Development of an ATP force field for coarse-grained simulation of ATPases and its application to the maltose transporter

The biological functions of ATPases, such as myosin, kinesin, and ABC transporter, are due to large conformational motions driven by energy obtained from ATP. Elucidation of the mechanisms underlying these ATP-driven movements is one of the greatest challenges in computational chemistry. It has been shown that the MARTINI coarse-grained method is a promising tool for the investigation of large conformational motions in various proteins. However, this method has not yet been applied to ATPases because of the lack of a force field for the ATP molecule. Here, we developed force field parameters for the ATP molecule and conducted simulations using these parameters for the subunits (MalK₂) and the full-length structure (MalFGK₂-E) of a maltose transporter. It was found for both targets that the dimerization of the nucleotide binding domains (NBDs) is induced upon ATP binding. Moreover, for the full-length transporter, the conformational transition from the pre-translocation state to the outward-facing state was observed and was accompanied by an initial transport motion of the substrate. It is expected that coarse-grained simulations utilizing the parameters for the ATP molecule developed here will serve as a powerful tool for investigating other ATPases as well. © 2019 Wiley Periodicals, Inc.     

Conformational dynamics of ATP∕Mg:ATP in motor proteins via data mining and molecular simulation

The conformational diversity of ATP∕Mg:ATP in motor proteins was investigated using molecular dynamics and data mining. Adenosine triphosphate (ATP) conformations were found to be constrained mostly by inter cavity motifs in the motor proteins. It is demonstrated that ATP favors extended conformations in the tight pockets of motor proteins such as F(1)-ATPase and actin whereas compact structures are favored in motor proteins such as RNA polymerase and DNA helicase. The incorporation of Mg(2+) leads to increased flexibility of ATP molecules. The differences in the conformational dynamics of ATP∕Mg:ATP in various motor proteins was quantified by the radius of gyration. The relationship between the simulation results and those obtained by data mining of motor proteins available in the protein data bank is analyzed. The data mining analysis of motor proteins supports the conformational diversity of the phosphate group of ATP obtained computationally.     

Biochemical characterization of three putative ATPases from a new type IV secretion system of <Emphasis Type="Italic">Aeromonas veronii</Emphasis> plasmid pAC3249A

Background  

Type four secretion systems (TFSS) are bacterial macromolecular transport systems responsible for transfer of various substrates such as proteins, DNA or protein-DNA complexes. TFSSs encode two or three ATPases generating energy for the secretion process. These enzymes exhibit highest sequence conservation among type four secretion components.     

Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists

Adenosine triphosphate (ATP) is the energy source for various biochemical processes and biomolecular motors in living things. Development of ATP antagonists and their stimuli-controlled actions offer a novel approach to regulate biological processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins. The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated the axonemal dynein motor activity for the force generation in a demembranated model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of ATP antagonists significantly differ in their affinity to the ATP binding site.     

Mechanisms,Methods of Tracking and Applications of DNA Walkers: A Review

In recent years, DNA nanotechnology expanded its scope from structural DNA nanoarchitecture towards designing dynamic and functional nanodevices. This progress has been evident in the development of an advanced class of DNA nanomachines, the so-called DNA walkers. They represent an evolution of basic switching between distinctly defined states into continuous motion. Inspired by the naturally occurring walkers such as kinesin, research on DNA walkers has focused on developing new ways of powering them and investigating their walking mechanisms and advantages. New techniques allowing the visualization of walkers as single molecules and in real time have provided a deeper insight into their behavior and performance. The construction of novel DNA walkers bears great potential for applications in therapeutics, nanorobotics or computation. This review will cover the various examples and breakthrough designs of recently reported DNA walkers that pushed the limits of their performance. It will also mention the techniques that have been used to investigate walker nanosystems, as well as discuss the applications that have been explored so far.     

Bacterial flagellar motor and H(+)/ATP synthase: two proton-driven rotary molecular devices with different functions.

Both the bacterial flagellar motor and the H(+)/ATP synthase are membrane-bound macromolecular complexes in which the movement of protons through channels across the membrane is coupled to the rotation of a part of the complex around an axis perpendicular to the membrane. Despite this similarity, the two devices are designed for quite different functions. The flagellar motor is responsible for a practically smooth rotation of the flagellar filament in order to propel the cell. Smooth rotation is not essential for the H(+)/ATP synthase, which accumulates torque by twisting a rod-shaped structure. Possible mechanisms for generating torque in the two devices are presented, based on the models which have been proposed. The performances of the various mechanisms are discussed.     

Mechanisms and measurements of nanomaterial-induced oxidative damage to DNA

Many of the current investigations on the environmental and human health risks of engineered nanomaterials focus on their short-term acute toxicity. However, the long-term chronic effects of nanomaterials on living systems, and in particular, on the genetic components of living systems, also warrant attention. An increasing number of nanomaterial safety studies include an assessment of genotoxicity as part of the overall risk evaluation. The potential of nanomaterials to directly or indirectly promote the formation of reactive oxygen species is one of the primary steps in their genotoxic repertoire. The subsequent modification of genomic DNA by reactive oxygen species could lead to the development of mutagenesis, carcinogenesis, or other age-related diseases if the DNA damage is not repaired. This review focuses on the interactions of nanomaterials with DNA and specifically on the capacity of some nanomaterials to induce oxidative damage to DNA. A critical assessment of the analytical methodology and the potential biochemical mechanisms involved in nanomaterial induction of oxidative damage to DNA is presented, results obtained for the various studies with each nanomaterial are compared, and recommendations for future research are discussed. Researchers should consider, among other experimental recommendations, (1) the application of more chromatography-based and mass-spectrometry-based analytical techniques to the assessment of oxidative damage to DNA to facilitate an enhanced understanding of DNA damage mechanisms and (2) the verification of cellular viability before conducting genotoxicity assays to reduce the impact of fragmented DNA, formed as a consequence of cell death, on DNA damage measurements.     

Gas-phase catalysis by atomic and cluster metal ions: the ultimate single-site catalysts

Gas-phase experiments with state-of-the-art techniques of mass spectrometry provide detailed insights into numerous elementary processes. The focus of this Review is on elementary reactions of ions that achieve complete catalytic cycles under thermal conditions. The examples chosen cover aspects of catalysis pertinent to areas as diverse as atmospheric chemistry and surface chemistry. We describe how transfer of oxygen atoms, bond activation, and coupling of fragments can be mediated by atomic or cluster metal ions. In some cases truly unexpected analogies of the idealized gas-phase ion catalysis can be drawn with related chemical transformations in solution or the solid state, and so improve our understanding of the intrinsic operation of a practical catalyst at a strictly molecular level.     

Dynamics and biological relevance of epigenetic N6-methyladenine DNA modification in eukaryotic cells

DNA methylation represents a major type of DNA modifications that play key roles in diverse biological processes. With the recent development of highly selective and sensitive bioanalytical techniques,N⁶-methyladenine（6mA） has been characterized as an important internal DNA modification dynamically occurring in multiple eukaryotes including humans. Increasing evidence has indicated that 6mA may act as a novel epigenetic modification involved in regulation of development, stress respon...     

FAR UV IRRADIATION OF DNA IN THE PRESENCE OF PROTEINS, AMINO ACIDS OR PEPTIDES

Abstract— The DNA of bacteriophage SP02c12 was subjected to 254 nm irradiation in solutions containing lysozyme or histone. In these solutions, the protein-DNA mass ratios and the ionic strengths of the solvents were varied to change the amount of protein associated with the DNA. Lysozyme-DNA binding constants were measured under the same conditions. The sensitivity of phage DNA to biological inactivation by UV increased as the amount of lysozyme bound per DNA strand increased. Although binding constants could not be measured for the DNA-histone interaction, this protein had a protective effect which was greater under conditions which cause enhanced binding. No crosslinking of either protein could be detected even at doses ten-fold greater than those giving a surviving fraction of 0.01.
Irradiation was also performed in the presence of various amino acids and short peptides. These were chosen to include amino acids which: (1) are positively charged, (2) absorb UV of this wavelength or (3) form UV-induced crosslinks to DNA. None of the amino acids tested affected sensitivity of the DNA to biological inactivation. Peptides containing a UV-absorbing amino acid and a positively charged amino acid enhanced sensitivity. For each of these peptides, a mixture of the constituent amino acids had the same effect as the peptide itself. Under the conditions used, no evidence for formation of DNA-amino acid crosslinks was found. The results indicate that proteins and peptides can sensitize DNA to UV inactivation by mechanisms other than covalent crosslink formation. Such mechanisms could include energy or electron transfer or alterations in the conformation of the DNA.     

Phylogenetic and functional classification of ATP-binding cassette (ABC) systems

ATP binding cassette (ABC) systems constitute one of the most abundant superfamilies of proteins. They are involved in the transport of a wide variety of substances, but also in many cellular processes and in their regulation. In this paper, we made a comparative analysis of the properties of ABC systems and we provide a phylogenetic and functional classification. This analysis will be helpful to accurately annotate ABC systems discovered during the sequencing of the genome of living organisms and to identify the partners of the ABC ATPases.     

Systematic investigation of sequence and structural motifs that recognize ATP

Interaction between ATP, a multifunctional and ubiquitous nucleotide, and proteins initializes phosphorylation, polypeptide synthesis and ATP hydrolysis which supplies energy for metabolism. However, current knowledge concerning the mechanisms through which ATP is recognized by proteins is incomplete, scattered, and inaccurate. We systemically investigate sequence and structural motifs of proteins that recognize ATP. We identified three novel motifs and refined the known p-loop and class II aminoacyl-tRNA synthetase motifs. The five motifs define five distinct ATP–protein interaction modes which concern over 5% of known protein structures. We demonstrate that although these motifs share a common GXG tripeptide they recognize ATP through different functional groups. The p-loop motif recognizes ATP through phosphates, class II aminoacyl-tRNA synthetase motif targets adenosine and the other three motifs recognize both phosphates and adenosine. We show that some motifs are shared by different enzyme types. Statistical tests demonstrate that the five sequence motifs are significantly associated with the nucleotide binding proteins. Large-scale test on PDB reveals that about 98% of proteins that include one of the structural motifs are confirmed to bind ATP.     

Supercytostatics and supercytotoxins

Natural compounds are considered which in concentrations of 5·10^?8 M inhibit the proliferation of culturable malignant mammalian cells. It is proposed to call them supercytostatics and supercytotoxins. Their cytotoxic activities are based on various biochemical mechanisms. Among the supercytostatics there are mitotic poisons, inhibitors of protein and nucleic acid synthesis, and membrane and cytoplasmic enzymes. However, in many cases there are grounds for assuming that the critical cell targets do not coincide with the observed biochemical effects of the supercytostatics. In spite of their diverse chemical structures, the majority of substances contain similar structural fragments which may be complementary to unknown receptors participating in the regulation of cell proliferation.     

The use of electrochemical impedance spectroscopy for biosensing

This review introduces the basic concepts and terms associated with impedance and techniques of measuring impedance. The focus of this review is on the application of this transduction method for sensing purposes. Examples of its use in combination with enzymes, antibodies, DNA and with cells will be described. Important fields of application include immune and nucleic acid analysis. Special attention is devoted to the various electrode design and amplification schemes developed for sensitivity enhancement. Electrolyte insulator semiconductor (EIS) structures will be treated separately. Figure An alternating current which is forced to pass an interface is sensitive to surface changes and will detect impedance changes due to biomolecule immobilisation or formation of a recognition complex. This can be used for the construction of biosensor electrodes     

New materials in sorptive extraction techniques for polar compounds

This paper provides an overview of the new developments in material and format technology that improve the extraction of polar compounds in several extraction techniques. They mainly include solid-phase extraction, but there are also other sorptive extraction techniques, such as stir bar sorptive extraction and solid-phase microextraction that use either fibers or in-tube devices. We focus on new synthesised materials that are both commercially available and "in-house". Most novel materials that enhance the extraction of polar compounds are hydrophilic and have large specific surface area; however, we also cover other leading technologies, such as sol-gel or monolith. We describe the morphological and chemical properties of these new sorbents so that we can better understand them and relate them to their capability of retaining polar compounds. We discuss the extraction efficiency for polar compounds when these polymers are used as sorptive material and compare them to other materials. We also mention some representative examples of applications.     

X‐Ray Scattering and Imaging Studies of Electrode Structure and Dynamics

We will review structures and dynamics of electrode interfaces studied in situ using x‐ray scattering and imaging techniques. The examples cover single‐crystal and nanocrystal structures relevant to electrocatalytic activities, anodic oxidation and corrosion, aqueous dissolution reactions, surface reconstructions, and surface modifications by under potential deposition. The x‐ray techniques include the widely used traditional surface x‐ray scattering, such as crystal truncation rods and x‐ray reflectivity, as well as recently developed resonance surface scattering, coherent surface x‐ray photon correlation spectroscopy, coherent x‐ray Bragg diffraction imaging, and surface ptychography. Results relevant to various electrochemical phenomena will be highlighted.     

Chemistry and biology of DNA repair

Numerous agents of endogenous and exogenous origin damage DNA in our genome. There are several DNA-repair pathways that recognize lesions in DNA and remove them through a number of diverse reaction sequences. Defects in DNA-repair proteins are associated with several human hereditary syndromes, which show a marked predisposition to cancer. Although DNA repair is essential for a healthy cell, DNA-repair enzymes counteract the efficiency of a number of important antitumor agents that exert their cytotoxic effects by damaging DNA. DNA-repair enzymes are therefore also targets for drug design. DNA-repair processes differ greatly in their nature and complexity. Whereas some pathways only require a single enzyme to restore the original DNA sequence, others operate through the coordinated action of 30 or more proteins. Our understanding of the genetic, biochemical, and structural basis of DNA repair and related processes has increased dramatically over the past decade. This review summarizes the latest developments in this field.     

Visualization of large elongated DNA molecules

Long and linear DNA molecules are the mainstream single‐molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA‐protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.     

Single-molecule tethered particle motion to study protein-DNA interaction

Single-molecule techniques have been demonstrated as powerful tools to investigate individual protein-DNA interactions that are difficult to access by conventional biochemical techniques. These methods are popularly used to obtain valuable and detailed molecular mechanisms of enzyme functions. Currently, we have used single-molecule tethered particle motion to investigate protein-DNA interactions, including homologous recombination, site-specific recombination, DNA package, and the nucleosome remodeling process, and useful information was obtained. Here, we will describe the experimental designs and present the information obtained.