Protein and Peptide Letters - Volume 10, Issue 6, 2003

Scaffolded peptides, in which fragments of the sequence are presented through a molecular scaffold in a discontinuous and nonlinear fashion, are promising candidates for the mimicry of discontinuous protein binding sites. Twelve scaffold molecules based on cyclic peptides with ring sizes ranging from 13 to 30 were generated. Up to three different peptide fragments were attached to the scaffolds in a site-selective manner, yielding scaffolded peptides in excellent purities, as documented by MS, HPLC, and 2D 1H NMR spectroscopy data.

We have performed a systematic investigation of the structural features of the peptides Int (a sequence able to cross cell membranes) and Int-H1(S6A,F8A) (which shows interesting antitumoral properties). After screening in aqueous solution at different ionic strength and pH values, we analyzed the structures of the peptides in different water / trifluoroethanol mixtures by Circular Dichroism and Nuclear Magnetic Resonance techniques.

Crystal structure of hemoglobin isolated from the Brazilian maned wolf (Chrysocyon brachyurus) was determined using standard molecular replacement technique and refined using maximumlikelihood and simulated annealing protocols to 1.87Å resolution. Structural and functional comparisons between hemoglobins from the Chrysocyon brachyurus and Homo sapiens are discussed, in order to provide further insights in the comparative biochemistry of vertebrate hemoglobins.

The mutation had dramatic effect on the kinetic and thermodynamic parameters inferring thermostability of endo-glucanase from Cellulomonas biazotea mutant 51 SMr .The denaturation activation energies of native and mutated enzymes were 73.3 and 68.8 kJ / mol respectively. They showed compensation effect at 55°C. Both enthalpy and entropy values of irreversible thermal inactivation for mutated enzyme were decreased suggesting that the mutation partly stabilized the enzyme.

Kinetic behavior of aggregation of amyloid-β-protein (Aβ) is represented by a stretched exponential function, F=A{1-exp(-Btn)}. Differences in temperature-dependence of A, B and n are studied for Aβ 1-40 and Aβ 1-42. As the temperature is lowered, parameter A is increased, parameter B is decreased and parameter n is increased in Aβ 1-40, while these parameters are less sensitive to temperature in a more hydrophobic protein Aβ 1-42. ln B is a linear function of n, which is shown by ln B = -6.34n + 3.69.

Previously we reported that halobacterial nucleoside diphosphate kinase can be refolded in the presence of concentrated trimethylamine N-oxide (TMAO) as well as NaCl, indicating that enhancement of compact structure formation by TMAO is sufficient for folding. Here we showed that the refolding effect of MgCl2 is maximal at 1 M and declines to zero at 2 M, indicating that charge shielding effect of MgCl2 is offset by its salting-in effect.

A new coding sequence of the procarboxypeptidase B gene was obtained from SD rat fresh pancreas by RT-PCR and highly expressed in Escherichia coli in inclusion bodies. The folded procarboxypeptidase B was subjected to trypsin enzymatic cleavage to produce active carboxypeptidase B, subsequently, carboxypeptidase B was effectively purified with anion exchange chromatography DEAE-FF and hydrophobic interaction chromatography Octyl FF, as a result, 40 mg carboxypeptidase B per litre cell culture with specific activity 7.42 u / mg was achieved. Further research showed that the obtained recombinant carboxypeptidase B could substitute carboxypeptidase B isolated from pancreas.

An analysis of hydrogen bonding patterns of cyclic decapeptide (CDP) β-sheet structures has resulted in a 'non-intuitive' design of cyclic decapeptides wherein their β-turns and residue positions can be fixed by choosing 2 of the 10 residues, i.e. positions i and i+4, to be Prolines or N-substituted residues. This sequence relationship between the two Pro or N-substituted residues is shown to uniquely define the conformation of the CDP. Furthermore, this design of the 2 β-turn, β-sheet CDP structure is expected to be characterised by residues disposed in an exclusive fashion in which four residues are on one side of the ring, two on the other and the four corner residues in the β-turn are in the plane of the ring. This opens up the possibility of fine-tuning the four residues facing one way and / or the two residues facing the other way such that a library containing a myriad of chemically diverse systems could be obtained. The design process along with the molecular modelling of specific CDP's and the building of a CDP library are discussed in detail.

Gastrodia anti-fungal protein (GAFP) displays strong inhibitory activity against certain fungal pathogens. Five GAFP analogues with different mutations at mannose-binding sites and the wild-type one were expressed and purified in Escherichia coli. The inhibitory analysis of the purified various GAFPs against the growth of Trichoderma viride indicates that single amino acid mutated-type GAFPs have inhibitory activity, but its activity is much less than the wild-type one. The double and triplicate amino acids mutated GAFPs have very low inhibitory activity. For the first time it was proved that GAFP mannosebinding sites play key role in anti-fungi process.

A glucose / mannose lectin was purified by affinity chromatography from Pisum arvense seeds (PAL) and the 50 kDa molecular mass in solution determined by size exclusion chromatography. SDS-PAGE and electrospray ionization mass spectrometry showed two distinct polypeptide chains: α (Mr. 5,591 Da) and β (19,986 Da). The lectin was extensively characterized in terms of its biochemical and biological aspects. The amino acid sequence was established by Edman degradation of overlapping peptides. PAL in solution behaves as a dimer and has its monomeric structure formed by two distinct polypeptide chains named alpha (Mr. 5,591 Da) and beta (19,986 Da) by Electrospray ionization (ESI) mass spectrometry. PAL possesses identical amino acid sequences to that of pea seed lectin but undoubtedly does not exhibit sequence heterogeneity. It is discussed that P. arvense should be considered as a synonym of P. sativum. Furthermore, like pea lectin, PAL discriminates biantennary fucosylated glycan, determined by surface plasmon resonance.

Lipases are versatile enzymes regarding the range of reactions they catalyse and substrates on which they act. They are as well important as catalyst in organic synthesis. Their immobilization on appropriate supports confer them greater stability besides the possibility of operating in continuous reactors. In order to explore these abilities, the reactions involving hydrolysis of p-nitrophenyl acetate (PNPA) and transesterification of PNPA with n-butanol were chosen. Lipases from two different sources were assayed, namely: microbial (Candida rugosa, CRL, Sigma Type VII) and pancreatic (PPL, Sigma, Type II). Two immobilization methods were also used, namely: 1) adsorption, using as support the following silica derivatives (150-300μm e 450μ): phenyl, epoxy, amino and without derivation, and 2) covalent binding, using glutaraldehyde as binding agent and silica amino as support. This later method led to better results. Hydrolytic activity was 6.1 U / gsupport for CRL and 0.97U / gsupport for PPL, and of transesterification, 2,8U / gsupport for CRL and 1,9U / gsupport for PPL. Stability of the immobilized enzyme as a function of temperature was evaluated for CRL at 40°C and 50°C and for PPL at 32°C and 40°C. The assays were initially carried out batchwise, both for soluble and immobilized enzymes, aiming to the obtention of parameters for the continuos reactor. Lipases immobilized by covalent binding were used in the assays of operacional stability in continuos reactors. For PPL in aqueous medium, at 32°C, and CRL in organic medium at 40°C, both operating continuously, no significant loss of activity was detected along the analysis period of 17 days. In the case of CRL in aqueous medium at 40°C there was a loss of activity around 40% after 18 days. For PPL in organic medium at 40°C the loss was 33% after 20 days. Compairing both sources with each other, very different results were obtained. Higher activitiy was found for CRL, both for hydrolysis and for transesterification reactions, with higher stability in organic medium. PPL showed lower activity as well as higher stability in aqueous medium. The immobilization method by covalent binding showed to be the most appropriate. Immobilized lipases are therefore relatively stable both in aqueous and organic medium.