bluuebunny/crossref_metadata_2025 huggingface dataset:
Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures
Authors: Sheridan Robert P. , Dixon J. Scott , Venkataraghavan R. , Kuntz I. D. , Scott K. P.
Published: May 2005

We examine the correlation between the sequence and tertiary structure for 212 domains from globular proteins and polypeptides. The sequence of each domain is described as a set of 25 features: the mole percent of 20 amino acids, the number of residues in the domain, and the abundance of four simple patterns in the hydrophobicity profile of the sequence. Each domain, then, is described as a location in 25‐dimensional sequence‐feature space. We use pattern‐recognition methods to find the two axes through the 25‐dimensional sequence‐feature space that best discriminate, respectively, predominantly α‐helix domains from predominantly β‐strand domains (the “secondary structure vector,” SV) and parallel α/β domains from other domains (the “parallel vector,” PV). When we divide the domains into two categories based on whether the cysteine content is above (CYS‐RICH) or below (NORMAL) 4.5%, we find the secondary structure vector for the subset of CYS‐RICH domains points in a significantly different direction than the equivalent vector for the NORMAL domains. Thus, CYS‐RICH and NORMAL, domains are best treated separately. The secondary structure vector and the parallel vector for NORMAL domains describes statistically meaningful information, but the secondary structure vector for CYS‐RICH domains may not be as reliable. We show how the secondary structure content of a NORMAL domain can be predicted by projecting the domain in the feature space onto the secondary structure vector. We subdivide the domains into five structural classes based on whether there is a parallel or mixed β‐sheet in the domain and whether there are more helix or strand residues: NORMAL ALPHA, NORMAL BETA, NORMAL PARALLEL, CYS‐RICH ALPHA, and CYS‐RICH BETA. When we project the NORMAL domains onto the plane containing the origin of the feature space and SV and PV, we see that ALPHA, BETA, and PARALLEL, domains cluster in the plane, with the BETA cluster partially overlapping the PARALLEL cluster. The separations between the clusters are such that, by looking at the location of any given NORMAL domain in the plane, we can correctly predict its structural class with 83% accuracy. CYS‐RICH ALPHA and BETA domains cluster when projected onto the CYS‐RICH SV vector, and the classes can be preducted with 83% accuracy, but this accuracy for CYS‐RICH domains may not be statistically meaningful.
Conformations of dinucleoside monophosphates in relation to duplex DNA structures
Authors: Rao Shashidhar N. , Sasisekharan V.
Published: May 2005

Mononucleotide conformations are important in understanding the structural aspects of nucleic acids and polynucleotides. In order to study the influence of stacking interactions between adjacent bases in a polynucleotide on the preferred conformations of mononucleotides, conformational energy calculations have been carried out on dinucleoside monophosphate fragments. Four base sequences—d(ApT), d(TpA), d(CpG), and d(GpC)— have been analyzed in the framework of helical structures. Flexibility of the furanose ring has been incorporated in the investigations. Energetically favored conformers of the four compounds correspond to a variety of left‐ and right‐handed uniform helical structures, similar to those of the commonly observed polymorphous forms. Implications of these investigations on the further understanding of double‐helical polynucleotide conformations are briefly discussed.
Interaction of calcium ions with gastrin fragments of increasing chain length
Authors: Peggion E. , Foffani M. T. , Wünsch E. , Moroder L. , Goodman M. , Mammi S.
Published: May 2005

The interaction of a series of biologically active gastrin fragments with calcium ions has been investigated by CD in trifluoroethanol. It was found that the gastrin octapeptide pGlu10,Nle15‐HG[10–17] binds one calcium ion per molecule. The hypothesis is made that the binding involves the C‐terminal, biologically important tetrapeptide. When the chain is elongated to the gastrin nonamer pGlu9,Nle15‐HG[9–17], a second binding site is available, which is most likely situated at the N‐terminal part of the molecule. Further elongation of the peptide chain up to the dodecapeptide pGlu6,Nle15‐HG[6–17] does not provide any additional binding site. Saturation of the two sites in the shorter peptides produces different changes in the chiroptical properties in the near‐ and far‐uv. As the chain is elongated, this difference tends to disappear. This result is consistent with an increased conformational order of the longer peptides. In the shorter fragments, the strength of this second binding is appreciably lower than that of the first, while in the longer peptides, the strength of the two bindings is comparable. On the assumption that the variation of the CD properties is proportional to the extent of binding, the constant for the binding of the second ion was determined to be of the order of 5 × 105 L/mol for the nonapeptide.
The dynamics of the DNA hydration shell at gigahertz frequencies
Authors: Tao N. J. , Lindsay S. M. , Rupprecht A.
Published: May 2005

We have used Brillouin scattering to measure the linewidths and frequencies of GHz acoustic phonons in Na‐ and Li‐DNA films as a function of temperature between 300 and 140 K for samples that were dry, lightly, and heavily hydrated. The linewidths decrease with falling temperature and water contents, indicating that coupling to a water relaxation is the main source of phonon damping. The strength of the relaxation was determined using measurements of the phonon linewidth as a function of frequency, and confirmed by comparison of measured and calculated spectral profiles. The relaxation strength is anisotropic, being greater for phonons propagating perpendicular to the helix axis. The hydrated DNA exhibits both a rapid relaxation (≤ 10−11 s per radian) giving rise to a classical f2 damping, and a slower motion with a relaxation time that varies from ∼ 4 × 10−11 s per radian (primary hydration shell) to ∼ 2 × 10−12 s per radian (secondary hydration shell) at room temperature. In the frequency interval that bounds these relaxation times (∼ 4 to 80 GHz) we expect degrees of freedom associated with the primary hydration shell to be important. The sample with primary hydration follows a simple Arrhenius behavior with ΔH ∼ 5 kcal mole−1. The effective activation energy for the sample with secondary hydration is somewhat higher (indicating a more cooperative water relaxation) and varies strongly with temperature. The elastic moduli change much more than can be accounted for by relaxation, indicating the importance of water motion in softening interatomic potentials. The extent of the softening caused by the “unfreezing” of water motion is similar to the degree of softening caused by hydrating the sample.
The biological functions of low‐frequency vibrations (phonons). VI. A possible dynamic mechanism of allosteric transition in antibody molecules
Authors: Chou Kuo‐Chen
Published: May 2005

By means of the quasi‐continuity theory developed recently [Chou, K.‐C. (1983) Biochem. J. 209, 573–580; Chou, K.‐C. (1984) Biochem. J. 221, 27–31; Chou, K.‐C. (1985) Biophys. J. 48, 289–297], the low‐frequency breathing motions of the β‐barrels in the 12 domains of an IgG antibody molecule have been calculated. The results are in very good agreement with the observed low‐frequency peaks in the Raman spectra. Based on this, the resonant couplings among the domains located at its different regions are discussed. It turns out that some very interesting functions of antibody molecules, such as the “chelate effect” and “trigger effect” whose dynamic principle has been so far unknown, can be clearly elucidated in terms of a fundamental natural law; i.e., it is through the channel of low‐frequency resonance that the “signal” (or energy) in an antibody is transmitted from one location to the other, so as to be able to induce the relevant conformational change required for operating those important biological functions. The physical picture illustrated here once again provides us with a classic example that structure and function in nature are highly harmonized.
Thermodynamics of water–biopolymer interactions: Irreversible sorption by two uniform sorbent phases
Authors: Bryan William P.
Published: May 2005

In order to understand the mutual interactions between water and a biopolymer, thermodynamic analysis of sorption isotherms of water vapor by the biopolymer is necessary. These isotherms are irreversible and show sorption hysteresis. The reasons for such behavior are not established. As a continuation of previous work, general relationships for thermodynamic quantities of sorption are derived for the general case when the sorbent consists of two uniform phases. As in the case of a single sorbent phase, the Clausius–Clapeyron equation can be used to obtain differential entropies of sorption. Two special cases for the two‐phase situation—equilibrium hysteresis and partial equilibrium hysteresis—are plausible models for the irreversibility seen in water–biopolymer interactions. When differential entropy of sorption is plotted as a function of amount of water sorbed per mole of biopolymer, irregularities are generally seen. It is suggested that these irregularities reflect changes in conformation and/or dynamics of the biopolymer molecule.
Brownian dynamics simulation of protein folding: A study of the diffusion‐collision model
Authors: Lee Sangyoub , Karplus Martin , Bashford Donald , Weaver David
Published: May 2005

The dynamic aspects of protein folding are described by a series of diffusion‐collision steps involving structural units (microdomains) of various sizes that combine to form the protein in its native state. A method is introduced for obtaining the rate constants for the basic diffusion‐collision step by use of Brownian dynamics. The method is applied to an investigation of the folding dynamics of two α‐helices connected by a flexible (random‐coil) polypeptide chain. The results of this full three‐dimensional treatment are compared with simplified model calculations for the diffusion‐collision step. Of particular interest are the nature of the collision dynamics and the role of the intervening peptide chain.
Conformational transitions of calmodulin as studied by vacuum‐UV CD
Authors: Hennessey John P. , Manavalan Parthasarathy , Johnson W. Curtis , Malencik Dean A. , Anderson Sonia R. , Schimerlik Michael I. , Shalitin Yechiel
Published: May 2005

CD measurements were made for calmodulin and its calcium (Ca2+) complexes at different ionic strengths and Ca2+ concentrations. Calmodulin at an ionic strength of 0.00M and in the absence of Ca2+ exists as an α‐helical protein with a negligible amount of β‐sheet. An increase in ionic strength, whether or not Ca2+ is present, increases α‐helix at the expense of “other” (coil) structure. The changes in β‐sheet and β‐turns are insignificant. Binding of Ca2+ at low ionic strength occurs in stages with at least one folding intermediate before attaining the final stable state. Binding of Ca2+ at an ionic strength of 0.165M causes only a slight increase in α‐helix, so that the secondary structure of the protein depends on ionic strength and is insensitive to the nature of the cation (i.e., Ca2+). Thus, the activation of calmodulin by Ca2+ must be due to a structural reorientation rather than to a major secondary structural alteration. The CD estimation of secondary structure with 4 mol Ca2+/calmodulin (61% α‐helix, 2% antiparallel β‐sheet, 2% parallel β‐sheet, 21% β‐turns, and 14% other) is in excellent agreement with the x‐ray results.
A CD study of the role of metal ions in the conformation of poly(L‐lysine)
Authors: Watanabe S. , Saito T.
Published: May 2005

The effect of LiCl, NaCl, and CsCl as univalent salts, and of CaCl2, ZnCl2, and MgCl2 as divalent salts, on the α and antiparallel β‐sheet, and random conformations of poly(L‐lysine) (PLL), in water at room temperature were examined by means of CD and compared quantitatively on the basis of elliptical strength at the maximal peak. Changes in the α‐helical and antiparallel β‐sheet helical conformations of PLL were markedly dependent on the salt concentrations of LiCl, NaCl, and CsCl, which induced decreases in negative intensity in that order. The CD spectrum of the random conformation, the most disordered form, displayed positive cotton effect in concentrations of these salts up to 3.0M and a negative peak in concentrations of 6.0M. The effect of these salts on the random conformation of PLL was stronger than that on the α‐ and β‐conformations in higher concentrations. The CD spectrum of the random conformation in the presence of CaCl2, ZnCl2, and MgCl2, on the other hand, showed negative cotton effect in salt concentrations as low as 3.0M. It was impossible, however, to measure the effect on α‐ and β‐conformations of ZnCl2 and MgCl2 above concentrations of 10 mM because of a solubility problem with salts in alkaline solution.
Order parameters of gels and gelation kinetics of aqueous agarose systems: Relation to the spinodal decomposition of the sol
Authors: Leone M. , Sciortino F. , Migliore M. , Fornili S. L. , Vittorelli M. B. Palma
Published: May 2005

Hydrogels of a significant biostructural polymer (agarose) were studied turbidometrically in the course of their isothermal self‐assembly. Supramolecular order was characterized by an order parameter and associated correlation length. This type of characterization, in general, may help more in the quantitative measurement of order in biostructures. The picture of processes leading to isothermal gelation appears much richer than expected, and it is probably of more general validity, as it agrees with predictions based on the statistical model of site‐bond correlated percolation. At the higher temperatures a spinodal decomposition occurs well before, and possibly triggers [P. L. San Biagio, et al. (1986) Biopolymers 25, 2255–2269], the start of gelation. In this case, the spatial modulation of concentration, as well as topological features of the gel, appear to reflect those of the spinodally decomposed sol. When an upper limit is approached for the temperature of isothermal gelation, both the order parameter and the correlation length exhibit a critical‐like behavior. At lower temperatures, the sequence of processes and the resulting features of the gel appear dictated by the (temperature‐ and concentration‐dependent) interplay of spinodal decomposition and gelation processes and kinetics. The present results are believed to provide a basis for a deeper understanding of the relation between the processes of gelation and of spinodal decomposition, and between their time scales.
Conformational analysis of the 2′‐deoxyribofuranose ring from proton–proton coupling constants: Analysis of a nucleoside‐carcinogen adduct formed from 2‐acetylaminofluorene utilizing a three‐state model
Authors: Evans Frederick E. , Levine Robert A.
Published: May 2005

The conformation of the sugar moiety of 8‐(N‐fluoren‐2‐ylamino)‐2′‐deoxyguanosine in solution has been examined as a function of temperature by 1H‐nmr spectroscopy. Analysis of coupling constants shows that lowering the temperature to −50°C in methanol shifts the conformational equilibrium of the sugar ring resulting in a C2′‐endo conformation at a mole fraction of 0.97. The computed phase angle of pseudorotation and amplitude of pucker are 154° and 36°, respectively, with very little discrepancy between the five calculated coupling constants and coupling constants extrapolated from the temperature profiles. A computer program has been written enabling a three‐state best‐fit analysis. The three‐state analysis indicates an equilibrium between C2′‐endo, C3′‐endo, and 04′‐endo conformations. In aqueous solution, the computed mole fraction of the 04′‐endo form is 0.18 at 30°C. The conformation associated with the sugar ring and the C4′C5′ bond is compared to that of 2′‐deoxyguanosine.
Cooperative lengths of DNA during melting
Authors: Blake R. D.
Published: May 2005

The mean cooperative length of domains of DNA, determined from the variance in (G + C) content in derivative melting curves of large bacterial DNAs, varies from 230 base pairs (bp) for (A − T)‐rich domains to 580 bp for (G − C) domains. These values correspond to values for the cooperativity parameter of 2(±2) × 10−5 and 3(±2) × 10−6, respectively, and to +7.2 and +9.6 kcal for the free energy of helix interruption in those regions.
Asymmetric oscillations in cyclodextrin—a molecular dynamics study
Authors: Prabhakaran M. , Harvey Stephen C.
Published: May 2005

A 30‐ps molecular dynamics simulation of motions of cyclodextrin is completed on the free molecule and with two model substrates. Even with its cyclic constraint, the molecule traversed through large conformational space, showing high flexibility. The asymmetric oscillations of the free molecule are evident from the time course behavior of the ratio of the second moments (anisotropic ratio) of the atomic motions along the first two principal axes. The study also shows the stability of the molecule derived from specific substrate. The preference of chair conformation by glucose is also evident from these studies.
Fluorescence dynamics studies of troponin C
Authors: Steiner Robert F. , Norris Lynn
Published: May 2005

The time decay of fluorescence anisotropy for a dansylaziridine (DANZ) conjugate with Met‐25, which lies within the N‐terminal lobe of troponin C (TnC), shows at 10 and 25°C a longer correlation time characteristic of the entire molecule and a shorter correlation time arising from a more localized motion of the probe. In the absence of Ca2+, the amplitude of the shorter correlation time increases, suggesting an increased mobility of the probe. At 40°C, in both the absence and presence of Ca2+, a significant increase in probe mobility occurs. A 2,6‐toluidinyl naphthalene sulfonate (2,6‐TNS) complex with Ca2+‐liganded TnC shows only the longer correlation time at 12 and 25°C. An N‐(iodoacetylaminoethyl‐5‐naphthylamine‐1‐sulfonate) conjugate with Cys‐98 shows both a long and a short correlation time; the amplitude of the shorter correlation time is greater than for the DANZ conjugate. At 9, 25, and 40°C in the presence of Ca2+, and at 9°C in its absence, the magnitude of the long correlation time is consistent with motion of the entire molecule; at higher temperatures in the absence of Ca2+ it is substantially smaller, suggesting the presence of internal rotation. For Ca2+‐liganded TnC at temperatures of 25°C or lower, the results with all three labels are interpretable in terms of the crystallographic structure of TnC.
Comparison by 1H‐nmr spectroscopy of the conformation of the 2600 dalton antifreeze glycopeptide of polar cod with that of the high molecular weight antifreeze glycoprotein
Authors: Rao B. N. Narasinga , Bush C. Allen
Published: May 2005

The antifreeze glycopeptide (AFGP‐8) from polar cod, B. saida, is a 14‐amino acid polypeptide having alternating glycotripeptide sequences of Ala‐[Gal(β1 → 3)GalNAc(β1 → O)]‐Thr‐Pro and Ala‐[Gal(β1 → 3)GalNAc(β1 → O)]‐Thr‐Ala, with alanyl residues at amino and carboxy terminals. Conformational studies of AFGP‐8 have been carried out by 1H‐nmr and empirical energy calculations to investigate the difference in its antifreeze behavior from that of the more active high‐molecular weight AFGP 1‐4 of P. borchgrevinki. The 1H‐nmr spectra, including the resonances of the exchangeable amide protons, were assigned by two‐dimensional correlated spectroscopy (COSY), one‐dimensional difference decoupling, and nuclear Overhauser effect (NOE) measurements. For the four threonyl residues, the amide proton coupling constants and the small coupling constants between Hα and Hβ indicate similar conformations, despite significant chemical shift differences. The strong NOE between the α protons and the amide protons of the residue following together with large temperature coefficients of chemical shifts, indicate an extended conformation not consisting of α‐helix, turns or bends. Energy computations indicate several low‐energy conformations consistent with the observed coupling constants for ϕ. Among these, a left‐handed helical conformation with three repeating residues per turn has been proposed, which is in accordance with the observed NOE between the methyl group of the α‐GalNAc and Ala Hβs. While the observed Overhauser effects in the threonyl side chain suggest a certain amount of conformational averaging, the effect involving the acetmido methyl of α‐GalNAc and Hβs of Ala indicate that it as is a major conformer. In view of the close similarity between the conformations of AFGP‐8 and the more active antifreeze polymer, AFGP 1‐4, we propose that the difference in their activities is due to the length of the regular repeating structure with glycosylation at every third amino acid residue, and not due to any fundamental difference in their conformations.
Molecular mechanics modeling of oligonucleotide adducts of the antitumor drug cis‐diamminedichloroplatinum(II)
Authors: Kozelka Jiří , Archer Sharon , Petsko Gregory A. , Lippard Stephen J. , Quigley Gary J.
Published: May 2005

In order to assess the geometric changes caused when the antitumor drug cis‐diammine‐dichloroplatinum(II) (cis‐DDP) binds to DNA, molecular mechanics calculations were performed on two double‐stranded and two single‐stranded oligonucleotides and their adducts with cis‐{Pt(NH3)2}2+. For the platinated duplexes, three model structures have been derived, one involving only local disruption of base pairing with retention of the helix directionality, and two models showing pronounced kinking of the double helix. One of the kinked models is stabilized by bridging sodium ions. The other kinked duplex model shows retention of all Watson–Crick base pairing, including that of the coordinated guanines. All models exhibit hydrogen bonds connecting one ammine ligand of platinum with one or two phosphate groups located at the 5′ side of the platinated strand.
Influence of hydrogen bonding, main chain–side chain interactions, and protecting groups on the excimer formation of bis(pyrenylalanine) peptides
Authors: Goedeweeck R. , Ruttens F. , López‐Arbeloa F. , De Schryver F. C.
Published: May 2005

Dipeptides of the aromatic fluorescent amino acid, pyrenylalanine, are studied using both stationary and transient fluorescence techniques. Since the conformational transitions of the peptide chain are slow compared to the decay of the pyrene excited state, both ground state conformations, adopted by the peptide, i.e., C5 and C7, can be monitored separately. Kinetic models are proposed to describe the molecular dynamics of the peptide chain as probed by the intramolecular excimer formation between both pyrene chromophores. These kinetic schemes explain the influence of solvent, chain chirality, main chain–side chain interactions, and nature of the protecting groups on the emission spectrum and the fluorescence decay profile of these model peptides. These schemes also provide a tool to calculate rate constants of conformational transitions and excimer formation. By comparing the kinetic and thermodynamic parameters of the various compounds, the influence of a structural modification on the molecular dynamics of the peptide chain is determined.
Vibrational CD studies of the solution conformation of N‐urethanyl‐L‐amino acid derivatives
Authors: Chernovitz Anita C. , Freedman Teresa B. , Nafie Laurence A.
Published: May 2005

The solution conformations of several N‐urethanyl‐L‐amino acids in 0.2–0.002M chloroform and 0.2M dimethylsulfoxide have been investigated by using vibrational circular dichroism (VCD), ir absorption, and 13C‐nmr spectroscopies. Both the N‐carbobenzoxy (N‐CBZ) and N‐t‐butoxycarbonyl derivatives of L‐alanine, L‐proline, L‐valine, and L‐phenylalanine, and N‐CBZ‐serine were studied. The 13C‐nmr results indicate that the molecules occur predominantly as the cis isomer about the CN peptide bond at room temperature. The interpretation of the strong VCD couplet in the carbonyl‐stretching region using the degenerate coupled oscillator model is consistent with the conformational range of ϕ = −60° to −90° and ψ = 30° to 90° for molecules forming acid dimers. Conformations with an intramolecularly hydrogen‐bonded C7 ring are also present, which give rise to biased VCD features in the NH‐, CH‐, and CO‐stretching regions that can arise due to vibrationally generated ring currents.
Loop energy in DNA
Authors: Blake R. D. , Delcourt Scott G.
Published: May 2005

The loop function ƒ(N), representing the statistical weight of N complementary residues in a closed ring, has been determined by analysis of high‐resolution melting curves of a series of recombinant homopoly(A · T)N inserts in pBR322 DNA, where 150 > N > 50 base pairs (bp). Loops are found more stable and therefore presumably less elastic than expected for an ideal, freely jointed chain. A value of 97 ± 2 bp is obtained for the empirical orientation‐stiffness parameter D in the expression for nonideal chains, ƒ(N) = (N + D)−1.7. The 10% increase in apparent stiffness over that of an ideal chain closely coincides with the extent of residual stacking in the loop. It is thus concluded that the more favorable loop energy, such as expected of smaller loops, is due to the incipient helical orientation of some residues, predisposing the loop to reclosure. A quantitative loop function is essential for the prediction and assignment of domains in DNA.
The Hodgkin–Huxley Na+ channel model versus the five‐state Markovian model
Authors: Chay Teresa Ree
Published: May 2005

In describing the Na+ channel‐gating kinetics, it is generally believed the Hodgkin–Huxley model is inadequate and other types of Markovian models are more appropriate. In this paper, we perform detailed kinetic analyses to find out whether the Hodgkin–Huxley model is really unacceptable. Specifically, we consider two models for the analyses: A five‐state Markovian model that allows inactivation to take place before opening and a Hodgkin–Huxley eight‐state model. The criteria used to check the goodness of the two models are (a) Akaike's information criterion; (b) χ2 tests on the waiting‐time, open‐time, and closed‐time distributions, and the number of openings per record; and (c) comparison between all latency distributions and the probability of the open state predicted from the two models. In order to do this, we first develop a method of constructing probability density histograms of a specified event (e.g., waiting time, closed time, open time, number of openings per patch) from the multichannel patch‐clamp recordings. The goodness of our method is checked by simulating multichannel patch recordings using a multinomial random number generator. Our kinetic analysis on the single Na+ channel recordings from the cardiac cells revealed that (a) on the basis of Akaike's information criterion, the Hodgkin–Huxley model is definitely a better model than the five‐state model, but (b) on the basis of χ2 tests on the probability density functions, the latter model is slightly better than the former. We find no evidence that the Hodgkin–Huxley model is inferior to the five‐state model for this cell type.
The helix–coil transition in heterogeneous peptides with specific side‐chain interactions: Theory and comparison with CD spectral data
Authors: Gans Paul J. , Lyu Pingchiang C. , Manning Mark C. , Woody Robert W. , Kallenbach Neville R.
Published: May 2005

Natural and synthetic peptides that contain detectable intramolecular α‐helical structure in aqueous solution have been used to evaluate the helical propensities for the common amino acids. Experimental spectroscopic data must be fit to a model of the helix–coil transition in order to determine quantitative stability constants for each amino acid. We present here a statistical mechanical description of helix formation in peptides or protein fragments that takes into account multiple internal conformations, heterogeneity in the stabilizing effects of different side chains, and specific side‐chain–side‐chain interactions. The model enables one to calculate values of [θ]222 for a given peptide using the length dependence of the helix signal computed by a quantum mechanical treatment of the nπ* transition that dominates the 222‐nm band. In addition, the helical probability at any residue in the chain is readily computed, and should prove useful as nmr spectral data become available. The free energy of specific side‐chain interactions, including ion pair formation, can be evaluated. Application of the analysis to experimental data on a pair of isomeric peptides, only one of which contains ion pairs, indicates that forming a single glutamate‐lysine ion pair stabilizes the α‐helix by 0.50 kcal/mole in 10 mM sodium ion and pH 7. A survey of the CD data measured for a variety of model peptides is presented, indicating that a single set of s values and σ constant can account for some but not all of the available results.
Transient electric birefringence of two small DNA restriction fragments of the same molecular weight
Authors: Stellwagen Nancy C.
Published: May 2005

The transient electric birefringence of two small DNA restriction fragments of the same molecular weight, one of which migrates anomalously slowly on polyacrylamide gels, has been investigated. Both fragments exhibit negative birefringence. The decay of the birefringence of the anomalously slowly migrating fragment is 8–9% faster than that of the normally migrating fragment. The faster birefringence decay of the anomalous fragment 12A persists under a variety of buffer conditions, suggesting that it is due primarily to static bending and/or curvature of fragment 12A. In reversing electric fields the absolute amplitude of the birefringence of fragments 12A and 12B decreased about 26% before returning to the steady state value. The minimum in the birefringence occurred faster than expected from the birefringence decay times and decreased with increasing electric field strength, suggesting that the minimum is due to a slow polarization of the ion atmosphere. For both fragments, the rise of the birefringence in the Kerr region is about 10% slower than the field‐free decay. The buildup of the negative birefringence is preceded either by an interval when no birefringence is observed or by a small positively birefringent transient, suggesting that a small transverse ionic polarizability is also present. Both DNA fragments exhibit Kerr law behavior over most of the range of electric field strengths investigated. Analysis of the shapes of the saturation curves suggests that differences may exist in the polarization mechanisms of the two fragments.
Conformation of the oligosaccharide receptor for E‐selectin
Authors: Mukhopadhyay Chaitali , Miller Kristine E. , Bush C. Allen
Published: May 2005

A tetrasaccharide related to the blood group oligosaccharides, known as sialyl LewisX, has been proposed as the receptor for the lectin responsible for leukocyte adhesion named alternatively as E‐selectin or ELAM‐1. The 13C‐ and 1H‐nmr spectra have been completely assigned for a tetrasaccharide model of this receptor, Neu5Ac α‐(2 → 3)‐Gal β‐(1 → 4)‐[ Fuc α‐(1 → 3)‐] GlcNAc β‐NHAc. Quantitative nuclear Overhauser data (NOESY) have been recorded and analyzed by a complete spin matrix simulation method. Conformational space was exhaustively searched and all conformational models whose simulated NOESY spectra matched the experiment were found. Molecular mechanics and molecular dynamics calculations were carried out to test whether the experimental conformations are low energy and thus likely to represent true single conformations for the tetrasaccharide. It was concluded that while the LewisX trisaccharide portion of the compound adopts a single conformation, there is likely to be some flexibility about the Neu5Ac α‐(2 → 3)‐linkage. A model featuring fast exchange between two different conformations of this linkage is found to be consistent with both the nmr experiments and the molecular dynamics simulations. © 1994 John Wiley & Sons, Inc.
The effect of the L‐azetidine‐2‐carboxylic acid residue on protein conformation. IV. Local substitutions in the collagen triple helix
Authors: Zagari Adriana , Palmer Kathleen A. , Gibson Kenneth D. , Némethy George , Scheraga Harold A.
Published: May 2005

The properties of collagen are affected by the replacement of Pro by imino acid analogues. The structural effect of the low‐level local substitution of L‐azetidine‐2‐carboxylic acid (Aze) has been analyzed by computing the energy of CH3CO‐(Gly‐Pro‐Pro)4‐NHCH3 triple helices in which a single residue of one strand has been replaced by Aze. When Aze is in position Y of a (Gly‐X‐Y) unit, low‐energy local deformations are introduced in the triple helix, i.e., it becomes more flexible. On the other hand, the flexibility of the triple helix is not increased with Aze in position X. The energy of the triple helix to coil transition is not changed significantly by this amount of substitution. In an earlier study, we have demonstrated that the regular substitution of Aze in every tripeptide distorts or destabilizes the triple helix to a large extent [A. Zagari, G. Némethy, & H. A. Scheraga (1990) Biopolymers, Vol. 30, pp. 967–974 ]. Thus, it appears that a high level of substitution is required to cause the observed chemical and biological effects of Aze on collagen. © 1994 John Wiley & Sons, Inc.
The interaction of substituted 2‐phenylquinoline intercalates with poly(A) · poly(U): Classical and threading intercalation modes with RNA
Authors: Zhao Min , Janda Lubomir , Nguyen Johnny , Strekowski Lucjan , Wilson W. David
Published: May 2005

The interaction of a series of 2‐phenylquinoline derivatives with RNA was investigated by means of viscometric, pKa, spectroscopic, binding, Tm, and kinetic methods. Compounds 1,2, and 3 have a piperazyl substituent at the para, meta, or ortho position, respectively, while 4 has an unsubstituted phenyl ring. The pKa results suggest that 1 has three charges, 2 and 3 have more than two charges, and 4 has two charges at pH 6.2. Spectroscopic and Tm results indicate that 1 binds more strongly to RNA than 2–4. Kinetic and modeling results indicate that 1 is a threading intercalator while 2 and 4 are classical intercalators. All experimental results indicate that 3, which has a large twist between the phenyl and quinoline rings, binds weakly with RNA. © 1994 John Wiley & Sons, Inc.
Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth
Authors: Chou Kuo‐Chen , Zhang Chun‐Ting , Maggiora G. M.
Published: May 2005

Microtubules, which play many diverse and important roles in biological systems, are usually made up of 13 nearly axial protofilaments formed from individual tubulin molecules. In this paper, a nonlinear dynamic model has been developed to elucidate the mechanism of the internal motion occurring during the assembly of microtubules. The results derived from the model indicate that such internal motion is associated with a solitary wave, or kink, excited by the energy released from the hydrolysis of GTP ⟹ GDP in microtubular solutions. As the kink moves forward, the individual tubulin molecules involved in the kink undergo motions that can be likened to the dislocation of atoms within the crystal lattice. Thus, the dynamic instability of microtubules may be characterized by a series of dislocation motions of the tubulin molecules. An energy estimate shows that a kink in the system possesses about 0.36–0.44 eV, which is quite close to but smaller than the 0.49 eV of energy released from the hydrolysis of GTP. Therefore, the relevant energy derived from our model is fully consistent with experimental observations; this finding also suggests that the hydrolysis energy may be responsible for exciting the solitary wave, or kink, leading to tubulin dislocation in microtubules.

Our model, and its intrinsic properties, i.e., dynamic nonlinearity, thermodynamic irreversibility, as well as an energy input from a sustained source, implies that the growth of microtubules is a typical dissipative process and that their structure in vivo is typical of dissipative structures. © 1994 John Wiley & Sons, Inc.
Microbial degradation of asphalt
Authors: Traxler R. W.
Published: May 2005

It would appear from these data that indeed asphalt degradation by bacteria does occur and can be rather rapid under laboratory conditions. The types of bacteria capable of degrading asphalt are diverse. The effects of temperature, pH, and oxygen tension on asphalt degradation are important but not always critical. The optimum conditions vary for different organisms. There are differences in the mechanisms of asphalt assimilation and degradation. There is a specificity of action by different bacteria which most likely involves the chemical components of the asphalts and the enzymatic action of the microorganism.
Mean light intensity—a useful concept in correlating growth rates of dense cultures of microalgae
Authors: Rabe A. E. , Benoit R. J.
Published: May 2005

An analysis of the distribution of light within some culture vessels developed at General Dynamics/Electric Boat is presented. The concept of a mean effective light intensity, Ē, is introduced and procedures are developed for computing Ē for any culture vessel geometry and incident light intensity distribution. A correlation is performed indicating the significance of Ēin assessing the growth rate of dense, continuous cultures of microalagae.
Quantitative determination of methylene blue sorption by dead Penicillium chrysogenum
Authors: Borzani Walter , Vairo Marina L. R.
Published: May 2005

The applicability of physicochemical adsorption laws to the sorption of methylene blue by dead Penicillium chrysogenum was studied. The specific area (area/mass) of the mold was measured.
Enzymatic process for mustard seed to produce oil, meal, and allyl isothiocyanate
Authors: Mustakas G. C. , Griffin E. L. , Gastrock E. A. , D'Aquin E. L. , Keating E. J. , Patton E. L.
Published: May 2005

Removal of the pungent factor, allyl isothiocyanate, will partly determine whether mustard seed can become a commerical source for oil and meal in the United States. In processing studies at the Northern Laboratory, the mustard glucoside was converted enzymatically and the pungent oil was removed. This process has now been extended to pilot‐plant scale by using filtration‐extraction equipment at the Southern Laboratory. After desolventization and further steam stripping, the extracted meal had a residual content of 2.9% crude fat and 0.004% allyl isothiocyanate.
Chemical properties of crystalline N‐methylethyloxytetracycline
Authors: Neidleman S. L. , Weisenborn F. L. , Bouchard J.
Published: May 2005

The inclusion of ethionine in Streptomyces rimosus fermentation resulted in the production of N‐methylethyloxytetracycline. The compound has been isolated, crystallized, and a number of its chemical properties determined.
Production of aflatoxin by the culture of strains of Aspergillus flavus‐oryzae on sterilized peanuts
Authors: Codner R. C. , Sargeant K. , Yeo R.
Published: May 2005

By growing Aspergillus parasiticus (C.M.I. 15957) under controlled conditions on sterilized peanuts an average of 265 mg. of aflatoxin per kilogram of peanuts has been produced and subsequently isolated. Other strains from the A. flavus‐oryzae group gave lower yields of aflatoxin and one such strain gave aflatoxin from which certain normal components were absent. The aflatoxin produced on sterilized peanuts by any particular strain of A. flavus‐oryzae was shown by thin‐layer chromatography to contain the same major components as were produced by that strain on unsterilized whole peanuts.
An application of the discrete maximum principle to a stagewise biochemical reactor system
Authors: Fan Liang‐Tseng , Wan Chee‐Gen
Published: May 2005

It is a well‐known fact that choosing a sequence of optimal control variables in each reactor tank of a multistage reactor system can result in a considerable increase of the desired product for a consecutive reaction system. The discrete maximum principle is applied to a generalized optimization problem of first order consecutive biochemical reaction system. A detailed numerical solution as an example is also presented for illustration.
Waste stabilization ponds: Use, function, and biota
Authors: Porges Ralph , Mackenthun Kenneth M.
Published: May 2005

Stabilization ponds have been widely accepted in recent years, following studies that established deeper understanding of the phenomena associated with the stabilization process. A compilation of information on the use of both sewage and industrial ponds is presented showing types and geographical location in the United States. A total of 1,304 stabilization ponds currently are used as the principal method of sewage treatment serving a population of 2,138,085. Ponds are used for tertiary treatment serving a population of 2,146,951, in 343 instances. Use of 827 industrial ponds by 31 industries in 44 States is also indicated. Indiana ranks first in usage with 159 ponds and Callfornia second with 140. Ponds were classed as effective by 66 percent of the 455 users who reported on this item. Of 149 reports on odors, 73% indicated nuisances. Insect problems were reported in only a small number of instances. Data are presented on design considerations and the mechanism of waste stabilization ponds. Aerobic ponds are given greatest emphasis. Photosynthesis and its dependence upon the algal mass, suitable temperature, incident light penetration, nutrient supply, and induced vertical mixing by wind are of prime importance in the stabilization mechanism. Odors are associated with prolonged anaerobic conditions, and these may persist up to 4 weeks following extended ice cover in cold climates, if BOD loadings are 25 lbs. per acre per day or greater. Nitrogen and carbon may be limiting factors in the development of an algal mass. Coliform, BOD, and nutrient removals are presented for various physical, chemical, and climatic conditions. Although fecal streptococci removal averaged 97% in a study pond, they were still discharged in the effluent at a rate of 700,000 per second in winter and 70,000 per second in summer. A striking similarity exists generally among the algal speciation in stabilization ponds, regardless of geographic location. The algal mass is, however, dependent upon unique pond conditions and location, and may vary upwards to nearly 5 million algal cells per milliliter, 34,000 p.p.m. by volume, or 30–35 tons per acre per year. The problem of blue‐green algal mats and resultant pigpen odors in extremely localized areas is duscussed. Midges and midge larvae may have an impact on the nutrient cycle in a stabilization pond, and may pose a potential localized nuisance in some areas. Mosquito problems have usually been associated with growth of aquatic vegetation. Suggestions for minimizing the potential problem are discussed.
Decomposition of organic wastes by Sphaerotilus
Authors: Pipes W. O. , Jones P. H.
Published: May 2005

Sphaerotilus is usually present in biological waste treatment processes and is considered to be a nuisance organism because it may cause bulking of activated sludge. However, it may play an important role in the decomposition of putrescible organic matter in properly operated biological waste treatment processes. The research described herein is a study of the variety of types of organic compounds which may be decomposed by Sphaerotilus and the effect of some environmental factors upon the rate of decomposition. Although there are some types of compounds which cannot be decomposed by Sphaerotilus, it is shown that this organism is able to assimilate and oxidize a large variety of organic compounds and that it is tolerant of an extremely wide range of environmental conditions. The role of Sphaerotilus in biological waste treatment is discussed in the light of the data presented.
Studies on the removal of alkyl benzene sulfonate by microorganisms
Authors: Hartmann Ludwig
Published: May 2005

These experiments show that ABS can be adsorbed and desorbed from microbial cell surfaces. The adsorption equilibria between the free and adsorbed phases are primarily influenced by the pH of the system. The effects of ABS upon the biochemical activities of bacteria depended upon the amount of ABS adsorbed and the type of bacteria present. The behaviour of ABS is essentially the same whether in the presence of pure or mixed bacterial cultures. Two desorption experiments with soil from a reclaimed water spreading basin which has received sewage over a six month period showed that at least 82% of the ABS “loss” was recoverable from the soil. In all the experiments carried out in this study no evidence was obtained for the biochemical degradation of ABS.
Biodegradation of anionic and nonionic surfactants under aerobic and anaerobic conditions
Authors: Wayman C. H. , Robertson J. B.
Published: May 2005

Because branched‐chain alkyl benzene sulfonate (ABS) is well known to create water pollution problems in surface water and ground water, a study was made on the biodegradation of this surfactant along with other anionic and nonionic surfactants in detergents by water bacteria. Biodegradation was evaluated by the conventional river die‐away test employing the methylene‐blue method or surface‐tension techniques as analytical tools. Under anaerobic conditions, sugar detergents (sucrose esters) seem to be an ultimate solution to water problems created by branched‐chain ABS; in aerated water, straight‐chain ABS, sulfo tallow methyl esters, and nonionic surfactants are preferable to branched‐chain ABS to improve water problems.
A method of automatic pH control of a bicarbonate‐CO2 buffer system for the submerged culture of hamster kidney cells
Authors: Telling R. C. , Stone C. J.
Published: May 2005

The equipment and operational techniques are described which were found suitable to control pH in the range 6.8–7.8 pH, within ±0.03 pH units of the desired value, at cell concentrations up to a maximum of 2.5 × 106/ml. The results of batch growth of a suspension strain of the BHK cell (clone 13) under conditions of controlled pH are given and the significance of these results is discussed.
Rapid estimation of 1‐dehydro‐17‐α‐methyltestosterone produced by microbiological oxidation of 17‐α‐methyltestosterone
Authors: Mizsei Antal , Szabó Antal
Published: May 2005

A method has been devised for the estimation in fermentation media, of 1‐dehydro‐17‐α‐methyltestosterone in the presence of 17‐α‐methyltestosterone. This method involves the extraction of the steroids with chloroform, and spectrophotometric measurement of the chromogen formed by a specific color reaction with sulfuric acid and 1‐dehydro‐17‐α‐methyltestosterone. The fermentation liquor and 17‐α‐methyltestosterone do not interfere. With this rapid (30 min.) method, quantitative tests on the progress of the steroid transformation can be made at frequent intervals during one fermentation run, these tests yielding the necessary information for an adequate control of the optimum conditions of production.
Problems of design and ecological considerations in mass culture of algae
Authors: Mayer A. M. , Zuri U. , Shain Y. , Ginzburg H.
Published: May 2005

A 2000 l. 1 m. deep mass culture of algae was operated with continuous stirring, as an open system. The system behaved as an ecological unit selecting the most favored species. The ecological conditions could be modified by stirring speed and pattern in the tank. Methods for improving yields and utilization of CO2 are described. Assessment of algal species for suitability in mass cultures is discussed. Yields obtained were 13 g. dry matter/sq. m. illuminated area/day.