophenylalanine (Δ‐Phe) and/or Phe to investigate the conformation–activity relationship.The characterization in DMSO‐d6 at 500 MHz indicates that, in this solvent, all peptides adopt essentially random, extended conformations, as a consequence of the strong solvation. The chemical shift of the methyl group of D‐Ala is influenced by the precise orientation of the side chain of the third residue in a fashion that can be correlated to the μ potency, consistently with our model of μ‐receptor.However, the complexes of the pentapeptides with 18‐crown‐6‐ether, when dissolved in chloroform, adopt ordered, folded conformations, a behavior that closely parallels the CD observations in methanol.
Regularly alternating L,D‐peptides. II. The double‐stranded right‐handed antiparallel β‐helix in the structure of t‐Boc‐(L‐Phe‐D‐Phe)4‐OMe
Authors: Di Blasio Benedetto , Benedetti Ettore , Pavone Vincenzo , Pedone Carlo , Gerber Cristoph , Lorenzi Gian Paolo 
Published: December 2004

AbstractThe crystal structure of Boc‐(L‐Phe‐D‐Phe)4‐OMe has been determined by x‐ray diffraction analysis. The peptide crystallizes in the triclinic system, space group P1 with a = 15.290 Å, b = 15.163 Å, c = 19.789 Å, α = 102.49°, β = 96.59°, γ = 74.22°, and Z = 2. The structure has been solved by coupling of the molecular replacement technique and expansion by tangent formula refinement of the set of known phases. Several cycles of Fourier calculations and least‐squares refinement led to the location of 194 atoms of the two independent octapeptide chains and few molecules of cocrystallized solvent (chloroform, water, and methanol). The isotropic refinement converged to R = 0.13 for the 3077 “observed” reflections.The two independent octapeptide molecule form a dimer in the solid state: the two chains are associated by interstrand hydrogen bonds (12 of the the type NH ⃛OC) with the formation of a double‐stranded antiparallel right‐handed ↑↓ β5.6‐helix. These double helices can be represented as a cylinder with a hydrophilic inner core represented by the peptide units and an hydrophobic exterior constituted by the aromatic moieties. The dimensions of the cylinder are equal to those observed for Boc‐(L‐Val‐D‐Val)4‐OMe. In the solid state the dimers pack with each other in an hexagonal fashion with the formation of layers; between the layers, solvent molecules fill empty spaces.
Interactive nmr and computer simulation studies of lanthionine‐ring structures
Authors: Palmer D. E. , Mierke D. F. , Pattaroni C. , Goodman M. , Wakamiya T. , Fukase K. , Kitazawa M. , Fujita H. , Shiba T. 
Published: December 2004

AbstractWe report progress in elucidating the structure of nisin, a naturally occurring peptide antibiotic. Nisin contains five rings constrained by lanthionine or methyllanthionine bridges, as well as α,β‐unsaturated amino acids. We have determined conformations for two model compounds of ring A and a derivative of ring B through interactive nmr and computer simulation studies. High‐resolution nmr techniques provides structural information, which was further refined through molecular dynamics simulations. These methods are being applied to the remaining constrained fragments of the molecule. This conformational information will be employed in an aufbau approach to determining the structure of the entire molecule.
Direct examination of chemical kinetic laws by visual imagery. IV. Association processes between antigen‐ and fragmented antibody carrying fluorescent latex particles
Authors: Kitano Hiromi , Yan Changhong , Maeda Yasushi , Ise Norio 
Published: December 2004

AbstractThe binary association process was further examined by direct visual observation using a fluorescence microscope connected to an image‐processing system and by a spectrophotometric method. In the present paper, we used human serum albumin (HSA)‐ and fragmented anti‐HSA antibody‐carrying fluorescent latex particles in order to attain higher sensitivities and exclude complexities that might be caused by dissociation of the association product. The rate constant of the binary association process was estimated to be 6.0 × 108M−1s−1 at 30°C and pH 7.6. The activation parameters of the association process were evaluated. The effects of pH and viscosity of the suspension on the association process were also examined.
Hydration of B‐DNA: Comparison between the water network around poly(dG) · poly(dC) and poly(dG‐dC) · poly(dG‐dC) on the basis of Monte Carlo computations
Authors: Eisenhaber F. , Tumanyan V. G. , Eisenmenger F. , Gunia W. 
Published: December 2004

AbstractA computational method is elaborated for studying the water environment around regular polynucleotide duplexes; it allows rigorous structural information on the hydration shell of DNA to be obtained. The crucial aspect of this Monte Carlo simulation is the use of periodical boundary conditions. The output data consists of local maxima of water density in the space near the DNA molecule and the properties of one‐ and two‐membered water bridges as function of pairs of polar groups of DNA.In the present paper the results for poly(dG) · poly(dC) and poly(dG‐dC) · poly(dG‐dC) are presented. The differences in their hydration shells are of a purely structural nature and are caused by the symmetry of the polar groups of the polymers under study, the symmetry being reflected by the hydration shell.The homopolymer duplex hydration shell mirrors the mononucleotide repeat. The water molecules contacting the polynucleotide in the minor groove are located nearly in the plane midway between the planes of successive base pairs. One water molecule per base pair forms a water bridge facing two polar groups of bases from adjacent base pairs and on different strands making a “spine”‐like structure. In contrast, the major groove hydration is stabilized exclusively by two‐membered water bridges; the water molecules deepest in the groove are concentrated near the plane of the corresponding base pair.The alternating polymer is characterized by a marked dyad symmetry of the hydration shell corresponding to the axis between two successive base pairs. The minor groove hydration of the dCpdG step resembles the characteristic features of the homopolymer, but the bridge between the O2 oxygens of the other base‐stacking type is formed by two water molecules. The major groove hydration is characterized by high probability of one‐membered water bridges and by localization of a water molecule on the dyad axis of the dGpdC step.The found structural elements are discussed as reasonable invariants of a dynamic hydration shell.
Flexibility of smooth and skletal tropomyosins
Authors: Swenson Charles A. , Stellwagen Nancy C. 
Published: December 2004

AbstractThe rotational relaxation times of nonpolymerizable skeletal and smooth muscle tropomyosin were measured by analysis of the decay of the zero‐field birefringence at different temperatures and salt concentrations. Skeletal tropomyosin in solution is equally well modeled as a rigid rod or as a semiflexible rod with a persistence length of 150 nm. Smooth muscle tropomyosin does not fit the rigid rod model but is well approximated by a semiflexible rod model with a persistence length of 55 nm. The results indicate that smooth muscle tropomyosin is either a more flexible molecule than skeletal muscle tropomyosin or is a curved structure with an end‐to‐end length shorter than the coiled‐coil contour length. Smooth muscle tropomyosin controls the actomyosin ATPase differently from skeletal muscle tropomyosin and it had been suggested that the reason is because it is more rigid; clearly, another explanation must be sought.
The electrostatic potential of B‐DNA
Authors: Jayaram B. , Sharp Kim A. , Honig Barry 
Published: December 2004

AbstractElectrostatic potentials around DNA are obtained by solving the nonlinear Poisson‐Boltzmann (PB) equation. The detailed charge distribution of the DNA and the different polarizabilities of the macromolecule and solvent are included explicitly in the calculations. The PB equation is solved using extensions of a finite difference approach applied previously to proteins. Electrical potentials and ion concentrations are compared to those obtained with simpler models. It is found that the shape of the dielectric boundary between the macromolecule and solvent has significant effects on the calculated potentials near the surface, particularly in the grooves. Sequence‐specific patterns are found, the most surprising result being the existence of positive regions of potential near the bases in both the major and minor grooves. The effect of solvent and ionic atmosphere screening of phosphate‐phosphate repulsions is studied, and an effective dielectric function, appropriate for molecular mechanics simulations, is derived.