Graph representation of high-dimensional alpha-helical membrane protein data

In silico modeling of Plasmodium falciparum chloroquine resistance transporter protein and biochemical studies suggest its key contribution to chloroquine resistance

Chloroquine (CQ) has been used for decades as the primary chemotherapeutic drug for the treatment of malaria. The emergence of drug resistance in Plasmodium falciparum has been considered to be because of the excessive use of antimalarial drugs worldwide. Moreover, the intense distribution and prevalence of chloroquine-resistant strains in endemic regions has aided the incidence of more complications to malaria treatment and control. Due to the lack of literature that portrays evident molecular mechanisms of drug resistance, it has been difficult to understand the drug resistance conferred by Plasmodium species. Intensive research on CQ drug resistance has identified the association of P. falciparum chloroquine resistance transporter protein (PfCRT), which belongs to the drug/metabolite transporter and EamA-like superfamily. Additionally, it has shown that K76 T mutation in PfCRT protein has mainly attributed to CQ resistance than other mutations. This study deals with the development of an in silico model of the PfCRT protein and its interaction with the CQ ligand molecule as well as the biochemical and biophysical characterization of the transmembrane domain 1 (TMD 1) peptide of the PfCRT protein. The physiochemical analysis of the PfCRT protein identified basic differences between the wild and mutant forms of the protein, as well as identifying the high hydrophobic nature of the mutant-type protein. The tertiary structure of the PfCRT protein was predicted and interaction with CQ revealed different active pocket binding regions in both the wild and mutant form of PfCRT proteins. The CQ²⁺ molecule interacts with TMD 10 of the wild-type PfCRT protein, whereas it interacts with TMD 1 of the mutant-type protein. Studies on the TMD 1 peptide revealed the insertion of the peptide in the micelles adopting stable alpha-helical structure. Binding studies with the CQ molecule detected high binding affinity toward the mutant-type TMD 1 peptide rather than the wild-type, thus confirming that the TMD 1 peptide is involved in substrate selectivity. Our findings help to characterize the structure of the PfCRT protein and the role played by the TMD 1 region in CQ resistance using in silico and biochemical approaches. Molecular docking and ligand binding studies confirm that TMD 1 is involved in substrate selectivity and aids in CQ efflux, thereby contributing to the parasite's CQ drug resistance mechanism.

The observation of evolutionary interaction pattern pairs in membrane proteins

Background

Over the last two decades, many approaches have been developed in bioinformatics that aim at one of the most promising, yet unsolved problems in modern life sciences - prediction of structural features of a protein. Such tasks addressed to transmembrane protein structures provide valuable knowledge about their three-dimensional structure. For this reason, the analysis of membrane proteins is essential in genomic and proteomic-wide investigations. Thus, many in-silico approaches have been utilized extensively to gain crucial advances in understanding membrane protein structures and functions.

Results

It turned out that amino acid covariation within interacting sequence parts, extracted from a evolutionary sequence record of α-helical membrane proteins, can be used for structure prediction. In a recent study we discussed the significance of short membrane sequence motifs widely present in nature that act as stabilizing ’building blocks’ during protein folding and in retaining the three-dimensional fold. In this work, we used motif data to define evolutionary interaction pattern pairs. These were obtained from different pattern alignments and were used to evaluate which coupling mechanisms the evolution provides. It can be shown that short interaction patterns of homologous sequence records are membrane protein family-specific signatures. These signatures can provide valuable information for structure prediction and protein classification. The results indicate a good agreement with recent studies.

Conclusions

Generally, it can be shown how the evolution contributes to realize covariation within discriminative interaction patterns to maintain structure and function. This points to their general importance for α-helical membrane protein structure formation and interaction mediation. In the process, no fundamentally energetic approaches of previous published works are considered. The low-cost rapid computational methods postulated in this work provides valuable information to classify unknown α-helical transmembrane proteins and to determine their structural similarity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12900-015-0033-5) contains supplementary material, which is available to authorized users.