Institution: IC
Departement: DSCTM
Typology: Research field/topic, Skill, Software
Location: via G. Amendola 122/o 70126, Bari
Contacts:
- Benedetta Carrozzini (benedetta.carrozzini@cnr.it)
- Anna Moliterni (anna.moliterni@cnr.it)
Description:
The IC-CRYST team is a multidisciplinary group internationally recognized for advancing biomolecu-lar crystallography, from small compounds to macromolecules, and developing innovative software such as SIR for single-crystal and EXPO for powder diffraction data. Collaborating with academic and industrial partners, including pharmaceutical companies, the team excels in solving complex cases, determining protein structures, and characterizing drug compounds. Their strength lies in tai-loring in-house crystallographic tools to address the unique challenges of each case. Key Competencies in Bio-Crystallography: Structural Determination of Biological Macromolecules - Ab Initio Approaches Effective phasing strategies, utilizing SIR software, for accurate ab initio structural analysis of complex biological molecules with high-resolution diffraction data. Advanced algorithms enhance Direct Methods for determining smaller molecules, like large peptides or small proteins, and improve Patterson Techniques for structures with heavy atoms and known fragments, like ligands. - Molecular Replacement (MR) and Anomalous Dispersion (SAD/MAD) Methods Expertise in solving structures focuses on innovative procedures tailored to enhance the accuracy and efficiency of MR and SAD/MAD methods. MR, relying on homologous templates, is ideal for conserved protein domains and structural genomics. SAD/MAD methods utilize anomalous scattering from specific atoms, such as sulfur or selenium, to solve macromolecules with heavy atoms or suitable scatterers. Enhancement of Electron Density Map Resolution Application of the Free Lunch (FL) method to refine electron density maps by extrapolating structure factors beyond resolution limits through Fourier inversion of modified maps. Applied during or after phasing, FL significantly enhances map resolution and interpretability, making it highly effective for challenging macromolecular structures. Advanced Computational Algorithms for Phase Extension and Refinement Implementation of sophisticated computational algorithms for phase extension and refinement, combining EDM techniques, difference Fourier synthesis, FL method, and the cyclic CAB procedure with external AMB tool, enhancing the accurate solution of complex macromolecular structures. Structural Determination via Electron Diffraction Leveraging high precise electron diffraction (3D-ED) techniques, recently gaining increased use in bio-crystallography, to analyze tiny or challenging crystals, unsuitable for traditional X-ray methods. The SIR package now features specialized phasing and refinement procedures, enabling accurate structure determination from 3D-ED data and broadening its application to complex samples. Resolution of Small and Medium-Sized Molecules Using Single-Crystal Diffraction Data or Microcrystalline Powder Diffraction Data Proven expertise in using SIR to support analysis and solution of small organic and hybrid compounds from single-crystal X-ray diffraction data, applying ab initio methods or global optimization techniques like Simulated Annealing. Additionally, specialized proficiency with EXPO enables accurate structure determination from powder diffraction data, facilitating the study of materials unsuitable for single-crystal studies. Integration of Artificial Intelligence and Traditional Crystallographic Methods Pioneering use of AI-driven techniques integrated with traditional crystallography methods. The new approach, called Phase Seeding, has been developed by the team to push forward the structure determination process of complex biological molecules by enhancing speed, accuracy, and tackling challenges in structural biology. Comprehensive Training and Support for SIR and EXPO Software Providing personalized training and hands-on guidance, including workshops and one-on-one tutoring, to equip researchers with the skills and knowledge needed to proficiently use SIR and EXPO software for their structural determination projects.
Team:
- Benedetta Carrozzini benedetta.carrozzini@cnr.it;
- Liberato De Caro liberato.decaro@cnr.it;
- Rocco Caliandro rocco.caliandro@cnr.it;
- Annamaria Mazzone annamaria-mazzone@cnr.it;
- Corrado Cuocci corrado.cuocci@cnr.it;
- Anna Moliterni anna.moliterni@cnr.it;
- Francesca Fedele francesca.fedele@cnr.it;
- Angela Altomare angela.altomare@cnr.it;
- Aurelia Facicchio aurelia.falcicchio@cnr.it
Fig.1 - Crystal Structure Determination Process (Fig1_Strct_Deter_Proceess.png); Fig.2 – Crystal structure of Set7 dimeric HMTase (Fig2_Set7_Structure.jpg); Fig.3 – Crystallographic Software developed by the IC-CRYST team (Fig3_Sir&Expo.png)