Molecular Interaction Properties Research Articles

Systems biology towards life in silico: mathematics of the control of living cells

Systems Biology is the science that aims to understand how biological function absent from macromolecules in isolation, arises when they are components of their system. Dedicated to the memory of Reinhart Heinrich, this paper discusses the origin and evolution of the new part of systems biology that relates to metabolic and signal-transduction pathways and extends mathematical biology so as to address postgenomic experimental reality. Various approaches to modeling the dynamics generated by metabolic and signal-transduction pathways are compared. The silicon cell approach aims to describe the intracellular network of interest precisely, by numerically integrating the precise rate equations that characterize the ways macromolecules' interact with each other. The non-equilibrium thermodynamic or 'lin-log' approach approximates the enzyme rate equations in terms of linear functions of the logarithms of the concentrations. Biochemical Systems Analysis approximates in terms of power laws. Importantly all these approaches link system behavior to molecular interaction properties. The latter two do this less precisely but enable analytical solutions. By limiting the questions asked, to optimal flux patterns, or to control of fluxes and concentrations around the (patho)physiological state, Flux Balance Analysis and Metabolic/Hierarchical Control Analysis again enable analytical solutions. Both the silicon cell approach and Metabolic/Hierarchical Control Analysis are able to highlight where and how system function derives from molecular interactions. The latter approach has also discovered a set of fundamental principles underlying the control of biological systems. The new law that relates concentration control to control by time is illustrated for an important signal transduction pathway, i.e. nuclear hormone receptor signaling such as relevant to bone formation. It is envisaged that there is much more Mathematical Biology to be discovered in the area between molecules and Life.

Resolving the Fast Kinetics of Cooperative Binding: Ca2+ Buffering by Calretinin

Cooperativity is one of the most important properties of molecular interactions in biological systems. It is the ability to influence ligand binding at one site of a macromolecule by previous ligand binding at another site of the same molecule. As a consequence, the affinity of the macromolecule for the ligand is either decreased (negative cooperativity) or increased (positive cooperativity). Over the last 100 years, O2 binding to hemoglobin has served as the paradigm for cooperative ligand binding and allosteric modulation, and four practical models were developed to quantitatively describe the mechanism: the Hill, the Adair-Klotz, the Monod-Wyman-Changeux, and the Koshland-Némethy-Filmer models. The predictions of these models apply under static conditions when the binding reactions are at equilibrium. However, in a physiological setting, e.g., inside a cell, the timing and dynamics of the binding events are essential. Hence, it is necessary to determine the dynamic properties of cooperative binding to fully understand the physiological implications of cooperativity. To date, the Monod-Wyman-Changeux model was applied to determine the kinetics of cooperative binding to biologically active molecules. In this model, cooperativity is established by postulating two allosteric isoforms with different binding properties. However, these studies were limited to special cases, where transition rates between allosteric isoforms are much slower than the binding rates or where binding and unbinding rates could be measured independently. For all other cases, the complex mathematical description precludes straightforward interpretations. Here, we report on calculating for the first time the fast dynamics of a cooperative binding process, the binding of Ca2+ to calretinin. Calretinin is a Ca2+-binding protein with four cooperative binding sites and one independent binding site. The Ca2+ binding to calretinin was assessed by measuring the decay of free Ca2+ using a fast fluorescent Ca2+ indicator following rapid (<50-μs rise time) Ca2+ concentration jumps induced by uncaging Ca2+ from DM-nitrophen. To unravel the kinetics of cooperative binding, we devised several approaches based on known cooperative binding models, resulting in a novel and relatively simple model. This model revealed unexpected and highly specific nonlinear properties of cellular Ca2+ regulation by calretinin. The association rate of Ca2+ with calretinin speeds up as the free Ca2+ concentration increases from cytoplasmic resting conditions (∼100 nM) to approximately 1 μM. As a consequence, the Ca2+ buffering speed of calretinin highly depends on the prevailing Ca2+ concentration prior to a perturbation. In addition to providing a novel mode of action of cellular Ca2+ buffering, our model extends the analysis of cooperativity beyond the static steady-state condition, providing a powerful tool for the investigation of the dynamics and functional significance of cooperative binding in general.

S04H4 シミュレーションによる分子間相互作用の熱力学特性の解析と予測(立体構造から生体分子間相互作用の熱力学へ,シンポジウム,第45回日本生物物理学会年会)

S04H4 シミュレーションによる分子間相互作用の熱力学特性の解析と予測(立体構造から生体分子間相互作用の熱力学へ,シンポジウム,第45回日本生物物理学会年会)

Molecular Simulations of the Transport of Molecules across the Liquid/Vapor Interface of Water

The transport of molecules across the liquid/vapor interface of water is a fundamental process that is important in a number of areas. Uptake of trace molecules by aqueous droplets is important in the atmosphere as it enables heterogeneous new chemical pathways that are not available in the gas phase. The uptake of molecules by water and partitioning to the air/water surface is important in aquatic environmental systems. The summary of molecular simulations presented in this work supports a picture of solute transport across the water’s vapor/liquid interface in which a hydrophilic solute molecule impinging on the surface is rapidly equilibrated, sticks to the surface of the interface with nearly unit probability, then diffuses into the bulk liquid on an free energy surface. Analysis of a large number of experimental observations of uptake, using a variety of techniques, supports a view of mass transport that is diametrically opposed – most solute molecules that collide with the surface return to the vapor rather than being absorbed into the liquid. This discrepancy stresses the need for greater understanding of the important process of uptake. We provide a perspective on molecular-scale simulations and evaluate the type of accuracy we should expect for interfacial properties,more » particularly those associated with the update of molecular at the surface. We briefly review computational methods commonly used in studies of aqueous interfaces, including functional forms of the molecular interaction potentials, descriptions of the simulation methodologies, and descriptions of the molecular models of the interface. We present the results of simulations of select properties of the air/water interface and properties of molecular interactions at interfaces and present an overview of modeling approaches to the macroscopic process of uptake. In particular, we present detailed descriptions of the uptake process in flow tube experiments with the help of fluid dynamics calculations toward critical comparison between the uptake experiments and the molecular simulations.« less

Daxx Mediates the Small Ubiquitin-like Modifier-dependent Transcriptional Repression of Smad4

Daxx has been shown to function as an apoptosis regulator and transcriptional repressor via its interaction with various cytoplasmic and nuclear proteins. Here, we showed that Daxx interacts with Smad4 and represses its transcriptional activity via the C-terminal domain of Daxx. In vitro and in vivo interaction studies indicated that the binding of Smad4 to Daxx depends on Smad4 sumoylation. Substitution of Smad4 SUMO conjugation residue lysine 159, but not 113, to arginine not only disrupted Smad4-Daxx interaction but also relieved Daxx-elicited repression of Smad4 transcriptional activity. Furthermore, chromatin immunoprecipitation analyses revealed the recruitment of Daxx to an endogenous, Smad4-targeted promoter in a Lys(159) sumoylation-dependent manner. Finally, down-regulation of Daxx expression by RNA interference enhanced transforming growth factor beta-induced transcription of reporter and endogenous genes through a Smad4-dependent, but not K159R-Smad4-dependent, manner. Together, these results indicate that Daxx suppresses Smad4-mediated transcriptional activity by direct interaction with the sumoylated Smad4 and identify a novel role of Daxx in regulating transforming growth factor beta signaling.

Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

State of the art molecular dynamics simulations are used to study the structure, dynamics, molecular interaction properties and flexibility of DNA and RNA duplexes in aqueous solution. Special attention is paid to the deformability of both types of structures, revisiting concepts on the relative flexibility of DNA and RNA duplexes. Our simulations strongly suggest that the concepts of flexibility, rigidity and deformability are much more complex than usually believed, and that it is not always true that DNA is more flexible than RNA.

Analytically defined surfaces to analyze molecular interaction properties

Molecular surfaces are widely used for characterizing molecules and displaying and quantifying their interaction properties. Here we consider molecular surfaces defined as isocontours of a function (a sum of exponential functions centered on each atom) that approximately represents electron density. The smoothness is advantageous for surface mapping of molecular properties (e.g., electrostatic potential). By varying parameters, these surfaces can be constructed to represent the van der Waals or solvent-accessible surface of a molecular with any accuracy. We describe numerical algorithms to operate on the analytically defined surfaces. Two applications are considered: (1) We define and locate extremal points of molecular properties on the surfaces. The extremal points provide a compact representation of a property on a surface, obviating the necessity to compute values of the property on an array of surface points as is usually done; (2) a molecular surface patch or interface is projected onto a flat surface (by introducing curvilinear coordinates) with approximate conservation of area for analysis purposes. Applications to studies of protein-protein interactions are described.

Molecular associations between indolizines and tetracyanoethylene

AbstractSpectroscopic, thermodynamic and kinetic properties of molecular interactions between indolizines and tetracyanoethylene are reported. The interactions involved in the complexes are weak as evidenced by the low formation constants. The kinetic behaviour indicates the initial formation of a pI‐complex that is rapidly transformed into a σ‐complex and thereafter into the final adduct(s). Apart from the results obtained by other techniques, infrared data clearly evidence vibrational contributes characteristic of the complexes, the tricyanovinyl derivatives and the tetracyanoethylene radical anion.