1.7 A x-ray structure of space-grown collagenase crystals

CARACTERIZAÇÃO BIOQUÍMICA DO PRODUTO DE EXCREÇÃO/SECREÇÃO DE LARVAS DE Cochliomyia hominivorax (DIPTERA: CALLIPHORIDAE)

Resumo A espécie Cochliomyia hominivorax, conhecida popularmente como mosca da bicheira, é um parasita obrigatório de animais de sangue quente e sua distribuição geográfica estende-se por toda a América do Sul, excetuando-se o Chile. O parasitismo por esta mosca provoca perdas econômicas significativas e tem grande importância no Brasil. São poucos os estudos com foco nos produtos de excreção e secreção desta espécie e este trabalho teve como objetivo estudar as enzimas presentes no produto de secreção e excreção (E/S) dos três estádios larvais de C. hominivorax. O perfil de proteínas foi obtido por eletroforese em gel de poliacrilamida e a atividade proteolítica foi analisada utilizando-se gelatina, azocaseína e Na-benzoil-arginina-nitroanilida (BAPNA) como substrato. Nos produtos de E/S dos três estádios, as proteínas foram detectadas com um peso molecular aparente que variou entre 116 e 20 kDa. No ensaio de azocaseína, em diferentes faixas de pH, a maior atividade proteolítica ocorreu em pH 7,5 para todos os estádios larvais. Os ensaios foram realizados usando-se estes mesmos substratos e as amostras foram tratadas com os inibidores Benzamidina, Pepstatin A, 4-(2-aminoetil)benzenosulfonil fluoreto hidrocloreto (AEBSF), N-α-tosil-L-lisina clorometil cetona (TLCK), N-α-tosil-L-fenilalanina clorometil cetona (TPCK), Ácido etilenodiamino tetra acético (EDTA), Leupeptina e Trans-epoxysuccinyl L-leucylamido-4-guanidino butano (E-64). As proteinases presentes nos produtos E/S de L1 são em sua maioria serina proteases do tipo tripsina e quimotripsina, enquanto que para os produtos E/S de L2 e L3 foi evidenciada a presença de serina proteases e aspartil proteases.

Receptor rigidity and ligand mobility in trypsin-ligand complexes

The trypsin-like serine proteases comprise a structurally similar family of proteins with a wide diversity of biological functions. Members of this family play roles in digestion, hemostasis, immune responses, and cancer metastasis. Bovine trypsin is an archetypical member of this family that has been extensively characterized both functionally and structurally, and that preferentially hydrolyzes Arg/Lys-Xaa peptide bonds. We have used molecular dynamics (MD) simulations to study bovine trypsin complexed with the two noncovalent small-molecule ligands, benzamidine and tranylcypromine, that have the same hydrogen-bond donating moieties as Arg and Lys side-chains, respectively. Multiple (10) simulations ranging from 1 ns to 2.2 ns, with explicit water molecules and periodic boundary conditions, were performed. The simulations reveal that the trypsin binding pocket residues are relatively rigid regardless of whether there is no ligand, a high-affinity ligand (benzamidine), or a low-affinity ligand (tranylcypromine). The thermal average of the conformations sampled by benzamidine bound to trypsin is planar and consistent with the planar internal geometry of the benzamidine crystallographic model coordinates. However, the most probable bound benzamidine conformations are +/-25 degrees out of plane, implying that the observed X-ray electron density represents an average of densities from two mirror symmetric, nonplanar conformations. Solvated benzamidine has free energy minima at +/-45 degrees , and the induction of a more planar geometry upon binding is associated with approximately 1 kcal/mol of intramolecular strain. Tranylcypromine's hydrogen-bonding pattern in the MD differs substantially from that inferred from the X-ray electron density. Early in simulations of this system, tranylcypromine adopts an alternative binding conformation, changing from the crystallographic conformation, with a direct hydrogen bond between its amino moiety and the backbone oxygen of Gly219, to one having a bridging water molecule. This result is consistently seen with the CHARMM22, Amber, or OPLS-AA force fields. The trypsin-tranylcypromine hydrogen-bonding pattern observed in the simulations also occurs as the crystallographic binding mode of the Lys15 side-chain of bovine pancreatic trypsin inhibitor bound to trypsin. In this latter cocrystal, a bridging crystallographic water does reside between the side-chain's amino group and the trypsin Gly219 backbone oxygen. Furthermore, the trypsin-tranylcypromine simulations sample two different stable noncrystallographic binding poses. These data suggest that some of the electron density ascribed to tranylcypromine in the X-ray model is rather due to a bound water molecule, and that multiple tranylcypromine binding conformations (crystallographic disorder) may be the cause of ambiguous electron density. The combined trypsin-benzamidine and trypsin- tranylcypromine results highlight the ability of simulations to augment protein-ligand complex structural data by deconvoluting the effects of thermal and structural averaging, and by finding energetically optimal ligand and bound water positions for weakly bound ligands.

Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology

The crystallographic quality of protein crystals that were grown in microgravity has been compared to that of crystals that were grown in parallel on earth gravity under otherwise identical conditions. A goal of this comparison was to assess if a more accurate 3D-structure can be derived from crystallographic analysis of the former crystals. Therefore, the properties of crystals prepared with the Advanced Protein Crystallisation Facility (APCF) on earth and in orbit during the last decade were evaluated. A statistical analysis reveals that about half of the crystals produced under microgravity had a superior X-ray diffraction limit with respect of terrestrial controls. Eleven protein structures could be determined at previously unachieved resolutions using crystals obtained in the APCF. Microgravity induced features of the most relevant structures are reported. A second goal of this study was to identify the cause of the crystal quality enhancement useful for structure determination. No correlations between the effect of microgravity and other system-dependent parameters, such as isoelectric point or crystal solvent content, were found except the reduced convection during the crystallisation process. Thus, crystal growth under diffusive regime appears to be the key parameter explaining the beneficial effect of microgravity on crystal quality. The mimicry of these effects on earth in gels or in capillary tubes is discussed and the practical consequences for structural biology highlighted.

The crystallization of biological macromolecules under microgravity: a way to more accurate three-dimensional structures?

The crystallization of proteins and other biological particles (including nucleic acids, nucleo-protein complexes and large assemblies such as nucleosomes, ribosomal subunits or viruses) in a microgravity environment can produce crystals having lesser defects than crystals prepared under normal gravity on earth. Such microgravity-grown crystals can diffract X-rays to a higher resolution and have a lower mosaic spread. The inferred electron density maps can be richer in details owing to which more accurate three-dimensional structure models can be built. Major results reported in this field of research are reviewed. Novel ones obtained with the Advanced Protein Crystallization Facility are presented. For structural biology, practical applications and implications associated with crystallization and crystallography onboard the International Space Station are discussed.