Biology subjects

Lapidus, L. J.

Publications and source records attributed to Lapidus, L. J..

3 recordsLinked to original sources

bioRxiv2022

Modeling concentration-dependent phase separation processes involving peptides and RNA via residue-based coarse-graining

Biomolecular condensation, especially liquid-liquid phase separation, is an important physical process with relevance for a number of different aspects of biological functions. Key questions of what drives such condensation, especially in terms of molecular composition, can be addressed via computer simulations, but the development of computationally efficient, yet physically realistic models has been challenging. Here, the coarse-grained model COCOMO is introduced that balances the polymer behavior of peptides and RNA chains with their propensity to phase separate as a function of composition and concentration. COCOMO is a residue-based model that combines bonded terms with short- and long-range terms, including a Debye-Huckel solvation term. The model is highly predictive of experimental data on phase-separating model systems. It is also computationally efficient and can reach the spatial and temporal scales on which biomolecular condensation is observed with moderate computational resources.

biophysics↗

bioRxiv2022

Characterizing Transient Protein-Protein Interactions by Trp-Cys Quenching and Computer Simulations

Transient protein-protein interactions occur frequently under the crowded conditions encountered in biological environments, yet they remain poorly understood. Here, tryptophan-cysteine quenching is introduced as an experimental approach that is ideally suited to characterize such interactions between proteins with minimal labeling due to its sensitivity to nano- to microsecond dynamics on sub-nanometer length scales. The experiments are paired with computational modeling at different resolutions including fully atomistic molecular dynamics simulations to provide interpretation of the experimental observables and add further insights at the molecular level. This approach is applied to model systems, villin variants and the drkN SH3 domain, in the presence of protein G crowders. It is demonstrated that Trp-Cys quenching experiments are able to not only distinguish between overall attractive and repulsive interactions between different proteins, but they can also discern variations in interaction preferences at different protein surface locations. The close integration between experiment and simulations also provides an opportunity to evaluate different molecular force fields for the simulation of concentrated protein solutions. Significance StatementBiological environments typically involve a variety of different proteins at very high concentrations where non-specific interactions are unavoidable. These interactions may go beyond simple crowding effects and involve transient contacts that may impact structure, dynamics, and ultimately function of proteins in vivo. While computer simulations have partially characterized such interactions, experimental data remain limited because established techniques are generally not well-suited to the characterization of dynamic processes on microsecond time and nanometer length scales. Tryptophan quenching by cysteine is introduced here as a new approach for studying transient protein encounters under concentrated conditions with the support of computational modeling. The study demonstrates that such experiments can resolve not just differences between different proteins but also residue-specific interaction preferences.

biophysics↗

bioRxiv2020

Charge-Driven Phase Separation of RNA and Proteins without Disorder

Phase separation processes are increasingly being recognized as important organizing mechanisms of biological macromolecules in cellular environments. Well established drivers of liquid-liquid phase separation are multi-valency and intrinsic disorder. Here, we show that globular macromolecules may condense simply based on electrostatic complementarity. More specifically, phase separation of mixtures between RNA and positively charged proteins is described from a combination of multiscale computer simulations with microscopy and spectroscopy experiments. Condensates retain liquid character and phase diagrams are mapped out as a function of molecular concentrations in experiment and as a function of molecular size and temperature via simulations. The results suggest a more general principle for phase separation that is based primarily on electrostatic complementarity without invoking polymer properties as in most previous studies. Simulation results furthermore suggest that such phase separation may occur widely in heterogenous cellular environment between nucleic acid and protein components. STATEMENT OF SIGNIFICANCELiquid-liquid phase separation has been recognized as a key mechanism for forming membrane-less organelles in cells. Commonly discussed mechanisms invoke a role of disordered peptides and specific multi-valent interactions. We report here phase separation of RNA and proteins based on a more universal principle of charge complementarity that does not require disorder or specific interactions. The findings are supported by coarse-grained simulations, theory, and experimental validation via microscopy and spectroscopy. The broad implication of this work is that condensate formation may be a universal phenomenon in biological systems.

biophysics↗