bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability of polypeptide conformational states as determined by computer simulation of the free energy
Authors: Meirovitch H. , Vásquez M. , Scheraga H. A.
Published: May 2005

A method is developed to extract the entropy of polypeptides and proteins from samples of conformations. It is based on techniques suggested previously by Meirovitch, and has the advantage that it can be applied not only to states in which the molecule undergoes harmonic or quasiharmonic conformational fluctuations, but also to the random coil, as well as to mixtures of these extreme states. In order to confine the search to a region of conformational space corresponding to a stable state, the transition probabilities are determined not by “looking to the future,” as in the previous method [H. Meirovitch and H. A. Scheraga (1986) J. Chem. Phys. 84, 6369–6375], but by analyzing the previous steps in the generation of the chain. The method is applied to a model of decaglycine with rigid geometry, using the potential energy function ECEPP (Empirical Conformational Energy Program for Peptides). The model is simulated with the Metropolis Monte Carlo method to generate samples of conformations in the α‐helical and hairpin regions, respectively, at T = 100 K. For the α‐helix, the four dihedral angles of the N‐ and C‐terminal residues are found to undergo full rotational variation. The results show that the α‐helix is a more stable structure than the hairpin. Both its Helmholtz free energy F and energy E are lower than those of the hairpin by ΔF ∼ 0.4 and ΔE ∼ 0.3 kcal/mole/residue, respectively. It should be noted that the contribution of the entropy ΔS to ΔF is significant (TΔS ∼ 0.1 kcal/mole/residue). Also, the entropy of the α‐helix is found to be larger than that of the hairpin. This is a result of the extra entropy arising from the rotational freedom about the four terminal single bonds of the α‐helix.
Structural determinants of spermidine–DNA interactions
Authors: Vertino Paula M. , Bergeron R. J. , Cavanaugh Paul F. , Porter Carl W.
Published: May 2005

Twelve different analogs of spermidine (SPD) and SPD itself were compared for their ability to modulate two conformational transitions of DNA; the B‐to‐Z conformational transition of poly(dG‐me5dC) and the thermal melting transition of calf thymus DNA. The analogs consisted of five N‐ethyl‐SPD derivatives [N1‐ethyl‐SPD, N4‐ethyl‐SPD, N8‐ethyl‐SPD, N1,N8‐bis(ethyl)SPD and N1,N4,N8‐tri(ethyl)SPD], which differed in the number and/or position of the ethyl substitution (the alkyl series); three N‐acetyl‐SPD derivatives (N1‐acetyl‐SPD, N4‐acetyl‐SPD, and N8‐acetyl‐SPD), which were comparable to the N‐ethyl‐SPD derivatives but not protonated at the substituted amine (the acyl series); three aliphatic analogs [nor‐SPD, homo‐SPD, and N1,N9‐bis(ethyl)homo‐SPD], which differed in the interamine carbon chain length (homolog series), and 1,8‐diaminooctane, which was comparable in overall chain length to SPD but lacked a central nitrogen. By comparing the relative abilities of the various analogs and SPD to modulate DNA structural transitions, it is possible to gain insight into the relative significance of the number and location of protonated amines (acyl series), the number and location of steric groups (alkyl series), aliphatic chain length (homolog series), and the central amine (1,8‐diaminooctane) as determinants of SPD–DNA interactions. The B‐to‐Z conformational transition was facilitated to a midpoint by 2.4 μM SPD under conditions of low (i.e., 11 mM Na+) ionic strength. The phenomenon was affected most significantly by the number of protonated amines followed in rank order by location of the protonated amines, number of steric groups (bulk), steric group location, and aliphatic chain length. Stabilization of DNA to thermal melting was also most affected by the number of protonated amines followed by aliphatic chain length, number of steric groups, and location of protonated amines. In general, substitutions at the central (N4) amine of SPD exerted a significant influence on the B‐to‐Z transition but not on thermal melting.
Gas‐phase IR spectra of substituted alkylamides
Authors: Venkatachalapathi Yalamoori V. , Mierke Dale F. , Taulane Joseph P. , Goodman Murray
Published: May 2005

The source of the splittings observed in the amide A, I, II, and III absorption bands of N‐methylacetamide (NMA) have been determined by high‐resolution gas‐phase FTIR. Analysis of isotopically labeled NMA, along with simpler amides (formamide, acetamide) show that the observed splitting arise from rotational transitions within the vibrational manifold. The ir spectra of a homologous series of monosubstituted alkylamides are also examined. The observed effects on the ir spectra from incorporating substituents from methyl to t‐butyl on both sides of the amide linkage are discussed in terms of rotational transitions and coupled oscillations. During these studies we did not observe any evidence for the presence of cis conformations of the amide bond.
Bisintercalation of ditercalinium into a d[CpGpCpG]2 minihelix: Structure and dynamics aspects—a 400‐MHz 1H‐nmr study
Authors: Delbarre A. , Delepierre M. , D'Estaintot B. Langlois , Igolen J. , Roques B. P.
Published: May 2005

The structure of the complex formed in aqueous solution at pH 5.5 between ditercalinium, a potent antitumoral 7H‐pyrido[4,3‐c]carbazole rigid dimer, and the self‐complementary tetranucleotide d[CpGpCpG], was investigated by 400‐MHz 1H‐nmr. For a 1:2.5 drug‐to‐helix ratio, the dimer was only found in bound form, whereas free and complexed tetranucleotide were in slow exchange. This allowed unambiguous assignment of the protons in the complex through exchange polarization transfer measurements. The tetranucleotide existed as a right‐handed double helix in the complex. The strong upfield shifts measured on most aromatic protons on both drug and nucleobases as well as on DNA imino protons were consistent with bisintercalation of the dimer. According to the negative nuclear Overhauser effects generated to protons on the convex edge of the bound drug rings by saturation of sugar protons, it was concluded that ditercalinium was intercalated with its rigid bis‐ethyl bispiperidine spacer fitting the major groove of the helix. Difference in antitumor activity of various pyridocarbazole dimers is discussed in relation to the binding kinetics and the complex geometry determined in this study.
A 43Ca‐nmr study of Ca(II)–DNA interactions
Authors: Braunlin William H. , Drakenberg Torbjörn , Nordenskiöld Lars
Published: May 2005

High‐field 43Ca‐nmr is applied to characterize the interactions of calcium ions with double‐helical DNA. Under the conditions examined, 43Ca lineshapes are always Lorentzian and single spin‐lattice relaxation rates are obtained. The measured transverse and longitudinal relaxation rates are, however, not equal, which implies that the relaxation is in the near‐extreme narrowing regime. Relative to the transverse relaxation rate, calcium ions near the DNA exchange rapidly with the bulk solution. The 43Ca linewidths, spin‐lattice relaxation rates, and chemical shifts observed over the course of a titration of DNA with calcium salt are not well described by simple electrostatic models. Deviations are most pronounced at low ratios of calcium to DNA phosphate. In contrast, at higher Ca/P ratios, the changes observed are well described by an electrostatic model based on the Poisson–Boltzmann equation. These results suggest that there is a small class of site‐bound calcium as well as a large background of delocalized calcium electrostatically associated with the DNA. In contrast to previous studies of 25Mg2+–DNA interactions, for which significant site‐binding effects were also indicated, it appears rather easy to displace bound 43Ca2+ by competition with sodium or magnesium cations. Unfortunately, neither these earlier results nor the present work allows a precise quantitation of the extent of site‐bound divalent cation.
Sedimentation equilibrium in macromolecular solutions of arbitrary concentration. II. Two protein components
Authors: Chatelier Ronald C. , Minton Allen P.
Published: May 2005

Relations describing sedimentation equilibrium in solutions containing two macromolecular solute components are derived for the following cases: (1) two nonassociating proteins at arbitrary concentration, (2) one dilute self‐associating protein in the presence of a second inert protein at arbitrary concentration, and (3) two proteins at arbitrary concentration that can associate to form a single heterocomplex of arbitrary composition. As in earlier work (R. C. Chatelier and A. P. Minton (1987) Biopolymers, 26, 507–524), the relations are obtained by using scaled particle theory to calculate the thermodynamic activity of each species present at a given radial distance in the centrifuge. The results of numerical simulations of sedimentation equilibrium are presented as the dependence of apparent molecular weights, or apparent weight‐average molecular weights, upon solution composition. Semiempirical methods are presented, by means of which the weight‐average molecular weights of self‐ and heteroassociating proteins in highly nonideal solutions may be estimated from experimental data. It is found that the semiempirical methods yield reasonably accurate estimates of the true weight‐average molecular weight over a broad range of experimental conditions, providing that the partial specific volumes of two components in a heteroassociating system do not differ by more than about 0.05 mL/g.
Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. III. Probable and average conformations of enkephalin
Authors: Paine Gregory H. , Scheraga Harold A.
Published: May 2005

The program SMAPPS (Statistical‐Mechanical Algorithm for Predicting Protein Structure) was originally designed to determine the probable and average backbone (ϕ, ψ) conformations of a polypeptide by the application of equilibrium statistical mechanics in conjunction with an adaptive importance sampling Monte Carlo procedure. In the present paper, the algorithm has been extended to include the variation of all side‐chain (χ) and peptide‐bond (ω) dihedral angles of a polypeptide during the Monte Carlo search of the conformational space. To test the effectiveness of the generalized algorithm, SMAPPS was used to calculate the probable and average conformations of Met‐enkephalin for which all dihedral angles of the pentapeptide were allowed to vary. The total conformational energy for each randomly generated structure of Met‐enkephalin was obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. The interaction energies were computed by the program ECEPP /2 (Empirical Conformational Energy Program for Peptides). Solvent effects were not included in the computation. The results of the Monte Carlo calculation of the structure of Met‐enkephalin indicate that the thermodynamically preferred conformation of the pentapeptide contains a γ‐turn involving the three residues Gly2‐Gly3‐Phe4. The γ‐turn conformation, however, does not correspond to the structure of lowest conformational energy. Rather, the global minimum‐energy conformation, recently determined by a new optimization technique developed in this laboratory, contains a type II′ β‐bend that is formed by the interaction of the four residues Gly2‐Gly3‐Phe4‐Met5. A similar minimum‐energy conformation is found by the SMAPPS procedure. The thermodynamically preferred γ‐turn structure has a conformational energy of 4.93 kcal/mole higher than the β‐bend structure of lowest energy but, because of the inclusion of entropy in the SMAPPS procedure, it is estimated to be ∼ 9 kcal/mole lower in free energy. The calculation of the average conformation of Met‐enkephalin was repeated until a total of ten independent average conformations were established. As far as the phenylalanine residue of the pentapeptide is concerned, the results of the ten independent average conformations were all found to lie in the region of conformational space corresponding to the γ‐turn. These results further support the conclusion that the γturn conformation is thermodynamically favored.
Conformational constraints of amino acid side chains in α‐helices
Authors: Piela Lucjan , Nemethy George , Scheraga Harold A.
Published: May 2005

The conformational freedom of amino acid side chains is strongly reduced when the side chains occur on an α‐helix. A quantitative evaluation of this freedom has been carried out by means of conformational energy computations for all naturally occurring amino acids and for α‐aminobutyric acid when they are placed in the middle of a right‐handed poly(L‐alanine) α‐helix. One of the three possible rotameric states for rotation around the Cα  Cβ bond (viz. g+) is excluded completely on the helix because of steric hindrance, and the relative populations of the other two rotamers (t and g−) are altered because of steric interactions and the reduction of hydrogen‐bonding possibilities. The computed tendencies of the changes in distributions of rotamers, on going from an ensemble of all backbone conformations to the α‐helix, agree with the observed tendencies in proteins. Minimum‐energy side‐chain conformations in an α‐helix have been tabulated for use in conformational energy computations on polypeptides.
Ir spectra and conformational behavior of N‐acetyl‐(glycine, L‐alanine, L‐leucine)‐N′‐methylamides in chloroform
Authors: Jose Chalakkal I. , Belhekar Anagha A. , Agashe Mangala S.
Published: May 2005

NH stretching bands of N‐acetyl‐(glycine, L‐alanine, L‐leucine)‐N′‐methylamides in dilute chloroform solution have shown that these dipeptides are present as a mixture of intramolecularly hydrogen‐bonded five‐membered ring species and nonhydrogen bonded species. Integrated absorption intensity measurements revealed that the concentration of the intramolecularly hydrogen bonded species decreased from 62% in glycine to 35% in the L‐leucine derivatives.
Enthalpy and entropy changes for the intercalation of small molecules to DNA. II. Ethidium and propidium fluoride
Authors: Hopkins Harry P. , Wilson W. David
Published: May 2005

Enthalpy changes (ΔHB) for the binding of ethidium (a monocation) and propidium (a dication) to calf thymus DNA have been determined calorimetrically in piperazine‐N, N′‐bis(2‐ethanesulfonic acid) buffer with the fluoride ion as the counterion. Heats of dilution for the fluoride salts of ethidium and propidium were substantially less than the corresponding values found for other halide salts of these cations. At a Na+ ion concentrations of 0.019, ΔHB = −8.3 and −7.9 ± 0.3 kcal mol−1 for ethidium and propidium, respectively. For these two cations, just as was observed for the naphthalene monoimide (monocation) and diimide (dication) [H. P. Hopkins, K. A. Stevenson, and W. D. Wilson, (1986) J. Sol. Chem. 15, 563–579], ΔHB is within the same experimental error for both cations. Apparently, charge–charge interactions in DNA–cation complexes produce only small changes in the enthalpy for the system. In the concentration range 0.019–0.207, the ΔHB values for propidium did not depend appreciably on the Na+ ion concentration, and a similar pattern was shown to exist for ethidium. When these results were combined with ΔGB values for the binding of these cations to DNA, we found the variation of ΔSB with Na+ ion concentration to be remarkably close to the predictions of modern polyelectrolyte theory, i.e., propidium binding to DNA causes approximately twice as many Na+ ions to be released into the bulk solution as does the binding of ethidium. The much stronger binding of propidium, relative to ethidium, at low ionic strengths is thus seen to be primarily due to entropic effects.
The effect of anisotropic properties of randomly oriented particles on polarized light: An operational calculus for spatially heterogeneous distributions
Authors: Maestre Marcos F.
Published: May 2005

Recent publication of the application of Mueller–Stokes calculus to a model of optical microdomains by Hjelm et al. [(1986) Biopolymers 25, 1359–1378] states that the CD of randomly orientated microdomains show apparent CD due to the linear dichroism components. In this paper we show that these conclusions are erroneous due to a misapplication of the Mueller calculus to the model proposed by Hjelm et al. We show in detail where the errors were committed, and prove that the ordinary Mueller matrices cannot be used to compute the interaction of light with heterogeneous distributions of optical microdomains that lay in a plane perpendicular to the direction of the irradiation of light. We further prove that ordinary Stokes vectors do not represent the polarization properties of light in systems that are a heterogeneous distribution of optical microdomains in the plane perpendicular to the light beam. A modified optical calculus is proposed, in which extended space matrices and extended space polarization vectors will give the correct formulation for the heterogeneous distribution of microdomains. We prove that, for randomly orientated microdomains in space, the linear dichroism and linear birefringence components cancel, and the only remaining terms are those due to the intrinsic CD and circular birefringence. This result negates the explanation of Hjelm et al. about the induced CD in the Soret region of sickle hemoglobin gels.
Conformational behavior of the polysaccharide backbone of murein
Authors: Leps B. , Labischinski H. , Bradaczek H.
Published: May 2005

The energetically possible conformations for the alternating heteropolysaccharide backbone of murein, consisting of N‐acetylglucosamine and N‐acetylmuramic acid, were calculated using an empirical approach. The calculations were carried out for regular as well as for random‐chain polymers, resulting in a model for the saccharide strands featuring extended chains with a length increment of 0.98–1.02 nm per disaccharide unit and peptide attachment sites at every second saccharide residuum pointing into all directions with propagation angles of 80–100° between consecutive sites.
Vibrational CD of polypeptides. X. A study of α‐helical oligopeptides in solution
Authors: Yasui S. C. , Keiderling T. A. , Katakai Ryoichi
Published: May 2005

We have measured the vibrational CD (VCD) of a series of heterooligopeptides—o‐nitrophenylsulfenyl(L‐Met‐L‐Met‐L‐Leu) n‐OEt, n = 6,8,10,11–in the amide A, I, and II regions. These spectra are identical in shape and magnitude, within our signal to noise limits. The VCD in each band are of exactly the shape expected for a right‐handed α‐helix and imply that VCD of the polypeptide α‐helix is relatively unaffected by chain length down to the 18‐subunit level.
Theoretical conformational analysis of a μ‐selective cyclic opioid peptide analog
Authors: Wilkes Brian C. , Schiller Peter W.
Published: May 2005

The allowed conformations of the μ‐receptor‐selective cyclic opioid peptide analog
equation image
were determined using a grid search through the entire conformational space. Energy minimization of the 13‐membered ring structure lacking the exocyclic Tyr1 residue and the Phe3 side chain using the molecular mechanics program Maximin resulted in only four low‐energy conformations. These four ring structures served as templates for a further energy minimization study with the Tyr1 residue and Phe3 side chain added to the molecule. The results indicated that the Tyr1 and Phe3 side chains enjoy considerable orientational freedom, but nevertheless, only a limited number of low‐energy side‐chain configurations were found. The obtained low‐energy conformers are discussed in relation to various proposed models of the bioactive conformation of enkephalins and morphiceptin.
Conformations of the glycine dipeptide
Authors: Lau Wan F. , Montgomery Pettitt B.
Published: May 2005

Integral equation theory is applied to the determination of the intramolecular potential of mean force for the glycine dipeptide, N‐acetyl glycyl‐N‐methylamide, in aqueous solution. The solvated free energy for the dipeptide as a function of the dihedral angles ϕ and ψ (Ramachandran plot) is determined and compared with the vacuum surface. Conformations forbidden in vacuum are found to be populated in aqueous solution. The results of the glycine dipeptide are compared to a parallel study on the alanine dipeptide. Solvent effects are found to be responsible for the extent of many of glycines properties related to flexibility.
Shape effects in elastic scattering by orientationally random ensembles of simple model viruses
Authors: McClain W. M. , Ghoul W. A.
Published: May 2005

Recent theoretical work has shown that the complete set of polarized elastic light scattering studies should yield information about particle structure that has so far hardly been utilized. We present calculations of such light‐scattering properties for a number of model structures, exploring particularly the size limit at which the new effects should become visible. The particles are assumed to be randomly oriented in aqueous suspension, and all identical to each other. We compare several particle models of differing geometrical shape, but with identical forward scattering power and identical radii of gyration. We find that one of the ten observables shows particularly desirable properties as a general large‐particle characterization parameter: it is nonzero for all structures, it approaches zero as particle size decreases, and it shows an angular dependence that distinguishes among models of different shape. Assuming incident light at 350 nm, it differentiates between different shaped particles with radii of gyration as small as 50 nm. Such particles are well below the optical resolution limit and about the size of many types of viruses.
Conformational perturbation due to an extra adenosine in a self‐complementary oligodeoxynucleotide duplex
Authors: Roy Siddhartha , Sklenar Vladimir , Appella Ettore , Cohen Jack S.
Published: May 2005

The conformation of an oligodeoxynucleotide pentadecamer, d(CGCGAAATTTACGCG), self‐complementary except for an additional adenosine nucleotide at position 11, has been investigated with nmr spectroscopy. This oligomer was found to exist predominantly in the duplex form in solution rather than in the hairpin loop form, as observed previously for an analogous 13‐mer sequence. Nuclear Overhauser effects indicate that the B‐form conformation is disrupted by the extra A base, which forms a wedge within the duplex, producing a bent junction and an overall S‐like structure. A downfield‐shifted phosphate resonance was assigned using a two‐dimensional 1H–31P correlation method, and was found to be P12‐13. This and other results indicate that the extra A causes conformational distortions at some distance along the duplex structure.
Cyclic retro–inverso dipeptides with two aromatic side chains. I. Synthesis
Authors: Nunami Ken‐Ichi , Yamazaki Toshimasa , Goodman Murray
Published: May 2005

A series of 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]}—were synthesized in order to define the minimum structural requirements for binding affinity with opiate receptors and biological activity. Although the first two compounds lack a free amine proposed to be necessary for receptor recognition, the c[mPhe‐gTyr] and c[mTyr‐gPhe] analogues serve as model molecules in conformational studies of the target analogue, c[(α‐amino)mTyr‐gPhe]. The cis‐ and trans‐c[(α‐amino)mTyr‐gPhe] contain all the functional groups such as the amine and phenolic groups in the tyrosine, and the aromatic group in the phenylalanine, necessary for opiate activity. In addition, the c[(α‐amino)mTyr‐gPhe] analogues possess similar geometries to the Tyr‐Pro part of morphiceptin (Tyr‐Pro‐Phe‐Pro‐NH2) whose high μ‐receptor activity is attributed to conformations with the Tyr‐Pro amide bond in a cis conformation because the peptide bonds assume a cis conformation. However, both analogues are inactive in the guinea pig ileum and the mouse vas deferens assays. This may result from wrong orientation of the benzyl group of the gPhe residue with respect to the (α‐amino)mTyr residue.

Conformational studies of these molecules using 1H‐nmr spectroscopy and molecular mechanics calculations will be reported in the following paper. Results of conformational analysis should provide information about backbone–side‐chain interactions in the retro–inverso peptide chains since all the fundamental structural elements of the retro–inverso peptides are included in these model systems even though the peptide bonds must assume a cis conformation.
Distance‐dependent dielectric constants and their application to double‐helical DNA
Authors: Mazur J. , Jernigan R. L.
Published: May 2005

Detailed studies of structures of biological macromolecules, even in simplified models, involve many costly and time‐consuming calculations. Any thorough methods require sampling of an extremely large conformation and momentum space. Calculations of electrostatic interactions, which depend on many physical factors, such as the details of solvent, solvent accessibility in macromolecules, and molecular polarizability, are always developed in a compromise between more rigorous, detailed models and the need for immediate application to complicated biological systems. In this paper, a middle ground is taken between the more exact theoretical models and the simplest constant values for the dielectric constant. The effects of solvent, counterions, and molecular polarizability are incorporated through a set of adjustable parameters that should be determined from experimental conditions. Several previous forms for the dielectric function are compared with the new ones. The present methods use Langevin functions to span the region of dielectric constant between bulk solvent and cavity values. Application of such dielectric models to double‐helical DNA is important because base‐stacking preferences were previously demonstrated [A. Sarai, J. Mazur, R. Nussinov, and R. L. Jernigan (1988) Biochemistry, vol. 27, pp. 8498–8502] to be sensitive to the electrostatic formulation. Here we find that poly (dG) · poly(dC) can be A form for high screening and B form for low screening. By contrast, poly (dA) · poly(dT) can only take the B form. Base stacking is more sensitive to the form of the dielectric function than are the sugar–phosphate backbone conformations. Also in B form, the backbone conformations are not so affected by the base types as in A form.
Salt dependence and ion specificity of the coil–helix transition of furcellaran
Authors: Zhang Wei , Piculell Lennart , Nilsson Svante
Published: May 2005

The conformational transition and the cation‐binding properties of aqueous furcellaran (a gel‐forming, low‐sulfated polysaccharide of the carrageenan family) in various salts and salt mixtures was studied by optical rotation and by 133Cs‐nmr. The results were compared with theoretical predictions based on the Poisson–Boltzmann cell model (PBCM). The conformational transition of furcellaran occurs in a single step, which implies a nonblocklike distribution of sulfate groups along the polymer chain. The chloride salts of sodium, lithium, and tetramethylammonium are equally potent in inducing helix formation of furcellaran, indicating that these ions act by nonspecific electrostatic interactions. In contrast, the potassium and cesium ions specifically promote helix formation and aggregation (gelation) of furcellaran. The divalent calcium and magnesium ions are nonspecific, but more potent than the nonspecific monovalent ions in inducing helices. Anions differ in their capacity to stabilize the furcellaran helix in the sequence Cl− < NO < Br− < SCN− < I−. The iodide and thiocyanate anions impede aggregation and gel formation. 133Cs‐nmr chemical shifts indicate specific binding of cesium ions to the furcellaran helix. Thus, with respect to its ion specificity and ion‐binding properties, furcellaran, with 0.6 sulfate group per repeating disaccharide, resembles κ‐carrageenan (1 sulfate/disaccharide) but differs from ι‐carrageenan (2 sulfates/disaccharide). The conformational transition temperatures of furcellaran are, however, generally higher than those of κ‐carrageenan under comparable conditions, and in mixtures of the two polysaccharides, separate transitions still occur, indicating that no mixed helices are formed. The observed ion sensitivity and cation‐binding properties of furcellaran agree with predictions, by the PBCM, for a K‐carrageenan with a reduced charge density.
Conformational preferences of oligopeptides rich in α‐aminoisobutyric acid. I. Observation of a 310/α‐helical transition upon sequence permutation
Authors: Basu Gautam , Bagchi Ken , Kuki Atsuo
Published: May 2005

The solution conformation of peptides rich in the α,α‐dialkylated amino acid Aib has proven to be a subtle problem, not because of helix/coil transitions, but rather because of α‐helical/310‐helical competition. A special series of peptides containing 75% Aib has been synthesized that feature identical amino acid composition but differing sequences; they are sequence permutation isomers. Nuclear magnetic resonance hydrogen‐bonding studies reveal that there is a sequence permutation induced transition between the two alternative helical forms within this set. The implications for the design and conformational prediction of helical Aib‐rich peptides are discussed.
Molecular dynamics simulation of oligosaccharides containing N‐acetyl neuraminic acid
Authors: Mukhopadhyay Chaitali , Bush C. Allen
Published: May 2005

αD‐N‐acetyl neuraminic acid (Neu5Ac, sialic acid) is a commonly occurring carbohydrate residue in various cell surface glycolipids and glycoproteins. This residue is linked terminally or internally to Gal residues via an α(2 → 3) or α(2 → 6) linkage. In the cell surface receptor, sialyl‐LewisX, a terminal α(2 → 3) linkage is present. Previous studies from our laboratory have shown that in solution LewisX adopts a relatively rigid structure. In order to model the Neu5Ac residue, vacuum molecular dynamics of this monosaccharide were compared with simulations that explicitly include solvent water. The dynamical average of the monosaccharide conformation obtained from the two simulations was similar. Vacuum calculations for the disaccharide Neu5Ac α(2 → 3) Gal β‐O‐methyl show that a number of low energy minima are accessible to this disaccharide. Molecular dynamics simulations starting from the low energy minima show conformational transitions with a time scale of 10–50 ps among several of the minima while large barriers between other minima prevent transitions on the time scale studied. Simulations of this disaccharide in the presence of solvent show fewer conformational transitions, illustrating a dampening effect of the solvent that has been observed in some other studies. Our results are most consistent with an equilibrium among multiple conformations for the Neu5Ac α(2 → 3) Gal β linkage. © 1994 John Wiley & Sons, Inc.
Direct nuclear Overhauser effect refinement of crambin from two‐dimensional nmr data using a slow‐cooling annealing protocol
Authors: Bonvin Alexandre M. J. J. , Boelens Rolf , Kaptein Robert
Published: May 2005

The solution structure of crambin has been refined using a direct nuclear Overhauser effect (NOE) simulation approach (DINOSAUR) following a slow‐cooling simulated annealing protocol starting from eight previously obtained nmr and the x‐ray structures of crambin. Theoretical NOE intensities calculated with inclusion of local motions were directly compared to the experimental nmr data and forces were derived using a simple first‐order approximation for the calculation of the NOE gradient. A dynamic assignment procedure was applied for the peaks involving unassigned diastereotopic proton pairs or equivalent aromatic protons. With this approach, R factors could be minimized in a reasonable simulation time to low values (around 0.26) while deviations from ideal bond lengths and angles are still acceptable. The improvement in R factors is accompanied by an improvement of the precision of the structures, the rms deviations (rmsd; from the average) calculated on the ensemble of nine structures decreasing from 0.65 to 0.55 Å for backbone atoms and from 1.0 to 0.85 Å for all heavy atoms. The solution structure is significantly different from the x‐ray structure with rmsd for all atoms of 1.35 Å compared to 0.85 Å between solution structures. The largest differences are found for residues Thr‐21 and Pro‐22 in the loop region between the two α‐helices and for the side chain of Tyr‐29. © 1994 John Wiley & Sons, Inc.
Change in mobility of side chains due to neutralization of charged poly(L‐lysine) with dansyl group
Authors: Torii Toshinori , Yamashita Takashi , Horie Kazuyuki
Published: May 2005

Poly(L‐lysine) having dansyl (5‐dimethylamino‐1‐naphthalene‐sulfonyl) groups to its side chains was prepared. The fluorescence spectra and fluorescence anisotropy ratios of the dansyl (DNS) group were measured in various conditions. In aqueous solution the increase in emission intensity was observed reflecting the alkali‐induced coil‐to‐helix transition. In aqueous‐methanolic solutions with methanol content above 60 wt %, the poly(L‐lysine) with DNS group (DNS‐PLL) was probed to show α‐helical conformation from CD spectra. With addition of alkali, the increase in fluorescence intensity of α‐helical DNS‐PLL and the drastic change in fluorescence anisotropy ratio were observed. In this case the rotational mobility of DNS probe decreases, gives a minimum at a certain concentration of added alkali, and then increases again up to approximately the initial level. At the concentration where the rotational mobility gives the minimum, intensity of scattered light gives a maximum. This shows that suppression of the mobility of DNS side chains is caused by the intermolecular aggregation of α‐helical DNS‐PLL. This concentration of added alkali corresponds to the midpoint of neutralization to charged side chains of the DNS‐PLL. The interaction that causes aggregate of α‐helical DNS‐PLL is suggested to be the intermolecular hydrogen bonding between neutralized and unneutralized side chains. © 1994 John Wiley & Sons, Inc.
Configurational statistics of the DNA duplex: Extended generator matrices to treat the rotations and translations of adjacent residues
Authors: Marky Nancy L. , Olson Wilma K.
Published: May 2005

The base‐to‐base virtual bond treatment of nucleic acids used in statistical mechanical calculations of polynucleotide chain properties has been refined by incorporating the six parameters that relate the positions and orientations of sequential rigid bodies. The scheme allows for the sequence‐dependent bending, twisting, and displacement of base pairs as well as for asymmetry in the angular and translational fluctuations of individual residues. Expressions are developed for the generator matrices required for the computation, as a function of chain length, of various parameters measuring the overall mean extension and shape of the DNA. Quantities of interest include the end‐to‐end vector r, the square of the end‐to‐end distance r2, the square radius of gyration s2, the center‐of‐gravity vector g, the second moments of inertia S×2, and the higher moments of r and g. The matrix expressions introduced in the 1960s by Flory and co‐workers for the determination of configuration‐dependent polymer chain averages are decomposed into their translational and orientational contributions so that the methods can be extended to the rigid body analysis of chemical moieties. The new expressions permit, for the first time, examination of the effects of sequence‐dependent translations, such as the lateral sliding of residues in A‐ and B‐helices and the vertical opening of base pairs in drug–DNA complexes, on the average extension and shape of the long flexible double helix. The approach is illustrated in the following paper using conformational energy estimates of the base sequence‐dependent flexibility of successive B‐DNA base pairs. © 1994 John Wiley & Sons, Inc.
Economic definition of continuous fermentation goals
Authors: Bungay H. R.
Published: May 2005

A cost analysis of the continuous fermentation of penicillin G shows that materials cost and product yields are more significant than throughput rate. Number of fermentation stages, productivity, and the implications for research and development are discussed.
Production of cobamides by Butyribacterium rettgeri
Authors: Perlman D. , Semar Joan B.
Published: May 2005

Cobamide production by Butyribacterium rettgeri Barker and Haas (ATCC 10825) was studied on a laboratory scale. Yields of the order of 5 μg./ml. were obtained when this anaerobe was grown for 6 days at 37°C. in a medium containing glucose, cornsteep liquor, cobalt nitrate, calcium carbonate, and sufficient ammonium hydroxide to keep the pH between 6.0 and 7.2. All of the vitamin was found associated with the bacterial cells, and examination of extracts of these cells showed the presence of 5,6‐dimethylbenzimidazolylcobamide coenzyme in large quantities. Supplementation of the fermentation medium with a number of benzimidazoles resulted in formation of traces of “new” cobamides with these bases in the nucleotide protion of the cobamide. Supplementation with a number of purines did not result in incorporation of these moieties in the cobamide portion of the molecule.
Pilot plant batch production of Neurospora crassa
Authors: Ensign Stewart , Kaplan Sam , Bonner David M.
Published: May 2005

A 50‐gal. growth chamber is described together with its air filter and humidifier. The unit was designed especially for the production of Neurospora crassa, and was found to be effective in producing bulk amounts of mycelia with a high specific activity of tryptophan synthetase.
Pilot‐plant process for the isolation of a microbial polysaccharide with a quaternary ammonium compound
Authors: Albrecht W. J. , Sohns V. E. , Rogovin S. P.
Published: May 2005

Microbial polysaccharides which have many potential industrial applications are receiving more and more attention. One of the economic obstacles to the commercialization of these polysaccharides has been the cost of isolating them from fermented broth. To reduce this cost a recycling process was developed. The polyanionic polysaccharide synthesized from glucose by the activity of the bacterium Xanthomonas campestris NRRL B‐1459 is precipitated from the fermented broth with a quaternary ammonium compound (QAC).

QAC is removed from the precipitate with methanol leaving the water‐soluble polysaccharide. Evaporation of the methanol wash removed the methanol and substantially all the QAC was recovered in the concentrate. This was recycled for subsequent precipitations. Chemical assay and the viscosity of water solutions of the isolated polysaccharide indicate no adverse effects on it from recycled QAC. The cost to make this polysaccharide by the described procedure is estimated to be $1.14/lb. This cost estimate includes land, buildings, raw materials, equipment, labor and supervision, utilities, factory supplies, working capital, and plant overhead.
Evaluation of dead cell fractions in suspensions of Penicillium chrysogenum
Authors: Borzani Walter , Vairo Marina L. R.
Published: May 2005

An adsorption colorimetric method is proposed for the determination of the percentage of dead cells in suspensions of Penicillium chrysogenum, based on the observed fact that a linear relation exists between that percentage and the dye concentration at the equilibrium point.
Uniform inoculation of nutrient surfaces
Authors: Clark D. S.
Published: May 2005

A method of inoculating nutrient surfaces uniformly with bacterial cells has been developed. The method is based on controlled exposure of samples in a humidified chamber to a spray produced from a bacterial suspension. Factors affecting uniformity of inoculation (ionic strength of suspension, force of spray, distance between spray nozzle and sample, and exposure time) were studied in detail. Under optimum condition using agar medium in Petri plates, differences between total counts for six plates inoculated simultaneously, or between counts for individual 2 cm.2 areas taken at any location on any of the plates, were not statistically significant at the 5% level. The coefficient of variability for counts on 2 cm.2 areas renged from 8 to 12% between tests of 216 counts each.
Disposable shaker flasks
Authors: Falch E. A. , Hedén C.‐G.
Published: May 2005

A disposable plastic tetrahedron bag is described which is suitable for holding a 50 ml. culture on a shaker table. Bags can be made out of polypropylene or Teflon and they are quite simple and inexpensive. The tetrahedrons make excellent use of the shaker table space and they give a threefold increase in aeration efficiency over Erlenmeyer flasks.
The development of a process for recovering nucleotides from Bakers' yeast
Authors: Munden J. E. , Crook E. M. , Donald M. B.
Published: May 2005

A process has been developed giving over‐all yields of about 50%: which could be increased to about 80% with higher material costs and processing time. The preferred method of recovering nucleotides from the cytoplasm has been thermal extraction by means of a heat exchanger followed by filtration, protein precipitation, and carbon adsorption. The concentrated eluate from the carbon is absorbed onto Dowex 1 ion‐exchange resin, and groups of nucleotides are removed by pH‐defined eluents and recovered by a second carbon adsorption. Finally, standard ion‐exchange resolutions have been used to recover individual nucleotides. Other biochemicals in the extract have been investigated, and preliminary work has been done on the combination of nucleotide extraction with the recovery of nucleic acids from the residual cells.
Some systems for the biological oxidation of phenol‐bearing waste waters
Authors: Smith R. M.
Published: May 2005

Phenol‐bearing waste waters continue to be an area of wide concern for various industries faced with the task of cleaning up effluents containing relatively small amounts of these materials. The microbiological aspects of the degradation of these materials in pure culture and waste treatment plants is reviewed. Actual operating experiences at three plants of The Dow Chemical Company, where phenols are present in combination with other widely varying waste constituents, are discussed.
Estimating biodegradability and treatability of organic water pollutants
Authors: Ludzack F. J. , Ettinger M. B.
Published: May 2005

Biological purification of water pollutants depends upon a complex balance of organisms and environment conducive to effective metabolism. The bench scale test is useful to determine effects of a given waste water on that balance and to suggest controls promoting optimum purification. Applicability of laboratory results depends, in part, upon an experimental design similating anticipated operating conditions. This paper discusses advantages and limitations of historical bench‐tests as a guide for design of tests giving data that are more useful during full‐scale operation.
An apparatus for continuous electrophoresis on a preparative scale
Authors: Blakebrough N. , Brookes R.
Published: May 2005

A method of performing electrophoretic separations in a thin horizontal layer of continuously flowing buffer has been developed. The theoretical considerations that make possible the use of a thin layer for stabilization against convection effects, without the assistance of a packing material, are discussed. The apparatus is described together with an example of its performance, and a comparison with that of other workers.
The separation of biological mixtures by a liquid—liquid chromatography column containing differentially permeable partitions
Authors: Barker P. E. , Boaz R. W. , Gregory J. L.
Published: May 2005

The operation and construction of a liquid–liquid chromatography apparatus containing differentially permeable partions is described. The method is of value for the separation of heat sensitive and nonvolatile solutes.
Continuous cultivation of Escherichia coli possessing high penicillin–acylase activity
Authors: Sikyta Bohumil , Slezák Josef
Published: May 2005

The authors describe continuous cultivations of Escherichia coli possessing high penicillin‐acylase activity in corn‐steep liquor, peptone, and ammonium phenylacetate containing nutrient medium. If the cultivation is performed in the absence of ammonium phenylacetate the enzymic activities of cells from the batch as well as the continuous cultures are very low. The enzymic activity of cells in the batch process was considerably increased by the addition of 0.015% ammonium phenylacetate to the nutrient medium. Further increase of ammonium phenylacetate concentration did not result in any further increase of acylase activity. Continuous cultivation of the bacteria at the above ammonium phenyl‐acetate concentration was unsuccessful, as the enzymic activity of the bacteria constantly decreased during the process. On increasing the concentration of ammonium phenylacetate in the medium to 0.15% the authors succeeded in maintaining the enzymic activity of the bacteria at the same level as in the batch process performed at 0.015% concentration, throughout the whole continuous cultivation. At the dilution rate D = 0.5 hr.−1 the concentration of cells in the culture effluent from the fermentor at the steady state was equal to cell concentration at the end of batch cultivation. In relation to the cultivation time the output of cells in continuous cultivation is almost seven times higher as compared with the batch process.
Investigations of conditions for production of penicillin and chlortetracycline in submerged fermentation
Authors: Matelová V.
Published: May 2005

During investigations of submerged fermentation of penicillin and chlortetracycline, we reached the conclusion that production in relation to oxygen transfer is relatively uninfluenced by the composition of the fermentation medium. The maximum penicillin production, using the strain Penicillium chrysogenum NG in flasks on a shaker was uniformly achieved in all investigated media with an oxygen transfer rate of 0.81; and in chlortetracycline, using strain Streptomyces aureofaciens BMK−11, with an oxygen transfer rate of 0.59 ml. O2/ml./hour. The primary factor which influences the antibiotics production is the transfer of oxygen into the liquid. The absolute volume of production is, however, partly influenced by mechanical conditions of fermentation and the composition of the medium.
Measurement of the kinetics of biological systems at elevated temperatures utilizing flow techniques
Authors: Wang Daniel I‐C. , Humphrey Arthur E. , Eagleton Lee C.
Published: May 2005

Continuous flow‐type reactors have been used to study the kinetics of biological systems for quite some time. For continuous media sterilization, tubular flow reactors are particularly useful being simple in character and easy to control. However, one aspect quite often neglected in sterilization calculations is the residence time distribution of the reactor system. Serious errors in estimating the degree of bacterial destruction can be encountered if the residence time distribution is neglected; especially when a high degree of destruction is desired. This paper reports a study made to characterize and use the residence time distribution of a tubular reactor in the interpretation of high‐temperature, short exposure time data for inactivation of Bacillus stearothermophilus spores. Mathematical models accounting for the residence time distribution of the tubular reactor have been proposed and employed to obtain high‐temperature death‐rate data.