Transitions,transversions, and the molecular evolutionary clock

Summary Nucleotide substitutions in the form of transitions (purine-purine or pyrimidine-pyrimidine interchanges) and transversions (purine-pyrimidine interchanges) occur during evolution and may be complied by aligning the sequences of homologous genes. Referring to the genetic code tables, silent transitions take place in third positions of codons in family boxes and two-codon sets. Silent transversions in third positions occur only in family boxes, except for AC transversions between AGR and CGR arginine codons (R=A or G). Comparisons of several protein genes have been made, and various subclasses of transitional and transversional nucleotide substitutions have been compiled. Considerable variations occur among the relative proportions of transitions and transversions. Such variations could possibly be caused by mutator genes, favoring either transitions or, conversely, transversions, during DNA replication. At earlier stages of evolutionary divergence, transitions are usually more frequent, but there are exceptions. No indication was found that transversions usually originate from multiple substitutions in transitions.     

Quantum-chemical investigation of tautomerization ways of Watson-Crick DNA base pair guanine-cytosine

A novel physico-chemical mechanism of the Watson-Crick DNA base pair Gua.Cyt tautomerization Gua.Cyt*<---->Gua.Cyt<---->Gua*.Cyt (mutagenic tautomers of bases are marked by asterisks) have been revealed and realized in a pathway of single proton transfer through two mutual isoenergetic transition states with Gibbs free energy of activation 30.4 and 30.6 kcal/mol and they are ion pairs stabilized by three (N2H...N3, N1H...N4- and O6+H...N4-) and five (N2H...O2, N1H...O2, N1H...N3, O6+H...N4- and 06+H...N4-) H-bonds accordingly. Stable base pairs Gua-Cyt* and Gua*.Cyt which dissociate comparably easy into monomers have acceptable relative Gibbs energies--12.9 and 14.3 kcal/mol--for the explanation of the nature of the spontaneous transitions of DNA replication. Results are obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-31 1++G(d,p) level of theory in vacuum approach.     

New nucleoside analogues for the recognition of pyrimidine-purine inversion sites

A new nucleoside designed to enhance triplex stability has been synthesised in 15 steps starting from sugar 2. This pathway contains the sugar derivative 9 which is a useful intermediate for the introduction of other natural and unnatural bases into the 2'-aminoethoxy nucleoside containing scaffold.     

Electrophysiological investigation of the texture discrimination mechanisms

In electrophysiological and psychophysical experiments, we investigated mechanisms of the visual system underlying local and global texture processing. Textures included rectangular matrixes composed of Gabor patches (sine wave grating windowed by a Gaussian envelope). Orientation of each grating varied from 0 to 165 degrees with the step of 15 degrees. Matrixes differed by the amount of Gabor patches with vertical or horizontal orientation. The observers' task was to discriminate the dominant orientation. The advantage of such stimuli involved a possibility to calculate global statistics of the textures, which we considered as the difference between whole amount of vertical and horizontal orientations in the stimulus irrespective of their location. The local statistics was calculated as relative amount of spatially organized nearby gratings (i. e. collinear contours). The subjects' accuracy was low in discriminating less organized textures and gradually improved with the amount of vertically of horizontally oriented Gabor patches, while the reaction time decreased. Visual evoked potentials (VEPs) recorded from occipital lobes revealed different dependencies of their components' magnitude on the amount of equally oriented gratings. Amplitude of the late positive component P3 with latency 400 ms directly depended on the texture discriminability, and N2 wave with latency 180 ms had an S-like dependence. Opposite to that, the magnitude of P2 wave with latency 260 ms was maximal in response to less organized textures and gradually decreased with the amount of equally oriented gratings. The dependencies received were compared with the textures' statistics. Data analysis allowed us to suppose that, in the conditions of our experimental paradigm, two mechanisms were involved in discrimination of the textures--the local and the global processing. We believe that by recording VEPs one can separately investigate activity of these two processes.     

Cancer cachexia: the molecular mechanisms

Cancer cachexia is a syndrome characterised by a marked weight loss, anorexia, asthenia and anaemia. In fact, many patients who die with advanced cancer suffer from cancer cachexia. The cachectic state is invariably associated with the presence and growth of the tumour and leads to a malnutrition status due to the induction of anorexia or decreased food intake. In addition, the competition for nutrients between the tumour and the host leads to an accelerated starvation state which promotes severe metabolic disturbances in the host, including hypermetabolism which leads to an increased energetic inefficiency. Although, the search for the cachectic factor(s) started a long time ago, and although many scientific and economic efforts have been devoted to its discovery, we are still a long way from knowing the whole truth. The main aim of the present review is to summarise and evaluate the different catabolic mediators (both humoural and tumoural) involved in cancer cachexia since they may represent targets for future promising clinical investigations.     

P-glycoprotein-ATPase modulation: the molecular mechanisms

P-glycoprotein-ATPase is an efflux transporter of broad specificity that counteracts passive allocrit influx. Understanding the rate of allocrit transport therefore matters. Generally, the rates of allocrit transport and ATP hydrolysis decrease exponentially with increasing allocrit affinity to the transporter. Here we report unexpectedly strong down-modulation of the P-glycoprotein-ATPase by certain detergents. To elucidate the underlying mechanism, we chose 34 electrically neutral and cationic detergents with different hydrophobic and hydrophilic characteristics. Measurement of the P-glycoprotein-ATPase activity as a function of concentration showed that seven detergents activated the ATPase as expected, whereas 27 closely related detergents reduced it significantly. Assessment of the free energy of detergent partitioning into the lipid membrane and the free energy of detergent binding from the membrane to the transporter revealed that the ratio, q, of the two free energies of binding determined the rate of ATP hydrolysis. Neutral (cationic) detergents with a ratio of q = 2.7 ± 0.2 (q > 3) followed the aforementioned exponential dependence. Small deviations from the optimal ratio strongly reduced the rates of ATP hydrolysis and flopping, respectively, whereas larger deviations led to an absence of interaction with the transporter. P-glycoprotein-ATPase inhibition due to membrane disordering by detergents could be fully excluded using ²H-NMR-spectroscopy. Similar principles apply to modulating drugs.     

Aldosterone: the mechanisms of molecular action

Aldosterone: a steroid hormone of adrenal cortex, has recently attracted much interest not only due to its great importance in regulation of salt and water balance, but also because of its key role in therapy of cardiovascular and renal pathology. The classical genomic mechanism of molecular action of aldosterone is mediated through interaction with mineral-corticoid receptors. Fast nongenomic pathway of cell signal transduction begins with interaction with hypothetic membrane receptors and includes activation of different kinase cascades. Interference of these two pathways of signal transduction assures abroad spectrum of aldosterone effects depending on the cell type, and also secures multycomponent regulation depending on the need of specific functional and stress situation. This review is dedicated to modern views of mechanisms of aldosterone molecular action, mostly of the level of aldosterone-sensitive segment of kidney nephron.     

Heterogeneity of molecular mechanisms the olfactor reception

In experiments on the frog isolated olfactory epithelium by using vital fluorescent microscope, odorants with fruit, rank, flower and camphor smell were shown to involve intracellular signaling systems in olfactory transduction. The odorants with different qualitative smells have different messenger and activity mechanisms. Intracellular messengers do not participate in reception of odorants with piquant and rotten smells. Thus the perception of different odour substances is maintained by physical and chemical processes. Hence, not only taste, carotid, medullar, but olfactory reception as well are characterised by heterogeneity of biophysical mechanisms.     

Moving beyond molecular mechanisms

A major goal in cell biology is to bridge the gap in our understanding of how molecular mechanisms contribute to cell and organismal physiology. Approaches well established in the physical sciences could be instrumental in achieving this goal. A better integration of the physical sciences with cell biology will therefore be an important step in our quest to decipher how cells work together to construct a living organism.Over the past 60 years, the field of cell biology has been firmly rooted in understanding the molecular basis of complex cellular processes including genome replication, migration, metabolism, and adhesion. This progress has been enabled by advances in molecular biology, biochemistry, physical chemistry, single-molecule physics, and microscopy. Bringing together these disciplines has been successful in identifying the molecular composition of macromolecular machines, characterizing the structure and physical properties of single proteins within cells, reconstituting complex macromolecular machinery in vitro, and imaging the dynamics and function of these machines in vivo.Despite this amazing progress, a major challenge facing cell biology is understanding how the chemical and physical properties of molecular machinery come together to guide cell processes. How do varied physical and chemical signals in the environment determine whether a cell survives, proliferates, or migrates? What circuitry allows for a complex body plan to be constructed out of a single-celled embryo? The signals in the environment are noisy, with fluctuations in both time and space. Moreover, as anyone who has tried to characterize cells is aware, cell phenotypes are variable both across individual cells and within a single cell over time. In the presence of all this noise, cells execute some processes exceedingly reliably (e.g., DNA segregation in cell division). Others, such as the determination of protrusive activity in a migrating cell, appear to be more variable. How does this complex network of stochastic chemical and mechanical machinery enable robust and complex decision making at the cell scale?The answers to these questions require knowledge of cell structure at the scale between single molecules and whole cells (Fig. 1). This intermediate, or mesoscopic, length scale has different names depending on who you ask. You can think of it as a “system” or interconnected network of biochemical interactions that provide a logic circuit as to how cells process a signal to decide on an output. It can be a subcellular machine consisting of a collection of macromolecules designed to work together for a desired mechanical output, such as cargo transport, DNA segregation, or cell movement. There is a significant gap in our understanding at this scale. To make an analogy between a cell and a car: most of us have a good understanding of the car’s component materials (e.g., rubber, metal), and in some cases we understand the individual machines that make up parts of the whole (e.g., the engine, transmission). However, we do not have a good understanding of the essential control parameters of the machines or how these are wired together to form productive, more complex machinery (e.g., creating the forward, backward, and turning motions). Understanding the control parameters that regulate macromolecular assemblies, and how these are wired together to enable complex cell outputs, represents an exciting frontier in cell biology.Open in a separate windowFigure 1.The scales of cell biology. Shown are images illustrating the range of scales in cell biology. At the smallest (∼10⁻⁹ m) is that of molecules represented by the structure of G-actin (left; reproduced from Paavilainen et al. 2008. J. Cell Biol. http://dx.doi.org/10.1083/jcb.200803100) and the largest (10⁻⁵ to 10⁻⁴ meters) is that of cell physiology, represented by a migrating fibroblast with a labeled actin cytoskeleton (right; image courtesy of Patrick Oakes). In between these length scales reside: macromolecular assemblies (10⁻⁸ to 10⁻⁷ m) of individual proteins, represented by a schematic of an Arp2/3-mediated F-actin branch (second from the left); and organelles (10⁻⁷ to 10⁻⁵ m), such as lamellipodia (third from the left), which are formed by the integration of macromolecular assemblies into a mechanochemical machine depicted as a pathway diagram. At the next level are organelle systems (10⁻⁴ to 10⁻⁵ m) that integrate organelles together for a specific aspect of cell physiology, represented by a fluorescent image of actin overlaid with vectors of actin flow at the leading edge that result from the coordination of numerous regulatory organelles across the cell (second from the right; reproduced from Thievessen et al. 2013. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201303129). Understanding the processes at this intermediate scale will greatly aid in our knowledge of how molecules construct living cells.Many areas of the physical sciences have been devoted to studying how collections of objects work together to construct a material or machine. In this construction, new properties emerge that could not be predicted or understood by studies of objects in isolation. For instance, electrical engineers need to know how circuit elements are connected in order to predict the circuit response. Or, in condensed matter physics, interactions between atoms and/or molecules result in properties such as elasticity or viscosity. In these areas of science, it is well appreciated that knowledge of individual components (in isolation) cannot predict the output of the entire system. By analogy, this would imply that understanding the molecular components of a cell, which has been the gold standard of cell biology, is insufficient. As cell biology starts to address questions wherein cells are thought of as “systems,” “materials,” or “machines,” there are numerous challenges that can be informed by approaches that have proven successful in the studies of materials and machines in the physical world.

Developing a common community

Cell biology is an inherently multidisciplinary science, requiring approaches from genetics, chemistry, physics, applied mathematics, and engineering. While biochemical and genetic approaches have been successfully integrated into the field, other disciplines require more effort. Physical scientists that join the field of cell biology retain the training and language from their physical discipline, which has been specialized for specific purposes. Applied mathematicians, condensed matter physicists, and mechanical engineers all have unique perspectives on how to model complex biological phenomena (Fig. 2). This has led to the development of parallel theoretical and experimental approaches for modeling cell biological phenomena that are difficult to directly compare or rigorously test. A challenge for the future is to develop a community of researchers that will integrate these diverse physical approaches to identify strengths, resolve differences, and determine the best approaches for modeling cell behaviors.Open in a separate windowFigure 2.The integration of physical sciences with cell biology. A flow chart showing examples of how various disciplines from the physical sciences (bottom) have optimized a variety of theoretical/modeling tools (left) as well as experimental techniques (right) that have been applied to cell biological problems. However, these experimental and theoretical tools have been optimized for their home disciplines. A current challenge is to systematically have them benchmarked against each other and identify their weaknesses and strengths before using them to provide a new framework optimized for mesoscale cell biology.

Precision in language

One of the simplest solutions to implement is to develop a consistent and precise language to describe measurements or ideas. In my field, which centers on how mechanical forces are sensed and generated by cells, terms like “mechanosensing” or even “stiffness sensing” are used without precision, resulting in confusion of what is known versus just “thought to be true.” Precision of language is essential for standardizing experimental protocols and measurements and in being able to clearly communicate conclusions and ideas.

Construction and validation of physical methods

One historical role of physical scientists in biology has been the introduction of new experimental and analytical tools. Some of these tools, such as microscopy and scattering techniques, have been developed extensively. However, in other cases, the nature of measurements require small apparatuses that can be difficult to replicate or operate (magnetic tweezers are a notorious example), making it difficult for other laboratories to build upon this knowledge. Similar issues arise in analysis and methods. It is extremely important for these methods to be used and validated by different laboratories to confirm results independently and by many individuals so that the language used to describe physical concepts and results can be made more precise. Being able to directly compare two different measurement techniques so that the same parameters can be used is essential for resolving discrepancies.Even though the goal is to understand cell physiology, model testing will require physical characterization that may not immediately inform a biological process. To use an analogous example: the work in basic materials science of magnetism that needed to be performed before we could construct and build computer hard drives. It is my hope that the cell biology community will remain interested in these advances in characterization of biological materials and systems, as they are crucial to uncovering synergies that are not currently apparent.

Feedback between modeling and experiments

In the physical sciences, research has evolved so that individuals typically focus on either theory or experimentation. Of course, each of these can be further subdivided into analytical theory versus computer modeling, as well as sample preparation versus characterization. This specialization has emerged as both the questions and fields themselves become more mature. It also has led to a vigorous feedback between theoretical prediction, experimental measurement, and new materials development. To be useful, models need to be falsifiable. There is increasing evidence that many of the models used in biology are over-parameterized and, consequently, difficult (or impossible) to falsify. That is, when parameters are assigned with molecular-level details, the number of parameters quickly becomes large. In these scenarios, changes in the parameter value have little effect on the model predictions and make it difficult to verify the accuracy of the model (for more details, see http://www.lassp.cornell.edu/sethna/Sloppy/). Identifying order parameters that encompass the physical quantities or metrics (e.g., elastic modulus, organelle transport) that make up many of the molecular details is essential for developing models with fewer control parameters. Such order parameters will provide crucial insight into understanding regulation of the individual macromolecular machinery.The word mechanism in cell biology typically refers to a molecular mechanism that is explored rigorously by genetic and biochemical testing. Understanding the physical mechanism requires both identification of the parameters controlling a system and then elucidation of the regulation of parameter values. Thus, seldom does a single molecular mechanism tie directly into a physical parameter. Moreover, understanding how molecular interactions give rise to a single physical parameter is not straightforward, and may require years of work. It is quite natural to apply models and approaches that we have used to engineer machines, such as the flow of decision making in electrical circuits or mechanic designs. However, cells are working under different sets of constraints, and a future challenge of understanding cellular machines is that completely different design principles may be used.Establishing a culture that encourages dynamic feedback between theory, experimentation, and physiology is crucial to advancing the integration of physical sciences with cell biology. A potentially very exciting possibility is that understanding the physical mechanisms controlling biological machines will enable a completely new set of design principles that provide insight into how living cells are able to respond and adapt to highly variable environments. This will enable understanding of how these states change during disease progression and the capability of engineering biological cells to maintain a healthy phenotype.     

Apoptosis: molecular mechanisms

Apoptosis is a genetically programmed cell death that is required for morphogenesis during embryogenic development and for tissue homeostasis in adult organisms. In most cases, apoptosis involves cytochrome c release from mitochondria. In the cytosol, cytochrome c combines with APAF-1 in the presence of ATP to activate caspase-9 that, in turn, activates effectors caspases such as caspase-3. Bcl-2 and related proteins control cytochrome c release from the mitochondria whereas IAP (for Inhibitor of APoptosis) molecules modulate the activity of caspases. Plasma membrane receptors such as Fas (CD95, APO-1), characterized by a so-called "death domain" in their cytoplasmic domain, can activate the caspase cascade through adaptator molecules such as FADD (Fas-Associated protein with a Death Domain). Dysregulation of the apoptotic machinery plays a role in the pathogenesis of various diseases and molecules involved in cell death pathways are potential therapeutic targets in immunologic, neurologic, cancer, infectious and inflammatory diseases.     

Probabilities of transversions and transitions.

The values of the mean relative probabilities of transversions and transitions have been refined on the basis of the data collected by Jukes and found to be equal to 0.34 and 0.66, respectively. Evolutionary factors increase the probability of transversions to 0.44. The relative probabilities of individual substitutions have been determined, and a detailed classification of the nonsense mutations has been given. Such mutations are especially probable in the UGG (Trp) codon. The highest probability of AG, GA transitions correlates with the lowest mean change in the hydrophobic nature of the amino acids coded.     

A molecular dynamics investigation into the mechanisms of material removal and subsurface damage of nanoscale high speed laser-assisted machining

Molecular dynamics is employed to study the mechanism of material removal and subsurface damage of monocrystalline silicon when it is under a nanoscale high-speed laser-assisted grinding of a diamond tip. Laser-assisted machining (LAM) is that the workpiece is locally heated by an intense laser beam before material removal. The effects of laser moving speed, laser pulse intensity and laser spot radius are thoroughly investigated in terms of atomic trajectories, phase transformation, temperature distribution, grinding temperature, grinding force and friction coefficient. The investigation shows that a higher laser moving speed reduces the subsurface damage and improves the material remove rate because of fewer atoms with five and six coordination atoms and more chips. Besides, both tangential grinding force (Fx) and normal grinding force (Fy) decrease as the laser moving speed increases. The distribution of high-temperature zone strongly depends upon the effect of laser pulse intensity and laser spot radius. Larger laser pulse intensity can make the material more fully softened before being removed. Moreover, as the laser pulse intensity becomes larger, the friction coefficients became smaller, the material remove rate improves and the depth of grinding increases. However, larger laser pulse intensity may result in a larger thermal deformation of workpiece. A larger laser spot radius reduces the grinding depth but increases the width of laser irradiation zone on machined surface. Thus, a suitable laser spot radius can improve the material removal rate. These results indicate that it is possible to control and adjust the laser parameters according to laser moving speed, laser pulse intensity and laser spot radius, and it provides a potential technology to improve a surface integrity and a smoothness of ground surface.     

Microglia-mediated neurotoxicity: uncovering the molecular mechanisms

Mounting evidence indicates that microglial activation contributes to neuronal damage in neurodegenerative diseases. Recent studies show that in response to certain environmental toxins and endogenous proteins, microglia can enter an overactivated state and release reactive oxygen species (ROS) that cause neurotoxicity. Pattern recognition receptors expressed on the microglial surface seem to be one of the primary, common pathways by which diverse toxin signals are transduced into ROS production. Overactivated microglia can be detected using imaging techniques and therefore this knowledge offers an opportunity not only for early diagnosis but, importantly, for the development of targeted anti-inflammatory therapies that might slow or halt the progression of neurodegenerative disease.     

On the molecular mechanisms of mitotic kinase activation

During mitosis, human cells exhibit a peak of protein phosphorylation that alters the behaviour of a significant proportion of proteins, driving a dramatic transformation in the cell''s shape, intracellular structures and biochemistry. These mitotic phosphorylation events are catalysed by several families of protein kinases, including Auroras, Cdks, Plks, Neks, Bubs, Haspin and Mps1/TTK. The catalytic activities of these kinases are activated by phosphorylation and through protein–protein interactions. In this review, we summarize the current state of knowledge of the structural basis of mitotic kinase activation mechanisms. This review aims to provide a clear and comprehensive primer on these mechanisms to a broad community of researchers, bringing together the common themes, and highlighting specific differences. Along the way, we have uncovered some features of these proteins that have previously gone unreported, and identified unexplored questions for future work. The dysregulation of mitotic kinases is associated with proliferative disorders such as cancer, and structural biology will continue to play a critical role in the development of chemical probes used to interrogate disease biology and applied to the treatment of patients.     

Exploring the mechanisms of molecular recognition by flavins

The design and development of chemical models for enzymes depends on the fundamental principles observed in biological systems. Molecular recognition of flavins by various receptors has attracted attention due to their applications as chemical models for flavoenzymes. The area of molecular recognition is being investigated through research at the interface of chemistry and biology. In this review, the literature has been surveyed to provide comprehensive coverage of the synthetic methodology of different flavins and receptors and their molecular-recognition studies. Various applications of flavin-receptor complexes have also been highlighted.