Applying M-sequences Decimation to Generate Interleaved Sequence

Abstract—M-sequences are widely used in for many purposes, from synchronization, whitening, communications and cryptography. We analyze decimation techniques and introduce two methods to generate decimation sequences which don’t have to calculate intermediate states. Then we apply these methods to interleaved sequence as a new method to pre-calculate for set of interleaved order which is more effective in implementation. Tóm tắt—M-dãy đang được sử dụng rất rộng rãi trong nhiều lĩnh vực, từ việc đồng bộ, làm trắng thông tin, viễn thông và kỹ thuật mật mã. Chúng tôi phân tích kỹ thuật phân rã m-dãy theo bước và giới thiệu hai phương pháp sinh dãy phân rã theo bước mà không cần tính các trạng thái trung gian. Áp dụng phương pháp này vào dãy lồng ghép, ta có một phương pháp mới để tính trước tập các thứ tự lồng ghép có tính hiệu quả trong cài đặt thực tế.

Continuous B- to A- Transition in Protein-DNA Binding - How Well Is It Described by Current AMBER Force Fields?

When DNA interacts with a protein, its structure often undergoes significant conformational adaptation. Perhaps the most common is the transition from canonical B-DNA towards the A-DNA form, which is not a two-state, but rather a continuous transition. The A- and B- forms differ mainly in sugar pucker P (north/south) and glycosidic torsion χ (high-anti/anti). The combination of A-like P and B-like χ (and vice versa) represents the nature of the intermediate states lying between the pure A- and B- forms. In this work, we study how the A/B equilibrium and in particular the A/B intermediate states, which are known to be over-represented at protein-DNA interfaces, are modeled by current AMBER force fields. Eight protein-DNA complexes and their naked (unbound) DNAs were simulated with OL15 and bsc1 force fields as well as an experimental combination OL15χOL3. We found that while the geometries of the A-like intermediate states in the molecular dynamics (MD) simulations agree well with the native X-ray geometries found in the protein-DNA complexes, their populations (stabilities) are significantly underestimated. Different force fields predict different propensities for A-like states growing in the order OL15 < bsc1 < OL15χOL3, but the overall populations of the A-like form are too low in all of them. Interestingly, the force fields seem to predict the correct sequence-dependent A-form propensity, as they predict larger populations of the A-like form in naked (unbound) DNA in those steps that acquire A-like conformations in protein-DNA complexes. The instability of A-like geometries in current force fields may significantly alter the geometry of the simulated protein-DNA complex, destabilize the binding motif, and reduce the binding energy, suggesting that refinement is needed to improve description of protein-DNA interactions in AMBER force fields.

Xtrapol8: automatic elucidation of low-occupancy intermediate-states in crystallographic studies

Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, hindering structure determination by conventional methods. To automatically extract such structures, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate state; (iii) calculates various types of extrapolated structure factors, and (iv) refines the corresponding structures.

Release of the ribosome biogenesis factor Bud23 from small subunit precursors in yeast

Ribosomes are the universally conserved ribonucleoprotein complexes that synthesize proteins. The two subunits of the eukaryotic ribosome are produced through a quasi-independent assembly-line-like pathway involving the hierarchical actions of numerous trans-acting biogenesis factors and the incorporation of ribosomal proteins. The factors work together to shape the nascent subunits through a series of intermediate states into their functional architectures. The earliest intermediate of the small subunit (SSU or 40S) is the SSU Processome which is subsequently transformed into the pre-40S intermediate. This transformation is, in part, facilitated by the binding of the methyltransferase Bud23. How Bud23 is released from the resultant pre-40S is not known. The ribosomal proteins Rps0, Rps2, and Rps21, termed the Rps0-cluster proteins, and several biogenesis factors are known to bind the pre-40S around the time that Bud23 is released, suggesting that one or more of these factors induce Bud23 release. Here, we systematically examined the requirement of these factors for the release of Bud23 from pre-40S particles. We found that the Rps0-cluster proteins are needed but not sufficient for Bud23 release. The atypical kinase/ATPase Rio2 shares a binding site with Bud23 and is thought to be recruited to pre-40S after the Rps0-cluster proteins. Depletion of Rio2 prevented the release of Bud23 from the pre-40S. More importantly, the addition of recombinant Rio2 to pre-40S particles affinity-purified from Rio2-depleted cells was sufficient for Bud23 release in vitro. The ability of Rio2 to displace Bud23 was independent of nucleotide hydrolysis. We propose a novel role for Rio2 in which its binding to the pre-40S actively displaces Bud23 from the pre-40S, and we suggest a model in which the binding of the Rps0-cluster proteins and Rio2 promote the release of Bud23.

Cutting rules on a cylinder: a simplified diagrammatic approach to quantum kinetic theory

Nonequilibrium quantum field theory is often used to derive an approximation for the evolution of number densities and asymmetries in astroparticle models when a more precise treatment of quantum thermal effects is required. This work presents an alternative framework using the zero-temperature quantum field theory, S-matrix unitarity, and classical Boltzmann equation as starting points leading to a set of rules for calculations of thermal corrections to reaction rates. Statistical factors due to on-shell intermediate states are obtained from the cuts of forward diagrams with multiple spectator lines. It turns out that it is equivalent to cutting closed diagrams on a cylindrical surface.

Protein unfolding in freeze frames: intermediate states are revealed by variable temperature ion mobility-mass spectrometry.

The gas phase is an idealized laboratory for the study of protein structure, from which it is possible to examine stable and transient forms of mass selected ions in the absence of bulk solvent. With ion mobility-mass spectrometry (IM-MS) apparatus built to operate at both cryogenic and elevated temperatures, we have examined the conformational transitions of the monomeric proteins: ubiquitin, lysozyme and alpha-synuclein as a function of temperature and in source activation. We rationalize the experimental observations with a temperature dependent framework model and comparison to known conformers. Data from ubiquitin shows unfolding transitions that proceed through diverse and highly elongated intermediate states, which converge to more compact structures. These findings contrast with data obtained from lysozyme – a protein where (un)-folding plasticity is restricted by four disulfide linkages, although this is alleviated in its reduced form. For structured proteins, collision activation of the protein ions in- source, enables subsequent “freezing” or thermal annealing of unfolding intermediates whereas disordered proteins restructure substantially at 250 K even without activation, indicating that cold denaturation can occur without solvent. These data are presented in the context of a toy model framework which describes the relative occupancy of the available conformational space.

Vascular KATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides

Vascular tone is dependent on smooth muscle KATP channels comprising pore-forming Kir6.1 and regulatory SUR2B subunits, in which mutations cause Cantú syndrome. Unique among KATP isoforms, they lack spontaneous activity and require Mg-nucleotides for activation. Structural mechanisms underlying these properties are unknown. Here, we determined cryogenic electron microscopy structures of vascular KATP channels bound to inhibitory ATP and glibenclamide, which differ informatively from similarly determined pancreatic KATP channel isoform (Kir6.2/SUR1). Unlike SUR1, SUR2B subunits adopt distinct rotational “propeller” and “quatrefoil” geometries surrounding their Kir6.1 core. The glutamate/aspartate-rich linker connecting the two halves of the SUR-ABC core is observed in a quatrefoil-like conformation. Molecular dynamics simulations reveal MgADP-dependent dynamic tripartite interactions between this linker, SUR2B, and Kir6.1. The structures captured implicate a progression of intermediate states between MgADP-free inactivated, and MgADP-bound activated conformations wherein the glutamate/aspartate-rich linker participates as mobile autoinhibitory domain, suggesting a conformational pathway toward KATP channel activation.