Biology subjects

Klein, M. L.

Publications and source records attributed to Klein, M. L..

7 recordsLinked to original sources

bioRxiv2026

Tightly Knotted Enzymes Inhibit Protein-Protein Aggregation

Neurodegenerative diseases are closely linked to aberrant protein aggregation arising from failures in cellular proteostasis, yet the physical determinants governing transitions between soluble states, liquid-liquid phase separation (LLPS), and aggregation remain incompletely understood. Here, we investigate how protein backbone topology influences phase behavior using ubiquitin C-terminal hydrolase L1 (UCH-L1), a highly neuron-enriched deubiquitinase in the ubiquitin-proteasome system harboring a rare, evolutionarily conserved knotted backbone topology, and its Parkinsons disease-associated I93M mutant. Through multiscale molecular dynamics (MD) simulations of single-chain and multichain systems, we show that knot integrity acts as a conformational constraint that limits access to expanded states, and suppresses LLPS propensity. Destabilization of the native knotted ensemble in I93M reshapes the conformational ensemble, enhancing intermolecular contacts, strengthening hydrophobic interaction, and reducing solvation penalties, thereby stabilizing protein-rich phases. Within condensates, these changes lead to persistent interchain contacts, increased topological entanglement, and slower relaxation dynamics, indicative of a transition toward viscoelastic assemblies, whereas intact topology maintains dynamic, liquid-like behavior. Our results identify topological integrity as a key physical determinant of protein phase behavior and establish a mechanistic link between topological stability and condensate material properties, with implications for aggregation-associated neurodegeneration.

biophysics↗

bioRxiv2025

Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities

The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and apply this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates in two genome-resolved investigations of the human gut and oral cavity. Our results demonstrate that EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark genome collections.

microbiology↗

bioRxiv2021

The SPICA Coarse-Grained Force Field for Proteins and Peptides

A coarse-grained (CG) model for peptides and proteins was developed as an extension of the SPICA (Surface Property fItting Coarse grAined) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulation with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. The side chain analogs reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable dimerization free energies in water compared to those from AA-MD. A series of peptides/proteins adsorbed or penetrated into the membrane simulated by the CG-MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins comparable to those in the orientation of protein in membrane (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated a good performance of the SPICA FF.

biophysics↗

bioRxiv2019

Coexistence of lipid phases stabilizes interstitial water in the outer layer of mammalian skin

The lipid matrix in the outer layer of mammalian skin, the stratum corneum, has been previously investigated by multiple biophysical techniques, aimed at identifying hydrophilic and lipophilic pathways of permeation. While consensus is developing over the microscopic structure of the lipid matrix, no molecular-resolution model describes the permeability of all chemical species simultaneously. Using molecular dynamics simulations of a model mixture of skin lipids, the self-assembly of the lipid matrix lamellae has been studied. At higher humidity, the resulting lamellar phase is maintained by partitioning excess water into isolated droplets of controlled size and spatial distribution. The droplets may fuse together to form intra-lamellar water channels, thereby providing a pathway for the permeation of hydrophilic species. These results reconcile competing data on the outer skins structure and broaden the scope of molecular-based methods to improve the safety of topical products and to advance transdermal drug delivery.

biophysics↗

bioRxiv2018

A consistent picture of TRPV1 activation emerges from molecular simulations and experiments

Although the structure of TRPV1 has been experimentally determined in both the closed and open states, very little is known about its activation mechanism. In particular, the conformational changes occurring in the pore domain and resulting in ionic conduction have not been identified yet. Here, we suggest a hypothetical molecular mechanism for TRPV1 activation, which involves the rotation of a conserved asparagine in S6 from the S4-S5 linker toward the pore. This rotation is correlated with the dehydration of four peripheral cavities located between S6 and the S4-S5 linker and the hydration of the pore. In light of our hypothesis, we perform bioinformatics analyses of TRP and other evolutionary related ion channels, analyze newly available structures and re-examine previously reported water accessibility and mutagenesis experiments. Overall, we provide several independent lines of evidence that corroborate our hypothesis. Finally, we show that the proposed molecular mechanism is compatible with the currently existing idea that in TRPV1 the selectivity filter acts as a secondary gate.

biophysics↗

bioRxiv2017

TRPV1 activation relies on hydration/dehydration of nonpolar cavities

TRPV1 promotes cationic currents across cellular membranes in response to multiple stimuli such as increased temperature, binding of chemicals, low pH and voltage. The molecular underpinnings of TRPV1 gating, in particular the mechanism of temperature sensitivity, are still largely unknown. Here, we used molecular simulations and electrophysiology to shed light on the closed to open transition. Specifically, we found that gating of TRPV1 relies on the motion of an evolutionarily conserved amino acid (N676) in the middle of the S6 helix. On rotation, the side chain of this asparagine faces either the central pore or the S4-S5 linker. Only in the former case is the central pore hydrated and thus conductive. Interestingly, when N676 rotates toward the linker, we observe hydration of four so far unreported small nonpolar cavities. Based on these findings, we propose a model for TRPV1 gating involving the dynamic hydration of these four cavities. Free energy calculations indicate that this gating mechanisms is markedly temperature dependent favoring the open state at high temperature. On the basis of this model, which is able to rationalize a wealth of seemingly conflicting and/or unrelated experimental observations, we predicted the behavior of two single residue mutants, M572A and F580Y, the consequences of which we confirmed experimentally.

biophysics↗

bioRxiv2017

Exploring the Complex Dynamics of an Ion Channel Voltage Sensor Domain via Computation

Voltage-gated ion channels are ubiquitous proteins that orchestrate electrical signaling across excitable membranes. Key to their function is activation of the voltage sensor domain (VSD), a transmembrane four alpha-helix bundle that triggers channel opening. Modeling of currents from electrophysiology experiments yields a set of kinetic parameters for a given channel, but no direct molecular insight. Here we use molecular dynamics (MD) simulations to determine the free energy landscape of VSD activation and to, ultimately, predict the time evolution of the resulting gating currents. Our study provides the long-sought-for bridge between electrophysiology and microscopic molecular dynamics and confirms, as already suggested on the basis of experiments, that rate-limiting barriers play a critical role in activation kinetics.

biophysics↗