Biology subjects

Grubmuller, H.

Publications and source records attributed to Grubmuller, H..

8 recordsLinked to original sources

bioRxiv2026

Combining CHARMM36m with OPC water improves accuracy

Atomistic simulations of intrinsically disordered proteins (IDPs) are notoriously sensitive to force field inaccuracies, either regarding the protein or the water model, yielding inaccurate observables such as compactness, secondary structure propensities, or kinetics. The currently most widely used IDP force fields are Amber99sb-disp (A99disp) and Charmm36m (C36m). A99disp includes a new water model and thus optimized both, the protein and the water interactions. In contrast, C36m used the Tip3p water model and optimized only protein interactions. In many cases, C36m+Tip3p underestimates radii of gyration compared to FRET or SAXS experiments. Such overly compact structural ensembles are believed to arise from an imbalance between protein-protein, protein-water, and water-water interactions, which might be due to Tip3p inaccuracies. Here, we aim at re-balancing these interactions by combining C36m with the Optimal Point Charge (OPC) water model. Recently, this C36m+OPC combination showed improved accuracy for the disordered domain of the measles virus nucleoprotein. Here we present a systematic assessment, comparing C36m+OPC, C36m+Tip3p, C36m+Tip4p, C22*, A03ws, A99sb-ws, and A99disp for five IDPs, as well as a subset of those for five globular proteins, a set of disordered AGQ-repeat peptides, and the fast folding miniprotein CLN025. We compared extensive MD simulations (> 8.5 ms) with SAXS, NMR, circular dichroism, photo-induced electron transfer (PET), T-jump infrared spectroscopy, and X-ray crystallography measurements. We found that combining C36m with OPC improved accuracy over C36m+Tip3p for IDP ensembles without compromising its accuracy for globular proteins. While also the kinetics of the AGQ-peptides were more accurate for C36m+OPC, those of CLN025 folding were less accurate. Overall, C36m+OPC showed similar accuracy as A99sb-ws and A99disp, the latter is currently considered among the most accurate protein force fields.

biophysics↗

bioRxiv2025

Analysis of Large Peptide Collisional Cross Section Dataset Reveals Structural Origin of Bimodal Behavior

Recent advances in ion mobility spectrometry have enabled the measurement of rotationally averaged collisional cross-sectional area (CCS) for millions of peptides, as part of routine proteomic mass spectrometry workflows. One of the most striking finding in recent large ion mobility datasets is that CCS exhibits two distinct modes, most notably for charge 3+ peptides. Here, using classical machine learning approaches, we identify that basic site positioning is a key sequence feature determining if a peptide belongs to the high or low CCS mode. Molecular dynamics simulations suggest that peptides in the high CCS mode tend to adopt more extended conformations and form charge-stabilized helical structures, whereas those in the low CCS mode adopt more compact, globular conformations. Further supporting this structural hypothesis, we provide evidence for preferential protonation near the C-terminus, and uncover multiple position-dependent sequence determinants that all suggest the predominance of helix formation in the high mode. Together, these findings will enable better integration of CCS measurements into protein identification and quantification pipelines, improving the performance of ion mobility-based proteomics.

bioinformatics↗

bioRxiv2025

Hierarchically ordered multi-timescale structural dynamics of the intrinsically disordered p53 transactivation domain

Intrinsically disordered proteins (IDPs) exhibit pronounced structural dynamics, which is crucial for their functional versatility. Yet their dynamics slower than nanoseconds remain largely elusive. We combined high-power relaxation dispersion nuclear magnetic resonance spectroscopy with molecular dynamics simulations to characterize these kinetics and the underlying structural interconversions of a prototypical IDP, the N-terminal transactivation domain of the tumor suppressor p53 (p53-TAD). We find a complex hierarchy of structural dynamics on timescales covering over seven orders of magnitude, ranging from fast nanoseconds backbone re-orientations, via sub-microsecond helix-formation dynamics involving many structural sub-states and transition times, to transient tertiary structure formation slower than 25 microseconds. These rich structural dynamics of p53-TAD, and likely those of other IDPs, parallel the timescale hierarchy of the conformational dynamics of folded proteins. One-Sentence summaryA hierarchical energy landscape governs kinetics and structural dynamics of the disordered p53 transactivation domain.

biophysics↗

bioRxiv2021

Nanomechanics combined with HDX reveal allosteric drug binding sites of CFTR NBD1

Cystic fibrosis is most frequently caused by the deletion of F508 ({Delta}F508) in CFTRs nucleotide binding domain 1 (NBD1), compromising CFTR folding, stability and domain assembly. The limitation of developing a successful therapy is due to the lack of molecules that synergistically facilitate folding by targeting distinct structural defects of {Delta}F508-CFTR. To improve drug efficacy by targeting the {Delta}F508-NBD1 folding and stability, and to study potential {Delta}F508-NBD1 allosteric corrector binding sites at the atomic level, we combined molecular dynamics (MD) simulations, atomic force spectroscopy (AFM) and hydrogen-deuterium exchange (HDX) experiments. These methods allowed us to describe unfolding intermediates and forces acting during NBD1 mechanical unfolding and to elucidate the stabilization mechanism of {Delta}F508-NBD1 by 5-bromoindole-3-acetic acid (BIA). An NBD1 region, including the -subdomain, was identified as a potentially important participant of the first folding steps, characterized by non-native interactions of F508, thus destabilized in the deletion mutant. The instability was counteracted by the low-potency corrector BIA, increasing the mechanical resistance of the {Delta}F508-NBD1 -subdomain, which was confirmed as a binding site by computational modeling and HDX experiments. Our results underline the complementarity of computational and experimental methods and provide a possible strategy to improve folding correctors.

biophysics↗

bioRxiv2021

Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel

The ribosome is a fundamental biomolecular complex responsible for protein production in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiologic consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form an -helix in the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP sequence has a low helical propensity in water and that the propensity is higher in more hydrophobic solvents. We propose that helix formation within the ribosome is driven by the tunnel environment and that a portion of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling the -helix formation, which causes the elongation arrest.

biophysics↗

bioRxiv2020

Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations

Membrane topology changes such as poration, stalk formation, and hemi-fusion rupture are essential to cellular function, but their molecular details, energetics, and kinetics are still not fully understood. Here we present a unified energetic and mechanistic picture of metastable pore defects in tensionless lipid membranes. We used an exhaustive committor analysis to test and select optimal reaction coordinates and also to determine the nucleation mechanism. These reaction coordinates were used to calculate free energy landscapes that capture the full process and end states. The identified barriers agree with the committor analysis. To enable sufficient sampling of the complete transition path for our atomistic simulations, we developed a novel "gizmo" potential biasing scheme. The simulations suggest that the essential step in the nucleation is the initial merger of lipid head-groups at the nascent pore center. To facilitate this event, an indentation pathway is energetically preferred to a hydrophobic defect. Continuous water columns that span the indentation were determined to be on-path transients that precede the nucleation barrier. This study gives a quantitative description of the nucleation mechanism and energetics of small metastable pores and illustrates a systematic approach to uncover the mechanisms of diverse cellular membrane remodeling processes. STATEMENT OF SIGNIFICANCEThe primary steps and nucleation of lipid membrane pore formation are key to membrane fusion, viral infection, and vesicular cellular transport. Despite decades experimental and theoretical studies, the underlying mechanisms are still not fully understood at the atomic level. Using a committor-based reaction coordinate and atomistic simulations, we report new structural and energetics insight into the full poration process. We find that the pore nucleates via an elastic indentation rather than by forming a hydrophobic defect. Subsequently, water pierces the thinned slab as a prerequisite for the following axial merger of the first lipid headgroups from opposite monolayers, which precedes and best characterizes the transition state. We also identify a metastable prepore basin, thereby explaining previous indirect experimental evidence.

biophysics↗

bioRxiv2019

tRNA dissociation from EF-Tu after GTP hydrolysis and Pi release: primary steps and antibiotic inhibition

In each round of ribosomal translation, the translational GTPase EF-Tu delivers a tRNA to the ribosome. After successful decoding, EF-Tu hydrolyses GTP, which triggers a conformational change that ultimately results in the release of the tRNA from EF-Tu. To identify the primary steps of these conformational changes and how they are prevented by the antibiotic kirromycin, we employed all-atom explicit-solvent Molecular Dynamics simulations of the full ribosome-EF-Tu complex. Our results suggest that after GTP hydrolysis and Pi release, the loss of interactions between the nucleotide and the switch 1 loop of EF-Tu allows domain D1 of EF-Tu to rotate relative to domains D2 and D3 and leads to an increased flexibility of the switch 1 loop. This rotation induces a closing of the D1-D3 interface and an opening of the D1-D2 interface. We propose that the opening of the D1-D2 interface, which binds the CCA-tail of the tRNA, weakens the crucial EF-Tu-tRNA interactions which lowers tRNA binding affinity, representing the first step of tRNA release. Kirromycin binds within the D1-D3 interface, sterically blocking its closure, but does not prevent hydrolysis. The resulting increased flexibility of switch 1 explains why it is not resolved in kirromycin-bound structures.

biophysics↗

bioRxiv2018

SESCA: Predicting the Circular Dichroism Spectra of Proteins from Molecular Structure

Circular dichroism spectroscopy is a highly sensitive, but low-resolution technique to study the structure of proteins. Combined with molecular modelling or other complementary techniques, CD spectroscopy can provide essential information at higher resolution. To this end, we introduce a new computational method to calculate the electronic circular dichroism spectra of proteins from a structural model or ensemble using the average secondary structure composition and a pre-calculated set of basis spectra. We compared the predictive power of our method to existing algorithms - namely DichroCalc and PDB2CD - and found that it predicts CD spectra more accurately, with a 50% smaller average deviation from the measured CD spectra. Our results indicate that the derived basis sets are robust to experimental errors in the reference spectra and to the choice of the secondary structure classification algorithm. For over 80% of the globular reference proteins, our basis sets accurately predict the experimental spectrum solely from their secondary structure composition. For the remaining 20%, correcting for intensity normalization considerably improves the prediction power. Additionally, we show that the predictions for short peptides and intrinsically disordered proteins strongly benefit from accounting for side-chain contributions and structural flexibility. Table Of Content Graphics O_TBL View this table: org.highwire.dtl.DTLVardef@1a1d73forg.highwire.dtl.DTLVardef@3aaa8forg.highwire.dtl.DTLVardef@193c090org.highwire.dtl.DTLVardef@1474f92org.highwire.dtl.DTLVardef@b920da_HPS_FORMAT_FIGEXP M_TBL C_TBL

biophysics↗