Optimization of Molecular Dynamics Simulations of c-MYC1-88-An Intrinsically Disordered System

Molecular Dynamics as a Tool for Virtual Ligand Screening

Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or nucleic acid is known. To that purpose, high-throughput virtual ligand screening campaigns aim at discovering computationally new binding molecules or fragments to modulate particular biomolecular interactions or biological activities, related to a disease process. The structure-based virtual ligand screening process primarily relies on docking methods which allow predicting the binding of a molecule to a biological target structure with a correct conformation and the best possible affinity. The docking method itself is not sufficient as it suffers from several and crucial limitations (lack of full protein flexibility information, no solvation and ion effects, poor scoring functions, and unreliable molecular affinity estimation).At the interface of computer techniques and drug discovery, molecular dynamics (MD) allows introducing protein flexibility before or after a docking protocol, refining the structure of protein-drug complexes in the presence of water, ions, and even in membrane-like environments, describing more precisely the temporal evolution of the biological complex and ranking these complexes with more accurate binding energy calculations. In this chapter, we describe the up-to-date MD, which plays the role of supporting tools in the virtual ligand screening (VS) process.Without a doubt, using docking in combination with MD is an attractive approach in structure-based drug discovery protocols nowadays. It has proved its efficiency through many examples in the literature and is a powerful method to significantly reduce the amount of required wet experimentations (Tarcsay et al, J Chem Inf Model 53:2990-2999, 2013; Barakat et al, PLoS One 7:e51329, 2012; De Vivo et al, J Med Chem 59:4035-4061, 2016; Durrant, McCammon, BMC Biol 9:71-79, 2011; Galeazzi, Curr Comput Aided Drug Des 5:225-240, 2009; Hospital et al, Adv Appl Bioinforma Chem 8:37-47, 2015; Jiang et al, Molecules 20:12769-12786, 2015; Kundu et al, J Mol Graph Model 61:160-174, 2015; Mirza et al, J Mol Graph Model 66:99-107, 2016; Moroy et al, Future Med Chem 7:2317-2331, 2015; Naresh et al, J Mol Graph Model 61:272-280, 2015; Nichols et al, J Chem Inf Model 51:1439-1446, 2011; Nichols et al, Methods Mol Biol 819:93-103, 2012; Okimoto et al, PLoS Comput Biol 5:e1000528, 2009; Rodriguez-Bussey et al, Biopolymers 105:35-42, 2016; Sliwoski et al, Pharmacol Rev 66:334-395, 2014).

Conformational ensemble of the NSP1 CTD in SARS-CoV-2: Perspectives from the free energy landscape

The nonstructural protein-1 (NSP1) of the severe acute respiratory syndrome-associated coronavirus 2 plays a crucial role in the translational shutdown and immune evasion inside host cells. Despite its known intrinsic disorder, the C-terminal domain (CTD) of NSP1 has been reported to form a double α-helical structure and block the 40S-ribosomal channel for mRNA translation. Experimental studies indicate that NSP1 CTD functions independently from the globular N-terminal region separated with a long linker domain, underscoring the necessity of exploring the standalone conformational ensemble. In this contribution, we utilize exascale computing resources to yield unbiased molecular dynamics simulation of NSP1 CTD in all-atom resolution starting from multiple initial seed structures. A data-driven approach elicits collective variables (CVs) that are significantly superior to conventional descriptors in capturing the conformational heterogeneity. The free energy landscape as a function of the CV space is estimated using the modified expectation maximized molecular dynamics. Originally developed by us for small peptides, here, we establish the efficacy of expectation maximized molecular dynamics in conjunction with data-driven CV space for a more complex and relevant biomolecular system. The results reveal the existence of two disordered metastable populations in the free energy landscape that are separated from the conformation resembling ribosomal subunit bound state by high kinetic barriers. Chemical shift correlation and secondary structure analysis capture significant differences among key structures of the ensemble. Altogether, these insights can underpin drug development studies and mutational experiments that help induce population shifts to alter translational blocking and understand its molecular basis in further detail.

Self-Diffusive Properties of the Intrinsically Disordered Protein Histatin 5 and the Impact of Crowding Thereon: A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study

Intrinsically disordered proteins (IDPs) are proteins that, in comparison with globular/structured proteins, lack a distinct tertiary structure. Here, we use the model IDP, Histatin 5, for studying its dynamical properties under self-crowding conditions with quasi-elastic neutron scattering in combination with full atomistic molecular dynamics (MD) simulations. The aim is to determine the effects of crowding on the center-of-mass diffusion as well as the internal diffusive behavior. The diffusion was found to decrease significantly, which we hypothesize can be attributed to some degree of aggregation at higher protein concentrations, (≥100 mg/mL), as indicated by recent small-angle X-ray scattering studies. Temperature effects are also considered and found to, largely, follow Stokes–Einstein behavior. Simple geometric considerations fail to accurately predict the rates of diffusion, while simulations show semiquantitative agreement with experiments, dependent on assumptions of the ratio between translational and rotational diffusion. A scaling law that previously was found to successfully describe the behavior of globular proteins was found to be inadequate for the IDP, Histatin 5. Analysis of the MD simulations show that the width of the distribution with respect to diffusion is not a simplistic mirroring of the distribution of radius of gyration, hence, displaying the particular features of IDPs that need to be accounted for.

Molecular Dynamics Simulations of Human FOXO3 Reveal Intrinsically Disordered Regions Spread Spatially by Intramolecular Electrostatic Repulsion

The human transcription factor FOXO3 (a member of the 'forkhead' family of transcription factors) controls a variety of cellular functions that make it a highly relevant target for intervention in anti-cancer and anti-aging therapies. FOXO3 is a mostly intrinsically disordered protein (IDP). Absence of knowledge of its structural properties outside the DNA-binding domain constitutes a considerable obstacle to a better understanding of structure/function relationships. Here, I present extensive molecular dynamics (MD) simulation data based on implicit solvation models of the entire FOXO3/DNA complex, and accelerated MD simulations under explicit solvent conditions of a central region of particular structural interest (FOXO3^120-530). A new graphical tool for studying and visualizing the structural diversity of IDPs, the Local Compaction Plot (LCP), is introduced. The simulations confirm the highly disordered nature of FOXO3 and distinguish various degrees of folding propensity. Unexpectedly, two 'linker' regions immediately adjacent to the DNA-binding domain are present in a highly extended conformation. This extended conformation is not due to their amino acid composition, but rather is caused by electrostatic repulsion of the domains connected by the linkers. FOXO3 is thus an IDP present in an unusually extended conformation to facilitate interaction with molecular interaction partners.

Transcribing Genes the Hard Way: In Vitro Reconstitution of Nanoarchaeal RNA Polymerase Reveals Unusual Active Site Properties

Nanoarchaea represent a highly diverged archaeal phylum that displays many unusual biological features. The Nanoarchaeum equitans genome encodes a complete set of RNA polymerase (RNAP) subunits and basal factors. Several of the standard motifs in the active center contain radical substitutions that are normally expected to render the polymerase catalytically inactive. Here we show that, despite these unusual features, a RNAP reconstituted from recombinant Nanoarchaeum subunits is transcriptionally active. Using a sparse-matrix high-throughput screening method we identified an atypical stringent requirement for fluoride ions to maximize its activity under in vitro transcription conditions.

Function, Regulation, and Dysfunction of Intrinsically Disordered Proteins

The discovery that a considerable fraction of the eukaryotic proteins lacks a well-defined three-dimensional structure in their native state has revolutionised our general understanding of proteins [...].

Roles, Characteristics, and Analysis of Intrinsically Disordered Proteins: A Minireview

In recent years, there has been a growing understanding that a significant fraction of the eukaryotic proteome is intrinsically disordered, and that these conformationally dynamic proteins play a myriad of vital biological roles in both normal and pathological states. In this review, selected examples of intrinsically disordered proteins are highlighted, with particular attention for a few which are relevant in neurological disorders and in viral infection. Next, the underlying causes for the intrinsic disorder are discussed, along with computational methods used to predict whether a given amino acid sequence is likely to adopt a folded or unfolded state in the solution. Finally, biophysical methods for the analysis of intrinsically disordered proteins will be discussed, as well as the unique challenges they pose in this context due to their highly dynamic nature.

Multivalent and Bidirectional Binding of Transcriptional Transactivation Domains to the MED25 Coactivator

The human mediator subunit MED25 acts as a coactivator that binds the transcriptional activation domains (TADs) present in various cellular and viral gene-specific transcription factors. Previous studies, including on NMR measurements and site-directed mutagenesis, have only yielded low-resolution models that are difficult to refine further by experimental means. Here, we apply computational molecular dynamics simulations to study the interactions of two different TADs from the human transcription factor ETV5 (ERM) and herpes virus VP16-H1 with MED25. Like other well-studied coactivator-TAD complexes, the interactions of these intrinsically disordered domains with the coactivator surface are temporary and highly dynamic (‘fuzzy’). Due to the fact that the MED25 TAD-binding region is organized as an elongated cleft, we specifically asked whether these TADs are capable of binding in either orientation and how this could be achieved structurally and energetically. The binding of both the ETV5 and VP16-TADs in either orientation appears to be possible but occurs in a conformationally distinct manner and utilizes different sets of hydrophobic residues present in the TADs to drive the interactions. We propose that MED25 and at least a subset of human TADs specifically evolved a redundant set of molecular interaction patterns to allow binding to particular coactivators without major prior spatial constraints.