A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction

Abstract

Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three widely used methodologies were considered: two general methodologies that are commonly applied to soluble proteins and a methodology that uses constraints that are specific for membrane proteins. The test pool consisted of 36 target-template pairs with different sequence similarities that was constructed on the basis of 24 experimental rhodopsin structures taken from the RCSB database. As a result, we showed that all three considered methodologies allow obtaining rhodopsin structures with the quality that is close to the crystallographic one (root mean square deviation (RMSD) of the predicted structure from the corresponding X-ray structure up to 1.5 Å) if the target-template sequence identity is higher than 40%. Moreover, all considered methodologies provided structures of average quality (RMSD < 4.0 Å) if the target-template sequence identity is higher than 20%. Such structures can be subsequently used for further investigation of molecular mechanisms of protein functioning and for the development of modern protein-based biotechnologies.

Structure and dynamics of membrane protein in SARS-CoV-2

“…Furthermore, the models with good quality, particularly in the TM region which can be produced even in the target-template sequence identity 20 − 40% region (Nikolaev et al., 2018 ). Another study has obtained more accurate alignments for proteins with low sequence identities to their templates, can be achieved using structure-based profile alignment methods.…”

Structural and evolutionary analyses of the Plasmodium falciparum chloroquine resistance transporter

“…Phyre2 42 and HHpred 43 interactive servers identified these same three DMT structures as the current best structures to model PfCRT, with an e-value < 5.4 e −21 and a confidence criterion (which represents the probability that the match between the sequence and the template arises from a true relationship 42 ) of 98.7% for the least acceptable of these three DMT structures (YddG; Supplementary Tables S3 and S4). Despite a low sequence identity between PfCRT and these transporters, reaching a maximum of 14% for the PfCRT-TPT comparison ( Supplementary Table S5), homology modeling remains still feasible 44 and the PfCRT tertiary structure may be predicted in both inward-facing and occluded states.…”

“…The nucleotide sugar GDP-mannose transporter Vrg4 (inward-facing state, PDB ID: 5oge) 36 and the triose-phosphate/phosphate translocator TPT (occluded state, PDB ID: 5y79) 32 were identified as sharing putative similar structural folds with PfCRT with confidence >99%. The very low sequence identity of these proteins with PfCRT, reaching only 14% with TPT, makes homology modeling challenging but still feasible 44 . In homology modeling, the sequence alignment of the target (here PfCRT) and the template (here other DMT proteins) is a critical step.…”

Docking studies and molecular dynamics simulations of the binding characteristics of waldiomycin and its methyl ester analog to Staphylococcus aureus histidine kinase

“…Generally, it is assumed that two proteins topologies are usually similar once their sequences share about 30% identity [35]. Moreover, Dimitrii et al [36] developed structures of average quality (RMSD < 4.0 Å) based on target-template sequence identity � 20%. The crystal structure of 5C93 was recently obtained at a resolution of 2.52 Å [34].…”