Computational Methods in Mass Spectrometry-Based Protein 3D Studies

摘要: Mass Spectrometry (MS)-based strategies featuring chemical or biochemical probing represent powerful and versatile tools for studying structural dynamic features of proteins their complexes. In fact, they can be used both as an alternative systems intractable by other established high-resolution techniques, a complementary approach to these latter, providing different information on poorly characterized very critical regions the under investigation (Russell et al., 2004). The versatility MS-based methods depends wide range usable techniques reagents, which makes them suitable virtually any class biomolecules complexes (Aebersold 2003). Furthermore, is still increased possibility operating at levels accuracy, ranging from qualitative high-throughput fold recognition complex identification (Young 2000), fine detail rearrangements in after environmental changes, point mutations formations (Nikolova al.,1998; Millevoi 2001; Zheng 2007). However, heavily rely upon availability computational approaches achieve full exploitation content associated with experimental data. determination three-dimensional (3D) structures models (MS3D) involves four main activity areas: 1) preparation sample its derivatives labelled probes; 2) generation derivatives/fragments molecules further MS analysis; 3) interpretation data identify those residues that have reacted 4) derivation 3D consistent previous steps. Ideally, this procedure should considered core iterative process, where final model possibly prompts new validating experiments helps assignment ambiguous mass spectra step. Both overall MS3D steps been subject several accurate review perspective articles (Sinz, 2006; Back 2003; Young 2000; Friedhoff, 2005, Renzone, 2007a). partial exception few recent papers (Van Dijk 2005; Fabris 2010; Leitner 2010), behind building (step has generally received less attention than former three Structural MS3D, special case sparse/indirect constraints (SD-SIC). Nevertheless, modelling derivable exhibits some peculiar