Robert G. Endres

Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation

The chemotaxis system in the bacterium Escherichia coli is remarkably sensitive to small relative changes in the concentrations of multiple chemical signals over a broad range of ambient concentrations. Interactions among receptors are crucial to this sensitivity as is precise adaptation, the return of chemoreceptor activity to prestimulus levels in a constant chemoeffector environment. Precise adaptation relies on methylation and demethylation of chemoreceptors by the enzymes CheR and CheB, respectively. Experiments indicate that when transiently bound to one receptor, these enzymes act on small assistance neighborhoods (AN) of five to seven receptor homodimers. In this paper, we model a strongly coupled complex of receptors including dynamic CheR and CheB acting on ANs. The model yields sensitive response and precise adaptation over several orders of magnitude of attractant concentrations and accounts for different responses to aspartate and serine. Within the model, we explore how the precision of adaptation is limited by small AN size as well as by CheR and CheB kinetics (including dwell times, saturation, and kinetic differences among modification sites) and how these kinetics contribute to noise in complex activity. The robustness of our dynamic model for precise adaptation is demonstrated by randomly varying biochemical parameters.

Variable sizes of Escherichia coli chemoreceptor signaling teams

Like many sensory receptors, bacterial chemotaxis receptors form clusters. In bacteria, large‐scale clusters are subdivided into signaling teams that act as ‘antennas’ allowing detection of ligands with remarkable sensitivity. The range of sensitivity is greatly extended by adaptation of receptors to changes in concentrations through covalent modification. However, surprisingly little is known about the sizes of receptor signaling teams. Here, we combine measurements of the signaling response, obtained from in vivo fluorescence resonance energy transfer, with the statistical method of principal component analysis, to quantify the size of signaling teams within the framework of the previously successful Monod–Wyman–Changeux model. We find that size of signaling teams increases 2‐ to 3‐fold with receptor modification, indicating an additional, previously unrecognized level of adaptation of the chemotaxis network. This variation of signaling‐team size shows that receptor cooperativity is dynamic and likely optimized for sensing noisy ligand concentrations.

Toward an atomistic model for predicting transcription-factor binding sites.

Identifying the specific DNA‐binding sites of transcription‐factor proteins is essential to understanding the regulation of gene expression in the cell. Bioinformatics approaches are fast compared to experiments, but require prior knowledge of multiple binding sites for each protein. Here, we present an atomistic force‐field method to predict binding sites based only on the X‐ray structure of a related bound complex. Specific flexible contacts between the protein and DNA are modeled by a library of amino acid side‐chain rotamers. Using the example of the mouse transcription factor, Zif268, a well‐studied zinc‐finger protein, we show that the protein sequence alone, without the detailed experimental structure, gives a strong bias toward the consensus binding site. Proteins 2004.

Conductance of single thiolated poly(GC)-poly(GC) DNA molecules

We use ultrahigh vacuum scanning tunneling microscopy∕spectroscopy (UHV-STM∕STS) to investigate the electronic properties of single thiolated 12-base-pair poly(GC)-poly(GC) DNA molecules on a Au(111) surface at room temperature. Reproducible current-voltage curves of the DNA are obtained at variable sample-tip separations. The normalized conductance, which can be interpreted as the density of states, shows a well-defined wide band gap. UHV-STM∕STS opens up a novel technique to probe the electronic properties of biomolecules on surfaces at the atomic level.

Chemotaxis Receptor Complexes: From Signaling to Assembly

Complexes of chemoreceptors in the bacterial cytoplasmic membrane allow for the sensing of ligands with remarkable sensitivity. Despite the excellent characterization of the chemotaxis signaling network, very little is known about what controls receptor complex size. Here we use in vitro signaling data to model the distribution of complex sizes. In particular, we model Tar receptors in membranes as an ensemble of different sized oligomer complexes, i.e., receptor dimers, dimers of dimers, and trimers of dimers, where the relative free energies, including receptor modification, ligand binding, and interaction with the kinase CheA determine the size distribution. Our model compares favorably with a variety of signaling data, including dose-response curves of receptor activity and the dependence of activity on receptor density in the membrane. We propose that the kinetics of complex assembly can be measured in vitro from the temporal response to a perturbation of the complex free energies, e.g., by addition of ligand.

Transverse Electronic Signature of DNA for Electronic Sequencing

In recent years, the proliferation of large-scale DNA sequencing projects for applications in clinical medicine and health care has driven the search for new methods that could reduce the time and cost. The commonly used Sanger sequencing method relies on the chemistry to read the bases in DNA and is far too slow and expensive for reading personal genetic codes. There were earlier attempts to sequence DNA by directly visualizing the nucleotide composition of the DNA molecules by scanning tunneling microscopy (STM). However, sequencing DNA based on directly imaging DNA’s atomic structure has not yet been successful. In Chap. 9, Xu, Endres, and Arakawa report a potential physical alternative by detecting unique transverse electronic signatures of DNA bases using ultrahigh vacuum STM. Supported by the principles, calculations and statistical analyses, these authors argue that it would be possible to directly sequence DNA by the STM-based technology without any modification of the DNA.

Electronic structure theory of DNA: from semi-empirical theory of the π-stack to ab initio calculations of the optical conductivity

Abstract In addition to DNAs fundamental role in genetics, its self-assembly property based on Watson-Crick base pairing has turned the DNA molecule into a potential component for nanoscale circuits. While the one-dimensional DNA π -stack has long been speculated to support electrical current, a final answer, despite recent multi-disciplinary efforts, has proved difficult. Biological DNA is nothing without its environment; the DNA environment system is a soft poly-electrolyte solution whose structural details and electronic properties depend on humidity, sequence and type of counter-ions. In this chapter we summarize our theoretical approaches [ 1, 2 ]. We employ a hybrid of semi-empirical Huckel and Slater-Koster theories for describing the electronic π -orbitals with parameters obtained from fitting to ab initio density functional theory (DFT) eigenvalues based on the SIESTA package. We use this model to study the dependence of the base-pair couplings on structural parameters and temperature. We then turn to DFT-based calculations of the optical conductivity of realistic solvated DNA segments obtained from molecular dynamics simulations and show that they give a reasonable description of contactless optical measurements of DNA molecules at low and high frequencies.