Stuart Licht

Thiyl Radicals in Ribonucleotide Reductases

The ribonucleoside triphosphate reductase (RTPR) from Lactobacillus leichmannii catalyzes adenosylcobalamin (AdoCbl)-dependent nucleotide reduction, as well as exchange of the 5′ hydrogens of AdoCbl with solvent. A protein-based thiyl radical is proposed as an intermediate in both of these processes. In the presence of RTPR containing specifically deuterated cysteine residues, the electron paramagnetic resonance (EPR) spectrum of an intermediate in the exchange reaction and the reduction reaction, trapped by rapid freeze quench techniques, exhibits narrowed hyperfine features relative to the corresponding unlabeled RTPR. The spectrum was interpreted to represent a thiyl radical coupled to cob(II)alamin. Another proposed intermediate, 5′-deoxyadenosine, was detected by rapid acid quench techniques. Similarities in mechanism between RTPR and the Escherichia coli ribonucleotide reductase suggest that both enzymes require a thiyl radical for catalysis.

ClpP Hydrolyzes a Protein Substrate Processively in the Absence of the ClpA ATPase: Mechanistic Studies of ATP-Independent Proteolysis†

ATP-dependent proteases are processive, meaning that they degrade full-length proteins into small peptide products without releasing large intermediates along the reaction pathway. In the case of the bacterial ATP-dependent protease ClpAP, ATP hydrolysis by the ClpA component has been proposed to be required for processive proteolysis of full-length protein substrates. We present here data showing that in the absence of the ATPase subunit ClpA, the protease subunit ClpP can degrade full-length protein substrates processively, albeit at a greatly reduced rate. Moreover, the size distribution of peptide products from a ClpP-catalyzed digest is remarkably similar to the size distribution of products from a ClpAP-catalyzed digest. The ClpAP- and ClpP-generated peptide product size distributions are fitted well by a sum of multiple underlying Gaussian peaks with means at integral multiples of approximately 900 Da (7-8 amino acids). Our results are consistent with a mechanism in which ClpP controls product sizes by alternating between translocation in steps of 7-8 (+/-2-3) amino acid residues and proteolysis. On the structural and molecular level, the step size may be controlled by the spacing between the ClpP active sites, and processivity may be achieved by coupling peptide bond hydrolysis to the binding and release of substrate and products in the protease chamber.

Time and Spatial Dependence of the Concentration of Less Than 105 Microelectrode-Generated Molecules

The time and spatial dependence of the concentration of as few as 40,000 electrogenerated, redox-active molecules has been determined. The distance between generator and detector microelectrodes in an array used in the study could be varied from 0.8 to 28 micrometers. Measurements of a sufficiently small ensemble of molecules allowed the experimental results to be compared with a quantitative simulation of the random movement of each member of the ensemble. The transit time of an electrogenerated species from the generator to a collector microelectrode was measured as a function of viscosity, diffusivity, and distance.

Synchrotron Protein Footprinting Supports Substrate Translocation by ClpA via ATP-Induced Movements of the D2 Loop

Synchrotron X-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer. Comparative solvent accessibilities between ClpA monomer and ClpA hexamer samples are in agreement throughout most of the sequence, with calculations based on two previously proposed hexameric models. The data differ substantially from the proposed models in two parts of the structure: the D1 sensor 1 domain and the D2 loop region. The results suggest that these two regions can access alternate conformations in which their solvent protection is greater than that in the structural models based on crystallographic data. In combination with previously reported structural data, the footprinting data provide support for a revised model in which the D2 loop contacts the D1 sensor 1 domain in the ATP-bound form of the complex. These data provide the first direct experimental support for the nucleotide-dependent D2 loop conformational change previously proposed to mediate substrate translocation.

Resolving Individual Steps in the Operation of ATP-Dependent Proteolytic Molecular Machines : From Conformational Changes to Substrate Translocation and Processivity

Clp, Lon, and FtsH proteases are proteolytic molecular machines that use the free energy of ATP hydrolysis to unfold protein substrates and processively present them to protease active sites. Here we review recent biochemical and structural studies relevant to the mechanism of ATP-dependent processive proteolysis. Despite the significant structural differences among the Clp, Lon, and FtsH proteases, these enzymes share important mechanistic features. In these systems, mechanistic studies have provided evidence for ATP binding and hydrolysis-driven conformational changes that drive translocation of substrates, which has significant implications for the processive mechanism of proteolysis. These studies indicate that the nucleotide (ATP, ADP, or nonhydrolyzable ATP analogues) occupancy of the ATPase binding sites can influence the binding mode and/or binding affinity for protein substrates. A general mechanism is proposed in which the communication between ATPase active sites and protein substrate binding regions coordinates a processive cycle of substrate binding, translocation, proteolysis, and product release.

An Information-Based Computational Technique for Estimation of Chromatographic Peak Purity

Assessment of the purity of chromatographic peaks is an important step in developing and validating purification procedures for complex mixtures. While curve-fitting techniques can be useful for determining the retention times and relative concentrations of the components of a chromatographic peak, their utility is limited by the lack of unambiguous criteria for determining the number of such components. In this work, we present a computational technique for analyzing chromatograms to estimate the number of components, their retention times, and their relative concentrations. In contrast to Fourier-transform-based techniques, the technique we present does not require manual peak identification. It is based on curve-fitting and uses the Akaike information criterion to estimate the number of components. Application of the technique to chromatograms obtained from size-exclusion and reverse-phase chromatography of test mixtures indicates that it is useful for the characterization of complex mixtures.

Polymer-Based Open-Channel Blockers for the Acetylcholine Receptor: The Effect of Spacer Length on Blockade Kinetics†

Blocking open ion channels provides a promising way to modulate synaptic transmission. Using the muscle-type acetylcholine receptor (AChR) as a test system, we seek to develop blockers that have blockade kinetics tunable via structural modifications. Here we investigate whether the blockade kinetics can be modulated by specifying the length of a poly(ethylene glycol) (PEG) spacer incorporated into the blocker. Single-channel electrophysiological experiments show that simple bis(trimethylammonium) compounds ( 1a- 3) both activate the AChR and block the open channel. The blockade kinetics are found to depend on spacer length: both the association and dissociation rate constants decrease with increasing spacer length. The decrease in the association rate constant can be quantitatively explained by the entropic cost of polymer confinement in the transmembrane lumen, while the decrease in the dissociation rate constant is consistent with weak, additive noncovalent interactions between the channel and the spacer. These results provide useful insights into the future design of kinetically tunable open-channel blockers for the AChR.

Poly(Ethylene Glycol) as a Scaffold for High-Affinity Open-Channel Blockers of the Mouse Nicotinic Acetylcholine Receptor

High-affinity blockers for an ion channel often have complex molecular structures that are synthetically challenging and/or laborious. Here we show that high-affinity blockers for the mouse nicotinic acetylcholine receptor (AChR) can be prepared from a structurally simple material, poly(ethylene glycol) (PEG). The PEG-based blockers (PQ1–5), comprised of a flexible octa(ethylene glycol) scaffold and two terminal quaternary ammonium groups, exert low- to sub-micromolar affinities for the open AChR pore (measured via single-channel analysis of AChRs expressed in human embryonic kidney cells). PQ1–5 are comparable in pore-binding affinity to the strongest AChR open-channel blockers previously reported, which have complex molecular structures. These results suggest a general approach for designing potent open-channel blockers from a structurally flexible polymer. This design strategy involves simple synthetic procedures and does not require detailed information about the structure of an ion-channel pore.

ATP-Sensitive Potassium Channels Exhibit Variance in the Number of Open Channels below the Limit Predicted for Identical and Independent Gating

In small cells containing small numbers of ion channels, noise due to stochastic channel opening and closing can introduce a substantial level of variability into the cells membrane potential. Negatively cooperative interactions that couple a channels gating conformational change to the conformation of its neighbor(s) provide a potential mechanism for mitigating this variability, but such interactions have not previously been directly observed. Here we show that heterologously expressed ATP-sensitive potassium channels generate noise (i.e., variance in the number of open channels) below the level possible for identical and independent channels. Kinetic analysis with single-molecule resolution supports the interpretation that interchannel negative cooperativity (specifically, the presence of an open channel making a closed channel less likely to open) contributes to the decrease in noise. Functional coupling between channels may be important in modulating stochastic fluctuations in cellular signaling pathways.