Phase separation processes are increasingly being recognized as important organizing mechanisms of biological macromolecules in cellular environments. Well-established drivers phase multi-valency and intrinsic disorder. Here, we show that globular may condense simply based on electrostatic complementarity. More specifically, mixtures between RNA positively charged proteins is described from a combination multiscale computer simulations with microscopy spectroscopy experiments. diagrams were...

Dynamic nuclear polarization (DNP)-enhanced solid-state NMR spectroscopy has been shown to hold great potential for functional studies of membrane proteins at low temperatures due its sensitivity improvement. There are, however, numerous applications which experiments ambient temperature are desirable and would also benefit from DNP signal enhancement. Here, we demonstrate as a proof concept that significant increase lipid bilayers under room-temperature conditions can be achieved by...

Intrinsically disordered proteins (IDPs) have been closely studied during the past decade due to their importance in many biological processes. The nature of this group makes it difficult observe its full span conformational space using either experimental or computational studies. In article, we explored C-terminal domain (CTD) RNA polymerase II (Pol II), which is also an intrinsically low complexity domain, enhanced sampling methods. We provided a detailed analysis model systems CTD with...

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details catalysis at near-atomic resolution precise arrangement key site components have been elusive. Here, we present the free-electron laser (FEL) structures matched ATP-bound Pol hyperactive Rpb1 T834P bridge helix (BH) mutant highest to date. The...

Lipid membrane permeation of drug molecules was investigated with Heterogeneous Dielectric Generalized Born (HDGB)-based models using solubility-diffusion theory and machine learning. Free energy profiles were obtained for neutral by the standard HDGB Dynamic (DHDGB) to account deformation upon insertion drugs. We also hybrid free where neutralization charged taken into insertion. The evaluation predictions done against experimental permeability coefficients from Parallel Artificial Membrane...

RNA polymerase II (Pol II) forms a complex with elongation factors to proceed the stage of transcription process. In this work, we studied factor SPT5 and explored protein–nucleic acid interactions for isolated systems KOW1 KOW4 domains DNA RNA, respectively. We performed molecular dynamics (MD) simulations using three commonly used force fields that are CHARMM c36m, AMBER ff14sb, ff19sb. Simulations showed strong low electrostatic binding free energies all used. was found be highly dynamic...

Polyelectrolytes continue to find wide interest and application in science engineering, including areas such as water purification, drug delivery, multilayer thin films. We have been interested the dynamics of small molecules a variety polyelectrolyte (PE) environments; this paper, we report simulations analysis dye molecule rhodamine B (RB) several very simple solutions. Translational diffusion RB zwitterion has measured fully atomistic, 2 μs long molecular four different Two solutions...

A refinement protocol based on physics-based techniques established for water soluble proteins is tested membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer aqueous solvent systems. Snapshots from the selected scoring with either knowledge-based or implicit membrane-based functions averaged to obtain refined models. The resulted consistent significant of similar performance methods...

The heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is extended by the addition of a van der Waals dispersion term to better describe nonpolar components free energy solvation. new model, termed HDGBvdW, improves estimates in hydrophobic interior membrane, where polar and charged species are rarely found interactions become significant. for environment extends model from Gallicchio et al. (J. Comput. Chem. 2004, 25, 479) combining separate contributions each...

Catalysis and fidelity of multisubunit RNA polymerases rely on a highly conserved active site domain called the trigger loop (TL), which achieves roles in transcription through conformational changes interaction with NTP substrates. The mutations TL residues cause distinct effects catalysis including hypo- hyperactivity altered fidelity. We applied molecular dynamics simulation (MD) machine learning (ML) techniques to characterize Saccharomyces cerevisiae Polymerase II (Pol II) system. did...

A protocol for predicting the hydrophobic length of membrane proteins using heterogeneous dielectric generalized Born (HDGB) implicit model is presented. The method involves optimal positioning in and identification lipid-facing inward-facing residues, followed by energy optimization to obtain from width. latest HDGB version 3 (HDGBv3) van der Waals (HDGBvdW) models were applied a test set containing 15 (seven β-barrel eight α-helical proteins), which matching widths are available...

A scoring protocol based on implicit membrane-based functions and a new for optimizing the positioning of proteins inside membrane was evaluated its capacity to discriminate native-like states from misfolded decoys. decoy set previously established by Baker lab (Proteins: Struct., Funct., Genet. 2006, 62, 1010-1025) used along with second that generated cover higher resolution models. The Implicit Membrane Model 1 (IMM1), IMM1 model CHARMM 36 parameters (IMM1-p36), generalized Born simple...

Spt5 is an elongation factor that associates with RNA polymerase II (Pol II) during transcription and has important functions in promoter-proximal pausing processivity. was also recognized for its roles the of expanded-repeat genes are related to neurodegenerative diseases. Recently, a set Spt5-Pol small molecule inhibitors (SPIs) were reported, which selectively inhibit mutant huntingtin gene transcription. Inhibition mechanisms as well interaction sites these SPIs Pol not entirely known....

ABSTRACT RNA Polymerase II (Pol II) C-terminal domain (CTD) is known to have crucial roles in regulating transcription. CTD has also been highly recognized for undergoing phase separation, which further associated with its regulatory functions. However, the molecular interactions that forms induce clustering drive separations and how phosphorylation of affects are not entirely known. In this work, we studied concentrated solutions two heptapeptide repeats (2CTDs) models at different...

RNA polymerase II (Pol II) C-terminal domain (CTD) is known to have crucial roles in regulating transcription. CTD has also been highly recognized for undergoing phase separation, which further associated with its regulatory functions. However, the molecular interactions that forms induce clustering drive separations and how phosphorylation of affects are not entirely known. In this work, we studied concentrated solutions two heptapeptide repeat (2CTD) models at different patterns protein...

ABSTRACT Catalysis and fidelity of multisubunit RNA polymerases rely on a highly conserved active site domain called the trigger loop (TL), which achieves roles in transcription through conformational changes interaction with NTP substrates. The mutations TL residues cause distinct effects catalysis including hypo- hyperactivity altered fidelity. We applied molecular dynamics simulation (MD) machine learning (ML) techniques to characterize Saccharomyces cerevisiae Polymerase II (Pol II)...

The activation of N-methyl-D-aspartate receptors is found to be intimately associated with neurodegenerative diseases which make them promising therapeutic targets. Despite the significantly increasing multidisciplinary interests centred on this ionotropic channel, design new ligands intended functional activity remains a great challenge. In article, computational study based density theory presented understand structural factors determining their function as antagonists and partial...

ABSTRACT Intrinsically disordered proteins (IDPs) have been closely studied during the past decade due to their importance for many biological processes. The nature of this group makes it difficult observe its full span conformational space either using experimental or computational studies. In article, we explored C-terminal domain (CTD) RNA polymerase II (Pol II), which is also an intrinsically low complexity domain, enhanced sampling methods. We provided a detailed analysis model systems...

ABSTRACT Spt5 is an elongation factor that associates with RNA polymerase II (Pol II) during transcription and has important functions in promoter-proximal pausing processivity. was also recognized for its roles the of expanded-repeat genes are related to neurodegenerative diseases. Recently, a set Spt5-Pol small molecule inhibitors (SPIs) were reported, which selectively inhibit mutant huntingtin gene transcription. Inhibition mechanisms as well interaction sites these SPIs Pol not entirely...

Abstract Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details catalysis at near atomic resolution precise arrangement key site components have been elusive. Here we present the free electron laser (FEL) structure matched ATP-bound Pol II, revealing full interaction network highest to date, including trigger...