Biology subjects

Linse, J.-B.

Publications and source records attributed to Linse, J.-B..

5 recordsLinked to original sources

bioRxiv2025

Depletion of the protein hydration shell with increasing temperature observed by small-angle X-ray scattering and molecular simulations

The hydration shell is an integral part of proteins since it plays key roles for conformational transitions, molecular recognition, and enzymatic activity. While the dynamics of the hydration shell have been described by spectroscopic techniques, the structure of the hydration shell remain less understood due to the lack of hydration shell-sensitive structural probes with high spatial resolution. We combined temperature-ramp smallangle X-ray scattering (T -ramp SAXS) from 255-335 K with molecular simulations to show that the hydration shells of the GB3 domain and villin headpiece are remarkably temperature-sensitive. For proteins in the folded state, T -ramp SAXS data and explicitsolvent SAXS predictions consistently demonstrate decays of protein contrasts and radii of gyration with increasing temperature, which are shown to reflect predominantly temperature-sensitive depleting hydration shells. The depletion is not merely caused by enhanced disorder within the hydration shells but also by partial displacements of surface-coordinated water molecules. Together, T -ramp SAXS and explicit-solvent SAXS calculations provide a novel structural view on the protein hydration shell, which underlies temperature-dependent processes such as cold denaturation, thermophoresis, or biomolecular phase separation.

biophysics↗

bioRxiv2025

Hydration shells of globular and intrinsically disordered proteins: effects of amino acid composition, peptide conformation, and force fields

The protein hydration shell is a key mediator of processes such as molecular recognition, protein folding, and proton transfer. How surface-exposed amino acids shape the hydration shell structure is not well understood. We combine molecular dynamics simulations with explicit-solvent predictions of small-angle X-ray scattering (SAXS) curves to quantify the contributions of all 20 proteinogenic amino acids to the hydration shell of the globular GB3 domain and the intrinsically disordered protein (IDP) XAO. We focus on two quantities encoded by SAXS curves: the hydration shell effect on the radius of gyration and the electron density contrast between protein and solvent. We derive an amino-acid-specific contrast score, revealing that acidic residues generate the strongest contrast with 1 to 1.5 excess water molecules relative to alanine, followed by cationic and polar residues. In contrast, apolar residues generate a water depletion layer. These trends are consistent across simulations with different water models. Around the XAO peptide, the hydration shell is generally far weaker compared to the globular GB3 domain, indicating unfavorable water-peptide packing at the IDP surface. The hydration shell effect on the radius of gyration of the IDP is strongly conformation-dependent. Together, the calculations show that the composition and spatial arrangement of surface-exposed amino acids govern the hydration shell structure, with implications for a wide range of biological functions and for hydration-sensitive experimental techniques such as solution scattering. SignificanceHydration shells of biomolecules constitute a large fraction of the water in crowded cellular environments and play key roles in biological functions such as enzymatic reactions and conformational transitions. Small-angle X-ray scattering (SAXS) has shown that hydration shells differ in density from bulk water, yet how surface-exposed amino acids and protein surface geometry shape the hydration shell is not well understood. We combined molecular dynamics simulations with explicit-solvent SAXS predictions to quantify how surface-exposed chemical moieties and protein geometry drive variations in hydration shell density. Notably, the hydration shell of a globular protein differs markedly from that of an intrinsically disordered protein. Our study offers a comprehensive characterization of protein hydration and informs the interpretation of hydration-sensitive experimental techniques.

biophysics↗

bioRxiv2023

Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data

Biological macromolecules in solution are surrounded by a hydration shell, whose structure differs from the structure of bulk solvent. In crowded cellular environments, hydration shells constitute a large fraction of the overall solvent. While the importance of the hydration shell for numerous biological functions such as molecular recognition or enzymatic activity is widely acknowledged, it is poorly understood how the hydration shell is regulated by macromolecular shape and surface composition, mostly because a quantitative readout of the overall hydration shell structure has been missing. We show that small-angle scattering (SAS) in solution using X-rays (SAXS) or neutrons (SANS) provide a protein-specific footprint of the protein hydration shell that enables quantitative comparison with molecular dynamics (MD) simulations. By means of explicit-solvent SAS predictions, we derived the effect of the hydration shell contrast relative to bulk on the radii of gyration Rg of five proteins using 18 combinations of protein force field and water model. By comparing computed Rg values from SAXS relative to SANS in D2O with consensus experimental data from a worldwide round-robin study, we found that several but not all force fields yield a hydration shell contrast in remarkable agreement with experimental data. The hydration shell contrast, as captured by Rg values, strongly depends on the protein charge and geometric shape, thus providing a protein-specific footprint of protein-water interactions and a novel observable for scrutinizing atomistic hydration shell models against experimental data.

biophysics↗

bioRxiv2022

Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein during translation regulation

RNA binding proteins (RBPs) often engage multiple RNA binding domains (RBDs) to increase target specificity and affinity. However, the complexity of target recognition of multiple RBDs remains largely unexplored. Here we use Upstream of N-Ras (Unr), a multidomain RBP, to demonstrate how multiple RBDs orchestrate target specificity. A crystal structure of the three C-terminal RNA binding cold-shock domains (CSD) of Unr bound to a poly(A) sequence exemplifies how recognition goes beyond the classical {pi}-{pi}-stacking in CSDs. Further structural studies reveal several interaction surfaces between the N-terminal and C-terminal part of Unr with the poly(A)-binding protein (pAbp). This provides first atomistic details towards understanding regulation of translation initiation that is mediated by the interplay of these two proteins with each other and RNA.

molecular biology↗

bioRxiv2020

Structure and dynamics of the quaternary hunchback mRNA translation repression complex

A key regulatory process during Drosophila development is the localized suppression of the hunchback mRNA translation at the posterior, which gives rise to a hunchback gradient governing the formation of the anterior-posterior body axis. The suppression of the RNA is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for proper Drosophila development. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins in the RNA suppression remains a long-standing open question. We characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos with hunchback mRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternary hunchback mRNA suppression complex is flexible with the unoccupied nucleotides of the RNA functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, Brat and Pum with Nanos bind the RNA completely independently. In accordance with previous studies, showing that Brat can suppress hunchback mRNA independently and is distributed uniformly throughout the embryo, this suggests that hunchback mRNA suppression by Brat is functionally separate from the suppression by Pumilio and Nanos.

molecular biology↗