SVIBOR - Papers quoted in CC - project code: 1-03-171

MINISTRY OF SCIENCE AND TECHNOLOGY

Strossmayerov trg 4, HR - 10000 ZAGREB
tel.: +385 1 459 44 44, fax: +385 1 459 44 69
E-mail: ured@znanost.hr

SVIBOR - Collecting Data on Projects in Croatia

Papers quoted in Current Contents on project 1-03-171

Quoted papers: 15
Other papers: 15
Total: 30

Title: Protein secondary structure preferences: dependence on medium-range steric interactions

Authors:: Juretić, Davor (19290); Williams, Robert W.

Journal: Journal of Mathematical Chemistry
ISSN: 0259-9791
Volume: 8
Year: 1991
Pages: from 229 to 242
Number of references: 39
Language: engleski
Summary: This paper addresses the question to what extent steric properties of sequence neighbors effect the preferences of an amino acid residue in protein to assume the alpha-helical or some other secondary structure conformation. For all amino acids, the preference for the helical structure increases if their primary structure neighbors form a larger steric environment
Keywords: Proteins, secondary structure, steric interactions, sequence environment, conformational preferences

Title: Localizing alpha-helices in water-soluble and membrane-bound proteins

Authors:: Juretić, Davor (19290)

Journal: Periodicum Biologorum
Number: 2
ISSN: 0031-5362
Volume: 93
Year: 1991
Pages: from 279 to 280
Number of references: 16
Language: engleski
Summary: Our middle-helix preference functions recognize alpha-helical segments in the membrane
Keywords: Preference functions, hydrophobicity, membrane proteins

Title: Magainin oligomers reversibly dissipate membrane potential in cytochrome oxidase liposomes

Authors:: Juretić, Davor (19290); Hendler, Richard, W.; Kamp, Frits; Caughey, Winslow, S.; Zasloff, Michael; Westerhoff, Hans, V.

Journal: Biochemistry
ISSN: 0006-2960
Volume: 33
Year: 1994
Pages: from 4562 to 4570
Number of references: 50
Language: engleski
Summary: Magainins dissipate membrane potential and stimulate respiration in cytochrome oxidase liposomes. Magainins are 23-25 amino acids long peptides present in the skin of Xenopus laevis and identified as antimicrobial agents. The release of respiratory control happens with a third of higher order cocentration dependence. The results are discussed in terms of a model in which most of the added magainin adsorbs as a monomer to the membrane but equilibrates with a multimeric pore that causes rather general permeability of membranes. The ensuing ion permeation dissipates membrane potential and stimulates respiration.
Keywords: Magainins, cytochrome oxidase, liposomes, membrane potential, respiratory control

Title: Functional synergism of the magainins PGLa and magainin-2 in Escherichia coli, tumor cells and liposomes

Authors:: Westerhoff, Hans, V.; Zasloff, Michael; Rosner, Lee, J.; Hendler, Richard, W.; De Waal, Anthony; Vaz Gomes, Ana; Jongsma, Ans, P. M.; Riethorst, Albert; Juretić, Davor (19290)

Journal: Eur. J. Biochem.
ISSN: 0014-2956
Volume: 228
Year: 1995
Pages: from 257 to 264
Number of references: 53
Language: engleski
Summary: Two magainins, magainin 2 and PGLa, are much more active in biological functions when added together than when added alone. This synergy applies for the antimicrobial activity, for the toxic effects on tumor cells, for dissipating the membrane potential in cytochrome oxidase liposomes and Escherichia coli, for stimulating respiration in cytochrome oxidase liposomes and for permeabilization of protein free liposomes for glucose.
Keywords: Magainins, synergy, antimicrobial, tumor cells, Escherichia coli, liposomes, cytochrome c oxidase

Title: Secondary structure prediction quality for naturally occuring amino acids in soluble proteins

Authors:: Juretić, Davor (19290); Lučić, Bono (184293); Trinajstić, Nenad (50450)

Journal: J. Mol. Struct. - Theochem.
ISSN: 0166-1280
Volume: 338
Year: 1995
Pages: from 43 to 50
Number of references: 43
Language: engleski
Summary: Proline in the loop conformation is the best predicted amino acid conformation. At the same time proline is the worst predicted amino acid in regular secondary structures. Novel, more specific, performance parameters for protein secondary structure prediction were introduced and the results of Rost-Sander neural network algorithm for predicting secondary structure of soluble proteins were analysed to reach this conclusion.
Keywords: Secondary structure, prediction, performance parameters, neural network, proline

Title: A novel QSPR approach to physicochemical properties of the alpha-amino acids

Authors:: Lučić, Bono (184293); Nikolić, Sonja; Trinajstić, Nenad (50450); Juretić, Davor (19290); Jurić, Albin

Journal: Croatica Chemica Acta
Number: 3
ISSN: 0011-1643
Volume: 68
Year: 1995
Pages: from 435 to 450
Number of references: 33
Language: engleski
Summary: A novel multivariate linear regression, based on the ordered orthogonalized connectivity basis and dominant component analysis, is applied to several physicochemical properties of alpha-amino acids.
Keywords: Multivariate linear regresion, quantitative structure-property models, orthogonalized descriptors, dominant component analysis, alpha-amino acids

Title: The structure-property models can be improved using the orthogonalized descriptors

Authors:: Lučić, Bono (184293); Lučić, Bono (184293); Trinajstić, Nenad (50450); Juretić, Davor (19290)

Journal: J. Chem. Inf. Comp. Sci.
ISSN: 0095-2338
Volume: 35
Year: 1995
Pages: from 532 to 538
Number of references: 20
Language: engleski
Summary: We describe an approach of how one can with the use of orthogonalized descriptors achieve a better structure-property-activity model.
Keywords: Structure-property models, orthogonalized descriptors, boiling points, octanes

Title: A scale of beta-preferences for structure-activity predictions in membrane proteins

Authors:: Juretić, Davor (19290); Pešić, Roko

Journal: Croatica Chemica Acta
Number: 1
ISSN: 0011-1643
Volume: 68
Year: 1995
Pages: from 215 to 232
Number of references: 56
Language: engleski
Summary: Our scale of beta-sheet preferences extracted from porins can predict functionally important amino acids located in transmembrane helices of membrane proteins such as bacteriorhodopsin and the potassium channel subunit. Our PREF-SPLIT suite of algorithms was used both to evaluate preference functions for transmembrane segments and to locate amino acid residues involved in the ion transport activity.
Keywords: Structure-activity predictions, preference functions, transmembrane helices, membrane proteins, porins, ion transport

Title: Damped oscillatory control of mitochondrial energy linked processes observed in the presence of magainins

Authors:: Juretić, Davor (19290)

Journal: Periodicum Biologorum
ISSN: 0031-5362
Volume: 93
Year: 1991
Pages: from 277 to 278
Number of references: 8
Language: engleski
Summary: Damped oscillations in the membrane potential, proton gradient, external pH, and mitochondrial volume of rat liver mitochondra are observed when succinate is added in the presence of oxygen, valinomycin and a peptide from the magainin family: PGLa.
Keywords: Mitochondrial oscillations, magainins, membrane potential, matrix volume, valinomycin, oxygen electrode, respiration

Title: Membrane free-energy converters: the benefits of intrinsic uncoupling and non-linearity

Authors:: Juretić, Davor (19290)

Journal: Acta Pharmaceutica
Number: 4
ISSN: 1330-0075
Volume: 42
Year: 1992
Pages: from 373 to 376
Number of references: 14
Language: engleski
Summary: The non-linear mode of energy conversion with loose coupling is shown to be more efficient than energy conversion in the linear Onsager domain. The model for proton pumping by mitochondrial cytochrome c oxidase is used to show that non-linear transducers with a variable slip are more suitable in controlling metabolism than linear free-energy transducers.
Keywords: Control theory, slip, free-energy conversion, efficiency, degree of coupling, free-energy storage, cytochrome c oxidase

Title: Secondary structure of membrane proteins: Prediction with conformational preference functions of soluble proteins

Authors:: Juretić, Davor (19290)

Journal: Croatica Chemica Acta
Number: 4
ISSN: 0011-1643
Volume: 65
Year: 1992
Pages: from 921 to 932
Number of references: 50
Language: engleski
Summary: Conformational preference functions are derived from the statistical analysis of the data base of soluble protein structures. These functions use local sequence information to modify the Chou-Fasman's preference of a given residue for secondary conformation. The secondary structure prediction algorithm that compares preferences is constructed. For the testing set of 14 membrane polypeptides the prediction accuracy is 78% in the three state model and 90% for the alpha-helix residues alone.
Keywords: Secondary structure, membrane proteins, preference functions, soluble proteins, prediction accuracy

Title: Protein secondary structure conformations and associated hydrophobicity scales

Authors:: Juretić, Davor (19290); Trinajstić, Nenad (50450); Lučić, Bono (184293)

Journal: Journal of Mathematical Chemistry
ISSN: 0259-9791
Volume: 14
Year: 1993
Pages: from 35 to 45
Number of references: 69
Language: engleski
Summary: We have developed conformational preference functions and a hierarchy of algorithms that can evaluate the success of each hydrophobicity scale in predicting protein secondary conformation.
Keywords: Hydrophobicity scales, proteins, secondary structure, transmembrane segments, preference functions, prediction accuracy

Title: Predicting membrane protein secondary structure: Preference functions method for finding optimal conformational parameters

Authors:: Juretić, Davor (19290); Lučić, Bono (184293); Trinajstić, Nenad (50450)

Journal: Croatica Chemica Acta
Number: 1
ISSN: 0011-1643
Volume: 66
Year: 1993
Pages: from 201 to 208
Number of references: 40
Language: engleski
Summary: An automated iterative method in combination with the preference functions method is developed for predicting secondary conformation in membrane proteins.
Keywords: Membrane proteins, secondary structure, preference functions, optimal parameters

Title: Conformational preference functions for predicting helices in membrane proteins

Authors:: Juretić, Davor (19290); Lee, Byungkook; Trinajstić, Nenad (50450); Williams, Robert W.

Journal: Biopolymers
ISSN: 0006-3525
Volume: 33
Year: 1993
Pages: from 255 to 273
Number of references: 68
Language: engleski
Summary: A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures. We show that a set of preference functions based on buried surface area is useful for predicting folding motifs in alpha-class and integral membrane proteins.
Keywords: Preference functions, membrane proteins, predicting helices

Title: Conformational preference functions and secondary structure prediction for membrane proteins

Authors:: Juretić, Davor (19290)

Journal: Acta Pharmaceutica
Number: 3
ISSN: 1330-0075
Volume: 43
Year: 1993
Pages: from 223 to 226
Number of references: 10
Language: engleski
Summary: Recently developed method of conformational preference functions is used with a training set of 40 proteins. Since hydrophibicity analysis alone is not enough to predict alpha-helix segments in membrane proteins, the importance of selecting an amino acid scale and a training data base of proteins appropriate for each chosen set of proteins to be tested is emphasized.
Keywords: membrane proteins, conformational preference functions, secondary sructure prediction, hydrophobicity analysis


Ministry of Science and Technology	Croatian language	Svibor homepage	Alphabetic list	Sorted on project code	Sorted on institutions	Search	Help

Information: svibor@znanost.hr