Simulations of an Extended Tau/Tubulins Interface Reveal a Complex Disorder–Disorder Interplay Mediated by the C-Terminal Tails

Building on a complex between a tubulin protofilament (PF) and a fragment of the Tau protein containing residues 169 to 367, we investigate the dynamics of the disordered elements of the system, namely the tubulin C-terminal tails (CTTs) and the Tau protein, using classical all-atom molecular dynamics simulations. Our results show that CTTs adopt a hook-like dynamic pattern on the bare PF while remaining highly mobile. The binding of Tau on the PF surface alters the dynamics of the αI-CTTs in a sequence-dependent manner. While the repeat domains of Tau are mostly maintained on the PF by weak and strong binding patches with the tubulin cores, the Proline-Rich Region (PRR) relies on the wrapping phenomenon of αI-CTTs to fuzzily stabilize its interaction with the PF. Our study thus provides a deep dive into the dynamic interplay between the Tau protein and the CTTs of microtubules, the latter being characterized extensively using a variety of disorder-adapted metrics.

pubs.acs.org

Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation

Unlocking the design principles of programmable RNA catalysts capable of site-specific chemical modification is critical for expanding the functional and therapeutic potential of RNA. The SAM analogue-utilizing ribozyme (SAMURI) enables site-specific RNA alkylation using either S-adenosylmethionine (SAM) or the synthetic cofactor propargylic Se-2,6-diaminopurinribosyl-selenomethionineamide (ProSeDMA), yet the molecular determinants of its reactivity remain incompletely understood. Here, we combined molecular dynamics, 3D-RISM solvation analysis, alchemical free energy calculations, quantum pKa shift predictions, and ab initio QM/MM free energy simulations to characterize the conformational and electronic factors that govern catalysis. Simulations show that, although the global fold of SAMURI remains stable in solution, the formation of catalytically competent near-attack configurations is rare, indicating that the observed rate depends on access to a minor fraction of these reactive conformations (freact). A putative Mg2+ binding site between the SAM carboxylate and the G30 phosphate, together with a hydrogen bond between the cofactor α-amine and U8:O2, enriches freact. QM/MM simulations support an SN2-like alkyl transfer mechanism and show that ProSeDMA reacts more readily than SAM primarily due to its more favorable electronic leaving group properties that enhance the intrinsic rate (kint). Atomic substitutions at A52 that tune the N3 pKa enhance nucleophilicity, further lower the activation barrier, and increase kint. Together, these results show that SAMURI catalysis is governed by a combination of conformational preorganization and electronic effects, providing a framework to guide the design of new programmable RNA alkyltransferases.

pubs.acs.org

Collective variable design for biomolecular conformational dynamics

Describing conformational changes in biomolecules using molecular dynamics simulations requires defining an appropriate low-dimensional mathematical d…

sciencedirect.com

Unraveling the Molecular Basis of Cooperativity in Cholera Toxin–Glycan Interactions

Cooperative ligand binding is an important determinant of specificity and regulation in biomolecular complexes. Yet, its prevalence and mechanistic basis in glycan-binding proteins (GBPs) remain unclear. Here, we present the first quantitative analysis of the temperature dependence of cooperative glycan binding. Variable-temperature native mass spectrometry (VT-nMS) resolved sequential ligand binding to either the five primary or the five secondary sites of the cholera toxin B subunit homopentamer (CTB5). Stepwise apparent affinities for the primary sites reveal positive cooperativity that strengthens with both ligand occupancy and temperature. Van’t Hoff analysis shows that this temperature-enhanced cooperativity is predominantly entropy driven. Mechanistic insight from temperature replica exchange molecular dynamics simulations shows that ligand binding at one primary site restrains a loop on an adjacent subunit (counterclockwise), widening its binding site. This prestructuring progressively lowers the unfavorable conformational entropy penalty of binding, independent of the order of subunit occupancy. In contrast, sequential ligand binding at the secondary sites exhibits negligible cooperativity except at the highest temperatures, although the enthalpic and entropic contributions are comparable in magnitude to those for primary-site binding, suggesting a shared energetic framework. Together, these results provide detailed thermodynamic and structural insight into cooperative GBP–glycan interactions and establish an integrated VT-nMS and molecular dynamics framework for quantitatively probing cooperative ligand binding in complex biomolecular systems.

doi.org

A Comparative Investigation of the Mannose Binding Interface in DC-SIGN and MRC1 Carbohydrate Recognition Domains with All-Atom Molecular Dynamics Simulations

Protein-carbohydrate interactions play a key role in numerous biological processes, including immune response, and glycan-based ligands that can target specific protein receptors on a cell surface represent promising candidates for therapeutics applications. For example, in retinoblastoma, the DC-SIGN mannose receptor is overexpressed on the surface of pathogenic cells and represents an interesting target for mannose-based ligands. At the same time, these ligands should not bind to the MRC1 receptor, which is expressed by adjacent, healthy, retinal pigment epithelial cells and presents a carbohydrate recognition domain (CRD) similar to the one of DC-SIGN. Therefore, the challenge remains to obtain a detailed picture of the recognition process between carbohydrates and proteins, in order to design effective and selective therapeutic compounds. In this work we used classical, all-atom molecular dynamics (MD) simulations to investigate the interaction between several mannose based ligands and the CRDs from DC-SIGN and MRC1. The analysis of the protein-carbohydrate contacts from the resulting trajectories highlights the variability of the mannose binding modes on both CRDs, and shows how the increased affinity of mannose for the MRC1 CRD can be related to a specific mannose binding state that is not accessible in the DC-SIGN CRD.

pubs.acs.org

FEBS Press

Evolutionary and mechanistic divergence in the Hsp70–Hsp110 chaperone system. Prokaryotic Hsp70s probably diversified into multiple orthologues that cooperated with co-chaperones such as JDPs and NEF...

febs.onlinelibrary.wiley.com

Lipid‐Facilitated Opening of the ADAM10 Sheddase Revealed by Enhanced Sampling Simulations

Phosphatidylserine acts as a lipid trigger to enhance activation of the sheddase ADAM10. By integrating fluorescence spectroscopy assays with enhanced sampling molecular dynamics simulations, this st...

advanced.onlinelibrary.wiley.com

Membrane-associated effluxosomes coordinate multi-metal resistance in Mycobacterium tuberculosis - The EMBO Journal

Bacterial pathogens must withstand metal-induced stress during infection, yet the mechanisms by which they sense and respond to toxic metal ions remain incompletely understood. Here, we uncover a prev...

shorturl.at

GitHub - FeNNol-tools/FeNNol-PMC: FeNNol Pretrained Models Collection

FeNNol Pretrained Models Collection. Contribute to FeNNol-tools/FeNNol-PMC development by creating an account on GitHub.

github.com

Sticky Salts: Overbinding of Monovalent Cations to Phosphorylations in All-Atom Force Fields

Phosphorylation is a major post-translational modification that is involved in the regulation of the dynamics and function of intrinsically disordered proteins (IDPs). We recently characterized a phen...

doi.org

Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane - Communications Biology

Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...

nature.com

Across (Conformational) Space and (Relaxation) Time: Using Coarse-Grain Simulations to Probe the Intra- and Interdomain Dynamics of the Tau Protein

The biological importance of intrinsically disordered proteins (IDPs) has been established for over two decades, yet these systems remain difficult to characterize, as they are better described by conformational ensembles instead of a single reference structure for their folded counterparts. Tau is a prominent member of the IDP family, which sees its cellular function regulated by multiple phosphorylation sites and whose hyperphosphorylation is involved in neurodegenerative diseases such as Alzheimer’s. We used coarse-grain MD simulations with the CALVADOS model to investigate the conformational landscape of tau without and with phosphorylations. Characterizing the local compactness of IDPs allows us to highlight how disorder comes in various flavors, as we can define different domains along the tau sequence. We define the IDP’s Statistical Tertiary Organization (STO) as the average spatial arrangements of domains, which constitute an extension of the tertiary structure of folded proteins. We also use IDP-specific metrics to characterize the local curvature and flexibility of tau. Comparing the local flexibilities with T2 relaxation times from NMR experiments, we show how this metric is related to the protein dynamics. A curvature and flexibility pattern in the repeat domains can also be connected to tau binding properties, without having to explicitly model the protein’s interaction partner. Finally, we rediscuss the original paperclip model that describes the spatial organization of tau and how phosphorylations impact it. The resulting changes in the protein intradomain and interdomain interaction pattern allow us to propose experimental setups to test our hypothesis.

pubs.acs.org

3rd Annual Danish Workshop on Advanced Molecular Simulation

aias.au.dk

Brève de science : au cœur des protéines

Faut-il forcément des microscopes et des tubes à essai pour observer des molécules ou des protéines ?

cnrs.fr

Inorganic sulfate is critical for Mycobacterium tuberculosis lung tissue colonization and redox balance | PNAS

Tuberculosis remains the deadliest infectious disease caused by a single pathogen, highlighting the urgent need for novel therapies. A deeper under...

pnas.org

Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers

Nature Structural & Molecular Biology - Liu et al. show that SPIN90 dimerizes and binds two Arp2/3 complexes to nucleate two bidirectional actin filaments and the dimerization domain is...

rdcu.be