CoNSEnsX+ Webserver for the Analysis of Protein Structural Ensembles Reflecting Experimentally Determined Internal Dynamics.

Ensemble-based models of protein structure and dynamics reflecting experimental parameters are increasingly used to obtain deeper understanding of the role of dynamics in protein function. Such ensembles differ substantially from those routinely deposited in the PDB and, consequently, require specialized validation and analysis methodology. Here we describe our completely rewritten online validation tool, CoNSEnsX+, that offers a standardized way to assess the correspondence of such ensembles to experimental NMR parameters. The server provides a novel selection feature allowing a user-selectable set and weights of different parameters to be considered. This also offers an approximation of potential overfitting, namely, whether the number of conformers necessary to reflect experimental parameters can be reduced in the ensemble provided. The CoNSEnsX+ webserver is available at consensx.itk.ppke.hu . The corresponding Python source code is freely available on GitHub ( github.com/PPKE-Bioinf/consensx.itk.ppke.hu ).

Ligand-dependent intra- and interdomain motions in the PDZ12 tandem regulate binding interfaces in postsynaptic density protein-95.

The postsynaptic density protein-95 (PSD-95) regulates synaptic plasticity through interactions mediated by its peptide-binding PDZ domains. The two N-terminal PDZ domains of PSD-95 form an autonomous structural unit, and their interdomain orientation and dynamics depend on ligand binding. To understand the mechanistic details of the effect of ligand binding, we generated conformational ensembles using available experimentally determined nuclear Overhauser effect interatomic distances and S2 order parameters. In our approach, the fast dynamics of the two domains is treated independently. We find that intradomain structural changes induced by ligand binding modulate the probability of the occurrence of specific domain-domain orientations. Our results suggest that the ß2-ß3 loop in the PDZ domains is a key regulatory region, which influences both intradomain motions and supramodular rearrangement.

Evaluation and Selection of Dynamic Protein Structural Ensembles with CoNSEnsX.

Understanding protein function at atomistic detail is not possible without accounting for the internal dynamics of these molecules. Ensemble-based models are based on the premise that single conformers cannot account for all experimental observations on the given molecule. Rather, a suitable set of structures, representing the internal dynamics of the protein at a given timescale, are necessary to achieve correspondence to measurements. CoNSEnsX+ is a service specifically designed for the investigation of such ensembles for compliance with NMR-derived parameters. In contrast to common structure evaluation tools, all parameters are treated as an average over the ensemble, if are not themselves an ensemble property like order parameters. CoNSEnsX+ is also capable of selecting a sub-ensemble with increased correspondence to a set of user-defined experimental parameters. CoNSEnsX+ is available as a web server at http://consensx.itk.ppke.hu , and the full Python source code is available on GitHub.

Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases.

Parvulins or rotamases form a distinct group within peptidyl prolyl cis-trans isomerases. Their exact mode of action as well as the role of conserved residues in the family are still not unambiguously resolved. Using backbone S2 order parameters and NOEs as restraints, we have generated dynamic structural ensembles of three distinct parvulins, SaPrsA, TbPin1 and CsPinA. The resulting ensembles are in good agreement with the experimental data but reveal important differences between the three enzymes. The largest difference can be attributed to the extent of the opening of the substrate binding cleft, along which motional mode the three molecules occupy distinct regions. Comparison with a wide range of other available parvulin structures highlights structural divergence along the bottom of the binding cleft acting as a hinge during the opening-closing motion. In the prototype WW-domain containing parvulin, Pin1, this region is also important in forming contacts with the WW domain known to modulate enzymatic activity of the catalytic domain. We hypothesize that modulation of the extent and dynamics of the identified 'breathing motion' might be one of the factors responsible for functional differences in the distinct parvulin subfamilies.