bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrostatic forces in two lysozymes: Calculations and measurements of histidine pKa values
Authors: Takahashi Takuya , Nakamura Haruki , Wada Akiyoshi
Published: December 2004

In 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

In 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

Twelve 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

The 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

Systematic 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

IR 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

This 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

In 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

The 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.
α‐helix to random coil transitions: Determination of peptide concentration from the CD at the isodichroic point
Authors: Holtzer Marilyn Emerson , Holtzer Alfred
Published: December 2004

A method is presented for determining the concentrations of peptides and proteins having isodichroic points near 203 nm. The existence of an isodichroic point for a given substance indicates a local two‐state (α‐helix, random coil) population. The mean residue ellipticity at the isodichroic point, [θλi], is, of course, independent of helix content. For a wide variety of synthetic and natural peptides, including both single helices and coiled coils, it is shown that [θλi] is also essentially independent of substance and of whether the transition is induced by temperature, ionic strength, pH, chain length changes, amino acid substitution, or solvent perturbation. Averaging [θλi] values culled from various laboratories gives –151 ± 16 (SD, 7 sources) deg · cm2 · mmol−1. In our laboratory, nonpolymerizable rabbit α‐tropomyosin and two α‐tropomyosin subsequences yield –135 ± 10 (SD, 190 values) deg · cm2 · mmol−1. Thus, given [θλi] for a peptide of known concentration, it is possible to estimate the concentration of any other peptide provided that it has an isodichroic point at which the ellipticity is accurately measurable. It is then possible to calculate [θλ] at any other wavelength for which θ is known. It is advisable to determine [θλi] for the best known peptide in one's own laboratory, since it depends on absolute instrument and cell calibrations and an absolute concentration determination. © 1992 John Wiley & Sons, Inc.
How many numbers are required to specify sequence‐dependent properties of polynucleotides?
Authors: Goldstein Robert F. , Benight Albert S.
Published: December 2004

There are 10 unique dinucleotides of double‐stranded DNA, but only 8 independent nearest‐neighbor energies that occur in circular DNA, as shown by D. M. Gray and I. Tinoco [(1970) Biopolymers 9, 223–244]. We extend that analysis to include end effects, and show that the number of unique dinuoleotide pairs (including ends) is 14. but there are only 12 independent energies. We discuss how these 12 energies (or spectra or any other pairwise additive property) can be measured and displayed, and how they should and should not be compared between experimenters. As an example, we analyzed the recently reported melting curves [M. J. Doktycz et al. (1992) Biopolymers, 32, 849–864] of 16 DNA dumbbells in two different Na+ environments. This analysis reveals a new means for evaluating end effects and the emergence of longer than nearest‐neighbor interactions at low salt concentration. © 1992 John Wiley & Sons, Inc.
Influence of electrostatic interactions on the sugar–phosphate backbone conformation in DNA
Authors: Pechenaya V. I.
Published: December 2004

The influence of sugar ring flexibility in DNA on the mechanism of the B ⇄ A conformational transition is studied. The dipole moment of the deoxyribose as a function of its puckered states is calculated by the quantum‐mechanical method using the MINDO/3 approximation. The interaction of the sugar dipole with the neighbor molecular groups in polynucleotide chains is estimated. The sugar dipole interaction with phosphate groups and counterions is shown to be strong and capable to deform the pseudorotation potential of deoxyribose. The effective pseudorotation potential of sugar ring in the B and A helices is obtained. The results are used to explain the behavior of Raman bands in the region of sugar–phosphate vibrations. The mechanism of the effect of electrostatic forces on the sugar–phosphate backbone conformation, which is essential for the B ⇄ A and other structure transitions, is offered. © 1993 John Wiley & Sons, Inc.
A Monte Carlo method for generating structures of short single‐stranded DNA sequences
Authors: Erie Dorothy A. , Breslauer Kenneth J. , Olson Wilma K.
Published: December 2004

A Monte Carlo method has been developed for generating the conformations of short single‐stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecules are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mole of the global minimum in the resulting optimized states are then allowed to vary by ±10° in an effort to estimate the breadth of the different local minima. The energies of a total of 2187 (37) angle combinations are examined per local conformational minimum. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theoretical sample match those found in nmr solution studies. This last step is necessitated by limitations in the theoretical methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from nmr coupling constants and the frequencies of glycosyl conformations in x‐ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150–325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single‐stranded d(CXnG) chains, where X = A, T and n = 3, 4, 5. The oligonucleotides are built sequentially from the 5′ end of the chain using random numbers to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 106 conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar–phosphate backbone. The distributions of oligonucleotide conformations are examined in terms of the magnitudes, positions, and orientations of the end‐to‐end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodology is discussed and compared with other nucleic acid model building techniques. © 1993 John Wiley & Sons, Inc.
Kinetic analysis of the hydrodynamic transition accompanying protein folding using size exclusion chromatography. 1. Denaturant dependent baseline changes
Authors: Shalongo William , Heid Paul , Stellwagen Earle
Published: December 2004

Size exclusion profiles of proteins with persistent conformations exhibit broad asymmetric peaks whose shape and elution times are dependent on denaturant concentration. The collective elution profiles were precisely simulated by an apparent binding model that treats the denaturant dependence in terms of an apparent matrix binding. The model requires three experimentally measurable parameters: the elution time for the unbound protein, an apparent association equilibrium constant for binding, and an apparent exchange time for binding. The denaturant dependence for each of these parameters is related to the accessible surface area of the protein. © 1993 John Wiley & Sons, Inc.
Microwave absorption spectroscopy of DNA
Authors: Bigio Irving J. , Gosnell Timothy R. , Mukherjee Pritish , Saffer Jeffrey D.
Published: December 2004

By utilizing a novel approach to microwave spectrometry, we have measured the absolute absorption spectrum of plasmid DNA (pUC8.c2), in buffered aqueous solution, from 5 to 20 GHz. Our technique does not suffer from the same experimental difficulties that plague other methods. We observe no absorption resonances in this frequency range, but we do see broadband differences, between DNA and pure buffer, that are attributable to changes in the ionic conductivity of the solutions. These results constitute the first verification, by a totally different technique, of the absence of resonances in the microwave absorption spectrum of DNA, and the first data obtained by any technique in the 10–20‐GHz band. © 1993 John Wiley & Sons, Inc.
Helix‐Forming tendencies of amino acids depend on their sequence contexts: Tripeptides AFG and FAG show incipient β‐bulge formation in their crystal structures
Authors: Parthasarathy R. , Go Kuantee , Chaturvedi Sanjeev
Published: December 2004

Many of the theoretical methods used for predicting the occurrence of α‐helices in peptides are based on the helical preferences of amino acid monomer residues. In order to check whether the helix‐forming tendencies are based on helical preferences of monomers only or also on their sequence contexts, we synthesized permuted sequences of the tripeptides GAP, GAV, and GAL that formed crystalline helices with near α‐helical conformation. The tripeptides AFG and FAG formed good crystals. The x‐ray crystallographic studies of AFG and FAG showed that though they contain the same amino acids as GAF but in different sequences, they do not assume a helical conformation in the solid state. On the other hand, AFG and FAG, which contain the same amino acids but in a different sequence, exhibit nearly the same backbone torsion angles corresponding to an incipient formation of a β‐bulge, and exhibit nearly identical unit cells and crystal structures. Based on these results, it appears that the helix‐forming tendencies of amino acids depend on the sequence context in which it occurs in a polypeptide. The synthetic peptides AFG (L‐Ala‐L‐Phe‐Gly) and FAG (L‐Phe‐L‐Ala‐Gly), C14H19N3O4, crystallize in the orthorhombic space group P212121, with a = 5. 232(1), b = 14. 622(2), c = 19. 157(3) Å, Dx = 1.329 g cm−3, Z = 4, R = 0.041 for 549 reflections for AFG, and with a = 5. 488(2), b = 14.189 (1), c = 18.562(1) Å, Dx = 1.348 g cm−3, Z = 4, R = 0.038 for 919 reflections for FAG. Unlike the other tripeptides GAF, GGV, GAL, and GAI, the crystals of AFG and FAG do not contain water molecule, and the molecules of AFG or FAG do not show the helical conformation. The torsion angles at the backbone of the peptide are ψ1 = 144. 5(5)°; ϕ2, ψ2 = −98.1(6)°, −65.2(6)° ϕ3, ψ13, ψ31 = 154.1(6)°, −173.6(6)°, 6.9(8)° for AFG; and ψ1 = 162.6(3)°; ϕ2, ψ2 = −96.7(4)°, −46.3(4)°; ϕ3, ψ13, ψ31 = 150.1(3)°, −168.7(3)°, 12.2(5)° for FAG. The conformation angles (ϕ ψ) for residues 2 and 3 for both AFG and FAG show incipient formation of an β‐bulge. © 1993 John Wiley & Sons, Inc.
Shape analysis of molecular surfaces
Authors: Duncan Bruce S. , Olson Arthur J.
Published: December 2004

The description of molecular shape is important in the analysis of protein–protein and protein–ligand interactions. We describe volumetric and surface‐based techniques for computing shape properties of molecular surfaces. The surface is defined as an isocontour of an approximate electron density function. Each technique can compute several scalar and vector surface properties such as the Gaussian and mean curvature, principal curvatures, and principal curvature directions. Shape properties are derived from the eigenvalues and eigenvectors of a 3 by 3 matrix for each surface point. In the volumetric approach, the matrix is the second derivative of an approximate electron density function. In the surface‐based approach, the matrix is the approximate gradient of the surface normal. Derivatives 4 are computed by convolving the density or the surface normals with the derivatives of a Gaussian function. The variance of the Gaussian determines the effective length scale at which the surface is analyzed. Scalar surface properties are displayed as colored dots or shaded triangles, and vector properties are displayed as line segments from each surface point. This report describes the implementation of these procedures and their use in computing the shape properties of Cu‐Zu superoxide dismutase. © 1993 John Wiley & Sons, Inc.
Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: Application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2
Authors: Prévost C. , Louise‐May S. , Ravishanker G. , Beveridge D. L , Lavery R.
Published: December 2004

A theory and graphical presentation for the analysis of helix structure and deformations in oligonucleotides is presented. The parameters “persistence” and “flexibility” as defined in the configurational statistics of polymers of infinite length are reformulated at the oligonucleotide level in an extension of J. A. Schellman's method [(1974) Biopolymers, Vol. 17, pp. 217–226], and used as a basis for a systematic “Persistence Analysis” of the helix deformation properties for all possible subsequences in the structure. The basis for the analysis is a set of link vectors referenced to individual base pairs, and is limited to sequences exhibiting only perturbed rod‐like behavior, i.e., below the threshold for supercoiling. The present application of the method is concerned with a physical model for the angular component of bending, so the link vectors are defined as the unit components of a global helix axis obtained by the procedure “Curves” of R. Lavery and H. Sklenar [(1988) J. Biomol. Struct. Dynam., Vol. 6, pp. 63–91; (1989) J. Biomol. Struct. Dynam., Vol. 6, pp. 655–667]. A discussion, of the relationship between global bending and relative orientation of base pairs is provided. Our approach is illustrated by analysis of some model oligonucleotide structures with intrinsic kinks, the crystal structure of the dodecamer d (CGCGAATTCGCG)2, and the results of two molecular dynamics simulations on this dodecamer using two variations of the GROMOS force field. The results indicate that essentially all aspects of curvature in short oligonucleotides can be determined, such as the position and orientation of each bend, the sharpness or smoothness, and the location and linearity of subsequences. In the case of molecular dynamics simulations, where a Boltzmann ensemble of structures is analyzed, the spatial extent of the deformations (flexibility) is also considered. © 1993 John Wiley & Sons, Inc.
A model for the dynemicin‐A cleavage of DNA using molecular dynamics simulation
Authors: Cardozo Mario G. , Hopfinger A. J.
Published: December 2004

Molecular dynamics (MD) simulations to model possible reaction pathways of the dynemicin‐A‐DNA cleavage mechanism were performed. Two base‐pairs sequences, ApCpTp‐ApCpTp‐3′/TpGpApTpGpAp‐5′ and CpApCpGpGpGp‐3′/GpTpGpCpCpCp‐5′, were considered in the calculations. A model based on a prior study of intercalation of dynemicin‐A and posterior activation of the drug was assumed in this study. The minimum energy minor groove intercalation complexes for dynemicin‐A were used as starting structures in the MD simulations for the reactive intermediate species involved in the postulated action mechanism. The dynemicin‐A diol derivative product of the opening of the epoxy ring was used as a “steric mimic” ligand for the DNA‐reactive diaryl intermediate. The calculated changes in the geometry of the intercalation complex, due to the opening of the epoxy ring, correspond to the approach of the postulated intermolecular reaction centers in the intercalation states that are responsible for the highest observed DNA cleavage frequency observed. Conversely, unfavorable reaction geometries were found for the intercalation modes corresponding to the lowest observed DNA cutting frequencies. © 1993 John Wiley & Sons, Inc.
Cyanogen as a selective probe for carbonic anhydrase hydrolase activity
Authors: Karagözler A. A. , Ghenbot G. , Day R. A.
Published: December 2004

The salt bridge probe cyanogen (ethanedinitrile, C2N2; NC–‐CN) inhibits the bovine carbonic anhydrase (EC 4.2.1.1.) hydrolase activity toward various types of esters without significant effect on its hydrolyase activity. Two sets of pyridine derivatives that were isosteric substrates for the two activities were differentially affected. Acetazolamide and salamide are reversible inhibitors of the enzyme; only salamide affords protection of the hydrolase activity against the action of C2N2. Since each is known to bind in different positions within the active site, the selective effect of salamide may arise from its position covering one CO2 site as well as a site important for hydrolase activity. The C2N2 concentration dependence of the time course of hydrolase inhibition is consistent with the existence of a high C2N2 affinity site with slow covalent change and a second site with lower C2N2 affinity, but higher rate of covalent modification of the enzyme. © 1993 John Wiley & Sons, Inc.
Lattice vibrations in crystalline L‐alanine
Authors: Durand Dominique , Field Martin J. , Quilichini Marguerite , Smith Jeremy C.
Published: December 2004

Zwitterionic L‐alanine forms crystals containing strong hydrogen‐bonding and methyl‐methyl interactions. Well‐defined low‐frequency lattice vibrations exist in the crystals involving correlated intermolecular motions on the picosecond timescale. A characterization of these vibrations is expected to provide useful information on the nature of nonbonded interactions in peptides and proteins. We examine some of the vibrations using coherent inelastic neutron scattering and computer simulation techniques. The neutron scattering measurements are used to determine phonon dispersion relations for the acoustic and some low‐frequency optic modes in the crystal. There is evidence for interaction between the two lowest frequency optical phonons and the longitudinal acoustic mode. The velocity of sound is anisotropic and can be correlated with the hydrogen‐bonding arrangement in the crystal. Corresponding phonon dispersion relations are derived from normal mode analyses of the crystal using the program CHARMM. Although some calculated vibrational frequencies are somewhat too high, the form of the calculated dispersion relations are in good agreement with experiment. © 1993 John Wiley & Sons, Inc.
Differences in melting behavior between homopolymers and copolymers of DNA: Role of nonbonded forces for GC and the role of the hydration spine and premelting transition for AT
Authors: Chen Y. Z. , Prohofsky E. W.
Published: December 2004

Melting measurements of the mono‐base‐pair DNA polymers showed that the melting temperature Tm of the B‐DNA homopolymer poly (dA ) · poly (dT) is higher than that of the copolymer poly [d(A‐T)]. On the other hand, the Tmof the B‐DNA homopolymer poly (dG) · poly (dC) is lower than that of the copolymer poly [d (G‐C)]. From a structural point of view, the cross‐strand base‐stacking interaction in a DNA homopolymer is weaker than that in a DNA copolymer with the same base pair. One would then expect that all the DNA homopolymers are less stable than the copolymer with the same base pair. We find that the inversion of the melting order seen in the AT mono‐base‐pair DNA polymers is caused by the enhanced thermal stability of poly (dA) · poly (dT) from a well‐defined spine of hydration attached to its minor groove. In this paper we employ the modified self‐consistent phonon theory to calculate base‐pair opening probabilities of four B‐DNA polymers: poly(dA)‐poly(dT), poly(dG) · poly(dC), poly[d(A‐T)], and poly[d(G‐C)] at temperatures from room temperature through the melting regions. Our calculations show that the spine of hydration can give the inverted melting order of the AT polymers as compared to the GC polymers in fair agreement with experimental measurements. Our calculated hydration spine disruption behavior in poly(dA) · poly(dT) at premelting temperatures is also in agreement with experimentally observed premelting transitions in poly (dA) · poly (dT). The work is in a sense a test of the validity of our models of nonbonded interactions and spine of hydration interactions. We find we have to develop the concept of a strained bond to fit observations in poly (dA) · poly(dT). The strained‐bond concept also explains the otherwise anomalous stability of the hydration chain. © 1993 John Wiley & Sons, Inc.
Conformational difference between diastereomers of Dnp‐Val‐Aib‐Gly‐Leu‐pNA studied by x‐ray crystal analyses
Authors: Yamada Takashi , Nakao Masayuki , Miyazawa Toshifumi , Kuwata Shigeru , Sugiura Makiko , In Yasuko , Ishida Toshimasa
Published: December 2004

In order to investigate the Conformational change of the α‐aminoisobutyric acid (Aib) containing peptide by the D/L replacement of an amino acid residue, single crystals of two diastereomers, Dnp‐L‐Val‐Aib‐Gly‐L‐Leu‐pNA (L‐L isomer) and Dnp‐D‐Val‐Aib‐Gly‐L‐Leu‐pNA (D‐L isomer), were prepared from aqueous methanol solutions as CH3OH and CH3OH · H2O solvates, respectively, and were analyzed by the x‐ray diffraction method. Molecular conformation of L‐L isomer adopts consecutive two different types of β‐turns, a type II′ β‐turn bent at Aib‐Gly, and a type III β‐turn bent at Gly‐Leu, stabilized by two intramolecular (Leu) NH …︁ OC (Val) and (pNA) NH …︁ OC(Aib) hydrogen bonds. In contrast, these two intramolecular hydrogen bonds lead the D‐L isomer to a distorted 310‐helix conformation consisting of consecutive two type‐III β‐turn of Aib‐Gly‐Leu sequence. The most significant structural difference between these diastereomers is the mutual orientation between the Dnp and pNA chromophores. While the extensive stacking of both the chromophores is intramolecularly formed for the folded conformation of L‐L isomer, they are oriented toward an opposite direction in the open conformation of D‐L isomer and are intermolecularly stacked with each other. The large separation between these diastereomers observed in the chromatography is discussed in the relation with their Conformational differences. © 1993 John Wiley & Sons, Inc.
Further characterization of the kinetic folding intermediate of αα‐tropomyosin and of its 142–281 subsequence
Authors: Mo Jianming , Holtzer Marilyn Emerson , Holtzer Alfred
Published: December 2004

The backbone CD spectrum from 250 to 212 nm for the kinetic folding intermediate of αα‐tropomyosin (αα‐Tm) and nonpolymerizable αα‐Tm was obtained. The spectrum shows that the intermediate is indeed α‐helical with about 70% of the equilibrium α‐helix content. Subsequence 142Tm281 of the α‐tropomyosin chain has five tyrosine residues (at positions 162, 214, 221, 261, 267). Stopped flow CD at the negative peak in the tyrosine spectral region (280 nm) shows that any tyrosine residues that contribute to the spectrum in the region have already reached their final state in the fast phase of folding ( < 0.04 s). © 1993 John Wiley & Sons, Inc.
Carrier design: Conformational studies of amino acid (X) and oligopeptide (X‐DL‐Alam) substituted poly(L‐lysine)
Authors: Mezö G. , Kajtár J. , Hudecz F. , Szekerke M.
Published: December 2004

The present study was undertaken to examine the influence of the reversal of the sidechain sequential order on the conformation of branched polypeptides. At the same time, the influence of the optically active amino acid joined directly to the poly (L‐Lys) backbone and the DL‐Ala oligomer grafted as chain‐terminating fragment were separately analyzed. Therefore two sets of polypeptides were synthesized corresponding to the general formula poly [Lys‐(Xi,)] (XK) and poly[Lys‐(DL‐Alam‐Xi)] (AXK) when X = Ala, D‐Ala, Leu, D‐Leu, Phe, D‐Phe, Ile, Pro, Glu.,D‐Glu, or His. For coupling amino acid X to polylysine, three types of active ester methods were compared: the use of pentafluorophenyl or pentachlorophenyl ester, and the effect of the addition of an equimolar amount of 1‐hydroxybenzotriazole. After cleavage of protecting groups, AXK polypeptides were synthesized by grafting short oligo (DL‐Ala) chains to XK by using N‐carboxy‐DL‐Ala anhydride. The CD measurements performed in water solutions of various pH values and ionic strengths were used for classification of the polypeptide conformations as either ordered (helical) or unordered. Different from what was observed with the unsubstituted poly (L‐Lys), poly[Lys‐(Xi)] type polypeptides can adopt ordered structure even under nearly physiological conditions (pH 7.3, 0.2M NaCl). These data suggest that the introduction of amino acid residue with either (ar) alkyl side chain (Ala, Leu, Phe) or negatively charged side chain (Glu) promotes markedly the formation of ordered structure. Comparison of chiroptical properties of poly [Lys‐ (DL‐Alam‐Xi)] and of poly [Lys‐ (Xi)] reveals that side‐chain interactions play an important role in the stabilization of ordered solution conformation of AXK type branched polypeptides. The results give rather conclusive evidence that not only hydrophobic interactions, but also ionic attraction, can be involved in the formation and stabilization of helical conformation of branched polypeptides. © 1993 John Wiley & Sons, Inc.
Nmr and computer‐aided modeling studies of the interactions between a cyclic hexapeptide and the two enantiomers of some Boc‐ and Fmoc‐amino acids
Authors: McEwen I.
Published: December 2004

The cyclic hexapeptide cyclo[‐Pro1‐Gly2‐Glu3(OBzl) ‐Pro4‐Phes5‐Leu6‐] (1) was modeled and synthesized to be used for chiral discrimination studies. Total correlated spectroscopy and nuclear Overhauser effect spectroscopy spectra of the cyclic hexapeptide 1 in CDCl3 showed the presence of three stereoisomers: two dominant stereoisomers 1a and 1b that exchanged chemically with each other, and a minor stereoisomer 1c (4%) that exchanged exclusively with the stereoisomer 1b. Of the two dominant stereoisomers, only 1a interacted specifically with t‐butyloxycarbonyl (Boc‐) and 9‐flourenylmethyloxycarbonyl (Fmoc‐) amino acids in CDCl3. The interaction site of la when complexing with the derivatized amino acids was the chain segment Phe5‐Leu6. The Phe5 NH and Leu6 NH protons are contiguous and solvent exposed. Their nmr signals shifted strongly downfield with the addition of Boc‐ or Fmoc‐ amino acids to the peptide solution. Thus, both NH protons hydrogen bond to the amino acids, forming a two‐point hydrogen‐bonding complex. The peptide stereoisomer 1b did not interact specifically with the Boc‐ and Fmoc‐amino acids because of the lack of two contiguous and solvent‐exposed peptidic NH protons that seem to be needed for specific interactions of the cyclic hexapeptide 1 with the Boc‐ and Fmoc‐amino acids. A clear difference in the interaction of 1a with D‐ and L‐enantiomers of BocTrp and Fmoc‐Trp was observed with nmr spectroscopy. Docking models and molecular mechanics calculations together with nmr observations showed that the NH proton of the indole ring of the Boc‐L‐Trp and the Fmoc‐L‐Trp hydrogen bonded to the Pro1 carbonyl group. In this three‐point hydrogen‐bonding complex, the indole ring becomes locked underneath the Leu residue. The nmr signals of all the Leu6 protons (except for Leu NH) shifted strongly upfield owing to the shielding effect of the indole aromatic ring currents. The indole NH of the D‐enantiomer did not hydrogen bond to the Pro1 carbonyl group because the formation of such a three‐point hydrogen‐bonding complex was thermodynamically unfavorable. © 1993 John Wiley & Sons, Inc.
Sequence dependence of purine C8H exchange kinetics in the dodecamer 5′‐d(CGCGAATTCGCG)‐3′
Authors: Walters Kylie J. , Russu Irina M.
Published: December 2004

Proton nmr spectroscopy is used to measure the deuterium exchange rates of C8 protons in individual purines of the dodecamer 5′‐d(CGCGAATTCGCG)‐3′ and their temperature dependence. In perfect agreement with results from tritium labeling and laser Raman spectroscopy, we find that the DNA secondary structure retards the rates of purine C8H exchange. The largest effects are observed for the C8 protons of adenines whose rates of exchange at 40°C are 3‐to 4‐fold lower than that in 5′‐adenosine monophosphate. Moreover, the retardation of exchange at the central adenine is greater than that at its 5′‐neighbor. For the guanines, the exchange rates are up to 2‐fold lower than that in 5′‐guanosine monophosphate, and the largest retardation is observed for the bases at positions 10 and 12. A dependence on base sequence is also observed for the activation energy for exchange. The activation energy is largest for the adenines and its value is 4 kcal/mol higher than that in 5′‐adenosine monophosphate. The lowest activation energy is observed for the guanine in position 4 and the value is the same as in 5′‐guanosine monophosphate. These results demonstrate the sensitivity of the purine C8H exchange kinetics to sequence‐dependent conformational features of B‐DNA in solution state. © 1993 John Wiley & Sons, Inc.
Probing the influence of sequence‐dependent interactions upon α‐helix stability in alanine‐based linear peptides
Authors: Jacchieri Saul G. , Richards Nigel G. J.
Published: December 2004

The observation that short, linear alanine‐based polypeptides form stable α‐helices in aqueous solution has allowed the development of well‐defined experimental systems with which to study the influence of amino acid sequence upon the stability of secondary structure. We have performed detailed conformational searches upon six alanine‐based peptides in order to rationalize the observed variation in the α‐helical stability in terms of side‐chain‐backbone and side‐chain‐side‐chain interactions. Although a simple, gas‐phase, potential model was used to obtain the conformational energies for these peptides, good agreement was obtained with experiment regarding their relative α‐helical stabilities. Our calculations clearly indicate that valine, isoleucine, and phenylalanine residues should destabilize the α‐helical conformation when included within alanine‐based peptides because of energetically unfavorable side‐chain‐backbone interactions, which tend to result in the formation of regions of 310‐helix. In the case of valine, the destabilization most probably arises from entropic effects as the isopropyl side chain can assume more orientations in the 310‐helical form of the peptide. A detailed examination of very short‐range interactions in these peptides has also indicated that an interaction, involving fewer than five consecutive residues, whose stabilizing effect reinforces that of the (i, i + 4) hydrogen bond may be the basis of the requirement for increased nucleation (σ) and propagation parameters (s) required by Zimm–Bragg theory to predict the α‐helical content for compounds in this class of short peptides. Our calculations complement recent work using modified Zimm–Bragg and Lifson–Roig theories of the helix–coil transition, and are consistent with molecular dynamics simulations upon linear peptides in aqueous solution. © 1993 John Wiley & Sons, Inc.
Nmr and molecular dynamics study of four carbocyclic muramyl dipeptide analogues
Authors: Pristovšek P. , Kidrič J. , Mavri J. , HadžI D.
Published: December 2004

We have performed a conformational analysis of the carbocyclic muramyl dipeptide analogues (1′R, 2′R)‐ and (1′S, 2′S)‐N‐[2‐(2′‐acetamidocyclohexyIoxy)acetyl]‐LAla‐D‐iGln (‐D‐Glu) utilizing 1H‐nmr spectroscopy and nuclear Overhauser effect restrained molecular dynamics. Intramolecular H bonding for all four diastereoisomers is suggested by the Ala‐NH temperature coefficients. Distance restraints were obtained by NOE spectroscopy and rotating frame NOE spectroscopy experiments. Structures with low potential energy and high agreement with NOE data were sought by restrained molecular dynamics. The ring configuration was found to induce conformational preferences. The β‐like turn characterized by the intramolecular C10 H‐bond Ala‐NH‐acetamido‐CO is preferred with the (1′S, 2′S), but appears to be less stable with (1′R, 2′R), diastereoisomers. Calculations show the double β‐turn proposed for muramyl dipeptide [S. Fermandjian, B. Perly, M. Level, and P. Lefrancier (1987) Carbohydrate Research, Vol. 162, pp. 23–32] to have higher potential energy. © 1993 John Wiley & Sons, Inc.
The contribution of helical potential to the in vitro receptor binding activity of a neuropeptide Y N‐terminal deletion fragment
Authors: Doughty Michael B. , Hu Longqin
Published: December 2004

In its dimeric form neuropeptide Y (NPY) folds into a compact structure in which the antiparallel oriented proline and α‐helices apparently associate to form a primitive hydrophobic core. To investigate the contribution of helical stability to the receptor binding activity of NPY and its N‐terminal deletion fragments, we synthesized and studied the solution conformational properties and in vitro activities of NPY, Nα‐acetyl‐NPY2–36, NPY15–36, Nα‐propinonly‐NPY15–36, and Nα‐succinyl‐NPY15–36 is significantly less helical than both NPY and Nα‐acetyl‐NPY2–36, and this decreased helical potential is attributed of the absence of the intramolecular stabilizing interaction afforded by the proline helix in the latter analogues. However, in accord with the helix dipole model, the helical potential of NPY15–36 is significantly increased by N‐terminal succinlyation, whereas propionylation has no effect. In addition to an increase in helical potential, Nα‐succinyl‐NPY15–36 is 2.5 and 4.6 times more active than NPY15–36 and Nα‐propionly‐NPY15–36, respectively and is equipotent with Nα‐acteyl‐NPY2–36 in displacing 1mM[3H]‐NPY from specific binding sites in rat brain membranes. The demonstration of positive correlation between % α‐helix content and in vitro binding activity suggests that the helical potential of N‐terminal NPY deletion fragments contributes to their in vitro activity in the rat brain, and that a second role of the proline helix might be to stabilize the receptor‐active conformation of the NPY α‐helix. © 1993 John Wiley & Sons, Inc.
Stretching and overstretching of DNA in pulsed field gel electrophoresis. I. A quantitative study from the steady state birefringence decay
Authors: Mayer Pascal , Sturm Jean , Weill Gilbert
Published: December 2004

Using a sensitive birefringence instrument, the birefringence arising from the orientation of the DNA chain during electrophoretic transport has been recorded. This birefringence is shown to proceed both from the alignment (stretching) of the molecule in the direction of the electric field and from the extension of the length of its primitive path (overstretching). The contribution of these two processes can be separated in the decay of the birefringence after the end of the application of the electric field. The fast relaxation of the overstretching occurs first and is demonstrated to be the main contribution to the birefringence. The orientation factor of the remaining stretched state and its decay can be quantitatively understood using the biased reptation model. It provides, in addition, a high value for the tube diameter or gel pore size a (4500 ± 450 Å for a 0.7% agarose gel with a c−0.6g dependence in the agarose concentration cg) and a low value for the effective charge per base pair (0.2e as compared to 0.5e using the condensation hypothesis). The contribution of overstretching to the birefringence is also quantitatively interpreted in term of the change in the mean length l of DNA inside a pore size a. The dynamics of decay of this overstretching is well represented by a stretched exponential with a stretching exponent α = 0.44. The mean decay time decreases slightly with increasing fields and scales with the overall DNA length close to N20. © 1993 John Wiley & Sons, Inc.