bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational study of bacterial lipopeptides: Refinement of the structure of iturin A in solution by two‐dimensional 1H‐nmr and energy calculations
Authors: Marion Dominique , Genest Monique , Caille Anita , Peypoux Françoise , Michel Georges , Ptak Marius
Published: May 2005

Iturin A is a lipopeptide extracted from strains of Bacillus subtilis. Seven peptide residues form a cycle closed by a β‐amino acid carrying a hydrophobic tail. This compound is an antifungal and induces the formation of conducting pores in black lipid membranes. Two‐dimensional 1H‐nmr was used for investigating its conformation in pyridine. A complete set of nuclear Overhauser effects (NOEs) was obtained from which interproton distances were deduced in a rather broad range of 2.2–4.2 Å. A special procedure was then used to optimize simultaneously experimental parameters and intramolecular energy calculated by semiempirical methods. A model of the conformation is proposed for the backbone for which there is an excellent coherence between NOEs, coupling constants, and intramolecular energy. The conformations of Asn, Gln, and Ser side chains appear to be much more flexible because of their interactions with the solvent. From this picture, iturin A seems to have a rather stiff ring surrounded by mobile side chains. Further studies of this lipopeptide and of other members of the family should enable us to approach some structure–activity relationships for this class of antibiotics.
Number of binding sites of DNA and polynucleotides with tris(2,2′‐bipyridyl)ruthenium(II) cations
Authors: Stradowski Czeslaw , Görner Helmut , Currell Leslie J. , Schulte‐Frohlinde Dietrich
Published: May 2005

The binding of tris(2,2′‐bipyridyl)ruthenium(II) cations [Ru(bpy)] with single‐ and double‐stranded (ss and ds) DNA, and the polynucleotides poly(A), poly(C), poly(G), poly(I), poly(I) · poly(C), and poly(U), was studied in aqueous solution. Steady‐state electrical conductivity measurements with the polynucleotides, ssDNA, and dsDNA reveal that approximately three nucleotides offer one binding site. This may be compared with the ratio [nucleotide]/[Mg2+] of 2.4 : 1 for dsDNA. After laser excitation (353 nm), the luminescence of Ru(bpy) bound to nucleic acids shows two decay components. The contribution of the fast component, which is interpreted as resulting from quenching processes of the absorbed ruthenium complex, exhibits a maximum with increasing [nucleotide]/[Ru(bpy)] at a ratio of about three to one. Bound Ru(bpy) can be released from the strand by addition of NaClO4 [half‐concentration: 2.5 and ≤ 10 mM for poly(U) and dsDNA, respectively].
Calculation of the CD of oligo (dG‐dC): Influence of basic optical parameters
Authors: Richterich Peter , Pohl Fritz M.
Published: May 2005

The CD spectra between 180 and 300 nm of (dG‐dC)4 · (dG‐dC)4 in the A, B, and Z form of DNA were calculated with the classical polarizability theory of DeVoe. The use of the simple point dipole approximation for the calculation of interaction coefficients led to results comparable to those obtained with the point monopole approximation in previous calculations. The background oscillator strengths, effective dielectric constant, helix winding angle, and some transition moment directions were varied systematically. Very satisfying agreements between calculated and measured CD spectra were obtained with transition‐moment directions that are in agreement with experimental results, except for the second transition of guanine. A value of 40° for this transition gave the best results. Possible reasons for this deviation from the experimental results and some problems inherent in the calculations of CD spectra are discussed.
Poly[d(A‐T)‐Cs+] conformations studied by IR spectroscopy
Authors: Adam S. , Bourtayre P. , Liquier J. , Taboury J. A. , Taillandier E.
Published: May 2005

Infrared absorption and ir linear dichroism measurements have been performed on poly[d(A‐T)‐Cs+] films at various relative humidities. At high relative humidity, samples are in a B form; at low relative humidity, in a C form. The B → C conformational transition is shown to be a noncooperative one corresponding to a gradual evolution of the backbone geometry of the polynucleotide within the B family. the C‐form‐type spectrum is characteristic of an alternated phosphodiester chain with a dinucleotidic repeat unit.
Sodium ion and solvent nuclear relaxation results in aqueous solutions of DNA
Authors: Van Dijk Leendert , Gruwel Marco L. H. , Jesse Wim , De Bleijser Jan , Leyte Jaap C.
Published: May 2005

The field‐dependent23Na nuclear relaxation in aqueous DNA solutions has been obtained for a range of temperatures, including the DNA melting region. At least two correlation times are needed to characterize the spectral density function for the23Na relaxation. For the slow process (with the largest correlation time), the temperature dependence of the coupling constant and the correlation time were determined, and important premelting effects were observed. Possible origins of the slow process are discussed. The last process is shown to be correlated with the properties of the hydration water of DNA as reflected by the17O relaxation rates in these solutions. The influence of the polyelectrolyte and NaCl concentrations on the23Na relaxation rate is compared with previous results from solutions of linear flexible polyelectrolytes.
The distribution of void sizes in a reticulate gel
Authors: West Roger
Published: May 2005

The conformational properties of reticulate gels are examined in detail. The distribution of void sizes in a reticulate gel is shown to be usually indistinguishable from that in a hypothetical gel comprising a scaffolding of long, straight, randomly oriented, nonintersecting gel fibers. Agarose gel is used as the principle model throughout, but the conclusions are shown to be extendable to other species of gel.
Helix–coil transition theory including long‐range electrostatic interactions: Application to globular proteins
Authors: Vasquez Max , Pincus Matthew R. , Scheraga Harold A.
Published: May 2005

An extension of the Zimm–Bragg two‐state theory for the helix–coil transition in polypeptides, which takes into account the effect of peptide charge–dipole interactions on helix stability, is presented. This new theory incorporates these interactions in an expression that is parameterized on recently obtained experimental data on polypeptides for which electrostatic effects are known to influence helix content. Unlike previous two‐state or multistate models, which are parameterized on protein x‐ray data, the present theoretical treatment in independent of such protein data. The theoretical model is applied to a series of peptides derived from the C‐peptide of ribonuclease A, which have been the object of recent spectroscopic studies. The new theoretical approach can account for most of the structural information derived from studies of these C‐peptides, and for overall average helix probabilities that are close in magnitude to those observed for these polypeptides in solution. An application of this new formulation for the prediction of the locations of α‐helices in globular proteins from their amino acid sequence is also presented.
Structural models for the N‐ and C‐terminal telopeptide regions of interstitial collagens
Authors: Jones E. Yvonne , Miller Andrew
Published: May 2005

Secondary‐structure prediction has been used to investigate the conformation of the N‐ and C‐terminal telopeptides for type I and type III collagen. The three predictive methods (Chou and Fasman, Robson and co‐workers, Lim) indicate mainly aperiodic conformations. A common structural motif is provided by the positioning of β‐turns, particularly in the vicinity of the residue sites involved in intermolecular cross‐links. An alternative model to that of Helseth et al [(1979) Biopolymers 18, 3005–3014] for the secondary structure of the N‐terminal telopeptide of type I collagen is proposed. The general features of these two contrasting structures have been surveyed by model‐building techniques employing molecular graphics and energy minimization. The role of the telopeptide component in the structural design of the biomaterial collagen is assessed. Notably, the alternative model clearly serves to demonstrate the compatibility of current cross‐linking evidence with the quasi‐hexagonal model for the packing of molecules within a collagen fibril.
A Monte Carlo study of the excluded‐volume effect on the amylosic chain conformation
Authors: Kitamura Shinichi , Okamoto Takahiro , Nakata Yasushi , Hayashi Takeshi , Kuge Takashi
Published: May 2005

A Monte Carlo procedure was used to determine the effect of excluded volume on the conformational dimensions of amylosic chains. The excluded volume was introduced into the model by assuming that hard spheres, which cannot overlap each other, exist at the center of mass of each glucose unit in the chain sequence. Monte Carlo chains, which were generated to be distributed consistent with the potential energy of nonbonded nearest‐neighbor interactions, underwent self‐intersections, and the attrition rate in the generation of self‐avoiding chains was found to obey an exponential decay law with increasing chain length x. Thus, in order to generate effectively a large number of self‐avoiding chains with long sequences, we used the Wall–Erpenbeck s‐p method of chain enrichment [F. T. Wall and J. J. Erpenbeck (1959) J. Chem. Phys. 30, 634–637]. By examination of the radial distribution of the end‐to‐end distance and the chain‐length dependence of the quantity 〈r2〉/xl2 (〈r2〉 is the mean square end‐to‐end distance and l is the virtual bond length), it was found that unperturbed amylosic chains change in overall conformation from a non‐Gaussian chain having a helical character to Gaussian as x is increased, whereas perturbed chains do not show Gaussian behavior even at x = 500. For the perturbed chains, 〈r2〉 can be expressed by the equation 〈r2〉 = axb in the range of 100 ≤ x ≤ 500, where a and b > 1 are constants. From comparisons of the persistence vectors and perspective drawings of representative unperturbed and perturbed chains, we felt the local conformation of the amylosic chains, i.e., the local helical character, is also affected by the long‐range excluded‐volume interaction.
Selective binding and solvent denaturation
Authors: Schellman John A.
Published: May 2005

A primitive model for solvent denaturation is that the denaturant binds independently to sites exposed by the unfolding of the protein. For reagents like urea and guanidinium salts, this binding must be very weak since denaturation occurs only at very high concentrations. Standard formulas for very weak binding lead to thermodynamic inconsistencies. In this paper, binding by denaturants is treated as selective solvation. This introduces a factor of K 1 into the binding isotherm and binding free energy, where K is the equilibrium constant for selective interaction with the sites. This leads to a thermodynamically consistent description of the binding and the denaturation since, when K = 1, there is no selective interaction and no effect on denaturation, even in concentrated solutions where site occupancy is inevitable.
Correlation between the sequence‐length distribution and structure of statistical copolymers of L‐valine and γ‐benzyl‐L‐glutamate
Authors: Saudek V. , Stejskal J. , Schmidt P. , Zimmermann K. , Škarda V. , Kratochvíl P. , Drobník J.
Published: May 2005

Statistical copolymers were prepared from N‐carboxyanhydrides of L‐valine and γ‐benzyl‐L‐glutamate in dioxan with triethylamine as an initiator. The copolymerization conversion was determined by ir spectroscopy, the copolymer composition by amino acid analysis, and the molecular weights by light scattering. The monomer reactivity ratios were found to be rVal = 0.14 and rGlu(OBzl) = 6.4. High‐molecular‐weight copolymers are formed even at low conversions. The content of β‐structure in the copolymers was estimated from the ir spectra in copolymerization mixtures. The sequence‐length distribution of L‐valine and γ‐benzyl‐L‐glutamate copolymers was calculated and its dependence on copolymerization conversion is discussed. Relations between the sequence‐length distribution and the content of β‐structure were studied. It was found that the content of β‐structure in samples with the same composition is different for low‐ and high‐conversion copolymers. The formation of β‐structure in copolymers in the copolymerization mixture requires a certain minimal sequence length, which has been found to be about 6 valine units.
Electrophoretic mobility of λ phage HIND III and HAE III DNA fragments in agarose gels: A detailed study
Authors: Hervet H. , Bean C. P.
Published: May 2005

The electrophoretic mobility (μ) of DNA fragments from λ phage and ΦX 174, split by restriction enzyme to molecular lengths from 3 × 102 to 2.36 × 104 base pairs, has been investigated in 0.6–4% agarose gels at various field strengths, ionic strengths, and temperatures. As already observed, μ is seen to be very sensitive to the field, increasing with field strength. The sensitivity increases with the molecular length of the DNA and decreases at high gel concentration. Our data are in qualitative agreement with recent theoretical predictions that concern the influence of the electric field on electrophoretic mobility. Mobility data have been extrapolated to zero field. This enables a comparison of our experimental results with theoretical predictions on the dependence of μ on the molecular weight of the DNA fragments. Our data fit, quite closely, a reptation model, where the tube path is described as a semiflexible entity with a persistence length equal to the pore diameter. The influence of the agarose concentration and the ionic strength of the buffer on the two parameters of the model—intrinsic electrophoretic mobility (μ0) and the number of base pairs per element of the tube (g)—are well described by the model. The temperature dependence of the electrophoretic mobility, together with the influence of the agarose concentration on μ0, indicate that the hydrodynamic drag is the leading frictional force on the DNA molecules in the gel.
Two‐dimensional 1H‐nmr investigation of the water conformation of the atrial natriuretic factor (ANF 101–126)
Authors: Theriault Y. , Boulanger Y. , Weber P. L. , Reid B. R.
Published: May 2005

The complete sequential assignment of the 1H‐nmr resonance frequencies of the active fragment of the rat atrial natriuretic factor (ANF 101–126) has been performed. Two‐dimensional nmr techniques have been employed, including phase‐sensitive nuclear Overhauser spectroscopy (NOESY), relayed coherence transfer spectroscopy (RELAY), and J‐correlated spectroscopy (COSY). Experiments were performed both in D20 and H20 solutions at different pH values. With few exceptions, resonance frequencies were practically pH independent. NOESY spectra were recorded using both 300‐ and 500‐ms mixing times, and no long‐range connectivities were observed, leading to the conclusion that ANF 101–126 has no defined secondary nor tertiary structure in water in the pH range used (2.73–5.21).
Differential geometry and protein conformation. V. Medium‐range conformational influence of the individual amino acids
Authors: Rackovsky S. , Goldstein D. A.
Published: May 2005

A previous differential geometric analysis of the conformational properties of the various amino acids has been extended to study their influence on folding over a larger backbone interval. In addition, statistical effects associated with variation in the number of the individual amino acids in the database have been treated in greater detail, using a simulation method. It is found that the amino acids can be divided into three groups on the basis of their conformational influence over four‐Cα units in the interval i − 6 ⩽ j ⩽ i + 6. Group Ia is composed of seven amino acids (His, Leu, Ala, Met, Lys, Gln, Ile) that encourage the formation of AR‐helical structure. Group Ib (Glu, Phe, Trp, Val, Asp) is composed of amino acids with some helix‐forming tendency but that also show positive extended‐strand formation tendency. They therefore act as a bridge between group Ia and group II (Cys, Gly, Asn, Pro, Arg, Ser, Thr, Tyr) that contains amino acids that encourage the formation of extended structure and bends. The detailed four‐Cα conformational properties of each of the amino acids are shown, and the ability of amino acids to exert conformational influence in both directions along the backbone is examined. It is shown that, in general, such influence extends farther in the N‐terminal direction than in the C‐terminal direction. A framework is briefly sketched for using the present data to investigate actual folding mechanisms.
Prediction of protein–ligand interactions: The complex of porcine pancreatic elastase with a valine‐derived benzoxazinone
Authors: Presta Leonard G. , Meyer Edgar F.
Published: May 2005

Prior to availability of the crystal structure of the complex, we evaluated models of the complex between porcine pancreatic elastase and a t‐Boc–Val‐derived benzoxazinone inhibitor. Models of the noncovalent and covalent complex were generated using computer graphics and each model was subjected to energy minimization using molecular mechanics. After the crystal structure became available, we found that the model with the lowest energy was in good agreement with the crystal structure, except for the position of the His57 side chain. Permissible conformations of the inhibitor were based on information from x‐ray crystal structures and an earlier conformational energy investigation of t‐Boc–amino acids. We did not, however, limit ourselves to these conformations. The conformation of the inhibitor in the lowest energy model and crystal structure, was not similar to any of the minimum‐energy conformations of t‐Boc–amino acids. This suggests that limiting proposed binding modes only to the lowest energy conformations of a ligand (prior to binding) may sometimes unfairly bias the procedure.
Sequential resonance assignment of the 500‐MHz nmr spectrum of d‐(CG)6 and its structure under low‐salt conditions
Authors: Sheth Anu , Ravikumar M. , Hosur R. V. , Govil Girjesh , Zu‐Kun Tan , Roy K. B. , Miles H. Todd
Published: May 2005

Two‐dimensional (2D) nmr methods (correlated spectroscopy, nuclear Overhauser enhancement spectroscopy, and relayed correlated spectroscopy) have been used to obtain resonance assignment of the nonexchangeable base and sugar protons of a double‐helical DNA segment, d‐(CG)6 in D2O solutions under conditions of low ionic strength. Detailed information about the glycosidic torsion angle, sugar geometry, stacking patterns of the bases, and the overall solution structure of the dodecanucleotide has been obtained from the relative intensities of cross‐peaks in the 2D spectra. The molecule shows general features of B‐DNA under the experimental conditions employed. However, in spite of the repeating base sequence, there are subtle and detectable variations in the structure along the double helix. The terminal residues show considerable conformational flexibility.
Protein stability curves
Authors: Becktel Wayne J. , Schellman John A.
Published: May 2005

The stability curve of a protein is defined as the plot of the free energy of unfolding as a function of temperature. For most proteins the change in heat capacity on denaturation, or unfolding, is large but approximately constant. When unfolding is s two‐state process, most of the salient features of the stability curves of proteins can be derived from this fact. A number of relations are obtained, including the special features of low‐temperature denaturation, the properties of the maximum in stability, and the interrelationships of the characteristic temperatures of the protein. The paper closes with a formula that permits one to calculate small changes in stabilization free energy from changes in the melting temperature of the protein.
Pulsed electrophoresis: Some implications of reptation theories
Authors: Viovy Jean Louis
Published: May 2005

This is an attempt to provide some theoretical guidelines for understanding and developing the pulsed electrophoresis techniques proposed as powerful means for separating very large macromolecules such as chromosome‐sized DNA. We show that even a simple approach using recent theories for biased reptation and ignoring the detailed shape of relaxation functions leads to nontrivial predictions. These predictions are used to discuss the presently available pulsed electrophoresis methods. We focus on several practical limits imposed on experiments by the critical values of the parameters associated with different electrophoresis regimes, such as the limiting effective velocity, or the mobility gap associated with the drift resonance. Some conceptual problems that do not seem to have been considered yet are identified. In particular, we show that the early expectation that orthogonal‐field pulsed electrophoresis could be an efficient way to fight chain orientation is probably unpractical. We propose a different approach, emphasizing resonance aspects.
Conformational transitions of solubilized trout elastins
Authors: Guantieri V. , Jaques A. M. , Serafini‐Fracassini A. , Tamburro A. M.
Published: May 2005

CD measurements on polypeptides obtained from trout elastin by mild acid hydrolysis (α‐elastin) or cyanogen bromide cleavage (CB‐elastin) are compared with the results of analogous studies on bovine α‐elastin. The spectra show that bovine and trout elastin, despite their compositional differences, have a similar β‐turn content. This is discussed with reference to the molecular evolution of the protein and the function of β‐turns in elastin.
13C‐nmr chemical shift and conformation of L‐alanine residues incorporated into poly(β‐benzyl L‐aspartate) in the solid state
Authors: Tuzi Satoru , Komoto Tadashi , Ando Isao , Saito Hazime , Shoji Akira , Ozaki Takuo
Published: May 2005

13C‐nmr spectra of poly(β‐benzyl L‐aspartate) containing 13C‐enriched [3‐13C]L‐alanine residues in the solid state were recorded by the cross polarization–magic angle spinning method, in order to elucidate the conformation‐dependent 13C chemical shifts of L‐alanine residues taking various conformations such as the antiparallel β‐sheet, the right‐handed α‐helix, the left‐handed α‐helix, and the left‐handed ω‐helix forms obtained by appropriate treatment. The latter two conformations for L‐alanine residues are achieved when L‐alanine residues are incorporated into poly(β‐benzyl L‐aspartate). We found that the alanine Cβ carbon show significant 13C chemical shift displacement depending on conformational change, and gave the 13C chemical shift values at about 17 ppm for the left‐handed ω‐helix, 14 ppm for the left‐handed α‐helix, 15.5 ppm for the right‐handed α‐helix, and 21.0 ppm for the antiparallel β‐sheet relative to tetramethylsilane.
Condensation of DNA by multivalent cations: Considerations on mechanism
Authors: Bloomfield Victor A.
Published: May 2005

DNA is generally found within viruses and cells in a tightly packaged state, typically occupying only 10−4–10−6 of the volume of the uncondensed DNA wormlike coil. Condensation can be induced in vitro at low salt by the naturally occurring polyamines spermidine3+ and spermine4+, by hexammine cobalt (III), and even by Mg2+ in methanol–water mixtures. These condensates generally have an orderly, toroidal, or rodlike shape and size similar to that of DNA gently lysed from phage heads. It is also striking that the condensate size distribution is independent of DNA molecular length from 400 to 40,000 base pairs (bp), but that shorter DNA molecules (e.g., 150‐bp mononucleosomal DNA) cannot condense in this fashion. We have constructed a successive association equilibrium theory to attempt to explain these results, using an equation devised by Tanford for micelle formation. Most of the obvious attractive and repulsive free energy contributions (mixing, bending, hydration, and other nearest‐neighbor interactions) are linear in the amount of DNA incorporated, but the net attractive ΔG° grows nonlinearly because of the increasing average number of nearest neighbors of each duplex as the particle grows. In order that the size distribution have a maximum, a quadratic repulsive free energy is also required, arising from the electrostatic self‐energy of the incompletely neutralized particles. The net attractive free energy per base pair interaction is tiny, on the order of 10−3 kT. Despite the apparent generally correct order of magnitude of the various free energy terms, the calculated size distribution is smaller and narrower than observed experimentally. It appears that the size distribution of condensed particles is determined kinetically rather than thermodynamically. Very short DNA molecules cannot nucleate stable aggregates because they cannot develop adequate overlap, either internally or intermolecularly. A substantial fraction of rodlike condensates is observed in aqueous solutions only with a rather inefficient condensing agent, permethylated spermidine. This suggests that slow condensation kinetics may be required to overcome the high activation energy of highly distorted DNA bends or kinks at the turning points of rods. Evidence is reviewed that condensation may be associated with localized helix structure distortion provoked by condensing agents.
Cyclic retro–inverso dipeptides with two aromatic side chains. II. Conformational analysis
Authors: Yamazaki Toshimasa , Nunami Ken‐Ichi , Goodman Murray
Published: May 2005

The conformations of cis and trans cyclic retro–inverso dipeptides—2‐[(4‐hydroxy)benzyl]‐5‐benzyl‐4,6(1H,2H,3H,5H)‐pyrimidinedione (c[mPhe‐gTyr]), 2‐benzyl‐5‐[(4‐hydroxy)benzyl]‐4,6(1H,2H,3H,5H)‐pyrimidinedione (c[mTyr‐gPhe]), and 2‐benzyl‐5‐amino‐5‐[(4‐hydroxy)benzyl]‐4,6(1H,2H,3H,5H)‐pyrimidinedione {c[(α‐amino)mTyr‐gPhe]}—and the parent cyclic dipeptides—c[tyrosyl‐phenylalanine] (cis‐c[L‐Tyr‐L‐Phe]) and c[tyrosyl‐D‐phenylalanine] (trans‐c[L‐Tyr‐D‐Phe])—were studied by using 1H‐nmr spectroscopy and semiempirical energy calculations. In the cis compounds of all the cyclic retro–inverso and parent dipeptides, the most stable conformer has both aromatic side chains sharing the space over the backbone ring in a “face‐to‐face” fashion. All the trans compounds predominantly assume a “sandwich” conformation in which the two aromatic rings are folded back over the backbone ring on opposite sides. However, different conformational preferences were observed for the backbones between the retro–inverso and parent cyclic dipeptides. The parent cyclic dipeptide trans‐c[L‐Tyr‐D‐Phe] adopts two types of boat structures with different side‐chain orientations in almost equal amounts: one with the Tyr side chain in a pseudoaxial position and the Phe side chain in a pseudoequatorial position, the other with the Tyr side chain in a pseudoequatorial position and the Phe side chain in a pseudoaxial position. On the other hand, the cyclic retro–inverso dipeptides trans‐c[mPhe‐gTyr] and trans c[mTyr‐gPhe] assume only one type of boat structure in which the malonyl side chain is in a pseudoequatorial and the gem‐diamino side chain is in a pseudoaxial position.

In addition to the preferred conformations, the conformational energies of the CαCβ bonds in the malonyl and gem‐diamino residues were estimated from the temperature variation of vicinal 1H1H coupling constants for the HCαCβH groupings observed for the trans isomers of cyclic retro–inverso dipeptides. The energies were evaluated to be 1.1 and 1.8 kcal mol−1 for the malonyl and gem‐diamino residues, respectively. Applying these energies to the parent cyclic dipeptide trans‐c[L‐Tyr‐D‐Phe], the observed fractions of three side‐chain conformations are reasonably reproduced. The conformational energies as well as conformational properties of the molecules estimated in this investigation may be useful to refine force constants for both parent and retro–inverso peptides with aromatic side chains.
The elastic resilience of DNA can induce all‐or‐none structural transitions in the nucleosome core particle
Authors: Marky Nancy L. , Manning Gerald S.
Published: May 2005

DNA on the surface of the histone octamer in the native nucleosome core particle is modeled as a circumferentially wound elastic line on the surface of a cylinder. In a model for the radial transition, the line is allowed to straighten, and thus lose energy, by swinging off the surface, but it is impeded in such an excursion by a radial force field representing the attractive interaction between DNA and histone octamer. In a model for the axial transition, the line may straighten by becoming more parallel to a generator of the cylinder while remaining on the surface. In this mode of straightening, dimer–tetramer or tetramer–tetramer interfaces are disrupted, and the resulting energy gain impedes the transition. Both radial and axial transitions are predicted to occur in all‐or‐none fashion. We propose that these models are related to the abrupt transitions actually observed in the nucleosome core particle.
Effects of Na+ on the persistence length and excluded volume of T7 bacteriophage DNA
Authors: Sobel E. S. , Harpst J. A.
Published: May 2005

Total intensity, Rayleigh light scattering has been used to measure the rms radius, second virial coefficient, persistence length, and excluded volume of homogeneous T7 bacteriophage DNA as a function of Na+ concentration (0.005 to 3.0 M). All parameters decrease sharply as [Na+] increases, and tend to level off at high Na+. The variation of persistence length with [Na+] is consistent with predictions from counterion condensation theory.
The CD of ligand–DNA systems. I. Poly(dG‐dC) B‐DNA
Authors: Lying Reidar , Rodger Alison , Nordén Bengt
Published: May 2005

A systematic theoretical study of the CD of double‐stranded poly (dG‐dC) and its complexes with small molecules is presented. The intrinsic CD of the polymer and the induced CD of a transition belonging to a molecule bound to DNA are calculated using the matrix method. The calculations show considerable differences between pyrimidine–purine and purine–pyrimidine binding sites, and we find that the induced CD of a groove bound molecule is one order of magnitude stronger than that of an intercalated molecule. The results form a sound basis for interpreting the CD of ligand–DNA systems in terms of molecular geometry, interactions, and spectroscopy.
The construction of a trefoil knot from a DNA branched junction motif
Authors: Du Shou Ming , Seeman Nadrian C.
Published: May 2005

A DNA trefoil (31) knot has been constructed from a 104‐nucleotide molecule whose strands form a 3‐arm branched junction motif. This construction tests the notion that a node in a DNA knot can be equated with a half‐turn of double‐helical DNA, and is consistent with that concept. Of five 104‐mer sequences tested, only one produces high yields of the target knot. The other molecules produce larger quantities of circular material and of a knot containing more nodes. The key features that differentiate the successful design from the others are (1) the ligation takes place in the linker region between helical domains and (2) only six nucleotide pairs are used for each of the double‐helical arms of the junction. The successful design separates the double‐helical regions from each other by a spacer containing two deoxythymidine nucleotides at the site of the branched junction. © 1994 John Wiley & Sons, Inc.
α/310‐Helix transitions in α‐methylalanine homopeptides: Conformational transition pathway and potential of mean force
Authors: Huston Shawn E. , Marshall Garland R.
Published: May 2005

The conformational transition between the α‐ and 310‐helical states of α‐methylalanine homopeptides is studied with molecular mechanics. Conformational transition pathways for Ace‐(MeA)n‐NMe withn= 7, 9, and 11 are obtained with the algorithms of Elber and co‐workers [R. Czerminski & R. Elber (1990)International Journal of Quantum Chemistry, Vol. 24, pp. 167–186; A. Ulitsky & R. Elber (1990)Journal of Chemical Physics, Vol. 92, pp. 1510–1511]. The free energy surface, or potential of mean force, for the conformational transition of Ace‐(MeA)9‐NMe is calculated from molecular dynamics simulations, and a method is presented for the decomposition of the free energy surface into the constituent energetic and entropic terms, via the calculation of the required temperature derivativesin situ. For the AMBER/OPLS model employed here, the conformational transition pathways each contain a single 310‐helical‐like transition state, and the transition state potential energy relative to the 310‐conformation is 3 kcal/mol, independent of peptide length. Entropic stabilization in the barrier region significantly lowers the activation free energies for the forward and reverse transitions from the estimates of the barrier heights based simply on potential energy alone. © 1994 John Wiley & Sons, Inc.
Resistance to oxygen transfer in fermentation broths
Authors: Blakebrough N. , Hamer G.
Published: May 2005

The distribution of dissolved oxygen in agitated, sparger‐aerated aqueous solutions has been investigated by polarographic techniques. The results of the investigations are discussed in relation to earlier studies in bubble distribution in such systems. Liquid‐phase mixing is good at agitation intensities well below that necessary to disperse bubbles throughout the liquid.

Suspended solids interfere with the transfer of oxygen unless they are freely suspended. Discrete fibers (paper‐pulp) are much easier to suspend than molds in either filamentous or pellet forms. Mass‐transfer at the cell‐liquid interface appears to be unaffected, in both bacterial and mold suspensions, by the intensity of agitation, provided that the organisms are freely suspended.
Plate assay methods for amino acids. 1. A sensitive cup plate assay for lysine with Streptococcus faecalis ATCC 6057
Authors: Bolinder Arne E. , Lie Sturla , Ericson L.‐E.
Published: May 2005

A sensitive cup plate assay method for lysine on large plates using S. faecalis ATCC 6057 as the test organism is described in detail. Well‐defined zones of dense growth were obtained in a rectilinear dose—response range from 5 to 3000 μg. of L‐lysine/ml. Comparative assays on twelve different samples were carried out using the turbidimetric tube assay method with Leuc. mesenteroides ATCC 8042 and the cup plate method with S. faecalis ATCC 6057. Good agreement between the two assay methods was obtained for five samples. For the remaining seven samples the tube assay values were appreciably higher than those obtained by the plate method. This discrepancy is discussed. Pure lysine added to various sample extracts could be quantitatively recovered. The specificity of the lysine requirement of S. faecalis ATCC 6057 in the plate assay was also investigated. Under certain experimental conditions, a weak and variable response was obtained with D‐lysine and the polyamines cadaverine, spermine, and spermidine. There was generally no difficulty in distinguishing the D‐lysine and polyamine growth zones from the L‐lysine growth zones. This growth effect of D‐lysine and polyamines could be diminished and even completely abolished by increasing the DL‐hydroxylysine hydrochloride level in the plate medium. The lysine peptides glycyl‐L‐lysine and L‐lysylglycine gave excellent growth zones of the same appearance as those produced by L‐lysine. The activity of these two peptides in cup tests were on a molar basis about 70% of that of L‐lysine.
Submerged citric acid fermentation of beet molasses in tank‐type fermenters
Authors: Clark D. S. , Lentz C. P.
Published: May 2005

Ferrocyanide‐treated beet molasses was fermented in fully baffled mechanically agitated, 2.5‐liter, tank‐type fermenters using pellets of Aspergillus niger grown in shake flasks as an inoculum. The object of the study was to adapt the fermentation method previously developed in an unstirred tower‐type fermenter to a conventional tank‐type fermenter. Under selected conditions of stirring (agitator speed 400–700 rpm) and sparging (medium porosity sintered disk), high yields of citric acid (8.6% citric acid, 70% conversion of available sugar) were obtained in 140 hr. of fermentation. There was little relation between citric acid yield and aeration conditions in the fermenter as judged by mash viscosity measurements and sulfite oxidation studies.
Laboratory fermentors for submerged fermentation
Authors: Sikyta Bohumil , Šlechta Jaromír , Herold Miloš
Published: May 2005

In the present paper the authors described laboratory fermentors used in the Antibiotics Research Institute since 1958 for research concerning the technology of the biosynthesis of antibiotics and amino acids and other aerobic fermentations. The lids of the fermentors are made from stainless steel, the vessels are made from glass. The fermentors are placed, always four each, in eight water baths with automatic temperature regulation within a range of ±0.5°C. Details regarding construction, auxiliary equipment, and working procedures used for the sterilization of fermentors and media, inoculation, injection of additives, and defoaming are given. The set‐up for one‐stage and multi‐stage, batch and continuous cultivation are discussed.
Kinetic study of the salicylic acid fermentation
Authors: Hosler Peter
Published: May 2005

The metabolic pathway of degradation of naphthalene to salicylic acid has been studied by several investigators. The rates of conversion and of cell growth are the basis for the present study. In the early phase of the fermentation, the salicylic acid accumulation followed an exponential curve, as did the bacterial cell accumulation. In the second phase, most of the salicylic acid was produced according to a linear or zero reaction, at rates of 0.3 to 0.5 g./l./hr. A linear accumulation of microbial cell weight accompanied the linear salicylic acid formation. Despite the correlation of growth and salicylic acid production, the type or amount of nitrogen supplied for growth had only a small effect on yield over broad limits. The optimum pH for salicylic acid accumulation was approximately 6.5. Below this value a slower rate of production and lower final yield was seen. Above pH 6.5, a rapid degradation of salicylic acid was observed. A temperature range from 25 to 30°C. was optimum. At 35°C., no growth occurred, while at 20°C. very slow salicylic acid accumulation resulted.
Pure culture studies of the degradation of detergent compounds
Authors: Payne W. J.
Published: May 2005

It has been found that a bacterium (isolant C12B) grew poorly on 6 and 8 carbon alcohols, well on 10 and 12 carbon alcohols, and slowly but well on the 14 to 18 carbon compounds. Unexpectedly, resting cells oxidized the 6 and 8 carbon compounds most readily and cell‐free extracts oxidized 6, 8, and 10 carbon alcohols. Extracts from cells adapted to sodium lauryl sulfate oxidized the 12 carbon alcohol as well, if small concentrations of substrate were used. The bacterium grew on benzene sulfonate and adapted resting cells oxidized that compound. Pure culture degradation studies revealed that isolant C12B used only 11% of tetrapropylene ABS supplied as a sole carbon source, whereas 66% of sodium lauryl sulfate was degraded. Intermediate quantities of kerosene‐based alkyl benzene sulfonate and a tallow‐derived detergent were utilized. Extracts of another bacterium, TEG‐5, grown on tetraethylene glycol, contained enzymes which oxidized polyethylene glycols up to an average molecular weight of 600, but not any larger polymers. This oxidation was visualized by coupling to reduction of ferricyanide.
Preparation of radioactive biochemicals by use of yeast
Authors: Laufer Louis , Gutcho Sidney , Castro Thomas , Grennen Ruth
Published: May 2005

Sugar molasses of high specific activity is prepared by photosynthesizing C14O2 into sugar in a leaf of the Canna plant and then extracting the sugar. When T. utilis is grown in such a medium about 45% of the radioactivity is incorporated into the yeast cell; the remaining radioactivity is carbon dioxide and volatile organic compounds. The cells are now randomly labeled in all carbon compounds. Distribution of C14 in the major cell components, such as protein, polysaccharide, and nucleic acids is shown.

Nucleic acid is extracted from the cells and subject to chemical and enzyme action, for the preparation of randomly labeled ribonucleotides. Proteins are isolated and hydrolyzed to yield high specific activity amino acids, up to 150 mc. per millimole. Similarly polysaccharides are also isolated and from them high specific activity glucose and mannose are obtained by acid hydrolysis.

By growing T. utilis in a medium containing C14‐8‐adenine and C14‐2‐uracil, these bases are about 90% incorporated into the nucleic acids of the cell. Using the same methods described for the uniformly labeled nucleic acid only base labeled nucleosides and nucleotides are prepared.

Preparative procedures for the isolation of some of these compounds are discussed. The latest biochemical techniques for their purification are described. Methods for assaying for radiochemical purity and problems concerining stability of high specific activity compounds are discussed.
Effect of pretreatment on the extraction of proteins from plant sourcees
Authors: Rastogi M. K. , Murti C. R. Krishna
Published: May 2005

Solubilization of proteins from cereals, legumes, and oil seed cakes by alkali peptization and isoelectric precipitation is adversely affected if the source material is pretreated by ethanol or cooked under pressure. The degree of hydrolysis by trypsin of protein isolates obtained from unautoclaved materials is, however, considerably raised by heat treatment prior to enzymatic digestion.
Extracellular guanosine 5′‐monophosphate and guanosine 5′‐diphosphate in Bacillus subtilis Broths
Authors: Demain A. L. , Vitali R. A. , Wilker B. L. , Rothrock J. W. , Jacob T. A.
Published: May 2005

The ability of Bacillus subtilis to accumulate guanosine 5′‐monophosphate (5′‐GMP) extracellularly was demonstrated by isolation of 85% pure 5′‐GMP from the broth. In addition, a compound with the properties of guanosine 5′ diphosphate was obtained from the same broth.
Preparation of amphotericin B‐14C
Authors: Perlman D. , Semar Joan B.
Published: May 2005

In a study of fermentation methods of producing amphotericin B‐14C, a variety of C‐14 labeled precursors were added to cultures of the amphotericin‐B producing streptomycete growing in a glucose‐cottonseed meal medium. Acetate‐14C and propionate‐14C were efficiently incorporated into the amphotericin‐B while formate‐14C, glucose‐U‐14C and methionine‐14CH3 were not.
Simultaneous gas‐liquid interfacial mass transfer and uptake by small particles
Authors: Tsao George Tsu Ning
Published: May 2005

The presence of active small particles, such as bacterial cells, in a liquid will affect the rate of gas‐liquid interfacial mass transfer. A theoretical analysis of the situation is presented in this article.
Erythorbic acid fermentation
Authors: Takahashi Takeshi
Published: May 2005

A brief review of the development of the research on erythorbic acid fermentation was presented. A previously proposed scheme of the acid biosynthesis has been proved to be correct. D‐glucono‐γ‐lactone dehydrogenase was purified to 50 fold and compared with other lactone dehydrogenases. For the purpose of commercial development, screening and mutagenie treatments of strains and studies on fundamental cultural conditions were carried out. Penicillium, but no other genera, was obtained as a producer. The experiments of ultraviolet irradiation and various cultural conditions were successful in elevating the yield of the acid over 40% in jar‐fermentor to glucose supplied. The continuous multibed extraction system of anion‐exchange resin was developed and a yield of 19.2% of the acid from fermentation broth was obtained.
Aromatization of 9α‐hydroxy‐19‐norandrostenedione by Arthrobacter simplex
Authors: Pan S. C. , Semar Joan , Junta Barbara , Principe P. A.
Published: May 2005

9α‐Hydroxy‐19‐norandrostenedionc (9α‐hydroxy‐Δ4‐estrene 3, 17‐dione) (IV) was prepared by fermentation of 19‐norandroslenedione with Corynespora melanis or Norcardia restriclus. When incubated with a growing culture of Arthrobacter simplex or its acetone‐dried cells, IV was converted to 9α‐hydroxyestronc (VII) and 9‐keto‐9, 10‐secoestrone (VI). 9α‐Hydroxyestrone undergoes spontaneous as well as enzymic dehydration to form Δ9(11)‐estrone (IX). Both VI and IX have been isolated and identified as such while VII was isolated as its 3‐acetate.
L‐asparaginase synthesis by Escherichia coli B
Authors: Robison Robert S. , Berk Bernard
Published: May 2005

We have studied the influence of strain of organism, temperature, and medium on the production of the antileukemic intracellular enzyme L‐asparaginase by E. coli B grown in shaken flasks. Five strains of E. coli B exhibited wide differences in their capacities to synthesize the EC‐2 form of L‐asparaginase active against leukemia. For the most productive strain, when grown in a casein hydrolysate medium, maximal production of L‐asparaginase occurred at 25°C. At this temperature, the organism required glycerol, glucose, or other mono‐saccharides to synthesize L‐asparaginase. Synthesis was stimulated when glycerol was used in place of glucose, but not in its presence. The effect of glycerol on L‐asparaginase synthesis was most evident when the cells were grown at 37°C, rather than at 25°C. With 0.25% glucose, cells had a specific activity of 409 I.U./g; with glycerol cells had a specific activity of 553 I.U./g. At 25°C, both cell and L‐asparaginase synthesis were increased by the use of 0.25% glycerol resulting in only a slight increase in specific activity of the cells. The addition of zinc, copper, manganese, iron, L‐asparagine, L‐glutamine, or L‐aspartic acid had no effect on L‐asparaginase synthesis in the casein hydrolysate medium. L‐aspartic acid (10−2 M) enhanced L‐asparaginase synthesis in a synthetic medium that lacked these metals or L‐asparagine, L‐glutamine, or L‐aspartic acid; cells grown under these conditions had a specific activity of 90 I.U./g.

In the casein hydrolysate medium, cell morphology was correlated with temperature of incubation.
The separation of proteins with heteropolyacids
Authors: Sternberg M. Z.
Published: May 2005

The precipitation of proteins with heteropolyacids has been studied for the purpose of large scale primary purification. A precipitate will form if the pH of the reaction between purified ovalbumin, hemoglobin, trypsin, pepsin, bovine serum albumin, ovomucoid, gelatin or ribonuclease and tungstrophosphoric, tungstosilicic or molybdosilicic acid is close to the isoelectric point of the protein and does not cause the dissociation of the heteropolyacid. Below the isoelctric point, the percent precipitation depends on the conformational changes of the protein. The precipitation of ovalbumin with tungstophosphoric decreases as the ionic strength of the buffer increases and is independent, of the protein concentration. Mixtures of ovalbumin and bovine serum albumin, though having close isoelectric points, can be separated by varying the concentration of the precipitant. The electropositive groups which combine with the tungstophosphoric acid are guanidino, ε‐amino and imidazole. No precipitation is given by the α‐amino groups. Filtrates of microbial fermentations containing lactase, glucose aerode‐hydrogenase, alkaline protease, amyloglucosidase, and transglucosylase have been purified by precipitation with heteropolyacids.