Full text
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| Author(s): |
Filipe Camargo Dalmatti Alves Lima
Total Authors: 1
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| Document type: | Master's Dissertation |
| Press: | São Paulo. |
| Institution: | Universidade de São Paulo (USP). Instituto de Física (IF/SBI) |
| Defense date: | 2010-08-20 |
| Examining board members: |
Helena Maria Petrilli;
Maria Teresa Moura Lamy;
Ronei Miotto
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| Advisor: | Helena Maria Petrilli |
| Abstract | |
Frutalin is a tetrameric carbohydrate-binding protein obtained from breadfruit seeds. Biomedical interest on Frutalin comes from the high afinity exhibited by these molecules toward carbohydrates expressed by specific tumor cells. So far, no theoretical computational studies have been carried out to investigate the binding characteristics of frutalin, which is probably due to the large number of atoms that should be considered for in silicon calculations. We investigate the binding of frutalin and optical properties with specific carbohydrate molecules using a theoretical cutmodel considering only the carbohydrate binding site. This model has been constructed with the aid of molecular docking and classical molecular mechanics. We use the ab initio all electron reciprocal space Projector Augmented Waves (PAW) method and the Car-Parrinello scheme as embodied in the CP-PAW code to obtain the binding energies. To evaluate the optical properties, we employed the Hartree-Fock Semi-empirical ZINDO method from the Materials Studio 4.0 computational package. The investigation of this very complex problem can be divided into 6 main steps. Firstly, we study the structural properties of the protein to evaluate its mobility and we choose a x-ray data to describe reliably the system. In the second step, we performed molecular docking to link up four carbohydrates (alpha-methyl-D-galactoside, beta-D-galactoside, O1-methyl-mannose and methyl-alpha-D-glucopyranoside) in the protein. We optimize the geometry of the system lectin-carbohydrate using molecular mechanics in the third step. In the fourth step, we created the cutmodel based on the final geometries obtained in the previous step. In the fifth and sixth steps we investigate the quantum interaction of the protein with each carbohydrate. Our theoretical results are compared with available measurements in each step. The study of the interaction between the active binding site and carbohydrates allows us to demonstrate that our methodology is well suited to predict the electronic properties of the system. (AU) | |
| FAPESP's process: | 08/02222-2 - Electronic and structural properties in systems with bionanotechnological interest through ab-initio electronic structure calculations |
| Grantee: | Filipe Camargo Dalmatti Alves Lima |
| Support Opportunities: | Scholarships in Brazil - Master |