bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two‐dimensional 1H‐nmr investigation of the water conformation of the atrial natriuretic factor (ANF 101–126)
Authors: Theriault Y. , Boulanger Y. , Weber P. L. , Reid B. R. 
Published: May 2005

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

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

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

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

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

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

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

Abstract13C‐nmr spectra of poly(β‐benzyl L‐aspartate) containing 13C‐enriched [3‐13C]L‐alanine residues in the solid state were recorded by the cross polarization–magic angle spinning method, in order to elucidate the conformation‐dependent 13C chemical shifts of L‐alanine residues taking various conformations such as the antiparallel β‐sheet, the right‐handed α‐helix, the left‐handed α‐helix, and the left‐handed ω‐helix forms obtained by appropriate treatment. The latter two conformations for L‐alanine residues are achieved when L‐alanine residues are incorporated into poly(β‐benzyl L‐aspartate). We found that the alanine Cβ carbon show significant 13C chemical shift displacement depending on conformational change, and gave the 13C chemical shift values at about 17 ppm for the left‐handed ω‐helix, 14 ppm for the left‐handed α‐helix, 15.5 ppm for the right‐handed α‐helix, and 21.0 ppm for the antiparallel β‐sheet relative to tetramethylsilane.
Condensation of DNA by multivalent cations: Considerations on mechanism
Authors: Bloomfield Victor A. 
Published: May 2005

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

AbstractThe conformations of cis and trans cyclic retro–inverso dipeptides—2‐[(4‐hydroxy)benzyl]‐5‐benzyl‐4,6(1H,2H,3H,5H)‐pyrimidinedione (c[mPhe‐gTyr]), 2‐benzyl‐5‐[(4‐hydroxy)benzyl]‐4,6(1H,2H,3H,5H)‐pyrimidinedione (c[mTyr‐gPhe]), and 2‐benzyl‐5‐amino‐5‐[(4‐hydroxy)benzyl]‐4,6(1H,2H,3H,5H)‐pyrimidinedione {c[(α‐amino)mTyr‐gPhe]}—and the parent cyclic dipeptides—c[tyrosyl‐phenylalanine] (cis‐c[L‐Tyr‐L‐Phe]) and c[tyrosyl‐D‐phenylalanine] (trans‐c[L‐Tyr‐D‐Phe])—were studied by using 1H‐nmr spectroscopy and semiempirical energy calculations. In the cis compounds of all the cyclic retro–inverso and parent dipeptides, the most stable conformer has both aromatic side chains sharing the space over the backbone ring in a “face‐to‐face” fashion. All the trans compounds predominantly assume a “sandwich” conformation in which the two aromatic rings are folded back over the backbone ring on opposite sides. However, different conformational preferences were observed for the backbones between the retro–inverso and parent cyclic dipeptides. The parent cyclic dipeptide trans‐c[L‐Tyr‐D‐Phe] adopts two types of boat structures with different side‐chain orientations in almost equal amounts: one with the Tyr side chain in a pseudoaxial position and the Phe side chain in a pseudoequatorial position, the other with the Tyr side chain in a pseudoequatorial position and the Phe side chain in a pseudoaxial position. On the other hand, the cyclic retro–inverso dipeptides trans‐c[mPhe‐gTyr] and trans c[mTyr‐gPhe] assume only one type of boat structure in which the malonyl side chain is in a pseudoequatorial and the gem‐diamino side chain is in a pseudoaxial position.In addition to the preferred conformations, the conformational energies of the CαCβ bonds in the malonyl and gem‐diamino residues were estimated from the temperature variation of vicinal 1H1H coupling constants for the HCαCβH groupings observed for the trans isomers of cyclic retro–inverso dipeptides. The energies were evaluated to be 1.1 and 1.8 kcal mol−1 for the malonyl and gem‐diamino residues, respectively. Applying these energies to the parent cyclic dipeptide trans‐c[L‐Tyr‐D‐Phe], the observed fractions of three side‐chain conformations are reasonably reproduced. The conformational energies as well as conformational properties of the molecules estimated in this investigation may be useful to refine force constants for both parent and retro–inverso peptides with aromatic side chains.
The elastic resilience of DNA can induce all‐or‐none structural transitions in the nucleosome core particle
Authors: Marky Nancy L. , Manning Gerald S. 
Published: May 2005

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

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

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

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

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

AbstractThe distribution of dissolved oxygen in agitated, sparger‐aerated aqueous solutions has been investigated by polarographic techniques. The results of the investigations are discussed in relation to earlier studies in bubble distribution in such systems. Liquid‐phase mixing is good at agitation intensities well below that necessary to disperse bubbles throughout the liquid.Suspended solids interfere with the transfer of oxygen unless they are freely suspended. Discrete fibers (paper‐pulp) are much easier to suspend than molds in either filamentous or pellet forms. Mass‐transfer at the cell‐liquid interface appears to be unaffected, in both bacterial and mold suspensions, by the intensity of agitation, provided that the organisms are freely suspended.
Plate assay methods for amino acids. 1. A sensitive cup plate assay for lysine with Streptococcus faecalis ATCC 6057
Authors: Bolinder Arne E. , Lie Sturla , Ericson L.‐E. 
Published: May 2005

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

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

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