Ab initio structure solution with ARCIMBOLDO of myosins and other highly helical proteins at resolutions below 2 Å

• Grant number: 13/12370-7
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• Start date: September 01, 2013
• End date: November 30, 2013
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Mário Tyago Murakami
• Grantee: Andrey Fabricio Ziem Nascimento
• Supervisor: Isabel Usón Finkenzeller
• Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Ministério da Ciência, Tecnologia e Inovação (Brasil). Campinas , SP, Brazil
• Institution abroad: Institut de Biologia Molecular de Barcelona (IBMB), Spain
• Associated to the scholarship: 09/14257-8 - Structural studies of the globular domain of human myosin Va responsible for intracellular transport of organelles and vesicles, BP.DD

Abstract

The macromolecular crystallography is one of most important tools in structural biology and it has been responsible for nearly 95% of protein structures deposited at the Protein Data Bank (PDB). However, the elucidation of a macromolecular crystallographic structure involves several empirical and laborious steps, which limit a higher success rate. Besides the difficulties observed in protein expression and crystallization, another problem is intrinsically from crystallography, the phase problem, which prevents the direct solution of the structure. Classically to overcome this problem, several techniques can be used, involving heavy-atoms (MIR, SAD, etc.) or homologous structures (molecular replacement), but the difficulty of obtaining heavy-atoms derivatives crystals and/or the absence of proteins with similar structure determined often prevents the structure solution. Ab initio methods, which derive the phases directly from the native dataset are efficient for small molecules; however, generally, the lack of atomic resolution (1.2 Å or better) and the large number of atoms prevent the use of these methods for proteins. With a new approach, implemented in the program ARCIMBOLDO which uses ±-helix fragments, the group of Prof. Isabel Usón solved protein structures with up to 222 residues and 2 Å resolution. Thus, we intend to extend the use of ARCIMBOLDO to lower resolutions (2-3 Å), using for it the data of the hCGMio5 structures recently obtained by our group, since these structures are rich in ±-helices and show a resolution in the interest range, being perfect for this study. Furthermore, the solution of the structures by another method will validate the data already obtained. (AU)