摘要:

AbstractIn a previous work we described the design, synthesis and catalytic activity of a branched cyclic peptide as a serine protease mimic. To maximize its catalytic activity we present now a systematic search of a large number of homologous peptides for potential enzyme activity as revealed by the topological arrangement of the catalytic triad residues. This process is accomplished by applying a combined molecular mechanics and molecular dynamics conformational search of about 200 molecules. Starting from a previously synthesized compound that showed some hydrolytic activity several analogues were modelled by amino acid substitutions in the main molecular framework using the Insight II molecular modelling environment with some script automation. Also presented is an algorithm that: (a) generates all possible combinations of residue substitutions, (b) scans the conformational space for each molecule via high temperature molecular dynamics, (c) picks the set of molecules the trajectories of which retained, to a considerable degree, the catalytic triad molecular arrangement, (d) subjects the selected molecules to layer solvation and energy minimization and chooses the molecules, the conformations of which could preserve the catalytic triad arrangement. Finally, a modelling with periodic boundary conditions, was performed to further support the reported algorithm. We found that at least one of the analogues could be a potential serine protease mimic, as revealed by the root‐mean‐square comparison between the catalytic triad in two molecular dynamics trajectories of the peptide and the corresponding residues in the crystal structure of trypsin. The most promising model candidate was synthesized and tested for its catalytic activity. Copyright © 2003 European Peptide Society and John Wiley&Sons,

ISSN:1075-2617    

DOI:10.1002/psc.441

出版商:John Wiley&Sons, Ltd.    

年代:2003

数据来源: WILEY

摘要:

AbstractThe segment 32–47 of theN‐terminal extracellular domain of the type A cholecystokinin receptor, CCKA‐R(32–47), was synthesized and structurally characterized in a membrane mimicking environment by CD, NMR and molecular dynamics calculations. The region of CCKA‐R(32–47) encompassing residues 39–46 adopted a well‐defined secondary structure in the presence of DPC micelles, whereas the conformation of theN‐terminal region (segment 32–37) could not be uniquely defined by the NOE derived distance constraints because of local flexibility. The conformation of the binding domain of CCKA‐R(32–47) was different from that found for the intactN‐terminal receptor tail, CCKA‐R(1–47). To assess whether CCKA‐R(32–47) was still able to bind the nonsulfated cholecystokininC‐terminal octapeptide, CCK8, a series of titrations was carried out in SDS and DPC micelles, and the binding interaction was followed by fluorescence spectroscopy. These titrations gave no evidence for complex formation, whereas a high binding affinity was found between CCKA‐R(1–47) and CCK8. The different affinities for the ligand shown by CCKA‐R(32–47) and CCKA‐R(1–47) were paralleled by different interaction modes between the receptor segments and the micelles. The interaction of CCKA‐R(32–47) with DPC micelles was much weaker than that of CCKA‐R(1–47), because the former receptor segment lacks proper stabilizing contacts with the micelle surface. In the case of SDS micelles CCKA‐R(32–47) was found to form non‐micellar adducts with the detergent that prevented the onset of a functionally significant interaction between the receptor segment and the micelle. It is concluded that tertiary structure interactions brought about by the 1–31 segment play a key role in the stabilization of the membrane bound, biologically active conformation of theN‐terminal extracellular tail of the CCKAreceptor. C

ISSN:1075-2617    

DOI:10.1002/psc.442

出版商:John Wiley&Sons, Ltd.    

年代:2003

数据来源: WILEY

摘要:

AbstractThe effects of three dipeptidesL‐phenylalanyl‐glycine, glycyl‐L‐phenylalanine, and aspartame (L‐aspartyl‐L‐phenylalanine, methyl ester) as inhibitors of the ascorbic acid‐induced modifications in lens proteins were studied. Their efficiency was compared to that of two known inhibitors—aminoguanidine and carnosine. The tested dipeptides diminished protein carbonyl content by 32–58% and most moderated the formation of chromophores, as measured by the absorbency at 325 nm of the glycated proteins. The appearance of non‐tryptophan fluorescence (excitation 340 nm/emission 410 nm) was observed for proteins glycated with ascorbic acid. All of the dipeptides examined, as well as aminoguanidine, decreased this glycation‐related fluorescence. The potential inhibitors prevented the intensive formation of very high molecular weight aggregates. A competitive mechanism of their inhibitory effect was proposed, based on the reactivity of individual substances toward ascorbic acid. These findings indicate that they have a potential for use as alternatives for aminoguanidine as an anti‐glycation agent. Copyright © 2003 European Peptide Societ

ISSN:1075-2617    

DOI:10.1002/psc.451

出版商:John Wiley&Sons, Ltd.    

年代:2003

数据来源: WILEY

摘要:

AbstractThe formation of aggregates including amyloid fibrils in the peptide fragment of non‐amyloid‐β component (NAC(1–13)) was investigated under a variety of solution conditions. Two types of sample preparation method from neutral and acidic conditions were examined. Electron microscopy observation showed amorphous aggregates in the sample at pH 4.5 adjusted from the neutral condition. The CD and HPLC quantitative analyses indicated that the formation of the amorphous aggregate did not accompany a conformational conversion from a random coil in the sample solution. The analyses of pKavalues determined by pH titration experiments in NMR spectroscopy indicated that the protonation of the carboxyl group of theN‐terminal glutamic acid triggers the aggregation of NAC(1–13). On the other hand, electron microscopy observation showed that the samples at pH 2.2 and 4.5 adjusted from an initial pH of 2.2 form fibrils. A β‐structure was detected by CD spectroscopy in the 1 mMNAC(1–13) at pH 2.2 immediately after preparation. The CD analyses of samples at different concentrations and temperatures indicated that 1 mMNAC(1–13) immediately after preparation at pH 2.2 was oligomerized. The quantity of the β‐structure was increased depending on the incubation time. The results strongly suggested that the β‐conformational oligomers play a critical role for the fibril nucleus. Copyright © 2003 European Peptide Society

ISSN:1075-2617    

DOI:10.1002/psc.444

出版商:John Wiley&Sons, Ltd.    

年代:2003

数据来源: WILEY

摘要:

AbstractThe synthesis of heterocyclic compounds containing the 7‐membered ring system [1,4]diazepane‐2,5‐dione is described. The aim of this study was to elaborate the solid phase and solution synthesis of eight representatives of the cyclic scaffold and to investigate their chemical stability and their conformational properties. The solid phase synthesis was performed on aminomethyl polystyrene resin using 5‐(4‐formyl‐3,5‐dimethoxyphenoxy)valeric acid as a backbone linker system (BAL‐linker). After attachment of the α‐ and β‐amino acid and deprotection of the amino function, the dipeptide ester was obtained. The molecule was cyclized on the solid support by treatment with NaOMe in MeOH/NMP. The product was cleaved from the resin by TFA. For the solution pathway the linear dipeptides were synthesized by coupling of the BOC‐protectedL‐α‐amino acid with the β2‐amino acid ester (EDC/HOBT). AfterN‐ andC‐terminal deprotection of the dipeptide, the linear species was cyclized with EDC/HOBT at a concentration of 3 mMin DMF. The products showed high chemical stability after storage in DMSO at room temperature for weeks. The x‐ray and two dimensional NMR investigations were performed to investigate the conformation of the molecules. Three types of configuration could be distinguished by NMR, depending on the substitution pattern of the cyclic compounds. The x‐ray results confirmed the NMR observations. In general the 7‐membered rings showed rigidity, thus they could represent optimal scaffolds for new receptor ligands. Copyright © 2003 Europea

ISSN:1075-2617    

DOI:10.1002/psc.445

出版商:John Wiley&Sons, Ltd.    

年代:2003

数据来源: WILEY