bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

AbstractThe 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

AbstractPoly(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

AbstractAluminium 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

AbstractWe 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

AbstractA 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

AbstractThe 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

AbstractUnoriented 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

AbstractThe 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

AbstractOn 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

AbstractTo 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

AbstractA 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

AbstractThere 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

AbstractThe 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

AbstractA 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.