bluuebunny/crossref_metadata_2025 huggingface dataset:
Some properties of acid‐reassembled tropomyosin
Authors: Holtzer Marilyn Emerson , Downing Lisa J. , Holtzer Alfred
Published: December 2004

The preference for parallelism of the two chains in tropomyosin coiled coils is thought to result from interchain salt bridges. To examine this idea, studies are presented of tropomyosin molecules reassembled from chaotropic solvents in acid solution, where cross‐links cannot exist. The acid‐reassembled molecules are appreciably less disulfide cross‐linkable in acid than native molecules, a result explainable if some antiparallel dimers indeed form at low pH. Physical studies (backbone‐ and tyrosine‐region CD and intrinsic viscosity) indicate that refolding in acid yields a molecular population demonstrably different in tyrosine‐region CD from native, but having comparable (but not identical) helix content, thermal stability, and dimensions. Moreover, the refolding in acid after either thermal or chaotropic‐solvent denaturation yields the same final state, arguing that it is an equilibrium state. All these results are consistent with, but do not prove, that the acid‐reassembled population includes an appreciable fraction (2/3) of antiparallel coiled‐coil dimers. © 1995 John Wiley & Sons, Inc.
For‐Met‐Lys‐Phe‐ For‐Met‐Lys‐Phe‐: A new cyclic analogue of the chemotactic formylpeptides
Authors: Torrini I. , Zecchini G. Pagani , Paradisi M. Paglialunga , Lucente G. , Gavuzzo E. , Mazza F. , Pochetti G. , Traniello S. , Spisani S.
Published: December 2004

As a continuation of the studies on chemotactic N‐formylpeptides, we report here the synthesis and activity of a new cyclic analogue of the prototypical ligand For‐Met‐Leu‐Phe‐OMe. The new compound contains a 20‐membered cyclic moiety made up of a dimeric‐Lys‐Phe‐sequence in which For‐Met is attached to each Lys α‐NH2‐and hence remains outside the ring. The conformation in the crystal of the cyclic precursor of 4, namely and the activity of the structurally related linear analogue For‐Met‐Lys(Z)‐Phe‐OBzl (6), have also been examined. The new analogues 4 and 6 are active as chemoattractants, secretagogues and superoxide anion generating agents, when tested on human neutrophils. The structure‐activity relationship is discussed and related to that of a previously studied cyclic model. © 1995 John Wiley & Sons, Inc.
Solvent effects on model d(CG·G)7 and d(TA·T)7 DNA triple helices
Authors: Cheng Yuen‐Kit , Pettitt B. Montgomery
Published: December 2004

Using free energy molecular mechanics, we find that the molecular effects of solvent are critical in determining relative stabilities in DNA triple helices or triplexes. The continuum solvent model is unable to differentiate the thermodynamics reflecting the basic solvation differences around the occupied major groove in triplexes. In order to avoid the local minimum problem, which is a major limitation of any modeling study, we started our computations with multiple structures rather than relying on the optimization of a single reference structure. By constructing triplex models with different initial helical twists, helical rises, and sugar‐pucker permutations, we explore the potential surface and the structural preference with respect to these variations. We find that in order to accommodate a third strand in triplex formation, the backbone geometry of the B‐DNA duplex target has to be adjusted into A‐DNA‐like form with a deep major groove. This is achieved by concerted adjustment in torsions β, ε, and ζ around the phosphate groups. However, the sugar pucker displays a more rich variation, resulting in conformations not usually associated with the canonical duplex structures. © 1995 John Wiley & Sons, Inc.
Hydrolysis of β‐lactoglobulin by thermolysin and pepsin under high hydrostatic pressure
Authors: Dufour Eric , Hervé Guy , Haertle Tomasz
Published: December 2004

Hydrolysis of β‐lactoglobulin with thermolysin and pepsin at pressures ranging between 0.1 and 350 MPa showed a significant increase of cleavage rates. Pressure‐induced changes of susceptibility to hydrolysis of β‐lactoglobulin proteolytic sites were also observed. The pressure, raised to 200 MPa, accelerates the hydrolysis of β‐lactoglobulin by thermolysin and changes obtained peptide profiles. Initially, higher pressure makes the N‐terminal, and to a smaller extent, C‐terminal peptide fragments of β‐lactoglobulin molecule, more susceptible to removal by thermolysin. This indicates combined influence of pressure‐induced thermolysin activation and partial unfolding of β‐lactoglobulin by compression at neutral pHs.

The rates of hydrolysis of β‐lactoglobulin by pepsin (negligible at 0.1 MPa) are increased considerably with pressure up to 300 MPa. The Susceptibility of β‐lactoglobulin proteolytic sites to peptic cleavage remains constant over all the studied pressure range. The lack of significant qualitative changes in the peptic peptide profiles produced at different pressures and at clearly pressure‐dependent rates points to negative reaction volume changes as the major factor in peptic hydrolysis of β‐lactoglobulin under high pressure. Thus the β‐lactoglobulin molecule resists pressure‐induced unfolding in acid pHs and yields to it in neutral pHs. © 1995 John Wiley & Sons, Inc.
Conformational properties of the proline region of porcine neuropeptide Y by CD and 1H‐NMR spectroscopy
Authors: Chu Shao Song , Velde David Vander , Shobe David , Balse Preeti , Doughty Michael B.
Published: December 2004

We synthesized porcine neuropeptide Y (pNPY) N‐terminal fragments by solid‐phase synthesis techniques and analyzed them for solution Conformational properties by CD and 1H‐nmr spectroscopy. The analogues pNPY1–9 and pNPY1–14 displayed CD spectra indicative of random structures and showed no evidence for induced α‐helical structures in trifluoroethanol (TFE) up to 50%. However, the CD spectra of pNPY1‐9 suggested a Conformational shift in tetrahydrofuran. Although in aqueous solution the CD spectra of pNPY1–21 indicated random structures with induction of only a small percentage of α‐helix in aqueous TFE, pNPY1‐25 displayed 13% a‐helical structure in aqueous solution that increased to 40 and 41% by the addition of TFE and methanol, respectively. The nmr spectra of pNPY1‐9 and the proline region of pNPY1–25 indicated extended structures with all‐trans conformers at Pro5 and Pro8 for pNPY1–9 and at Pro5, Pro8, and Pro13 for pNPY1–25; in each case the Tyrl‐Pro2 amide bond was in both cis and trans conformations. However, observed nuclear Overhauser effect correlations and UN exchange experiments indicated an α‐helical segment in pNPY1–25 initiated by Pro 13 and extending from residues 14 to 25. Thus, the N‐terminal polyproline region of NPY has no propensity to fold into a regular secondary structure, although Pro 13 is a helix initiator, a result consistent with the proposed role of this amino acid in the NPY structural model. © 1995 John Wiley & Sons, Inc.
The “cratic correction” and related fallacies
Authors: Holtzer Alfred
Published: December 2004

The “cratic correction” for removing the contribution of translational motion from standard free energies and entropies of chemical reactions is examined. Although removal of translational effects is useful in interpreting free energy and entropy changes in molecular terms, this particular correction does not do so. No basis for it is found in thermodynamics or statistical mechanics. The appropriate correction for center‐of‐mass translational motion is derived from classical statistical mechanics. However, the importance of recognizing the proper molecular meaning of the remaining free energy is stressed. In any case, this latter correction, however legitimate, is shown to be futile, since it has long been recognized from classical statistical mechanics that all terms involving momenta (thermal wavelength terms) —be they classified as translational, rotational, vibrational, or whatever—necessarily cancel out informing the standard free energy change of any chemical reaction from the constituent standard chemical potentials. © 1995 John Wiley & Sons, Inc.
The energy of formation of internal loops in triple‐helical collagen polypeptides
Authors: Paterlini M. Germana , Némethy George , Scheraga Harold A.
Published: December 2004

The sequence‐dependent local destabilization in the interior of the collagen triple helix has been evaluated by means of conformational energy computations. Using a model poly(Gly‐Pro‐Pro) triple helix as the reference state, a method was developed for generating local loops, i.e., internal deformations, and analyzing their conformations. A seven‐residue Gly‐Pro‐Pro‐Gly‐Pro‐Pro‐Gly fragment was replaced by the Gly‐Pro‐Ala‐Gly‐Ala‐Ala‐Gly sequence in one, two, or all three of the strands of the loop region. A set of loop conformations was generated in which the ends of the loop were initially fixed in the triple‐helical structure. The potential energy of the entire deformed triple helix was then minimized, resulting in a variety of structures that contained deformed loops. The conformations of the triple helices at the two ends of the loops remained essentially unchanged in many of the low‐energy conformations. In numerous high‐energy conformations, however, the triple‐helical segments were also partially or totally disrupted. The minimum‐energy conformations of the whole structures were compared in terms of rms deviations of atomic coordinates with respect to the original triple helix, and of the shapes of the loops (using a distance function derived from differential geometry). Three new geometrical parameters—stretch S, kink K, and unwinding U—were defined to describe the changes in the overall orientation of the triple helices at the two ends of the loop. It is shown that, when the number of Pro residues in a short fragment is reduced, the triple helical structure can accomodate internal loops (i.e., distortions) within a 5 kcal/mol cutoff from the essentially unperturbed triple helical structure. For structures with a Gly‐Pro‐Ala‐Gly‐Ala‐Ala‐Gly sequence in all three strands, the probability of finding conformations with internal loops is small, i.e., 0.06. Internal loops affect the overall orientation of these structures, as measured by the helix‐distortion parameters S, K, and U. © 1995 John Wiley & Sons, Inc.
Packing interactions of aib‐containing helices: Molecular modeling of parallel dimers of simple hydrophobic helices and of alamethicin
Authors: Breed J. , Kerr I. D. , Sankararamakrishnan R. , Sansom M. S. P.
Published: December 2004

α‐Aminoisobutyric acid (Aib) is a helicogenic α,α‐dimethyl amino acid found in channel‐forming peptaibols such as alamethicin. Possible effects of Aib on helix–helix packing are analyzed. Simulated annealing via restrained molecular dynamics is used to generate ensembles of approximately parallel helix dimers. Analysis of variations in geometrical and energetic parameters within ensembles defines how tightly a pair of helices interact. Simple hydrophobic helix dimers are compared: Ala20, Leu20, Aib20, and P20, the latter a simple channel‐forming peptide [G. Menestrina, K. P. Voges, G, Jung, and G. Boheim (1986) Journal of Membrane Biology, Vol. 93, pp. 111–132]. Ala20 and Leu20 dimers exhibit well‐defined ridges‐in‐grooves packing with helix crossing angles (Ω) of the order of +20°. Aib20 α‐helix dimers are much more loosely packed, as evidenced by a wide range of Ω values and small helix‐helix interaction energies. However, when in a 310 conformation Aib20 helices pack in three well‐defined parallel modes, with Ω ca. −15°, +5°, and 10°. Comparison of helix–helix interaction energies suggests that dimerization may favor the 310 conformation. P20, with 8 Aib residues, also shows looser packing of α‐helices. The results of these studies of hydrophobic helix dimers are analyzed in the context of the ridges‐in‐grooves packing model. Simulations are extended to dimers of alamethicin, and of an alamethicin derivative in which all Aib residues are replaced by Leu. This substitution has little effect on helix–helix packing. Rather, such interactions appear to be sensitive to interactions between polar side chains. Overall, the results suggest that Aib may modulate the packing of simple hydrophobic helices, in favor of looser interactions. For more complex amphipathic helices, interactions between polar side chains may be more critical. © 1995 John Wiley & Sons, Inc.
Manipulation of peptide conformations by fine‐tuning of the environment and/or the primary sequence
Authors: Li Shun‐Cheng , Kim Peter K. , Deber Charles M.
Published: December 2004

The widely observed phenomenon that peptides are capable of adopting multiple conformations in different environments suggests that secondary structure formation in a peptide segment is a process involving not only the peptide itself hut also the surrounding solvent media. The influence of the primary sequence and the molecular environment on peptide conformations are now investigated using synthetic peptides of amino acid sequence H2N‐(Ser‐Lys)2‐Ala‐X‐Gly‐Ala‐X‐Gly‐Trp‐Ala‐X‐Gly‐(Lys‐Ser)3‐OH, where X = Ile or Val. These two peptides, namely 3I (X = Ile) and 3V (X = Val), are found to lack defined secondary structure in aqueous buffer. However, discrete conformational states, e.g., α‐helices and β‐sheets, are readily generated and interconverted for both peptides when the buffer is modulated with the addition of methanol, sodium dodecyl sulfate (SDS) micelles, or phospholipid vesicles. The role of the primary sequence in affecting peptide conformations is manifested in that peptides 3I and 3V, which differ respectively in their content of β‐branched Ile or Val residues, differ in their secondary structures at monomeric concentrations in 2 mM SDS and in mixed lipid vesicles of phosphatidic acid and phosphatidylcholine. The overall results suggest that peptide segments can be conformationally flexible entities poised to react to minor modulations in cither the molecular environment or the primary sequence, a circumstance that may he relevant to protein functioning and folding. © 1995 John Wiley & Sons, Inc.
Multiple interconverting conformers of the cyclic tetrapeptide tentoxin, [cyclo‐(L‐MeAla1‐L‐Leu2‐MePhe[(Z)Δ]3‐Gly4)], as seen by two‐dimensional 1H‐nmr spectroscopy
Authors: Pinet Eric , Neumann Jean‐Michel , Dahse Ingo , Girault Guy , André François
Published: December 2004

The conformations of the phytotoxic cyclic tetrapeptide tentoxin [cyclo‐(L‐MeAla1‐L‐Leu2‐MePhe[(Z)Δ]3‐Gly4 )] have been studied in aqueous solution by two‐dimensional proton nmr at various temperatures. Contrary to what is observed in chloroform, tentoxin exhibits multiple exchanging conformations in water. Aggregation phenomena were also observed. Four conformations with different proportions (51, 37, 8, and 4%) were observed at −5°C. Models were constructed from nmr parameters and restrained molecular dynamics simulations. All the models exhibit cis‐trans‐cis‐trans conformation of the amide bond sequence. The conversion from one form to another is accomplished by a conformational peptide flip consisting of a 180° rotation of a nonmethylated peptide bond. © 1995 John Wiley & Sons, Inc.
Conformational analysis of helical poly(β‐L‐ aspartate)s by IR dichroism
Authors: López‐Carrasquero F. , Alemán C. , Muñoz‐Guerra S.
Published: December 2004

Poly(β–l–aspartate)s are known to take up helical conformations reminiscent of the α‐helix of polypeptides. The isobuttyl, n‐butyl, and 2‐methoxyethyl esters have been examined by polarized ir spectroscopy in order to discriminate between the left (1L) and right (2R) ‐handed conformations, which are known to be compatible with the 13/4‐helix adopted by these polyamides when crystallized in the hexagonal form. Dichroic ratios obtained from samples stretched in poly(ethylene oxide) together with orientation measurements made by x‐ray diffraction were used to estimate the transition moment directions of amide A, I, and II bands with respect to the fiber axis. These were compared to those calculated by modeling simulations to conclude that the right‐handed conformation consisting of 14‐membered hydrogen‐bonded rings is the correct model for the 13/4‐helix. These results give definite support to earlier molecular mechanics calculations, which had shown that the 2R model is energetically favored over the 1L by about 2. 5 kcal/(mol residue). © 1995 John Wiley & Sons, Inc.
Complexes of aluminium with peptide ligands: A fourier transform IR spectroscopic study
Authors: Hollósi Miklós , Holly Sándor , Majer Zsuzsa , Laczkó Ilona , Fasman Gerald D.
Published: December 2004

Aluminium has been recognized to be a neurotoxic agent and a risk factor in Alzheimer's disease and other neuronal dysfunctions. CD spectroscopic studies on two synthetic fragments of the human neurofilament protein midsized subunit (NF‐M), and their alanine‐for‐serine‐substituled and /or serine‐phosphorylated derivatives showed the formation of stable, citric acid resistant complexes of Al3+with peptide ligands [M. Hollósi, Z.M. Shen, A. Perczel, and G.D. Fasman (1994) Proc. Natl. Acad. Sci. USA, vol. 9, pp.4902‐4906]. In the case of Ser‐phosphorylated fragments, aβ‐sheet inducing effect of Ca2+ and Al3+ ions was observed. However, the serine‐containing parent peptides, NF‐M 13 (KSPVPKSPVEEKG) and NF‐M 17 (EEKGKSPVPKSPVEEKG), failed to show CD spectral changes reflecting β‐sheet formation upon addition of Al3+ ions. On the basis of the amide I region of the Fourier transform ir spectra, in triftuoroethanol, the peptide backbone of NF‐M17 and NF‐M17 (A6A11) shows marked changes in the presence ofAl3+. The most significant spectral differences are seen in the car‐boxyl region (> 1700 cm−l). The high‐frequency component bands above 1760 cm−1 in both spectra belong to the C O of undissociated CF3COOH. Another strong band at 1710 cm−1 which appears only in the spectrum of NF‐Ml 7 (A6A11)(NF‐M17 with Ser6 andSer11 replaced by Ala) can be assigned to the side chain or C‐terminal COOH groups. The differential proton‐ation state of the carboxyl groups in the two peptides suggests the format ion ofAl3+ complexes of different structure and stability. The Al3+ complex ofNF‐Ml 7 (A6A11) is likely less stable, or one or more of the carboxylates are not coordinated to the Al3+ and thus can serve as a base to bind the liberated protons. In NF‐M17 the OH groups of serines facilitate the formation of type [Al‐pep(H‐1)] complexes with the involvement of all carboxylategroups in the molecule. The relevance of intramolecular and intermolecular Al3+ binding to the controversial biological role of aluminium is also discussed. © 1995 John Wiley & Sons, Inc.
Exploration of compact protein conformations using the guided replication monte carlo method
Authors: Solomon Jerry E. , Liney David
Published: December 2004

We have studied the use of a new Monte Carlo (MC) chain generation algorithm, introduced by T. Garel and H. Orland[(1990) Journal of Physics A, Vol. 23, pp. L621–L626], for examining the thermodynamics of protein folding transitions and for generating candidate Cαbackbone structures as starting points for a de now protein structure paradigm. This algorithm, termed the guided replication Monte Carlo method, allows a rational approach to the introduction of known “native” folded characteristics as constraints in the chain generation process. We have shown this algorithm to be computationally very efficient in generating large ensembles of candidate Cαchains on the face centered cubic lattice, and illustrate its use by calculating a number of thermodynamic quantities related to protein folding characteristics. In particular, we have used this static MC algorithm to compute such temperature‐dependent quantities as the ensemble mean energy, ensemble mean free energy, the heat capacity, and the mean‐square radius of gyration. We also demonstrate the use of several simple “guide fields” for introducing protein‐specific constraints into the ensemble generation process. Several extensions to our current model are suggested, and applications of the method to other folding related problems are discussed. © 1995 John Wiley & Sons, Inc.
Applicability of a continuum solvation model to the octanol water transfer: CFF91 based model for amino acids
Authors: Schmidt A. B. , Fine R. M.
Published: December 2004

A continuum hydration model based upon the atomic charges provided with the CFF91 force field [A. B. Schmidt and R. M. Fine (1994) Molecular Simulation, 13. 347–365] has been extended to the octanol–water transfer. The electrostatic component of the transfer free energy is calculated using the finite‐difference solution to the Poisson–Boltzmann equation while the nonpolar contributions are assumed to be proportional to the solute‐excluded volume in water. All atomic charges and radii besides the aromatic carbon radius are equal in both solvents. The octanol dielectric constant and the probe radius are the main fitting parameters defining the octanol phase. The model has been tested for 38 organic molecules related to the amino acid residues and generally provides a high accuracy. In particular, the mean unsigned error for N‐acetyl amino acid amides is 0.5 kcal/mol. © 1995 John Wiley & Sons, Inc.
Crystal and molecular structure of the centrosymmetric meso‐valinomycin analogue—cyclo (D‐Val‐D‐Hyi‐D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi‐L‐Val‐L‐Hyi‐L‐Val‐D‐Hyi‐L‐Val‐L‐Hyi) (C60H102N6O18)
Authors: Pletnev V. Z. , Fonarev Yu. D. , Tsygannik I. N. , Ivanov V. T. , Pletnev S. V. , Langs D. A. , Duax W. L.
Published: December 2004

The crystal structure of cyclo (D‐Val‐D‐Hyi‐D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi‐L‐Val‐L‐Hyi‐L‐Val‐D‐Hyi‐L‐Val‐L‐Hyi)‐2H2O has been solved by x‐ray direct methods. The crystals (grown from a mixture of octane / CH2C12) are an orthorhombic, centrosymmetric space group Pbca, cell parameters a = 11.458(2). b = 25.613(3). c = 23.691(3) Å. Z = 4; therefore the molecule lies on a center of inversion in the cell. The atomic coordinates for the C, N, and O atoms were refined in the anisotropic thermal motion approximation (allowing for II‐atom contribution to Fcal) to a standard R‐ factor value of 0.081. In contrast to meso‐valinomycin, the analogue under study does not adopt an octahedral cage bracelet conformation. It has an unusual centrosymmetric elongated form with two type II terminal β‐bends formed by NHCO 4 → 1 type intramolecular H bonds. Two symmetry‐related water molecules reside in the elongated molecular cavity of the centrosymmetric depsipeptide ring. © 1995 John Wiley & Sons, Inc.
A study of Na‐DNA films containing NaCl via scanning electron and tunneling microscopies
Authors: Mayeres C. H. , Lee S. A. , Pinnick D. A. , Carter B. J. , Kim J
Published: December 2004

Unoriented films of Na‐DNA were prepared by dessicating a gel with different amounts of NaCl. For low salt concentrations, the resulting films were smooth and patternless. For high salt concentrations, the resul ting films had visible patterns that were very similar to those recently r eported by Sclavi et al. [(1994) Biopolymers, Vol.34. pp.1105–1113]. Scanning electron and tunneling microscopies and electron dispersive sp e ctroscopy studies were used to study the spatial distribution of NaCl th ro ughout these films. Two main conclusions were reached about the NaCl: (l) some NaCl is distributed throughout every film, and (2) the visib le p atterns observed in films with a large amount of NaCl were caused by the growth of NaCl crystals during the dehydration process. © 1995 John Wiley & Sons, Inc.
Concept and progress in the development of RGD‐containing peptide pharmaceuticals
Authors: Craig William S. , Cheng Soan , Mullen Daniel G. , Blevitt Jon , Pierschbacher Michael D.
Published: December 2004

The cell adhesion domain, arginine–glycine–aspartic acid (RGD), has been incorporated into synthetic peptides to perform either of two modes of drug action, antagonist or agonist. Short, conformationally constrained peptides have been developed as antagonists for the platelet membrane glycopivtein complex, the integrin αIIbβ3, using cell‐based and integrin‐based assays. In combination with a comparative molecular modeling study, these results have helped identify common conformalional elements in the pharmacophore of this class of molecules. Peptides are presented that are highly potent, integrin specific, and that possess reduced pharmacological side effects. Also presented is the development of a peptide that modifies, noncovalently, the surfaces of a wide variety of this molecule is evident from its ability to stimulate cell attachment on these surfaces. This is shown to translate into an in vivo activity of faster and more complete tissue integration, and a reduction in foreign body response. © 1994 John Wiley & Sons, Inc.
Approach to discovering novel therapeutic agents for osteoporosis based on integrin receptor blockade
Authors: Chorev Michael , Dresner‐Pollak Rivka , Eshel Yoav , Rosenblatt Michael
Published: December 2004

On a global scale, osteoporosis is a major and growing public health problem. In the United States, osteoporosis is present in 24 million people (mostly women) and contributes to more than 1.3 million fractures/year. Serious morbidity and mortality result from these fractures. Current therapies for osteoporosis are few, efficacy is limited, and side effects problematic. Fundamental to the pathophysiology of osteoporosis is an imbalance between the tightly coupled processes of bone resorption and bone formation that characterize normal bone remodeling. Our laboratory is engaged in a research effort focused on elucidating the role of the osteoclast integrin in bone resorption, defining the nature of ligand–integrin interactions, and developing antagonists for cell surface adhesion molecules, particularly the αν, β3 vitronectin‐like integrin receptor present on the surface of human osteoclasts. Peptides containing the internal arginine‐glycine‐aspartic acid (RGD) motif have been shown to inhibit osteoclast‐mediated bone resorption in vivo. We are now designing more potent and selective inhibitors of bone resorption as a potential new mechanism‐based therapeutic approach to osteoporosis based on a novel mechanism. In an effort to rapidly identify the highest affinity ligands for the human ανβ3 integrin, we have generated combinatorial peptide libraries containing substantial structural diversity. For instance, based on all possible sequence combinations of extracellular matrix proteins known to bind ανβ3, we recently synthesized and chemically analyzed a library of 360,000 peptides, all of which contain RGD. Human ανβ3 receptors are now available in a clonal cell line that expresses high levels of recombinant receptor, these cells can serve as a very important research tool in this project because of the limited number of bone‐derived osteoclasts that can be harvested for experimentation. The library of peptides will be screened by “affinity selection”: the highest binding affinity peptide(s) will be isolated and microsequenced. Receptor‐favored sequences will be synthesized and evaluated in a battery of in vitro and in vivo bioassays. Through these investigations, insight will be gained into the role of integrins in bone biology and patho‐physiology, and new directions will be developed for the design of potent human ανβ3‐selective antagonists for the treatment of osteoporosis. © 1994 John Wiley & Sons, Inc.
Two‐Dimensional nmr studies of the interactions between a peptide of cholera toxin and monoclonal antibodies
Authors: Anglister Jacob , Scherf Tali , Zilber Barbara , Levy Rina
Published: December 2004

To increase our understanding of the molecular basis for antibody specificity and for the cross‐reactivity of antipeptide antibodies with native proteins, it is important to study the three‐dimensional structure of antibody complexes with their peptide antigens. For this purpose it may not be necessary to solve the structure of the whole antibody complex but rather to concentrate on elucidating the combining site structure, the interactions of the antibody with its antigen, and the bound peptide conformation. To extract the information about antibody–peptide interactions and intramolecular interactions in the bound ligand from the complicated and unresolved spectrum of the Fab–peptide complex (Fab: antibody fragment made of Fv—the antibody fragment composed of the variable regions of the light and heavy chains forming a single combining site for the antigen—the light chain, and the first heavy chain constant regions), an nmr methodology based on measurements of two‐dimensional transferred nuclear Overhauser effect (NOE) difference spectra was developed. Using this methodology the interactions of three monoclonal antibodies with a cholera toxin peptide were studied. The observed interactions were assigned to the antibody protons involved by specific deuteration of aromatic amino acids and specific chain labeling, and by using a predicted model for the structure of the antibody combining site. The assigned NOE interactions were translated to restraints on interproton distances in the complex that were used to dock the peptide into calculated models for the antibodies combining sites. Comparison of the interactions of three antibodies against a cholera toxin peptide (CTP3). which differ in their cross‐reactivity with the toxin, yields information about the size and conformation of antigenic determinants recognized by the antibodies, the structure of their combining sites, and relationships between antibodies' primary structure and their interactions with peptide antigens. © 1994 John Wiley & Sons, Inc.
Comparative analysis of various proposed models of the receptor‐bound conformation of H‐tyr‐Tic‐Phe OH related δ‐opioid antagonists
Authors: Wilkes Brian C. , Schiller Peter W.
Published: December 2004

A molecular mechanics study (grid search and energy minimization) was performed with six δ opioid peptide antagonists containing a tetrahydroisoquinoline‐3‐carboxylic acid (Tic) residue in the 2‐position of the peptide sequence. Compounds examined were the highly potent and selective T1P(P) peptides H‐Tyr‐Tic‐Phe‐OH (TIP). H‐Tyr‐TicΨ[CH2‐NH]Phe‐OH (TIP[Ψ]). H‐Tyr‐Tic‐Phe‐Phe‐OH (TIPP). and H‐Tyr‐TicΨ[CH2‐NH]Phe‐Phe‐OH (TlPP[Ψ]), and the weakly active analogues H‐Tyr‐Tic‐NH2 and H‐Tyr‐Tic‐Ala‐OH. Low energy conformers of the peptides were examined for their compatibility with three proposed model of the δ receptor‐bound conformation. Model 1, based on spatial overlap of the Tyr1 and Phe3 aromatic rings and N‐terminal amino group of the peptides with the corresponding aromatic rings and nitrogen atom of the nonpeptide δ‐antagonist naltrindole, was ruled out because of the demonstrated importance of the Tic2 aromatic ring for δ antagonism and because of the somewhat elevated energies of the conformers consistent with this model. Models of the receptor‐bound conformation based on superimposition of the Tyr1 and Tic2 aromatic rings and N‐terminal amino group of the peptides with the corresponding moieties in naltrindole included an all‐trans peptide bond conformer [model 2, proposed by B. C. Wilkes and P. W. Schiller (1994) Biopolymers. Vol. 34. pp. 1213–1219] and a conformer with a cis peplide bond between the Tyr1 and Tic2 residues (model 3), originally proposed by P. A. Temussi et al. [(1994) Biochemical and Biophysical Research Communications. Vol. 198, pp. 933–939]. For all six peptides low energy conformers consistent with both model 2 and model 3 were identified: however, peptide conformers corresponding to model 2 showed better coplanarity of the Tyr1 aromatic ring and the phenol ring in naltrindole than peptide conformers corresponding to model 3. Both models remain plausible candidate structures for the receptor‐bound conformation of δ antagonists of the TIP(P) class. TIP(P) analogues containing additional conformational constraints need to be developed in order to arrive at a unique model. © 1994 John Wiley & Sons, Inc.
Role of microbial enzymes in flavor development in foods
Authors: Shahani K. M. , Arnold R. G. , Kilara A. , Dwivedi B. K.
Published: December 2004

There are four main sources of enzymes in foods—these being the inherent enzymes, enzymes from microbial contaminants, enzymes elaborated by microorganisms added to foods, and specific enzymes added to foods. This study primarily deals with the latter two sources of enzymes in food. Although both plants and animals serve as sources of enzymes, they are not as economical or versatile sources as are enzymes obtained from microorganisms. In the meat industry, proteases are used to tenderize muscle and to obtain flavor precursors. In the preparation of cured meat products such as sausages, lipases, and proteases from bacterial cultures are utilized. Similarly, proteases and lipases are used in the dairy industry to develop flavor compounds. Proteases and amylases also have applications in the baking and milling industries where they are used to produce precursors for the nonenzymatic browning reactions. Carbohydrases such as amylase, amyloglucosidase, and glucose isomerase have found usage in the starch and syrup industry for the production of high dextrose and high fructose syrups. Other enzymes such as glucose oxidase, pectinase, and naringinase are of value to the wine and fruit juice industries. A better understanding of the mode of action of enzymes as well as the mechanisms of development of flavor compounds will further enhance the use of microbial enzymes to develop specific and desired flavors in foods.
Design and performance characteristics of a continuous multistage tower fermentor
Authors: Páca Jan , Grégr Vratislav
Published: December 2004

The design of a continuous multistage tower fermentor is described. The fermentor consists of five stages separated by perforated plates. Each stage includes mechanical mixing provided by two disc turbine impellers and has its own impeller shaft with bearing assembly and flexible coupling that enables the operation of an arbitrary number of stages. The normal operation of this system enables the co‐current flow of gas and liquid, but the system can function countercurrently as well.

The purpose of this study was to examine the hydrodynamic performance, i.e., the pressure gradient along the tower, the mixing time, gas holdup, the residence lime distribution of the continuous phase, the value of the backflow coefficient, and the oxygen transfer rate under conditions usually used during fermentations. From the interrelations between parameters influencing the proper performance of this system, an optimal design of plate geometry for processes requiring high oxygen transfer rate was formulated.
A new mechanochecmical method of enzyme immobilization
Authors: Klibanov A. M. , Samokhin G. P. , Martinek K. , Berezin I. V.
Published: December 2004

A new mechanochemical method for enzyme immobilization has been elaborated. The principle of this method consists of the following precepts. Partially hydrolyzed nylon fiber, the surface of which is known to be strewn with micro‐cracks, is reversibly stretched (∼25%) and placed into an enzyme solution. Then, in the same solution, the fiber is made to relax and is taken out. The fiber retains considerable enzymatic activity even after numerous thorough washings (in a similar procedure without fiber stretching, equivalent washing removed all the enzymatic activity from the fiber). Immobilization on the fiber proceeds due to trapping of enzyme molecules by the microcavities on the surface of the support. The catalytic activity of mechanochemically immobilized chymotrypsin and trypsin is commensurable with their activity on covalent immobilization on nylon (calculated per unit of the macrosurface). A wide range of commercial polymers may be made of use as supports in the mechanochemical method of immobilization.
A mechanistic model of the aerobic growth of Saccharomyces cerevisiae
Authors: Bijkerk A. H. E. , Hall R. J.
Published: December 2004

A two‐stage deterministic model of the growth of Saccharomyces cerevisiae is presented. The cell cycle of this organism was used to suggest the basic model structure. The model represents the preparatory processes of substrate uptake and conversion separately from replication and division. The regulation of the fraction of the culture devoted to each of these broad areas of metabolism, and the overall growth rate, is related to the nature and availability of the energy substrate.

The simulation of respiration and glycolysis is achieved by including two alternative energy producing pathways. The regulation of these pathways is described in terms of the postulated primary regulation of the proportion of the culture required for substrate uptake and conversion, and the overall kinetic constants for each pathway. This regulation is dictated primarily by the growth rate rather than the nature or concentration of the energy substrate.

The model successfully describes both batch and continuous growth of S. cerevisiae under conditions of glucose limitation and oxygen excess. A preliminary assessment indicates that adjustment of the relevant parameters will allow the model to describe the growth of S. cerevisiae on other sugars and under oxygen limitation. Similarly the model could be expected to describe the growth characteristics of other yeast species.
The tubular loop fermentor: Oxygen transfer, growth kinetics and design
Authors: Ziegler H. , Meister D. , Dunn I. J. , Blanch H. W. , Russell T. W. F.
Published: December 2004

Oxygen transfer measurements using a dynamic method and evaluated with an appropriate mathematical model have been made on a tubular loop bioreactor. Correlations of the type used in tank systems are used to describe the influence of power and aeration rate on the mass transfer coefficient. Yeast cultures grown on hydrocarbon and glucose substrates show growth characteristics similar to conventional tank results. Model considerations for large‐scale tubular fermentors allow for the prediction of the steady‐state oxygen profiles and maximum reactor length. Combination with two‐phase flow and oxygen transfer correlations yields a design procedure for commercial scale tubular loop fermentors.
Mechanism of disintegration of biological cells in ultrasonic cavitation
Authors: Doulah M. S.
Published: December 2004

On the basis of elastic waves released by imploding cavitation bubbles, a mechanism for biological cell disintegration in high intensity ultrasounds has been proposed. Comparison of this mechanism with the published results on yeast cells shows many points of agreement suggesting that yeast cell disintegration in ultrasonic cavitation occurs by shear stresses developed by viscous dissipative eddies arising from shock waves.
Oxygen transfer coefficients by dynamic model moment analysis
Authors: Dang N. D. P. , Karrer D. A. , Dunn I. J.
Published: December 2004

A new method to estimate the oxygen transfer coefficient (KLa) from the experimental dynamic response data is presented. Employing a linear model which allows for gas phase, diffusion film, and oxygen electrode dynamics, the first moment of the response curve is simply related to the sum of the model parameters. Two separate experiments are used to characterize the measurement dynamics and to measure the unknown KLa parameter. The simple calculation procedure involves only measuring the area above the response curves.
Isolation of a yeast‐lyzing Arthrobacter species and the production of the lytic enzyme complex in batch and continuous‐flow fermentors
Authors: Rowley B. I. , Bull A. T.
Published: December 2004

A gram‐negative bacterium strongly lytic toward living cells of the food yeast Saccharomyces fragilis was isolated by continuous‐flow enrichment from compost. The organism was identified as a species of Arthrobacter. The extracellular lytic enzyme complex produced by this bacterium contained β‐1,3‐glucanase, mannan mannohydrolase, and proteolytic activities. The polysaccharases were inducible by whole yeast cells. In chemostat cultures on chemically defined media, synthesis of the polysaccharases was very slight and only detectable at dilution rates below 0.02 hr−1. Enzyme production in defined media was not solely dependent on growth rate but also was influenced by the growth limiting substrate and the culture history. The production of individual depolymerases and of the lytic activity was studied in batch and chemostat cultures containing yeast as the limiting substrate. The maximum specific growth rate of the Arthrobacter under these conditions was 0.22 hr−1. β‐1,3‐Glucanase and proteolytic activities were synthesized by exponentially growing bacteria but maximum lytic titers did not develop until the specific growth rate was declining, at which time mannan mannohydrolase syntheses was induced. In yeast limited chemostats polysaccharase syntheses were greatest at the lowest dilution rates examined, namely 0.02 hr−1. Further optimization of enzyme production was achieved by feeding the Arthrobacter culture to a second‐stage chemostat. A comparison of lytic enzyme productivities in batch and chemostat cultures has been made.
Characteristics of unbuffered gel‐immobilized urease particles. II. Overall rate of reaction
Authors: Atkinson B. , Rousseau I.
Published: December 2004

The overall rates of reaction of unbuffered gel‐immobilized urease particles have been investigated with the aid of a packed‐bed differential recycle reactor. Both substrate and enzyme concentrations have received attention. Cylindrical gel particles contained within impermeable tubelets were used to provide the physical strength necessary for the packed‐bed arrangement and a one dimensional diffusion path to aid understanding of the complex interactions between substrate and product diffusion, and their effect on the reactions taking place. The experimental data have been interpreted with the aid of an enzyme rate equation (ERE) which relates the free solution characteristics of the enzyme to the conditions within a diffusion limited particle. The internal hydrogen ion profiles have been accommodated by a lumped parameter, the apparent pH (pHapp). Two methods have been suggested for the calculation of pHapp and the loss of activity on particle preparation, these methods are based on the use of the ERE in conjunction with experimental data.
Hydrolysis of cellulose in a cellulase‐bead fluidized bed reactor
Authors: Karube Isao , Tanaka Shigeru , Shirai Takashi , Suzuki Shuichi
Published: December 2004

Cellulase was immobilized in a collagen fibril matrix, and no leakage of cellulase from the collagen fibril matrix was observed. The immobilized cellulase was more stable than the native cellulase. The substrate cellulose was hydrolyzed quantitatively with immobilized cellulase. The final reaction product was identified as glucose. Immobilized cellulase was used in a fluidized bed reactor where the pressure drop of the fluidized bed reactor was low and constant. Cellulose was hydrolyzed to glucose by the cellulase‐bead fluidized bed reactor. The minimum flow velocity (Umf) was 0.5 cm/sec and the optimum flow velocity of the cellulose hydrolysis was 1 cm/sec.
Competition for mixed substrates by microbial populations
Authors: Yoon H. , Klinzing G. , Blanch H. W.
Published: December 2004

A model for the growth of an organism on multiple substrates was developed, assuming that each substrate has a competitive inhibition effect on the uptake of other substrates. The model was extended to examine mixed substrates, showing that the coexistence of several species at steady state in continuous cultures is possible, even when all the organisms all strongly prefer the one substrate. The diversity of nutrient sources in a real system may be a key factor in supporting a heterogeneous microbial population.
Emulsifying and surface active agents from Corynebacterium hydrocarboclastus
Authors: Zajic J. E. , Guignard Hélène , Gerson D. F.
Published: December 2004

A Corynebacterium hydrocarboclastus culture isolated in our laboratory (see, Zajic and Knettig, Developments in Industrial Microbiology, 1971, p. 87) has been shown to produce an extracellular biopolymer with emulsifying properties when grown on a mixture of linear hydrocarbons. This microorganism was found to grow well on a variety of carbohydrates and hydrocarbons. However, the best substrates were pure linear hydrocarbons and particularly, n‐C12, n‐C13, and n‐C14. The substrates supporting good growth gave good polymer production. Maximum cell mass of 10–11 g/liter and a maximum amount of polymer of 5–6 g/liter were recorded. The polymers recovered from the different substrates were found to be complex molecules or mixtures with a protein, a lipid, and a carbohydrate moiety. All the polymers are surface active and have two critical micelle concentrations.
Some observations on oscillatory changes in the growth rate of Saccharomyces cerevisiae in aerobic continuous undisturbed culture
Authors: Borzani Walter , Gregori Rosana E. , Vairo Marina L. R.
Published: December 2004

Oscillatory changes in the growth rate were observed in undisturbed continuous culture of Saccharomyces cerevisiae on sugar‐cane molasses media when nitrogen sources (2.56 to 6.17 g/liter of ammonium sulfate or 1.22 g/liter of urea) were added to the feeding mash and when the air rate was 1.3 to 1.6 v/v/m. The oscillations were not affected by the addition of yeast extract. The suppression of the nitrogen source during the continuous test leads to a nonoscillatory transient state. No oscillations occurred at all when no nitrogen source was added to the medium and/or the air rate was equal to zero or equal to about 3.3 v/v/m. The oscillatory responses of the system were affected by a previous anaerobic continuous cultivation of the yeast.
Thirty liter tower‐type pilot plant for the mass cultivation of light‐ and motion‐sensitive planktonic algae
Authors: Jüttner Friedrich
Published: December 2004

A simple, low‐priced 30 liter tower‐type algal pilot plant for the cultivation of light‐ and motion‐sensitive species is described. Two hundred g wet weight of Microcystis aeruginosa were obtained per harvest. Since the self‐shading of denser cultures could be compensated for only to a limited extent by increasing the light intensity without damaging the cells, the efficiency of various culture‐vessel widths was determined for the growth of Microcystis : the best results were obtained with a width of 3.5 cm. Light requirements of Microcystis were studied in shadowless suspensions. The compensation point of photosynthesis varied between 200 and 300 lx, depending on the preillumination, whereas the light saturation point was found to be near 4000 Ix. The light optimum for photosynthesis was not identical with that for good growth.
Influence of lactose hydrolysis and solids concentration on alcohol production by yeast in acid whey ultrafiltrate
Authors: O'leary V. S. , Sutton C. , Bencivengo M. , Sullivan B. , Holsinger V. H.
Published: December 2004

Alcohol yields of 6.5% were obtained with Saccharomyces cerevisiae in lactasehydrolyzed acid whey permeate containing 30–35% total solids. Maximum alcohol yields obtained with Kluyveromyces fragilis were 4.5% in lactase‐hydrolyzed acid whey permeate at a solids concentration of 20% and 3.7% in normal permeate at a solids concentration of 10%. Saccharomyces cerevisiae efficiently converted the glucose present in lactase‐hydrolyzed whey permeates containing 5–30% total solids (2–13% glucose) to alcohol. However, the galactose, which comprised about half the available carbohydrate in lactase‐hydrolyzed whey, was not utilized by S. cerevisiae, so that even though alcohol yields were higher when this organism was used, the process was wasteful in that a substantial proportion of the substrate was not fermented. For the process to become commercially feasible, an efficient means of rapidly converting both the galactose and glucose to alcohol must be found.
Synthesis of a soluble catalase–dextran conjugate
Authors: Marshall J. John , Humphreys John D.
Published: December 2004

Results of a systematic study of the conditions for preparation of soluble catalase–dextran conjugates, using the cyanogen bromide activation procedure, are reported. A protocol for the synthesis of such a conjugate with satisfactory retention of enzymatic activity and high efficiency of coupling is described.