Biomedical subjects

Stefano Trapani

Publications and source records attributed to Stefano Trapani.

5 recordsLinked to original sources

PubMed2006

SCA: symmetry-based center assignment of 2D projections of symmetric 3D objects.

A method for finding the center of cryo-EM images which correspond to the projections of a symmetric 3D structure, based on mathematical properties of symmetry adapted functions and the Fourier-Bessel transform, is presented. It is a model independent one-step procedure with no parameters to be chosen by the user. The proposed method is tested in one synthetic tetrahedral case with different noise levels and in two real cases with D7 and icosahedral symmetries.

Chaperonin 60↗

PubMed2006

Calculation of spherical harmonics and Wigner d functions by FFT. Applications to fast rotational matching in molecular replacement and implementation into AMoRe.

The FFT calculation of spherical harmonics, Wigner D matrices and rotation function has been extended to all angular variables in the AMoRe molecular replacement software. The resulting code avoids singularity issues arising from recursive formulas, performs faster and produces results with at least the same accuracy as the original code. The new code aims at permitting accurate and more rapid computations at high angular resolution of the rotation function of large particles. Test calculations on the icosahedral IBDV VP2 subviral particle showed that the new code performs on the average 1.5 times faster than the original code.

Algorithms↗

PubMed2006

Combining experimental data for structure determination of flexible multimeric macromolecules by molecular replacement.

A major effort has been made by the structural biology community to develop user-friendly software for the use of biologists. However, structural projects become more and more challenging and their solution often relies on a combination of information from various sources. Here, it is described how X-ray data, normal-mode analysis (NMA) and electron-microscopy (EM) data can be successfully combined in order to obtain a molecular-replacement (MR) solution for crystal structures containing multimeric molecules. NMA is used to simulate computationally the inherent internal flexibility of the monomer and thus enhance, together with the crystal noncrystallographic symmetry (NCS), the MR capabilities. NCS is also used to obtain a reliable EM reconstruction, which is then employed as a filter to construct oligomers starting from monomers. The feasibility of the direct use of EM reconstructions as a template for MR when the X-ray and EM data resolutions overlap is also discussed.

Agrobacterium tumefaciens↗

PubMed2003

Amino acid sequence and tertiary structure of Cratylia mollis seed lectin.

Carbohydrate-protein interactions play a key role in many biological processes. Cramoll is a lectin purified from Cratylia mollis seeds that is taxonomically related to concanavalin A (Con A). Although Cramoll and Con A have the same monosaccharide specificity, they have different glycoprotein binding profiles. We report the primary structure of Cramoll, determined by Edman degradation and mass spectrometry and its 1.77 A crystallographic structure and compare it with the three-dimensional structure of Con A in an attempt to understand how differential binding can be achieved by similar or nearly identical structures. We report here that Cramoll consists of 236 residues, with 82% identity with Con A, and that its topological architecture is essentially identical to Con A, because the Calpha positional differences are below 3.5 A. Cramoll and Con A have identical binding sites for MealphaMan, Mn2+, and Ca2+. However, we observed six substitutions in a groove adjacent to the extended binding site and two in the extended binding site that may explain the differences in binding of oligosaccharides and glycoproteins between Cramoll and Con A.

Amino Acid Sequence↗

PubMed2003

Domain motions and quaternary packing of phosphofructokinase-2 from Escherichia coli studied by small angle x-ray scattering and homology modeling.

The binding of MgATP and fructose-6-phosphate to phosphofructokinase-2 from Escherichia coli induces conformational changes that result in significant differences in the x-ray-scattering profiles compared with the unligated form of the enzyme. When fructose- 6-phosphate binds to the active site of the enzyme, the pair distribution function exhibits lower values at higher distances, indicating a more compact structure. Upon binding of MgATP to the allosteric site of the enzyme, the intensity at lower angles increases as a consequence of tetramer formation, but differences along higher angles also suggest changes at the tertiary structure level. We have used homology modeling to build the native dimeric form of phosphofructokinase-2 and fitted the experimental scattering curves by using rigid body movements of the domains in the model, similar to those observed in known homologous structures. The best fit with the experimental data of the unbound protein was achieved with open conformations of the domains in the model, whereas domain closure improves the agreement with the scattering of the enzyme-fructose-6-phosphate complex. Using the same approach, we utilized the scattering curve of the phosphofructokinase-2-MgATP complex to model the arrangement and conformation of dimers in the tetramer. We observed that, along with tetramerization, binding of MgATP to the allosteric site induces domain closure. Additionally, we used the scattering data to restore the low resolution structure of phosphofructokinase-2 (free and bound forms) by an ab initio procedure. Based on these findings, a proposal is made to account for the inhibitory effect of MgATP on the enzymatic activity.

Escherichia coli↗