Computational protocol: Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations

Similar protocols

Protocol publication

[…] We have used the FoldX force field [] for all mutant properties regarding structural location, protein stability and its various components, the Tango [] and Waltz [[], submitted] algorithms to assess the propensity for aggregation of wild type and variant proteins, and the Limbo algorithm [[], submitted] to evaluate the chaperone-binding properties of amino acid sequences. A novel tool developed by Lenaerts et al (unpublished) was used to estimate the entropy of a specific amino acid site in a high-resolution structure. [...] In addition to the entropy calculations intrinsic to the FoldX force field, we use a novel method based on extensive sampling of side chain conformations as developed by Lenaerts et al. (unpublished). The sampling method produces for each side chain the probability (P(X)) of finding the residue's side chain in a particular conformational state. From these probabilities entropy can easily be derived: The method uses a rotamer database based on conditional statistics of dihedral angles derived from the WHAT IF data set []. All amino acids from this data and their corresponding dihedral angles (10° bin) were used to derive the following probabilities: P(χi), P(χi|χi-1) and P(χi|χi-1, χi-2), except for χ1(P(χ1) and P(χ1|ϕ, ψ)). A set of n random rotamers can be derived from the probability distribution thus calculated. This will allow sampling of rotamers with greater resolution than classical rotamer libraries.The sampling itself is performed by Monte Carlo based sampling method with Metropolis criterion (at 298 K). The Metropolis criterion states that a certain conformational change is accepted with a probability p that depends on the free energy change ΔΔG associated with the conformational change as given by the following formula: The free energy of each change is determined with FoldX. […]

Pipeline specifications

Software tools FoldX, TANGO, WHAT IF
Applications Drug design, Protein structure analysis, Protein physicochemical analysis
Diseases Mitochondrial Diseases