bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of the ising model for doubly ordered macromolecules
Authors: Tenenbaum A. , Triolo L.
Published: December 2004

We developed a statistical model, based on a one‐dimensional Ising model, for a recently studied polypeptide which displays an endothermic helix‐to‐coil transition with an “anomalous” behavior in the heat of solution. The model supports the assumption of an ordering of the chains due to a specific hydrogen bond interaction among them, beside the helical ordering of the backbone; this double ordering of the macromolecule produces the “anomalous” experimental behavior. With the hypothesis of a highly coopertive interaction among amide groups and side chains, we find that the backbone cooperation increases the chains cooperation, but not vice versa; this influence when the cooperation in the backbone increases.
Thermodynamics of oligo(A)N·2poly(U)∞ from the dependence of the temperature of the helix–coil transition on oligomer concentration
Authors: Blake R. D.
Published: December 2004

On the basis of elementary two‐state, ideal solution thermocynamics, a modified expression for the melting of oligo. polynucleotide helices is derived which is applicable to variations in TmN and/or oligomer concentration, Cm with oligomer length, N:

ΔHr is the enthalpy per helix residue, i.e., per base‐pair or base‐triplet, Vrf is the thermodynamic “available” or “reaction” volume, in liters/mole of helical residues; and n is the number of polynucleotide strands, e.g., n = 2 for oligo (A)N·2 poly(U)∞. Some earlier treatments have engendered confusion in the interpretation of the “reaction volume,” but with the derivation herein, the entropic origin and physical significance of Vrf is unequivocal.

The following approximation was arrived at for the reduction expected in the configurational entropy, ΔSrconf, ∞, for (A)∞·2(U)∞, when the poly(A), strand is substituted for by an equivalent strand of contiguous oligo(A)N,′s:

This adjustment of ΔSrconf, ∞ represents the source of the coefficient to 1/Tm∞ in expression (I). The expectation that ΔSrconf, N < ΔSrconf, ∞ is due to the effect of releasing normal internucleotide configurational restrictions every Nth residue in one‐third of the strands of the (A)N·2(U)∞ helix.

Although the reduction in ΔSrconf, ∞ (II) may seem small (i.e., only 5.5% for the tetramer), its effect on the magnitude of Vrf in expression (I) is exponential. Thus, without these considerations the quantitative applicability of earlier expressions is questionable.

By examining the variation in TmN with cm for a single N, all assumptions, required for evaluating Vrf or the entropic effects of discontinuities in the (A)N strand are avoided in the determination of a reliable enthalpy. We have therefore examined the system

and obtained a ΔHr = 12.58 ± 0.08 kcal per mole (A)·2(U) base‐triplets between 5 and 2.5°C. That this value for ΔHr is in such excellent agreement with all calorimetric values reported for (A)∞·2(U)∞ suggests that the enthalpy for reaction(III) is not significantly affected by disconnections in the backbone of (A)4·2(U)∞. From (I), Vrf = 6.0 × 10−4 1/mole or 1 Å 3per helical residue. ΔHr°, corrected for residual single‐strand stacking in (A)4, is in excellent agreement with that found earlier for (A)1·2(U)∞. A residual heat capacity of 90 kcal(±20) per mole (A)·2(U) base‐triplets per °C is deduced from the decrease of ΔHr° with temperature.
The determination of the thermodynamic parameter of the helix‐coil transition of polypeptides by means of dipole moment measurements
Authors: Dufour C. , Marchal E.
Published: December 2004

The theoretical change of the mean‐square dipole moment of a polypeptide during the helix‐coil transition is compared with the change in helix content. It is shown that, according to the theory, the determination of the helix initiation parameter σ and the enthalpy of helix formation ΔH can be determined. Experimental data on poly‐benzyl‐L‐gluatamate in two different solvent mixtures are given.
Complementary DNA base interactions: Application of recently refined electrostatic interaction theory
Authors: Stamatiadou Mary N. , Swissler T. J. , Rabinowitz James R. , Rein Robert
Published: December 2004

Electrostatic interactions between the DNA bases in the Watson‐Crick hydrogen bonding configuration are examined in both the molecular and the atomic multipole representation using three different methods of calculation: (a) CNDO wave functions and definitions of moments, (b) IEHT wave functions and division of two‐center densities and (c) IHET wave functions with equally divided overlap densities. It is shown that the inclusion in the interaction series of terms at least as high as the quadrupole‐quadrupole is required to quantitatively characterize the interactions. Convergence is more rapid with the atomic multipole representation and is unaffected by the type of assignment of formal charges. A quantitative approach to the problem of the role of electrostatic interactions in hydrogen bonding in DNA is thus provided, with obvious impact on the investigation of molecular recognition processes.
The circular dichroism of synthetic ribonucleic acids and the influence of uracil on conformation
Authors: Gray Donald M. , Tinoco Ignacio , Chamberlin Michael J.
Published: December 2004

We present CD spectra of four trinucleoside diphosphates, UpUpG, GpUpG, ApUpA, and ApUpG, of four single‐stranded polymers, poly AC, poly GU, poly AU, and poly AdU, and of five double‐stranded polymers, poly A:U, poly G:C, poly AU:AU, poly AdU:AdU, and poly GC:GC. The measured spectra are compared with empirical firstneighbor calculations. Our results, taken together with data from the literature, suggest that UpA and UpG sequences are relatively unstacked in a single‐stranded RNA compared with these isolated dimers in solution. These sequences may influence the structure and function of natural RNAs. Our results on double‐stranded RNAs indicate that the spectral changes which occur upon formation of a double helix are unique to the type of base pair involved and are relatively independent of sequence.
Characterization of two sequential polytripeptides containing glycine and ethyl‐glutamate residues
Authors: Rippon W. Barton , Chen H. H. , Anderson J. M. , Walton A. G.
Published: December 2004

The polytripeptides poly(glu(OEt)‐gly‐gly) and poly(glu(OEt)‐glu(OEt)‐gly) have been synthesized and characterized using infrared linear dichroism, ultraviolet circular dichroism spectroscopy, and electron microscopy. Both polymers have been obtained in a cross β conformation with antiparallel chains, however, there appear to be significant differences in the stability of this conformation for the two polymers. Poly(glu(OEt)‐gly‐gly) has also been shown to exist in a 31 polyglycine II type helix in aqueous solution whereas films cast from this solution appear to be random. Finally this same polymer can be obtained in either a random or an extended form trifluoroacetic acid depending on the nature of the substrate used for film casting.
“Increased‐valence” formulas for the iron–ligand bonding of some ferrohaemoglobin compounds
Authors: Harcourt R. D.
Published: December 2004

Valence formulas are constructed for the iron–ligand groups of the oxy‐, carboxy‐, nitric oxide‐, and nitrosobenzene derivatives of haemoglobin. To do this, the newly developed “increased‐valence” theory3 is used. The most stable of these valence formulae are able to account simply for certain iron‐ligand properties, with the iron remaining essentially as ferrous, as it is in haemoglobin.
Three‐stranded helix–coil equilibrium in polyuridylic acid–adenosine complex
Authors: Damle Vinayak N.
Published: December 2004

Interaction of poly U (polyuridylic acid) and adenosine is studied by following the changes in ultraviolet absorbance in the wavelength region near the isochromic wave‐length for the complex formation. The interaction is studied as a function of temperature, concentration of adenosine, and ionic strength, while the concentration of poly U was held constant. It is confirmed that only the three‐stranded complex with the stoichiometry 1A to 2U is formed and that it dissociates directly into free poly U and adenosine. No discontinuity of any kind was apparent in the melting curves, and poly U was found to possess no ordered structure above 10°C under the conditions used. The results were, therefore, analyzed in terms of an exact helix–coil equilibrium theory using the mismatching model, i.e., assuming that either completely formed base triplet or completely free unbonded bases only exist, and that the two sections of the polymer chains forming closed loops need not contain the same number of unbonded bases. Self‐association of free adenosine was taken into consideration. (Base triplet is analog of base pair for a three‐stranded helical complex. It refers to a unit of three coplanar bases, in this case two uracils and one adenine, hydrogen bonded to one another to form a triplet. Such triplets may stack over one another along the helical axis, and when they are so stacked the bases of two triplets next to each other may have stacking interactions between them.)

The values for enthalpy and entropy changes, both per mole of base triplets, were obtained for the following processes at neutral pH and moderate to high salt concentrations. (1) Growfh: Binding of one adenosine molecule to two uracil residues (one from each poly U strand) to form a base triplet next to an already formed base triplet with which it has stacking interactions, a process that involves both hydrogen bonding and base stacking interactions, ΔHs, = −19 ± 2 kcal, ΔSs = −55 ± 6 clausius; (2) Initiation: Binding of one adenosine molecule to two uracil residues (one from each poly U strand) to form an isolated base triplet, a process that involves only hydrogen bonding interactions, ΔHb* = 4.5 ± 2 kcal, ΔSb* = 6.6 ± 3 clausius; and (3)Interruption: Unstacking of two stacked base triplets initially next to each other by formation of an interruption (viz. a closed loop) between them, a process that involves only base stacking interactions, ΔHb = 23.5 ± 3 kcal, ΔSb = 61.6 ± 7 clausius, where the entropy changes include contributions other than the configurational entropy of closed loops. The discrepancy between our results and the calorimetric ΔHs of −13 kcal is attributed to (i) the possible effects of salt arid polymer on the self‐association of free adenosine, (ii) the uncertainty in the value of the parameter for the probability of ring closure, and (iii) the contributions due to the partial molal enthalpy of the solvent and the unstacking of any poly U structure to the calorimetric enthalpy.
Electrical conductivity in the solid state of sodium salts of calf thymus DNA
Authors: Lecompte M. F. , Muller D. , Jozefowicz M.
Published: December 2004

A dc conductivity study of native and denatured samples of sodium salts of calf thymus DNA in the solid state was performed at different temperatures and water content. From the results obtained it appears that the major carrier of conductivity is either electronic or ionic, depending upon the temperature of the sample, the water content, and the fact that the conductivity of native samples is higher than that of the denatured ones. These results have been confirmed by dc conductivity studies of poly U and poly A.
Co‐oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. III. Co‐oligopeptides of L‐phenylalanine, L‐tryptophan, and glycine: Synthesis and ultraviolet absorption properties
Authors: Guarnaccia Rocco , Rizzo Vincenzo , Gianola Pietro , Luisi Pier Luisi
Published: December 2004

The preparation of the co‐oligopeptides of the series H‐Gly‐Phe‐(Gly)n‐Trp‐Gly‐OH (n = 0, 1, 2) and of other free peptides of glycine, L‐tryptophan, and L‐phenylalanine is reported. The syntheses have been carried out by conventional methods, using N‐hydroxysuccinimide esters for the coupling steps. The ultraviolet absorption properties of the free peptides have been investigated in water. No hypo‐ or hyperchromicity was found for the aromatic chromophores, with the exception of H‐Gly‐Phe‐Trp‐OH, which shows a small but significant hypochromicity. The contribution of the peptide bond to the molar absorptivity in the far ultraviolet has been separated from that of the side chain plus the COO− group by plotting the measured molar absorptivity ϵ of the farthest accessible uv maximum as a function of the number of peptide bonds (nA). The peptide bond contribution proved to be independent of nA in the range nA = 1–5, thus ruling out the onset of helical conformations in the longer chain peptides.
Very low‐angle light scattering. A characterization method for high‐molecular‐weight DNA
Authors: Levine Harold I. , Fiel Robert J. , Billmeyer Fred W.
Published: December 2004

A very low‐angle light‐scattering photometer is described with respect to optical features, scattering cell, correction factors, and absolute calibration in the angular range 2°–35°. An improved microfiltration apparatus was used to obtain essentially dust‐free aqueous solutions for very low‐angle light scattering. The instrument was calibrated with silicotungstic acid, an absolute molecular‐weight standard, and the calibration was confirmed with the use of several secondary standards.

Very low‐angle light‐scattering measurements were made to determine the weight‐average molecular weight M̄r and z‐average radius of gyration Rg,z of a commerical preparation of calf‐thymus DNA. Microfiltration of the solutions allowed measurements down to 6°. The value M̄r = 20.0 × 106 obtained by extrapolating 6°–9° data to 0° is more than three times that from 30°–75° data (6.38 × 106) but ∼20% smaller than that from 10–35° data (23.7 × 106). The experimental errors in M̄r and Rg,z are estimated to be ±8% and ±14%, respectively. Combined 6°–75° data from two photometers fit well a theoretical scattering curve for a model wormlike coil of the same M̄r as the DNA sample.
Theoretical calculations of the helix–coil transition of DNA in the presence of large, cooperatively binding ligands
Authors: McGhee James D.
Published: December 2004

Theoretical calculations are conducted on the helix–coil transition of DNA, in the presence of large, cooperatively binding ligands modeled after the DNA‐binding proteins of current biological interest. The ligands are allowed to bind both to helx and to coil, to cover up any number of bases or base pairs in the complex, and to interact cooperatively with their nearest neighbors. The DNA is treated in the infinite homogeneous Ising model approximation, and all calculations are done by Lifson's method of sequence‐generating functions. DNA melting curves are calculated by computer in order to expolore the effects on the transition of ligand size, binding constant, free activity, and ligand–ligand cooperativity. The calculations indicate that (1) at the same intrinsic free energy change per base pair of the complexes, small ligands, for purely entropic reasons, are more effective than are large ligands in shifting the DNA melting temperature; (2) the response of the DNA melting temperature to increased ligand binding constant K and/or free ligand activity L is adequately represented at high values of KL (but not at low KL) by a simple independent site model; (3) if curves are calculated with the total amount of added ligand remaining constant and the free ligand activity allowed to vary throughout the transition, biphasic melting curves can be obtained in the complete absence of ligand–ligand cooperativity. In an Appendix, the denaturation of poly[d(A‐T)] in the presence of the drug, netropsin, is used to verify some features of the theory and to illustrate how the theory can be used to obtain numerical estimates of the ligand binding parameters from the experimental melting curves.
Evidence for long‐range interactions in DNA. Analysis of melting curves of block polymers d(C15A15)·d(T15G15), d(C20A15)·d(T15G20), and d(C20A10)·d(T10G20)
Authors: Wartell Roger M. , Burd John F.
Published: December 2004

The influence of one DNA region on the stability of an adjoining region (telestability) was examined. Melting curves of three block DNA's, d(C15A15)·d(T15G15), d(C20A15)·d(T15G20), and d(C20A10)·d(T10G20) were analyzed in terms of the nearest neighbor Ising model. Comparisons of predicted and experimental curves were made in 0.01 M and 0.1 M sodium ion solutions. The nearest neighbor formalism was also employed to analyze block DNA transition in the presence of actinomycin, a G·C specific molecule. The results show that nearest neighbor base‐pair interaction cannot predict the melting curves of the block DNA's. Adjustments in theoretical parameters to account for phosphate repulsion assuming a B conformation throughout the DNA's do not alter this conclusion. Changes in the theoretical parameters, which provide good overall agreement, are consistent with a substantial stabilization of the A·T region nearest the G·C block. The melting temperature T A·T for the average A·T pari in d(C20A10)·d(T10G20), with 10 A·T pairs, appears to be 4°C greater than TA·T for d(C15A15)·d(T15G15) and d(C20A15)·d(T15G20), both with 15 A·T pairs. Actinomycin bound to the G·C end effectively stabilizes the A·T end by 9°C. These results indicate a long‐range contribution to the interactions governing DNA stability. A possible mechanism for these interactions will be discussed.
Reconstitution of collagen‐fold structure with stretching of gelatin film
Authors: Tanioka Akikiko , Miyasaka Keizo , Ishikawa Kinzo
Published: December 2004

The gelatin film is stretched more 100% over 75% relative humidity, while the dried gelatin extended only several percent. In this experiment the gelatin film was stretched in a solution of water and ethanol. The sample was extended to 650% of its initial length when ethanol/water was 1.5(w/w) at 30°C. The wide‐angle X‐ray diffraction photographs of drawn samples showed the three important layer lines with approximate spacing of 10 Å, 4 Å, and 3 Å, which verify the reconstitution of collagen triple helical structure. The sharp spots appeared near 10 Å on the equatirial axis, indicating the high orientation of peptide chains. These patterns become sharp and clear on increasing the extension ratio.

The content of the triple helix was investigated by wide‐angle X‐ray diffraction and differential scanning calorimetry. The maximum renaturation percentage is 25% at the draw ratio of 7.5. Since the formation of a collagen triple helix requires three chains, in which each chain has only three repeatin amino acids, (Gly‐Pro‐X)n, and glycoprotein and other impurities interrupt helix formation, the more advanced renaturation will not be expected.
The optical birefringence of DNA solutions induced by oscillatory electric and hydrodynamic fields
Authors: Wilkinson Robert S. , Thurston George B.
Published: December 2004

The optical birefringence induced in DNA solutions by both oscillating hydrodynamic fields (flow birefringence) and oscillating electric fields (Kerr effect) is measured over a wide frequency range. The observed frequency response of the birefrigence is compared with theories for rigid ellipsoidal particles and for Gaussian chains. DNA at 6 × 105 molecular weight is found to exhibit rigid particle hydrodynamic behavior, while DNA at 5 × 106 molecular weight behaves like a flexible chain. Characterization of the hydrodynamic relaxation spectra for the DNA's by oscillatory flow birefringence allows precise comparison between theory and the experimental Kerr effect response. The dielectric model for DNA contains both permanent and dispersionless induced dipole moments. The dielectric behavior of DNA has the character of a permanent dipole but with anomalous low‐frequency dispersion in the Kerr effect. The existing theories do not adequately describe this dispersion. A fluctuation dipole mechanism with relaxation times comparable to those associated with the hydrodynamic motion could possibly demonstrate the observed polar behavior.
The effects of isolated N‐methylated residues on the conformational characteristics of polypeptides
Authors: Tonelli Alan E.
Published: December 2004

Conformational energies have been estimated for the tripeptide fragments L‐Ala‐N‐methyl‐L‐Ala‐L‐Ala, L‐Ala‐L‐Ala‐N‐methyl‐L‐Ala, L‐Ala‐Sar‐L‐Ala, and L‐Ala‐Gly‐N‐methyl‐L‐Ala. The peptide bonds connecting L‐Ala and Gly with N‐methyl‐L‐Ala and L‐Ala with Sar were permitted to adopt the planar cis as well as the usual trans conformation. Contour maps of the conformational energies of the central residue in these tripeptide fragments are presented and compared to the conformational energy maps previously calculated for unmethylated L‐Ala and Gly surrounded by residues which are also unmethylated. In generl it is observed that L‐Ala and Gly residues that are either N‐methylated in their conformational freedom relative to the same residues in an unmethylated polypeptide chain.
Switching of turn conformation in an aspartate anion peptide fragment by NH · · · O− hydrogen bonds
Authors: Onoda Akira , Yamamoto Hitoshi , Yamada Yusuke , Lee Keonil , Adachi Seiji , Okamura Taka‐aki , Yoshizawa‐Kumagaye Kumiko , Nakajima Kiichiro , Kawakami Toru , Aimoto Saburo , Ueyama Norikazu
Published: January 2005

Aspartic acid protease model peptides Z–Phe–Asp(COOH)–Thr–Gly–Ser–Ala–NHCy (1) and AdCO–Asp(COOH)–Val–Gly–NHBzl (3), and their aspartate anions (NEt4)[Z–Phe–Asp(COO−)–Thr–Gly–Ser–Ala–NHCy] (2) and (NEt4)[AdCO–Asp(COO−)–Val–Gly–NHBzl] (4), having an invariant primary sequence of the Asp–X(Thr,Ser)—Gly fragment, were synthesized and characterized by 1H‐NMR, CD, and infrared (IR) spectroscopies. NMR structure analyses indicate that the Asp Oδ atoms of the aspartate peptide 2 are intramolecularly hydrogen‐bonded with Gly, Ser, Ala NH, and Ser OH, supporting the rigid β‐turn‐like conformation in acetonitrile solution. The tripeptide in the aspartic acid 3 forms an inverse γ‐turn structure, which is converted to a β‐turn‐like conformation because of the formation of the intramolecular NH · · · O− hydrogen bonds with the Asp Oδ in 4. Such a conformational change is not detected between dipeptides AdCO–Asp(COOH)–Va–NHAd (5) and (NEt4)[AdCO–Asp(COO−)–Val–NHAd] (6). The pKa value of side‐chain carboxylic acid (5.0) for 3 exhibits a lower shift (0.3 unit) from that of 5 in aqueous polyethyleneglycol lauryl ether micellar solution. NMR structure analyses for 3 in an aqueous micellar solution indicate that the preorganized turn structure, which readily forms the NH · · · O− hydrogen bonds, lowers the pKa value and that resulting hydrogen bonds stabilize the rigid conformation in the aspartate anion state. We found that the formation of the NH · · · O− hydrogen bonds involved in the hairpin turn is correlated with the protonation and deprotonation state of the Asp side chain in the conserved amino acid fragments. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
Conformational aspects of polypeptide structure XIV. Synthesis of L‐glutamate oligomers via active ester and azide coupling reactions
Authors: Goodman Murray , Rosen Ira G. , Safdy Max
Published: December 2004

In this paper we have once again shown the general utility of the modified active ester synthesis using a dipeptide active ester. We have also demonstrated that the acyl azide coupling method using the modifications of Rudinger and Honzl, and Schwyzer make a good general method for the synthesis of complex oligopeptides. This method employs reactions known to give products of high optical purity in reasonable yields. The use of the t‐butyloxycarbonyl hydrazyl (CBH) blocking group provides a good route to hydrazides of esters of glutamic acid. The classical route to prepare hydrazides involves the displacement of an ester with hydrazine. Such a pathway is clearly impossible because of the γ‐esters. Finally we demonstrated that trifluoroethanol is an excellent solvent for catalytic hydrogenation reactions.
Conformational aspects of polypeptide structure XV. Synthesis of co‐oligomeric peptides of glutamic‐aspartic acids and glutamic acid‐glycine
Authors: Goodman Murray , Rosen Ira G.
Published: December 2004

We have synthesized three series of co‐oligomers of the following type:
magnified image
where Z represents the carbobenzoxy blocking group and the subscripts can assume various small integral values.

The first series includes the dimer (a = 1, b = 0), trimer (a = 1, b = 1) and pentamers (a = 2, b = 1) and was prepared using the p‐nitrophenyl ester technique. The second series is made up of dimer (n = 1, m = 0), trimer (n = 1, m = 1), pentamer (n = 2, m = 1), heptamer (n = 3, m = 1) and undecamer (n = 5, m = 1) and was prepared using mixed anhydrides and modified azide reactions. Lastly, the third series is composed of an octamer (w = 0, x = 3, y = 2) a decamer (w = 0, x = 3, y = 4) and an undecamer (w = 2, x = 3, y = 2). This group of compounds was synthesized by using p‐nitrophenyl ester and modified azide reactions.
Three‐component theory for the approach to sedimentation equilibrium in a density gradient
Authors: Hearst John E.
Published: December 2004

A three‐component theory for the approach to sedimentation equilibrium in a density gradient is developed starting from the ‐phenomenological equations of irreversible thermodynamics. It is concluded that in the limit of infinitely dilute macromolecule, the properties of the solvated molecule are being measured as might be expected.
Crosslinked synthetic polypeptides. I. Preparation and characterization of crosslinked poly Glu51‐Lys33Tyr16 and of poly Glu52Lys33Tyr15 no. 3
Authors: Marfey Peter S. , Gill Thomas J. , Kunz Heinz W.
Published: December 2004

Crosslinked synthetic polypeptides of poly Glu51Lys33Tyr16 (mol. wt. 31,000) and of poly Glu52Lys33Tyr15 (No. 3) (mol. wt. 52,000) containing from one to six crosslinks per molecule have been prepared by use of FFDNB, WRK and ICD reagents.

The monomeric fractions of these derivatives were isolated by Sephadex G‐100 chromatography. The number of crosslinks per molecule of DNPene derivatives was determined by total hydrolysis of the derivatives, isolation of O, N∈‐DNPene‐Tyr‐Lys bridges by paper chromatography and then spectrophotometric quantitation. The number of the amide‐type crosslinks in Am derivatives was established by their deamination followed by total hydrolysis and quantitation of the remaining lysine residues. Crosslinked derivatives appear to have a more compact structure, as judged by their behavior on the Sephadex columns and by their intrinsic viscosities. They were further characterized in regard to their amino acid composition, average number of the crosslinks per molecule, nitrogen content, solubility, root‐mean‐square end‐to‐end distance, and their spectral properties. Their properties recommend them as useful models for the study of the tertiary structure of proteins in solution.
Statistical mechanics of noncovalent bonds in polyamino acids. II. Combinatorial formulation for short chains, including hydrophobic bonding in random coil
Authors: Poland Douglas C. , Scheraga Harold A.
Published: December 2004

A combinatorial formulation of the partition function is developed for short polypeptide chains, where summations can be evaluated. From the complete combinatorial expression it is possible to assess the validity of any approximations which are made in evaluating the partition function. It is shown that it is an excellent approximation to consider the hydrogen‐bonded portion of a short (20 residues) chain as consisting of a single helical sequence of any size, with all sizes of helical sequences being about equally probable at the transition temperature. Another approximation, involving a linear dependence of the energy and entropy on the number of hydrogen bonds, helps to clarify the nature of the intermediate states in the denaturation process. Expressions are developed which incorporate the effect of hydrophobic bonds on the stability of the α‐helix, and the binding of water to the random coil. It is concluded that hydrophobic bonds in helical sequences can greatly stabilize the helix, but that similar bonds in the random coil can largely offset this stabilization.
Statistical mechanics of noncovalent bonds in polyamino acids. III. Interhelical hydrophobic bonds in short chains
Authors: Poland Douglas C. , Scheraga Harold A.
Published: December 2004

A partition function is derived for a simple model of interacting helices in a short (20 residues) chain of poly‐L‐alanine. It is found that interhelical hydrophobic bonds effect a marked stabilization of helical forms, and give rise to a sharp transition of the type found in many proteins.
Statistical mechanics of noncovalent bonds in polyamino acids. IV. Matrix treatment of hydrophobic bonds in the random coil and of the helix–coil transition for chains of arbitrary length
Authors: Poland Douglas C. , Scheraga Harold A.
Published: December 2004

The Lifson‐Roig matrix theory of the helix–coil transition in polyglycine is extended to situations where side‐chain interactions (hydrophobic bonds) are present both in the helix and in the random coil, as discussed for short chains in paper II of this series. It is shown that the conditional probabilities of occurrence of any number and size of hydrophobic pockets in the random coil can be adequately described by a 2 × 2 matrix. This is combined with the Lifson‐Roig 3 × 3 matrix to produce a 4 × 4 matrix which represents all possible combinations of any amount and size sequence of α‐helix with random coil containing all possible types of hydrophobic pockets in molecules of any given chain length.
A practical method for partial purification of the organism of psittacosis grown in chicken embryo yolk sac
Authors: Shirey William N. , Dorsey Warren G. , Patrick William C.
Published: December 2004

A procedure described for the partial purification of suspensions of the organisms of psittacosis utilizes tryptic digestion, calcium chloridedextran sulfate precipitation, and centrifugation through a sucrose barrier. More than 40% of the organisms in the original suspension are recovered in 80% of the original volume, with approximately 95% of the lipids and 85% of the proteins removed. This method is suggested as a preliminary purification procedure in laboratories desiring relatively large amounts of purified agent for studies on metabolism, physical properties, or antigenicity of the organism. Significant aspects of the investigations leading to the selection of the procedures are included.
A vibrating mixer for agitation of suspension cultures of mammalian cells
Authors: Ulrich K. , Moore G. E.
Published: December 2004

A new type of mixer that utilizes the Bernoulli effect has been found highly useful for providing gentle agitation in suspension cultures of fragile mammalian cells in culture volumes up to 6 l.
Mass transfer and mixing rates in fermentation vessels
Authors: Blakebrough N. , Sambamurthy K.
Published: December 2004

The effects on mass‐transfer and overall mixing rates of varying impeller geometry and operating speed have been studied for flat‐bladed turbines in laboratory fermentors, in aerated aqueous solutions, and in unaerated and aerated suspensions (1.6% w/v) of paper pulp. In the absence of suspended solid, oxygen absorption rates could be correlated directly with power input. In the pulp suspension, oxygen absorption at a given power input was influenced by impeller geometry and operating speed. The data for the three‐phase system can be correlated by a dimensionless equation relating oxygen‐transfer rates and mixing times to the geometrical and operating parameters of the impellers.
Power requirement in non‐newtonian fermentation broth
Authors: Taguchi Hisaharu , Miyamoto Saburo
Published: December 2004

Power requirements in the agitation of non‐Newtonian fermentation broths with and without aeration were measured by a strain gage‐type dynamometer. Broth from the production of gluc‐amylase by Endomyces species and carboxymethyl cellulose solutions were used as non‐Newtonian fluids. In gas–liquid agitation systems, the correlation between Pg and P02 ND3/Q0.56 observed by Michel and Miller was found to be applicable to non‐Newtonian fluids in laminar and transition regions. This was particularly true for fluids with apparent viscosities larger than 300 cp. The impeller diameter and impeller blade width had considerable effects on power consumption in a nongassed system. It was suggested, therefore, that Pg/P0 should be correlated by a dimensionless term involving some impeller‐size factors.
Dissolved oxygen measurements in pilot‐ and production‐scale novobiocin fermentations
Authors: Steel R. , Maxon W. D.
Published: December 2004

Dissolved oxygen measurements were made in pilot (20 and 250 l.) and production scale (15,000 l.) novobiocin fermentations. Bulk mixing was found to be incomplete in pilot tanks with turbine impellers of D/T = 0.40 (where D is impeller diameter, and T is tank diameter) but appeared homogeneous with impellers of D/T = 0.69. In the former case, the respiration rate was presumably limited by insufficient oxygen supply in areas of poor bulk mixing, whereas, in the latter case, the major resistance was between the bulk of the liquid and the cell (intraclump resistance). Higher agitator speeds decreased the gas–liquid resistance proportionally more than they reduced the liquid‐cell resistance. In production fermentors, dissolved oxygen measurements indicated that bulk mixing was complete with each of the three impeller sizes tested (D/T = 0.28, 0.33, and 0.43), but that the respiration rate was again limited, mainly by a resistance between the bulk of the liquid and the cell.
Stochastic models for sterilization
Authors: Fredrickson A. G.
Published: December 2004

Probabilistic models for the killing of microorganisms are formulated and described. The utility of the models is illustrated by applying them to the optimization of an idealized fermentation process.
Mass culture of red halophilic bacteria
Authors: Kushner D. J.
Published: December 2004

Extremely halophilic bacteria, which are able to grow in, and require, saturated or near‐saturated salt solutions are both of historical interest and of practical importance as food spoilage organisms. In addition, because of the environment in which they live, their membranes, enzymes, and ribosomes have unusual or unique properties that make them especially worthy of physiological study. A simple method for growing large quantities of extreme halophiles is described, and various growth media, both complex and synthetic are discussed.
Propagation of Bacillus popilliae in laboratory fermentors
Authors: Sharpe E. S.
Published: December 2004

The insect pathogen Bacillus popilliae Dutky causes a fatal milky disease of Japanese beetle larvae. Spores of the bacterium offer a biological means of controlling this insect. While satisfactory sporulation in vitro has not yet been accomplished, conditions have been developed for the proliferation of vegetative cells in shaken flasks and aerated fermentors. Vegetative cultures are maintained by frequent transfer or by lyophilization. Media based on yeast extract are used routinely, but corn steep liquor and casein hydrolyzates afford comparable yields of 5 × 108 cells/ml. in 16–24 hr. Nutritional requirements have been established for growth in a synthetic medium. Oxygen availability affects the pathway of carbohydrate catabolism and is necessary for optimal growth. In rapidly growing cultures, a short period of maximum viability is characteristically followed by rapid death of the cells. When inoculum size and transfer time are suitably manipulated, viable cell yields reach 1–2 × 109/ml. Alternative methods of propagation, including the addition of particulate carbon, and procedures designed either to neutralize acids or to remove metabolic products by dialysis, do not markedly enhance the yield of cells per volume of medium, although viability may be prolonged.
Effect of manganese and other heavy metals on submerged citric acid fermentation of molasses
Authors: Clark D. S. , Ito K. , Horitsu H.
Published: December 2004

The addition of as little as 2 ppb of manganese to ferrocyanide‐treated beet molasses during citric acid fermentation by Aspergillus niger NRC A‐1‐233 caused a 10% reduction in acid yield and undesirable change in the morphology of the organism from the normal pelletlike form to the filamentous from. Still smaller additions (0.4‐2ppb) caused undesirable pellet clumping, while greater additions (2‐100 ppb) gave further decreases in yield. The yield obtained at 100 ppb was less than 25% of that obtained at 1 ppb or less. None of the other metals tested (Al3+, Ca2+, Co2+, Cu2+, Fe2+, Mg2+, Ni2+, Zn2+) visibly changed pellet morphology, and only Al3+, Fe2+, and Zn2+ at relatively higher concentrations (5–25ppm) reduced acid yield. The adverse effect of manganese on growth and acid production was not affected by addition of the other metals.
Scale‐up of antibiotic fermentations by control of oxygen utilization
Authors: Jensen A. L. , Schultz J. S. , Shu P.
Published: December 2004

Oxygen Utilization as a scale‐up parameter is evaluated in two antibiotic‐producing fermentations. This method of scale‐up was used in tank‐to‐tank and in flash‐to‐flash scale‐up studies. Antibiotic yields and cell weight trends were generally duplicated in the replicate runs, with some discrepancy noted in chlortetracycline yields at high aeration levels. The apparatus for measuring oxygen consumption rates and for automatically controlling oxygen utilization, according to a predetermined pattern, is described.
Study of the dynamic behavior of the chemostat system
Authors: Koga S. , Humphrey A. E.
Published: December 2004

This paper deals with a theoretical study on the dynamic, character of the chemostat system. It. is primarily based on the Monod model for growth limitation, although certain more complex models are considered. Since the Monod model is described in terms of two variables, an analysis by use of a phase plane plot will show the various possible types of behavior theoretically expected for transient conditions of the system. In this paper it will be shown that the chemostat system might show an overshoot (or an underswing) with respect to changes in cell and substrate concentrations, depending on the extent to which the system might be disturbed from steady‐slate conditions. Other types of transient behavior ran also be expected when one of the system parameters such as dilution rate or input substrate concentration is disturbed in a stepwise manner. The simple Monod chemostat model was found never to oscillate in either a damped or a sustained manner as has been experimentally reported. Discussion is included about the transient behavior of other chemostat models such as that involving a variable yield coefficient, i.e., including the effect of cell maintenance requirements.
Methane as a carbon substrate for the production of microbial cells
Authors: Hamer G. , Hedén C.‐G. , Carenberg C.‐O.
Published: December 2004

The cultivation of aerobic, methane‐utilizing, microbial cells by submerged culture techniques, in an entirely mineral salts medium, with a view to their use as an edible protein source is discussed. Particular emphasis is placed on the potentially explosive nature of gaseous mixtures containing methane and oxygen. The experiments described investigate if fully safe operation at all times, by oxygen concentration control, is possible in agitated and sparged batch fermentors. Appreciable wastage of methane is prevented by gaseous‐phase recirculation. It is concluded that fully safe operation is possible, cultures being able to grow exponentially without substrate limitation by the gaseous‐phase nutrients.
Electronic sizing and counting of bacteria
Authors: Edwards Victo R. H. , Wilke Charles R.
Published: December 2004

An electronic apparatus is described that permits rapid determination of the concentration and size distribution of bacteria in electrolyte suspensions by a resistance method. The resulting size‐concentration distribution may be displayed on an oscilloscope and recorded with an X–Y plotter and an electric typewriter‐tape punch unit. The paper tape is analyzed with a computer program. Comparisons are made between electronic measurements of bacterial cell concentration and size distribution and values obtained by other methods. Effects of heat‐killing and disruption of the cell membrane on the electrical counting characteristics of the organisms are discussed.
The role of aeration and agitation in the production of glucose oxidase in submerged culture
Authors: Zetelaki Kornelia , Vas Karoly
Published: December 2004

The influence of agitation and aeration on growth and on production of glucose oxidase of Asp. niger has been studied. It was found that both rate of growth and glucose oxidase production was higher at an agitation speed of 700 rpm than at 460 rpm. Further increase in speed of agitation resulted in neither a higher rate of growth nor a higher glucose oxidase activity. Total glucose oxidase activity was highest in a medium containing 5% sugar (at an agitation speed of 700 rpm) and did not get higher when the sugar concentration of the medium was increased to 7%. When pure oxygen was bubbled through the culture the rate of growth of the culture (in the linear phase) was 95 mg. mycelial dry wt./100 ml./hr., and only 61 mg. when air was applied. The glucose oxidase activity of oxygenated culture was double the activity of aerated culture. Viscosity of the homogenized culture became higher with higher concentration of mycelia. The viscosity of oxygenated culture was found to be lower than that of aerated culture.
Some aspects of the metabolism of a partially colloidal substrate
Authors: Berg R. H. , Phillips D.
Published: December 2004

The biochemical oxygen demand (BOD) of a complex, partially colloidal substrate is divided into oxidation (fo) and synthesis (fs) fractions. The substrate being investigated is a suspension containing 10 mg./l. of dry skim milk. The oxidized and synthesized fractions of the BOD are shown to be 38.4% and 61.6%, respectively. The division of BOD is related to the time at which maximum cell growth appears. The time required to obtain maximum cell production is shown to be at least 10 hr. The relationship between the time to maximum cell production and the apparent initial activity of the seed organisms is discussed.
Transient response of continuous cultures to changes in temperature
Authors: Ryu D. Y. , Mateles R. I.
Published: December 2004

The purpose of this experimental study was to examine the transient response of a chemostat‐type continuous culture of Escherichia coli B to step changes in temperature by following transient limiting substrate concentration and calculating from it the transient growth rate. The transient response to step changes of temperature was tested for four different situations. In the first two cases, temperature was shifted down from 37 to 27°C., and 37 to 32°C. In the last two, it was shifted up from 32 to 37°C., and 27 to 37°C. When the temperature was shifted up, the growth rate increased rather rapidly to its transient maximum value and then decreased slowly until it, settled back into the steady‐state value. On the other hand, when the temperature was shifted down, the growth rate decreased relatively rapidly to its transient minimum and then it slowly increased and returned gradually to the steady‐state value. The magnitude of the transients was less than would be expected if the transient growth rates followed an Arrhenius function.
Toxic and inflammatory properties of two antibiotics: Muconomycin A and B
Authors: Guarino A. M. , Mendillo A. B. , DeFeo J. J.
Published: December 2004

Toxicological investigations were conducted on two new antibiotics, Muconomycin A and Muconomycin B. These non‐nitrogenous antibiotics were found to be highly toxic and capable of inducing profound inflammation in the peritoneal cavity of male albino rats. Either antibiotic produced large volumes (10–20 ml) of inflammatory exudate even when injected intraperitoneally in quantities of 1.6 × 10−10 moles. An extensive profile of the electrolytes and proteins found in inflammatory exudates was developed. Simultaneous assays of the blood serum of treated rats provided a basis for comparing the concentrations of constituents of serum with those of the exudate. The results of these assays showed that the exudate contained lower concentrations of sodium and proteins, and greater amounts of potassium, calcium, and phosphorus than the serum. Chloride ion concentrations were variable. Since previous work showed that one of the manifestations of toxicity of these substances was the production of creatinuria, further studies were carried out with ATP/Creatine Phosphotransferase. These studies show that these antibiotics are potent in vitro inhibitors of the enzyme ATP/Creatine Phosphotransferase.
Continuous cultivation of Saccharomyces cerevisiae. II. Growth on ethanol under transient‐state conditions
Authors: Mor Juan R. , Fiechter Armin
Published: December 2004

Growth of Saccharomyces cerevisiae LBG H 1022 on ethanol under transient‐state conditions was studied. As a cultivation device, an aerated Chemap fermentor combined with continuously working gas analyzers for oxygen and carbon dioxide was used. Yeast cell dry matter, substrate concentration, specific oxygen uptake, specific carbon dioxide release, and respiration quotient were measured during the different transient states. Depending on which range of the dilution rate the initial steady state was found, we obtain different responses to the shift experiment. For the lower range, up to D = 0.07, we deal with damped oscillations ranging above and below the steady‐state values. For the higher specific growth rates, the rate of damping is strongly enhanced and the shape of the curves becomes an asymptotic approach to the final steady states.
The influence of dissolved oxygen partial pressure on the level of various enzymes in mouse LS cells
Authors: Self Daphne A. , Kilburn D. G. , Lilly M. D.
Published: December 2004

The intracellular levels of seven enzymes in mouse LS cells growing in suspension culture at controlled dissolved oxygen partial pressures (pO2) have been measured. During the growth of each culture large fluctuations were observed in the levels of some enzymes, particularly aldolase and cytochrome oxidase. Mean values for the concentration of each enzyme during the growth phase have been calculated. These results are discussed in relation to previous observations made on the growth of mouse LS cells.
Cultivation of the yeast Candida lipolytica on hydrocarbons. II. One‐stage continuous cultivation on gas oil
Authors: Dostálek M. , Munk V. , Volfová Olga , Fencl Z. , Pecka K.
Published: December 2004

Continuous cultivation of the yeast Candida lipolytica on gas oil was studied from the viewpoint of biomass production and oil deparaffination. Optimum conditions wore found at the dilution rate D = 0.16–0.19 when biomass productivity 1.7 g/l/hr and yield coefficient. y = 0.92 were achieved. At deparaffination to the same freezing point, more than double the production of biomass and deparaffined oil during a given time unit was achieved in a continuous process than in batch cultivation. Consumption of substrate was followed in both cultivation processes and it was confirmed that individual n‐alkanes of gas oil were degraded at various rates and yields. Results proved optimum cultivation conditions to depend on concentration and composition of the paraffinic fraction of gas oil used. To achieve these conditions the continuous process may be controlled by choice; of suitable dilution rate and concentration of gas oil.