Molecular Dynamics-Assisted Interpretation of Experimentally Determined Intrinsically Disordered Protein Conformational Components: The Case of Human α-Synuclein

Abstract

Mass spectrometry and single molecule force microscopy are two experimental approaches able to provide structural information on intrinsically disordered proteins (IDPs). These techniques allow the dissection of conformational ensembles in their main components, although at a low-resolution level. In this work, we interpret the results emerging from these experimental approaches on human alpha synuclein (AS) by analyzing a previously published 73 μs-long molecular-dynamics (MD) simulation of the protein in explicit solvent. We further compare MD-based predictions of single molecule Förster resonance energy transfer (smFRET) data of AS in solution with experimental data. The combined theoretical and experimental data provide a description of AS main conformational ensemble, shedding light into its intramolecular interactions and overall structural compactness. This analysis could be easily transferred to other IDPs.

Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding

“…Here, we show that t-SNE is particularly well-suited for clustering seemingly disparate IDP conformations into homogeneous subgroups since it is designed to conserve the local neighborhood when reducing the dimension, which ensures similar data points remain equivalently similar and dissimilar data points remain equivalently dissimilar in the low-dimensional and high-dimensional space . Due to its ability to provide a very informative visualization of heterogeneity in the data, t-SNE is being increasingly employed in several applications such as clustering data from single cell transcriptomics, − mass spectrometry imaging, and mass cytometry. , Lately, t-SNE has also been used for depicting the MD trajectories of folded proteins − and for interpretation of mass-spectrometry-based experimental data on IDPs by juxtaposing with classical GROMOS-based conformation clusters from the corresponding molecular simulation trajectories of the IDP under consideration …”

“…90,91 Lately, t-SNE has also been used for depicting the MD trajectories of folded proteins 92−98 and for interpretation of mass-spectrometry-based experimental data on IDPs by juxtaposing with classical GROMOS-based conformation clusters from the corresponding molecular simulation trajectories of the IDP under consideration. 99 In this paper, we demonstrate the effectiveness of t-SNE (in combination with K-means clustering) for identifying and visualizing representative conformational substates in IDP ensembles. We investigate the small molecule binding properties of amyloid β42 (Aβ42) and α-synuclein (αS), proteins involved in the neurodegenerative proteinopathies, namely, Alzheimer's and Parkinson's diseases, respectively.…”

Demultiplexing the heterogeneous conformational ensembles of intrinsically disordered proteins into structurally similar clusters

“…Due to its ability to provide a very informative visualization of heterogeneity in the data, t-SNE is being increasingly employed in several applications such as clustering data from single cell transcriptomics 74–77 , mass spectrometry imaging 78 , and mass cytometry 79,80 . Lately, t-SNE has also been used for depicting the MD trajectories of folded proteins 81–87 and for interpretation of mass-spectrometry based experimental data on IDPs by juxtaposing with classical GROMOS-based conformation clusters from the corresponding molecular simulation trajectories of the IDP under consideration 88 .…”

Biomolecular Electrostatic Phenomena: An Evergreen Field

“…35 Among the applications to protein systems, it is worth mentioning one work using continuum electrostatics and QM calculations to understand in more detail the differences between serine and cysteine peptidases, 36 and two works on intrinsically disordered proteins, one considering the electrostatic interactions at the binding interface of the p53 transactivation domain with two protein partners, 37 while the other combines experimental data with long MD simulations to better understand the conformational and energetic landscape of the alpha synuclein protein. 38 This virtual special issue also includes works focusing on materials or interactions between biomolecules and materials. Among them, quantum-mechanical calculations at the DFT level were performed to better describe the adsorption of DNA nucleobases on 2D materials, examining the effects of different counterions, 39 while continuum electrostatics was used to characterize the dynamic equilibrium between different orientations when [NiFe] hydrogenase approaches an electrode, 40 and to explore how an external electric field can be used to control the orientation of trypsin proteins adsorbing to a solid surface.…”

“…Among the applications to protein systems, it is worth mentioning one work using continuum electrostatics and QM calculations to understand in more detail the differences between serine and cysteine peptidases, and two works on intrinsically disordered proteins, one considering the electrostatic interactions at the binding interface of the p53 transactivation domain with two protein partners, while the other combines experimental data with long MD simulations to better understand the conformational and energetic landscape of the alpha synuclein protein …”