Helicases and translocases are a ubiquitous, highly diverse group of proteins that perform an extraordinary variety of functions in cells. Consequently, this review sets out to define a nomenclature for these enzymes based on current knowledge of sequence, structure, and mechanism. Using previous definitions of helicase families as a basis, we delineate six superfamilies of enzymes, with examples of crystal structures where available, and discuss these structures in the context of biochemical data to outline our present understanding of helicase and translocase activity. As a result, each superfamily is subdivided, where appropriate, on the basis of mechanistic understanding, which we hope will provide a framework for classification of new superfamily members as they are discovered and characterized.

Structure and mechanism of helicases and nucleic acid translocases.

This article offers a comprehensive survey of results obtained for solitons and complex nonlinear wave patterns supported by nonlinear lattices (NLs), which represent a spatially periodic modulation of the local strength and sign of the nonlinearity, and their combinations with linear lattices. A majority of the results obtained, thus far, in this field and reviewed in this article are theoretical. Nevertheless, relevant experimental settings are also surveyed, with emphasis on perspectives for implementation of the theoretical predictions in the experiment. Physical systems discussed in the review belong to the realms of nonlinear optics (including artificial optical media, such as photonic crystals, and plasmonics) and Bose-Einstein condensation. The solitons are considered in one, two, and three dimensions. Basic properties of the solitons presented in the review are their existence, stability, and mobility. Although the field is still far from completion, general conclusions can be drawn. In particular, a novel fundamental property of one-dimensional solitons, which does not occur in the absence of NLs, is a finite threshold value of the soliton norm, necessary for their existence. In multidimensional settings, the stability of solitons supported by the spatial modulation of the nonlinearity is a truly challenging problem, for theoretical and experimental studies alike. In both the one-dimensional and two-dimensional cases, the mechanism that creates solitons in NLs in principle is different from its counterpart in linear lattices, as the solitons are created directly, rather than bifurcating from Bloch modes of linear lattices.

Solitons in nonlinear lattices

Helicases and nucleic acid translocases are motor proteins that have essential roles in nearly all aspects of nucleic acid metabolism, ranging from DNA replication to chromatin remodelling. Fuelled by the binding and hydrolysis of nucleoside triphosphates, helicases move along nucleic acid filaments and separate double-stranded DNA into their complementary single strands. Recent evidence indicates that the ability to simply translocate along single-stranded DNA is, in many cases, insufficient for helicase activity. For some of these enzymes, self assembly and/or interactions with accessory proteins seem to regulate their translocase and helicase activities.

Non-hexameric DNA helicases and translocases: mechanisms and regulation

Fundamental and vortex solitons in a two-dimensional optically induced waveguide array are reported. In the strong localization regime the fundamental soliton is largely confined to one lattice site, whereas the vortex state comprises four fundamental modes superimposed in a square configuration with a phase structure that is topologically equivalent to the conventional vortex. However, in the weak localization regime, both the fundamental and the vortex solitons spread over many lattice sites. We further show that fundamental and the vortex solitons are stable against small perturbations in the strong localization regime.

/pdf/fundamental-and-vortex-solitons-in-a-two-dimensional-optical-1yimlw2fl3.pdf

Fundamental and vortex solitons in a two-dimensional optical lattice.

The RecQ helicases are conserved from bacteria to humans and play a critical role in genome stability. In humans, loss of RecQ gene function is associated with cancer predisposition and/or premature aging. Recent experiments have shown that the RecQ helicases function during distinct steps during DNA repair; DNA end resection, displacement-loop (D-loop) processing, branch migration, and resolution of double Holliday junctions (dHJs). RecQ function in these different processing steps has important implications for its role in repair of double-strand breaks (DSBs) that occur during DNA replication and meiosis, as well as at specific genomic loci such as telomeres.

/pdf/the-recq-dna-helicases-in-dna-repair-5ch79bram2.pdf

The RecQ DNA Helicases in DNA Repair

Escherichia coli RecQ Is a Rapid, Efficient, and Monomeric Helicase

Escherichia coli RecQ is a rapid, efficient, and monomeric helicase. VOLUME 281 (2006) PAGES 12655-12663

We demonstrate the existence of the gap solitons and soliton trains in finite-sized two-dimensional periodic nonlinear photonic crystals by using the mutiple-scattering approach with an iterative scheme. In 12-fold symmetric nonlinear quasicrystals, we also demonstrated the existence of symmetric, regular gap solitons, asymmetric single-soliton states, and two-solitons states. We revealed that the existence of symmetric, regular gap solitons in a 12-fold quasicrystal is limited by the geometrical size of the hexagon that forms the core of the dodecahedral cell, which is the building block of the quasicrystal.

/pdf/gap-solitons-and-soliton-trains-in-finite-sized-two-kpg3x9np26.pdf

Gap solitons and soliton trains in finite-sized two-dimensional periodic and quasiperiodic photonic crystals.

The possibility of eliminating spatiotemporal chaos and spiral waves by weak spatial perturbations in a spatially extended dynamical system is demonstrated numerically through the example of a wide-aperture laser. The time-independent weak spatial perturbation can effectively migrate the system from the state of spatiotemporal chaos or spiral waves to that of traveling waves. The threshold and the controllable range of the control parameters are given. By varying the amplitude or the spatial wave vector of the perturbation, drastic changes in the spatiotemporal dynamics are found.

Ping Xie

Papers

Escherichia coli RecQ Is a Rapid, Efficient, and Monomeric Helicase

Escherichia coli RecQ is a rapid, efficient, and monomeric helicase. VOLUME 281 (2006) PAGES 12655-12663

Gap solitons and soliton trains in finite-sized two-dimensional periodic and quasiperiodic photonic crystals.

Eliminating spatiotemporal chaos and spiral waves by weak spatial perturbations

A model of processive movement of dimeric kinesin