What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression.diffusion ͉ genetics ͉ genomics ͉ protein-DNA interactions ͉ spatial effects T he colocalization of prokaryotic transcription factor (TF) genes and their binding sites is known from the pioneering work of Jacob and Monod (1) on the lactose operon and has been shown to be widespread (2-4) and essential for the formation of regulatory motifs (5). Some have hypothesized that TF-binding site colocalization is advantageous, in part, because it could expedite a TF's search for its site (2, 5-7) (the rapid search hypothesis). In prokaryotes, this speed-up by colocalization is possible because transcription and translation are coupled spatially and temporally. Therefore, TFs are synthesized near their genes and can rapidly bind colocalized sites (Fig. 1A). The arrival time of a TF to its site ultimately controls the timing of gene regulation, whereas fluctuations in the arrival time can lead to bursts of gene activity and noise in gene regulation. The rapid search hypothesis suggests that colocalization is favorable because expediting TF arrival makes regulation faster and more reliable.Both experimentally (see ref.8 for an overview) and theoretically (9-13), many have studied the broader question: how can a TF find its cognate site on DNA among Ϸ10 7 decoy sites in a fraction of a minute while moving in the crowded environment of the cell and hampered by other DNA-bound proteins? The general model of the process includes 3D spatial diffusion of the TF through the cell volume and 1D sliding of a TF along DNA. According to this m...

We present a computational tool, eReaxFF, for simulating explicit electrons within the framework of the standard ReaxFF reactive force field method. We treat electrons explicitly in a pseudoclassical manner that enables simulation several orders of magnitude faster than quantum chemistry (QC) methods, while retaining the ReaxFF transferability. We delineate here the fundamental concepts of the eReaxFF method and the integration of the Atom-condensed Kohn-Sham DFT approximated to second order (ACKS2) charge calculation scheme into the eReaxFF. We trained our force field to capture electron affinities (EA) of various species. As a proof-of-principle, we performed a set of molecular dynamics (MD) simulations with an explicit electron model for representative hydrocarbon radicals. We establish a good qualitative agreement of EAs of various species with experimental data, and MD simulations with eReaxFF agree well with the corresponding Ehrenfest dynamics simulations. The standard ReaxFF parameters available in the literature are transferrable to the eReaxFF method. The computationally economic eReaxFF method will be a useful tool for studying large-scale chemical and physical systems with explicit electrons as an alternative to computationally demanding QC methods.

KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regularly updated list of known knots in protein structures.

The public EST (expressed sequence tag) databases represent an enormous but heterogeneous repository of sequences, including many from a broad selection of plant species and a wide range of distinct varieties. The significant redundancy within large EST collections makes them an attractive resource for rapid pre-selection of candidate sequence polymorphisms. Here we present a strategy that allows rapid identification of candidate SNPs in barley (Hordeum vulgare L.) using publicly available EST databases. Analysis of 271,630 EST sequences from different cDNA libraries, representing 23 different barley varieties, resulted in the generation of 56,302 tentative consensus sequences. In all, 8171 of these unigene sequences are members of clusters with six or more ESTs. By applying a novel SNP detection algorithm (SNiPpER) to these sequences, we identified 3069 candidate inter-varietal SNPs. In order to verify these candidate SNPs, we selected a small subset of 63 present in 36 ESTs. Of the 63 SNPs selected, we were able to validate 54 (86%) using a direct sequencing approach. For further verification, 28 ESTs were mapped to distinct loci within the barley genome. The polymorphism information content (PIC) and nucleotide diversity (pi) values of the SNPs identified by the SNiPpER algorithm are significantly higher than those that were obtained by random sequencing. This demonstrates the efficiency of our strategy for SNP identification and the cost-efficient development of EST-based SNP-markers.

The progress in genome sequencing has led to a rapid accumulation in GenBank submissions of uncharacterized`hypothetical' genes. These genes, which have not been experimentally characterized and whose functions cannot be deduced from simple sequence comparisons alone, now comprise a signi®cant fraction of the public databases. Expression analyses of Haemophilus in¯uenzae cells using a combination of transcriptomic and proteomic approaches resulted in con®dent identi®ca-tion of 54`hypothetical' genes that were expressed in cells under normal growth conditions. In an attempt to understand the functions of these proteins, we used a variety of publicly available analysis tools. Close homologs in other species were detected for each of the 54`hypothetical' genes. For 16 of them, exact functional assignments could be found in one or more public databases. Additionally, we were able to suggest general functional characterization for 27 more genes (comprising~80% total). Findings from this analysis include the identi®cation of a pyruvate-formate lyase-like operon, likely to be expressed not only in H.in¯uenzae but also in several other bacteria. Further, we also observed three genes that are likely to participate in the transport and/or metabolism of sialic acid, an important component of the H.in¯uenzae lipo-oligosaccharide. Accurate functional annotation of uncharacterized genes calls for an integrative approach, combining expression studies with extensive computational analysis and curation, followed by eventual experimental veri®cation of the computational predictions.

Light-driven chemical reactions on semiconductor surfaces have potential for addressing energy and pollution needs through efficient chemical synthesis; however, little is known about the time evolution of excited states that determine reaction pathways. Here, we study the photo-oxidation of methoxy (CH3O) derived from methanol on the rutile TiO2(110) surface using ab initio simulations to create a molecular movie of the process. The movie sequence reveals a wealth of information on the reaction intermediates, time scales, and energetics. The reaction is broken in three stages, described by Lewis structures directly derived from the "hole" wave functions that lead to the concept of "photoinduced C-H acidity". The insights gained from this work can be generalized to a set of simple rules that can predict the efficiency of photo-oxidation reactions in reactant-catalyst pairs.

We present a method for real-time propagation of electronic wave functions, within time-dependent density functional theory (RT-TDDFT), coupled to ionic motion through mean-field classical dynamics. The goal of our method is to treat large systems and complex processes, in particular photocatalytic reactions and electron transfer events on surfaces and thin films. Due to the complexity of these processes, computational approaches are needed to provide insight into the underlying physical mechanisms and are therefore crucial for the rational design of new materials. Because of the short time step required for electron propagation (of order ∼10 attoseconds), these simulations are computationally very demanding. Our methodology is based on numerical atomic-orbital-basis sets for computational efficiency. In the computational package, to which we refer as TDAP-2.0 (Time-evolving Deterministic Atom Propagator), we have implemented a number of important features and analysis tools for more accurate and efficient treatment of large, complex systems and time scales that reach into a fraction of a picosecond. We showcase the capabilities of our method using four different examples: (i) photodissociation into radicals of opposite spin, (ii) hydrogen adsorption on aluminum surfaces, (iii) optical absorption of spin-polarized organic molecule containing a metal ion, and (iv) electron transfer in a prototypical dye-sensitized solar cell.

Hydrogen production in photoelectrochemical cells constitutes an important avenue toward carbon-free fuel. The most convenient process for hydrogen production is the splitting of water molecules, which necessitates a catalytic reaction involving a semiconductor. Here, we introduce a framework for the study of photocatalyzed reactions on semiconductor surfaces based on time-dependent density functional theory that explicitly accounts for the evolution of electronically excited states. Within this framework, we investigate the possibility of hole-mediated splitting of molecularly adsorbed water on a representative metal oxide surfacethe rutile TiO 2 (110). We find that oxidative dehydrogenation of water is possible in synergy with thermal effects at temperatures between 60 and 100 K only when defects like Ti interstitials are present in the subsurface region. This study presents a general computational strategy for describing photoexcited semiconductor/adsorbate interfaces and also demonstrates that the occurrence of water dissociation on the rutile TiO 2 (110) surface depends sensitively on the local atomic environment and external parameters such as temperature.