Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel

As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities

A Role for Confined Water in Chaperonin Function

A Role for Confined Water in Chaperonin Functio

Meltdown - a tool for classification and analysis of DSF data [Conference Abstract]

An application that translates raw thermal melt curve data into more easily assimilated knowledge is described. This program, called ‘Meltdown’, performs a number of data remediation steps before classifying melt curves and estimating melting temperatures. The final output is a report that summarizes the results of a differential scanning fluorimetry experiment. Meltdown uses a Bayesian classification scheme, enabling reproducible identification of various trends commonly found in DSF datasets. The goal of Meltdown is not to replace human analysis of the raw data, but to provide a sensible interpretation of the data to make this useful experimental technique accessible to naïve users, as well as providing a starting point for detailed analyses by more experienced users

Kinetic and Sequence-Structure-Function Analysis of LinB Enzyme Variants with β- and δ-Hexachlorocyclohexane

<div><p>Organochlorine insecticide hexachlorocyclohexane (HCH) has recently been classified as a ‘Persistent Organic pollutant’ by the Stockholm Convention. The LinB haloalkane dehalogenase is a key upstream enzyme in the recently evolved Lin pathway for the catabolism of HCH in bacteria. Here we report a sequence-structure-function analysis of ten naturally occurring and thirteen synthetic mutants of LinB. One of the synthetic mutants was found to have ∼80 fold more activity for β- and δ-hexachlorocyclohexane. Based on detailed biophysical calculations, molecular dynamics and ensemble docking calculations, we propose that the latter variant is more active because of alterations to the shape of its active site and increased conformational plasticity.</p></div

Simultaneous expression of ClopHensor and SLC26A3 reveals the nature of endogenous oxalate transport in CHO cells.

ClopHensor, a fluorescent fusion protein, is a dual function biosensor that has been utilized as a tool for the simultaneous measurement of intracellular chloride and pH in cells. ClopHensor has traditionally been used in conjunction with fluorescence microscopy for single cell measurements. Here, we present a promising multi-well format advancement for the use of ClopHensor as a potential high-throughput method capable of measuring fluorescence signal intensity across a well of confluent cells with highly reproducible results. Using this system, we gained mechanistic insight into an endogenous oxalate transporter in Chinese hamster ovary (CHO) cells expressing ClopHensor and the human chloride transporter, SLC26A3. SLC26A3, a known anion exchanger, has been proposed to play a role in colonic oxalate absorption in humans. Our attempt to study the role of SLC26A3 in oxalate transport revealed the presence of an endogenous oxalate transporter in CHO cells. This transporter was strongly inhibited by niflumate, and exhibited clear saturability. Use of ClopHensor in a multi-well cell assay allowed us to quickly demonstrate that the endogenous oxalate transporter was unable to exchange chloride for bicarbonate, unlike SLC26A3

Comparative conformational flexibility within the cap domain of two LinB variants.

<p>Sausage diagram for LinB_B90A (A) and LinB_G2.2 (B) in which the thickness of the chain as well as the colour denotes the average RMSD of each residue. The active site catalytic residues are rendered in ball and stick. The RMSD of each residue as a function of time is plotted for LinB_B90A (C) and LinB_G2.2 (D).</p

Molecular dynamics simulations of LinB with β-HCH bound in the active site.

<p>The distance between the nucleophilic oxygen of Asp108 and the center of mass of β-HCH is shown as a function of time (LinB_B90A in blue and LinB_G2.2 in red) in panel A. Panel B shows the RMSD from the near-attack conformation for β-HCH as a function of time (LinB_B90A in blue and LinB_G2.2 in red) in panel B.</p