An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules

Several mechanisms have been proposed to explain how ion channels and transporters distinguish between similar ions, a process crucial for maintaining proper cell function. Of these, three can be broadly classed as mechanisms involving specific positional constraints on the ion coordinating ligands which arise through: a "rigid cavity", a 'strained cavity' and 'reduced ligand fluctuations'. Each operates in subtly different ways yet can produce markedly different influences on ion selectivity. Here we expand upon preliminary investigations into the reduced ligand fluctuation mechanism of ion selectivity by simulating how a series of model systems respond to a decrease in ligand thermal fluctuations while simultaneously maintaining optimal ion-ligand binding distances. Simple abstract-ligand models, as well as simple models based upon the ion binding sites in two amino acid transporters, show that limiting ligand fluctuations can create ion selectivity between Li(+), Na(+) and K(+) even when there is no strain associated with the molecular framework accommodating the different ions. Reducing the fluctuations in the position of the coordinating ligands contributes to selectivity toward the smaller of two ions as a consequence of entropic differences.This work was funded by an Australian Postgraduate Award from the Australian Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Stochastic models of intracellular transport

The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an over-damped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of ATP hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review we present a wide range of analytical methods and models of intracellular transport. In the case of diffusive transport, we consider narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion. In the case of active transport, we consider Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean field approximations. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self–organization of subcellular structures

Multiscale modeling for complex macromolecular systems: Methodologies and applications

The objective of this dissertation is to understand the binding mechanism between flexible macromolecules and guest species in solution using multiscale molecular modeling strategies, including: ab initio electronic structure theory, all-atom classical molecular dynamics simulations, coarse-grained molecular dynamics simulations, and statistical eld theory. A brief summary of the subsequent chapters in this thesis is provided. Chapters 2 - 7 and Appendix A are self-contained units complete with literature review and bibliography

The evolution of catalytic function

It is very likely that the main driving force of enzyme evolution is the requirement to improve catalytic and regulatory efficiency which results from the intrinsic performance as well as from the spatial and functional organization of enzymes in living cells. Kinetic co-operativity may occur in simple monomeric proteins if they display “slow” conformational transitions, at the cost of catalytic efficiency. Oligomeric enzymes on the other hand can be both efficient and co-operative. We speculate that the main reason for the emergence of co-operative oligomeric enzymes is the need for catalysts that are both cooperative and efficient. As it is not useful for an enzyme to respond to a change of substrate concentration in a complex kinetic way, the emergence of symmetry has its probable origin in a requirement for “functional simplicity”. In a living cell, enzyme are associated with other macromolecules and membranes. The fine tuning of their activity may also be reached through mutations of the microenvironment. Our hypothesis is that these mutations are related to the vectorial transport of molecules, to achieve the hysteresis loops of enzyme reactions generated by the coupling of reaction and diffusion, through the co-operativity brought about by electric interactions between a charged substrate and a membrane, and last but not least, through oscillations. As the physical origins of these effects are very simple and do not require complex molecular devices, it is very likely that the functional advantage generated by the spatial and functional organization of enzyme molecules within the cell have appeared in prebiotic catalysis or very early during the primeval stages of biological evolution. We shall begin this paper by presenting the nature of the probable earliest catalysts in the RNA world

Structural studies of the hipersaline adaptation of proteins belonging to halophilic archaea

183 p.Adaptation of organisms to extreme halophilic environments (> 1 ¿ 2 M) occurs through theaccumulation of large intracellular concentrations of KCl. Their major adaptive feature is theextensive modification of the constituting proteome. A biased set of amino acids is selected inorder to improve the stability and solubility of halophilic proteins: large hydrophobic residuesare penalized, specially lysines, whereas small, polar and often negatively charged residuesare favoured, such as aspartic acid, threonine and glutamic acid (Figure I4). Themodifications occur mainly at the surface, so the overall structure is conserved. Themolecular determinants for such a selection remain elusive despite of considerable efforts.Previous models based on weak unspecific K+¿carboxylate interactions have provedthemselves insufficient to explain some features of haloadaptation, such as the complex saltmodulationof enzymatic activity or the dependence of protein stability with Hofmeister anions.Figure I4. Halophilic amino acid composition. Residue abundance in halophilic proteins compared tomesophilic proteins expressed as the percentage of relative variation in the average amino acidcomposition

Design of Surface Modifications for Nanoscale Sensor Applications

Nanoscale biosensors provide the possibility to miniaturize optic, acoustic and electric sensors to the dimensions of biomolecules. This enables approaching single-molecule detection and new sensing modalities that probe molecular conformation. Nanoscale sensors are predominantly surface-based and label-free to exploit inherent advantages of physical phenomena allowing high sensitivity without distortive labeling. There are three main criteria to be optimized in the design of surface-based and label-free biosensors: (i) the biomolecules of interest must bind with high affinity and selectively to the sensitive area; (ii) the biomolecules must be efficiently transported from the bulk solution to the sensor; and (iii) the transducer concept must be sufficiently sensitive to detect low coverage of captured biomolecules within reasonable time scales. The majority of literature on nanoscale biosensors deals with the third criterion while implicitly assuming that solutions developed for macroscale biosensors to the first two, equally important, criteria are applicable also to nanoscale sensors. We focus on providing an introduction to and perspectives on the advanced concepts for surface functionalization of biosensors with nanosized sensor elements that have been developed over the past decades (criterion (iii)). We review in detail how patterning of molecular films designed to control interactions of biomolecules with nanoscale biosensor surfaces creates new possibilities as well as new challenges

Biomicrofluidics: recent trends and future challenges

Biomicrofluidics is an active area of research at present, exploring the synergy of microfluidics with cellular and molecular biology, biotechnology, and biomedical engineering. The present article outlines the recent advancements in these areas, including the development of novel lab-on-a-chip based applications. Particular emphasis is given on the microfluidics-based handling of DNA, cells, and proteins, as well as fundamental microfluidic considerations for design of biomedical microdevices. Future directions of research on these topics are also discussed

Chemistry in nanochannel confinement

This review addresses the questions of whether it makes sense to use lithographically defined nanochannels for chemistry in liquids, and what it is possible to learn from experiments on that topic. The behavior of liquids in different classes of pores (categorized according to their size) is reviewed, with a focus on chemical reactions and protein dynamics. A number of interesting phenomena are discussed for nanochannels with feature sizes that are manufacturable with modern photolithography-based fabrication technology. The use of spectroscopic methods to investigate chemistry in nanochannels, where both spectroscopic method and nanochannels are integrated into a single device, will be evaluated