Structure–function inferences based on molecular modeling, sequence-based methods and biological data analysis of snake venom lectins

Specificity analysis of the C-type lectin from rattlesnake venom, and its selectivity towards Gal- or GalNAc-terminated glycoproteins

“…The same residue differences that confer specificity for Man instead of Gal or GalNAc in mammalian lectins are present in the B. fasciatus lectins, i.e. QPDXY/F becomes EPNXS [12,13].…”

“…Models of related lectins have been made on the basis of the RSVL N. M. Young (*) : H. van Faassen : D. C. Watson : monomer structure though their quaternary structures may not be decamers [12]. From their sequences, these lectins are also predicted to be Gal-specific, but additional Manspecific ones have been found, e.g in Bungarus fasciatus [13].…”

Structural model of haptoglobin and its complex with the anticoagulant ecotin variants: structure–activity relationship study and analysis of interactions

“…Protein similarity was determined for both heavy and light chains by multiple sequence alignments performed in Clustal W2 software (www.ebi.ac.uk/ Tools/msa/clustalw2), using selected proteins previously described 3,12,31 . Briefly, the construction of dimeric HP structure was performed in three steps including the construction of HP: (1) light(a) and heavy(b) subunits, (2) monomer and (3) dimer 32 . On that purpose, we used the Swiss-Model and Deepview/Swiss-PDB Viewer Version 4.04 programs (http://swissmodel.expasy.org/; http://spdbv.vital-it.ch/) 33,34 and zymogen and active catalytic domain of complement protease c1r (PDB ID:1gpza and 1md8a, respectively) as templates 14,35,36 .…”

“…Initially the 18N-terminal amino acids of the HP1 sequences, which represent a signal peptide, were previously removed, once these are released during the proteolytic maturation of the polypeptide. Then, after constructing HP1 monomers as described by Abreu et al 32 , we structurally aligned them with the dimer protease C1r crystal structure (PDB ID: 1gpz) in an antiparallel position as proposed by Polticelli and coworkers 16,35 . To construct the HP dimeric structure, we used the report of the Ettrich et al 12 electronic microscopy data to align the subunits and establish the disulfide bond between the cysteines 15(Cys15) of the light chains(a).…”

“…According to the literature, in order to understand protein selectivity, both sequences analysis and three-dimensional structures should be considered. Some of these studies evaluate the protein targets and their three-dimensional complexes to get into their biological functions and interactions 32,45,46 .…”