Biology subjects

Stirnemann, G.

Publications and source records attributed to Stirnemann, G..

7 recordsLinked to original sources

bioRxiv2026

Mapping Active-Site Conformational Ensembles Along Competing Catalytic Pathways of the Hairpin Ribozyme

The catalytic mechanism of the hairpin ribozyme has remained controversial for more than two decades, with different experimental approaches often supporting distinct mechanistic interpretations. In this work, we investigate the conformational landscape of the active site along several proposed reaction pathways using all-atom molecular dynamics simulations in explicit solvent combined with enhanced sampling techniques. Specifically, we employ Hamiltonian replica exchange simulations to extensively explore active-site conformations without relying on predefined collective variables, enabling a broad characterization of the structural ensembles associated with multiple protonation states along three candidate reaction mechanisms. Our simulations suggest that a dianionic general acid/general base pathway involving direct participation of A38 and G8 is unlikely to proceed through well-defined intermediates with catalytically competent geometries. In particular, states associated with G8 deprotonation and subsequent O2 deprotonation exhibit strongly distorted active-site arrangements that appear poorly suited for reaction progression. Although highly synchronous proton-transfer steps cannot be excluded, the required deprotonation of G8 remains difficult to reconcile with neutral pH conditions. In contrast, monoanionic pathways in which the non-bridging oxygens of the scissile phosphate act as transient proton relays produce intermediates that sample geometries favorable for the nucleophilic addition and leaving-group elimination steps of the reaction. These mechanisms do not require direct catalytic involvement of G8 while remaining compatible with potential acid catalysis by protonated A38+ and a possible structural role of G8. Our results provide a unified conformational perspective on competing mechanistic scenarios. The ensembles generated here offer a foundation for future QM/MM and ML/MM calculations aimed at quantitatively resolving the free-energy landscapes governing hairpin ribozyme catalysis. Finally, the present strategy could easily be applied to other biomolecular systems with high conformational plasticity, including other ribozymes.

biophysics↗

bioRxiv2026

Exploring RNA conformational ensembles in silico: progress and challenges

RNA function is intrinsically linked to its structural polymorphism, with molecules exploring the heterogeneous conformational ensembles resulting from complex energy landscapes. These landscapes arise from competing interactions, small energetic separations between microstates, and strong coupling to the environment, posing significant challenges for both experimental characterization and molecular simulation. In this chapter, we review current computational strategies that aim to explore RNA conformational ensembles in silico, with a specific focus on energy landscape-based approaches and atomistic simulations. We discuss key limitations related to sampling efficiency, force-field accuracy, and ensemble analysis, and illustrate their impact through case studies on a self-cleaving ribozyme and an H-type pseudoknot. Finally, we highlight emerging directions, including closer integration with experimental data and the growing role of machine learning, which will probably reinforce the predictive power of in silico RNA energy landscape exploration.

molecular biology↗

bioRxiv2025

Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies

AO_SCPLOWBSTRACTC_SCPLOWMost naturally occurring ribozymes catalyze self-splicing reactions through a 2-OH group. Consequently, experimental structures of precatalytic states often require chemical modifications of the 2-OH, such as its removal or methylation. However, the impact of these chemical modifications on the active site structure remains largely unexplored, which raises important questions since methylated structures are often taken as being representative of pre-catalytic states. Here, we employ extensive atomistic simulations critically compared to and fine-tuned on experimental data, and we revisit experimental results to show that 2-O-methylation critically affects reactant geometries and, therefore, the possible reaction mechanisms inferred from the structures. Our results also challenge the common assumption that 2-O-methylation stabilizes the C3-endo puckering conformation. Our findings, consistent with recent experimental data on ribosome structure, reveal that this effect is highly sensitive to the local secondary structure and is often overstated. For three investigated small-cleaving ribozymes, the C2-endo conformation observed for chemically-modified active site residues through 2-O-methylation is not stable upon methyl group removal to obtain the catalytically-relevant hydroxylated state. This suggests that these geometries arise primarily from a combinaison of steric hindrances and electrostatic interactions with the surrounding environment rather than intrinsic conformational preferences of the ribose upon methylation.

biochemistry↗

bioRxiv2025

Atomic scale description of the allosteric coupling between a lipid bilayer and a membrane protein

Biological membranes are complex environments whose functions are closely tied to the dynamic interactions between lipids and proteins. Here, we utilize high-pressure NMR of lipid nanodiscs paired with molecular dynamics simulations to elucidate at the atomic scale the allosteric dialog between the lipid bilayer and a bacterial model membrane protein, OmpX. We discover that OmpX delays the gelation process by liquefying the annular shell of lipids through hydrophobic and roughness matching processes at the protein surface. Furthermore, the alteration of the mechanical properties of the lipid bilayer directly impacts the energy landscape of amino acid side chains at the lipid/protein interface, but also, unexpectedly, at the protein core. Our work highlights a potential thermodynamically coupled but kinetically uncoupled allosteric pathway linking lipid dynamics with the interior of membrane proteins, directly impacting our understanding of membrane function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/634742v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@5c02ddorg.highwire.dtl.DTLVardef@c033c5org.highwire.dtl.DTLVardef@86f90forg.highwire.dtl.DTLVardef@149480e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

A direct computational assessment of vinculin-actin unbinding kinetics reveals catch bonding behavior

Vinculin forms a catch bond with the cytoskeletal polymer actin, displaying an increased bond lifetime upon force application. Notably, this behavior depends on the direction of the applied force, which has significant implications for cellular mechanotransduction. In this study, we present a comprehensive molecular dynamics simulation study, employing enhanced sampling techniques to investigate the thermodynamic, kinetic, and mechanistic aspects of this phenomenon at physiologically relevant forces. We dissect a catch bond mechanism in which force shifts vinculin between either a weakly- or strongly-bound state. Our results demonstrate that models for these states have unbinding times consistent with those from single-molecule studies, and suggest that both have some intrinsic catch bonding behavior. We provide atomistic insight into this behavior, and show how a directional pulling force can promote the strong or weak state. Crucially, our strategy can be extended to capture the difficult-to-capture effects of small mechanical forces on biomolecular systems in general, and those involved in mechanotransduction more specifically.

biophysics↗

bioRxiv2023

Atomistic simulations of RNA duplex thermal denaturation: sequence- and forcefield-dependence

Double-stranded RNA is the end-product of template-based replication, and is also the functional state of some biological RNAs. Similarly to proteins and DNA, they can be denatured by temperature, with important physiological and technological implications. Here, we use an in silico strategy to probe the thermal denaturation of RNA duplexes. Following previous results that were obtained on a few different duplexes, and which nuanced the canonical 2-state picture of nucleic acid denaturation, we here specifically address three different aspects that improve our description of the temperature-induced dsRNA separation. First, we investigate the effect of the spatial distribution of weak and strong base-pairs among the duplex sequence. We show that the deviations from the two-state dehybridization mechanism are more pronounced when a strong core is flanked with weak extremities, while duplexes with a weak core but strong extremities exhibit a two-state behavior, which can be explained by the key role played by base fraying. This was later verified by generating artificial hairpin or circular states containing one or two locked duplex extremities, which results in an important reinforcement of the entire HB structure of the duplex and higher melting temperatures. Finally, we demonstrate that our results are little sensitive to the employed combination of RNA and water forcefields. The trends in thermal stability among the different sequences as well as the observed unfolding mechanisms (and the deviations from a two-state scenario) remain the same regardless of the employed atomistic models. However, our study points to possible limitations of recent reparametrizations of the Amber RNA forcefield, which sometimes results in duplexes that readily denature under ambient conditions, in contradiction with available experimental results.

biophysics↗

bioRxiv2022

Binding site plasticity regulation of the FimH catch-bond mechanism

The bacterial fimbrial adhesin FimH is a remarkable and well-studied catch-bond protein found at the tip of E. coli type 1 pili, which allows pathogenic strains involved in urinary tract infections to bind high-mannose glycans exposed on human epithelia. The catch-bond behavior of FimH, where the strength of the interaction increases when a force is applied to separate the two partners, enables the bacteria to resist clearance when they are subjected to shear forces induced by urine flow. Two decades of experimental studies performed at the single-molecule level, as well as X-ray crystallography and modeling studies, have led to a consensus picture whereby force separates the binding domain from an inhibitor domain, effectively triggering an allosteric conformational change in the former. This force-induced allostery is thought to be responsible for an increased binding affinity at the core of the catch-bond mechanism. However, some important questions remain, the most challenging one being that the crystal structures corresponding to these two allosteric states show almost superimposable binding-site geometries, which questions the molecular origin for the large difference in affinity. Using molecular dynamics with a combination of enhanced-sampling techniques, we demonstrate that the static picture provided by the crystal structures conceals a variety of binding-site conformations that have a key impact on the apparent affinity. Crucially, the respective populations in each of these conformations are very different between the two allosteric states of the binding domain, which can then be related to experimental affinity measurements. We also evidence a previously unappreciated but important effect: in addition to the well-established role of the force as an allosteric regulator via domain separation, application of force tends to directly favor the high-affinity binding-site conformations. We hypothesize that this additional local catch-bond effect could delay unbinding between the bacteria and the host cell before the global allosteric transition occurs, as well as stabilizing the complex even more once in the high-affinity allosteric state.

biophysics↗