l-Asparaginase is a key therapeutic agent for treatment of childhood acute lymphoblastic leukemia (ALL). There is wide individual variation in pharmacokinetics, and little is known about its metabolism. The mechanisms of therapeutic failure with l-asparaginase remain speculative. Here, we now report that 2 lysosomal cysteine proteases present in lymphoblasts are able to degrade l-asparaginase. Cathepsin B (CTSB), which is produced constitutively by normal and leukemic cells, degraded asparaginase produced by Escherichia coli (ASNase) and Erwinia chrysanthemi. Asparaginyl endopeptidase (AEP), which is overexpressed predominantly in high-risk subsets of ALL, specifically degraded ASNase. AEP thereby destroys ASNase activity and may also potentiate antigen processing, leading to allergic reactions. Using AEP-mediated cleavage sequences, we modeled the effects of the protease on ASNase and created a number of recombinant ASNase products. The N24 residue on the flexible active loop was identified as the primary AEP cleavage site. Sole modification at this site rendered ASNase resistant to AEP cleavage and suggested a key role for the flexible active loop in determining ASNase activity. We therefore propose what we believe to be a novel mechanism of drug resistance to ASNase. Our results may help to identify alternative therapeutic strategies with the potential of further improving outcome in childhood ALL.

Using proteins in a therapeutic context often requires engineering to modify functionality and enhance efficacy. We have previously reported that the therapeutic antileukemic protein macromolecule Escherichia coli L-asparaginase is degraded by leukemic lysosomal cysteine proteases. In the present study, we successfully engineered L-asparaginase to resist proteolytic cleavage and at the same time improve activity. We employed a novel combination of mutant sampling using a genetic algorithm in tandem with flexibility studies using molecular dynamics to investigate the impact of lid-loop and mutations on drug activity. Applying these methods, we successfully predicted the more active L-asparaginase mutants N24T and N24A. For the latter, a unique hydrogen bond network contributes to higher activity. Furthermore, interface mutations controlling secondary glutaminase activity demonstrated the importance of this enzymatic activity for drug cytotoxicity. All selected mutants were expressed, purified, and tested for activity and for their ability to form the active tetrameric form. By introducing the N24A and N24A R195S mutations to the drug L-asparaginase, we are a step closer to individualized drug design. (Blood. 2011; 117(5):1614-1621)

Moderate heating (40–50°C) of immunoglobulins makes them accessible for binding with Congo Red and some related highly associated dyes. The binding is specific and involves supramolecular dye ligands presenting ribbon‐like micellar bodies. The L chain λ dimer, which upon heating disclosed the same binding requirement with respect to supramolecular dye ligands, was used in this work to identify the site of their attachment. Two clearly defined dye–protein (L λ chain) complexes arise upon heating, here called complex I and complex II. The first is formed at low temperatures (up to 40–45°C) and hence by a still native protein, while the formation of the second one is associated with domain melting above 55°C. They contain 4 and 8 dye molecules bound per L chain monomer, respectively. Complex I also forms efficiently at high dye concentration even at ambient temperature. Complex I and its formation was the object of the present studies. Three structural events that could make the protein accessible to penetration by the large dye ligand were considered to occur in L chains upon heating: local polypeptide chain destabilization, VL‐VL domain incoherence, and protein melting. Of these three possibilities, local low‐energy structural alteration was found to correlate best with the formation of complex I. It was identified as decreased packing stability of the N‐terminal polypeptide chain fragment, which as a result made the V domain accessible for dye penetration. The 19‐amino acid N‐terminal fragment becomes susceptible to proteolytic cleavage after being replaced by the dye at its packing locus. Its splitting from the dye–protein complex was proved by amino acid sequence analysis. The emptied packing locus, which becomes the site that holds the dye, is bordered by strands of amino acids numbered 74–80 and 105–110, as shown by model analysis. The character of the temperature‐induced local polypeptide chain destabilization and its possible role in intramolecular antibody signaling is discussed. © 2001 John Wiley & Sons, Inc. Biopolymers 59: 446–456, 2001

Molecular Dynamics (MD) simulations have been performed on a set of rigid-body docking poses, carried out over 25 protein-protein complexes. The results show that fully flexible relaxation increases the fraction of native contacts (NC) by up to 70% for certain docking poses. The largest increase in the fraction of NC is observed for docking poses where anchor residues are able to sample their bound conformation. For each MD simulation, structural snap-shots were clustered and the centre of each cluster used as the MD-relaxed docking pose. A comparison between two energy-based scoring schemes, the first calculated for the MD-relaxed poses, the second for energy minimized poses, shows that the former are better in ranking complexes with large hydrophobic interfaces. Furthermore, complexes with large interfaces are generally ranked well, regardless of the type of relaxation method chosen, whereas complexes with small hydrophobic interfaces remain difficult to rank. In general, the results indicate that current force-fields are able to correctly describe direct intermolecular interactions between receptor and ligand molecules. However, these force-fields still fail in cases where protein-protein complexes are stabilized by subtle energy contributions.

In previous CAPRI rounds (3-5) we showed that using MD-generated ensembles, as inputs for a rigid-body docking algorithm, increased our success rate, especially for targets exhibiting substantial amounts of induced fit. In recent rounds (6-11), our cross-docking was followed by a short MD-based local refinement for the subset of solutions with the lowest interaction energies after minimization. The above approach showed promising results for target 20, where we were able to recover 30% of native contacts for one of our submitted models. Further tests, performed a posteriori, revealed that cross-docking approach produces more near-native (NN) solutions but only for targets with large conformational changes upon binding. However, at the time of the blind docking experiment, these improved solutions were not chosen for the subsequent refinement, as their interaction energies after minimization ranked poorly compared with other solutions. This indicates deficiencies in the present scoring schemes that are based on interaction energies of minimized structures. Refinement MD simulations substantially increase the fraction of native contacts for NN docked solutions, but generally worsen interface and ligand RMSD. Further analysis shows that although MD simulations are able to improve sidechain packing across the interface, which results in an increased fraction of native contacts, they are not capable of improving interface and ligand backbone RMSD for NN structures beyond 1.5 and 3.5 A, respectively, even if explicit solvent is used.

Lipoxygenases (LOs), which are non-heme-iron-containing enzymes, play a vital role in plant and mammalian organisms. Their active sites have been probed by various spectroscopic techniques both in resting (Fe 2+ ) and active (Fe 3+ ) forms. Several crystal structures have been reported for ferrous forms of LOs; nevertheless, many unresolved questions have still remained. In particular, subtle differences in the first coordination sphere of the iron center seem to be very important for their catalytic activity thus any information about details of these structures is of great value. In this report, we present results of first principle calculations for reliable models of ferrous and ferric active sites of LOs undertaken to resolve ambiguities in structure of both resting and active forms of the iron sites in lipoxygenases. Geometrical parameters of optimized models are compared with crystallographic and EXAFS data. Time-dependent density functional theory (TDDFT) results for spectroscopic states are confronted with the relevant experimental results to validate the models and to gain an insight into the electronic structure of ferric and ferrous active sites. Overall good agreement between the calculated and experimental positions of the absorption bands is found, and where possible, the sources of discrepancies are discussed.

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The self-assembling tendency and protein complexation capability of dyes related to Congo red and also some dyes of different structure were compared to explain the mechanism of Congo red binding and the reason for its specific affinity for beta-structure. Complexation with proteins was measured directly and expressed as the number of dye molecules bound to heat-aggregated IgG and to two light chains with different structural stability. Binding of dyes to rabbit antibodies was measured indirectly as the enhancement effect of the dye on immune complex formation. Self-assembling was tested using dynamic light scattering to measure the size of the supramolecular assemblies. In general the results show that the supramolecular form of a dye is the main factor determining its complexation capability. Dyes that in their compact supramolecular organization are ribbon-shaped may adhere to polypeptides of beta-conformation due to the architectural compatibility in this unique structural form. The optimal fit in complexation seems to depend on two contradictory factors involving, on the one hand, the compactness of the non-covalently stabilized supramolecular ligand, and the dynamic character producing its plasticity on the other. As a result, the highest protein binding capability is shown by dyes with a moderate self-assembling tendency, while those arranging into either very rigid or very unstable supramolecular entities are less able to bind.