Biomedical subjects

S Oldziej

Publications and source records attributed to S Oldziej.

7 recordsLinked to original sources

PubMed2004

The protein folding problem: global optimization of the force fields.

The evolutionary development of a theoretical approach to the protein folding problem, in our laboratory, is traced. The theoretical foundations and the development of a suitable empirical all-atom potential energy function and a global optimization search are examined. Whereas the all-atom approach has thus far succeeded for relatively small molecules and for alpha-helical proteins containing up to 46 residues, it has been necessary to develop a hierarchical approach to treat larger proteins. In the hierarchical approach to single- and multiple-chain proteins, global optimization is carried out for a simplified united residue (UNRES) description of a polypeptide chain to locate the region in which the global minimum lies. Conversion of the UNRES structures in this region to all-atom structures is followed by a local search in this region. The performance of this approach in successive CASP blind tests for predicting protein structure by an ab initio physics-based method is described. Finally, a recent attempt to compute a folding pathway is discussed.

Algorithms↗

PubMed2001

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

Recent improvements of a hierarchical ab initio or de novo approach for predicting both alpha and beta structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic alpha-helical protein of 70 residues was predicted to within 4.3 A alpha-carbon (C(alpha)) rms deviation (rmsd) whereas, for other alpha-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 A C(alpha) rmsd. Whereas beta structures can now be predicted with the new procedure, the success rate for alpha/beta- and beta-proteins is lower than that for alpha-proteins at present. For the beta portions of alpha/beta structures, the C(alpha) rmsd's are less than 6.0 A for contiguous fragments of 30-40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a C(alpha) rmsd less than 6.0 A. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence.

Models, Molecular↗

PubMed2001

Impact of Cu(II) and Ni(II) on a structure of chiral peptide nucleic acids having four, six and eight thymines in a peptide side chain.

The studies on binding ability of longer chiral peptide nucleic acids (having four, six and eight thymines in a peptide side chain) have shown that the interactions between the nucleic base rings within a ligand molecule have a critical impact on the complex stability. Thymines inserted in the peptide side chain interact with each other as well as with peptide back-bone increasing the structural organization of the cPNA molecule. The metal ion coordination to cPNA, on the other hand, induces a very specific ligand structure, which may have a basic impact on the cPNA self-recognition processes.

Copper↗

PubMed1996

Fluorescence and Monte Carlo conformational studies of the (1-15) galanin amide fragment.

Galanin (GAL) is a 29 amino acid C-terminally aminated linear neuropeptide showing diverse biological activities. The N-terminal (1-15)GAL-NH2 fragment was shown to have a very high affinity to the galanin receptor. In this work we describe the results of a combined fluorescence and Monte Carlo studies, the latter carried out using the ECEPP/3 force field with and without including hydration, on the (1-15)GAL-NH2 fragment. Using the time-domain technique we measured fluorescence decay times of the tyrosine residue in position 9. Based on the Forster energy transfer theory we calculated the distance and distance distribution between the Trp2 (acceptor) and Tyr9 (donor) aromatic side chains. The distance obtained was about 10.5 angstrom and half-width, hw, of the distance distribution was 5.6 angstrom. This results were found to be in good agreement with the chromophore distances calculated for the low-energy solution confirmations obtained in Monte Carlo simulations. All the low-energy conformations obtained in the absence of water were almost all-helical with the exception of a few C-terminal residues. In contrast, none of the low-energy solution conformations contained any significant amount of secondary structure. These findings are in agreement with the results of earlier CD and NMR conformational studies of galanin in water and non-aqueous solvents. On the other hand, the conformations obtained in the presence of water turned out to be largely compact in the N-terminal hydrophobic part. This explains the relatively short distance between chromophores and narrow distance distribution obtained in fluorescence measurements.

Amides↗

PubMed1992

Investigation of the inhibition pathway of glucosamine synthase by N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid by semiempirical quantum mechanical and molecular mechanics methods.

Glucosamine synthase (E.C. 2.6.1.16) is a promising target in antifungal drug design. It has been reported that its potent inhibitor, N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid (FMDP), inactivates the enzyme by the Michael addition of the S-H group to the FMDP molecule followed by cyclisation reactions. In this study we have investigated, by means of semiempirical MNDO, PM3 and molecular mechanics methods, the energetics and kinetic possibility of the formation of various stereoisomers of the products of cyclisation of the Michael addition products detected experimentally. It was found that the substituted 1,4-thiazin-3-one can be formed in one step under alkaline conditions; the stereoisomers of this compound predicted to be the most stable on the basis of theoretical calculations are also the dominant ones in reality.

Calorimetry↗

PubMed1992

MNDO study of the mechanism of the inhibition of cysteine proteinases by diazomethyl ketones.

Diazomethyl ketones are one of the most effective irreversible inhibitors of cysteine proteinases and are therefore very important in drug design. In the present study a mechanism of inactivation is proposed based on the results of model MNDO calculations of the possible pathways. It was found that the mercaptide nucleophile, on approaching the carbonyl carbon as in the catalytic reaction path, binds to the inner diazo nitrogen. The intermediate thus formed can rearrange giving a stable product, beta-thioketone, and molecular nitrogen, with a considerable energy gain. The energy barrier to this process is equal to 36.9 kcal/mol, and corresponds to a pyramidal transition state with the vertex at the methylene carbon and the base formed by the carbonyl, thiol, and diazo groups. The energy barrier can be lowered on deprotonation of the intermediate. Based on the results obtained it was concluded that good irreversible inhibitors of cysteine proteases must fulfil two structural requirements: i) the dimensions and charge distribution must be similar to those of the peptide bond and ii) a second electrophilic center must be present in the neighbourhood of the carbonyl carbon. These are requirements which are satisfied by other strong cysteine proteinase inhibitors: beta-chloroketones and beta-ketooxiranes.

Chemical Phenomena↗

PubMedDate not supplied

Conformational aspects of differences in requirements for oxytocin and vasopressin receptors.

Conformational energy calculations were carried out on three non-peptide antagonists of oxytocin and vasopressin: penicilide (compound 1; selective for oxytocin receptors), 1-¿1-[4-(3-acetylaminopropoxy(benzoyl]-4-piperidyl¿-3,4-dihydro-2( 1H)-quinoline (compound 2; selective for vasopressin V1 receptors) and 5-dimethylamino-1-¿(2-methylbenzylamino)-benzoyl¿-2,3,4,5-tetrahyd ro-1H-benzapine (compound 3; selective for vasopressin V2 receptors). The obtained low-energy conformations of compound 1 were compared with low-energy conformations of oxytocin (OT) and low-energy conformations of compounds 2 and 3 were compared with low-energy conformations of arginine vasopressin (AVP). It was found that the affinity of the non-peptide antagonists and their selectivity for vasopressin and oxytocin receptors is probably connected with mimicking the aromatic rings of the Tyr2 and the Phe3 residues of AVP in the case of compounds 2 and 3 and with mimicking the Tyr2 residue and the Ile3 or Leu8 residues of OT by the outer benzene ring and the isobutyl group of compound 1. Application of the results in the design of more potent non-peptide antagonists of OT and VP is also discussed.

Antidiuretic Hormone Receptor Antagonists↗