A physiological phase separation in airway mucus.

The pathology of the disease cystic fibrosis is known to be associated very generally with ionic imbalance in the mucosal secretion which lines the respiratory tract, so-called airway surface liquid (ASL). The imbalance is caused by mutation of a transmembrane protein (CFTR) implicated in the control of ion traffic across the airway epithelium. It is feasible that CFTR malfunction undermines a putative phase-separated texture of healthy ASL which is apparent in electron microscopy images. A molecular statistical description of ASL is presented here with the aim of illustrating this hypothesis at the phenomenological level. The model predicts that a volume criterion and a salt criterion must be met in order to achieve the phase-separated texture. These predictions help to rationalise the findings of clinical trials. In conjunction with further experimental investigation, molecular statistical approaches in this spirit have the potential to play a useful role in the drive towards treatment strategies.

Glassy arrest in colloidal fluids with size polydispersity.

Short-range attraction between colloidal particles such as proteins can drive a glass-like structural arrest. For monodisperse systems, mode-coupling theory affords a simple asymptotic prediction of the transition. Here, using a depletion mapping framework, we extend this result to incorporate size polydispersity. For comparison, we also give an energy landscape formulation of the transition. We comment on the relevance to subcellular crowding, recombinant protein expression, and osmotic stress in microbial organisms.

Salting-in the microbial cytoplasm.

Microbial organisms are known to rely for osmotic regulatory purposes on an assortment of low molecular weight molecules earmarked for function as osmolytes. The so-called 'compatible' subclass of osmolyte, notably glycine betaine, is distinguished by a propensity to avoid the large bound fraction of cytoplasmic water adsorbed at the surface of biological macromolecules. Here we argue that this property is implicated in thermodynamic stabilisation of the cytoplasm. A rudimentary molecular statistical approach indicates that flooding the cytoplasm with large amounts of compatible osmolyte is an effective way to deal with the threat of phase separation.

Volatile diffusional character of cytoplasm.

The fluctuating extracellular environment of microbial organisms influences diffusional mobility of macromolecules in the cytoplasm. This effect may be measured experimentally on the one hand by directly tracking the trajectories of individual macromolecules. We discuss how it may also be indirectly estimated from fluctuations in the amount of cytoplasmic water and from the varying patterns of protein expression seen in 2d gel analysis.

Sequence variability of proteins evolutionarily constrained by solution-thermodynamic function.

Focusing on silk fibroin and hemoglobin molecules as templates, we model protein homolog dispersal across sequence-fitness landscapes determined by solution thermodynamics. Landscapes are constructed by inspecting an idealized theoretical phase topology associated with sequence length and hydrophobic-polar composition, comprising liquid-liquid phase separation, gelation and liquid crystalline self-assembly. We then calculate the distribution of homologs in sequence space as steady states of a simple mutation-selection dynamics. The results are consistent with Swiss-Prot bioinformatic data.

Fluctuation-entanglement mechanism for director anchoring at nematic polymer surfaces.

The existence of polymeric entanglements in a polymer nematic liquid crystal modifies the Frank elastic description governing director deformation. We present a calculation of the director fluctuation contribution to polymer nematic surface tension, in which we supplement the usual Frank terms with a damping term due to entanglements. We infer an effective surface anchoring potential, going to zero as n ln n in the limit of low entanglement density n. The anchoring easy axis depends on the relative magnitudes of the Frank constants governing director elasticity. We comment on generalizing the approach to take into account polydomain structure.

Retention of enzyme gene duplicates by subfunctionalization.

Duplication-degeneration-complementation (DDC) describes a process by which evolving duplicates of a pleiotropic ancestral gene divide up the multiple functions of the ancestor between them (i.e. subfunctionalize), and this ultimately frustrates the rate of pseudogene formation. Focusing explicitly on enzyme-like pleiotropic function, we model DDC driven by sequence divergence between duplicates. The model incorporates an idealized sequence-function mapping in which enzyme-substrate binding affinity is related to hydrophobic versus polar (HP) amino-acid composition of tertiary structure about the binding pocket. In this sense, a transparent coupling between physical-chemical function of an enzyme and sequence evolution is presented.

Modelling self assembly of natural silk solutions.

We present a tentative interpretation of the origin of nematic liquid crystalline order exhibited by various natural silk fibroin solutions, notably those of orb-weaving spiders and the domestic silkworm Bombyx mori. It is thought that liquid crystalline rheology is exploited during the spinning process. We discuss in this approach the response of the liquid crystalline phase diagram to equilibrium physiological conditions and to parameters characterising the amino acid sequence of the fibroin molecules. The phase diagram is sensitive in this latter respect to sequence mutations, such that it may constitute a source of evolutionary selection pressure.

Towards modeling molecular cooperativity on the cellular scale.

Formulated originally to describe the subtle blend of kinetics and thermodynamics that drives protein folding and ligand binding, the molecular cooperativity concept extrapolates readily to the cellular scale. Here it constitutes a thermally driven mode of cytological organization which can be provisionally explored within the equation of state (EOS) framework of classical statistical mechanics. We give a unified EOS account of the 'proto-cooperative' phenomena of phase separation and gelation in cytoplasm, emphasizing osmoregulatory control mechanism. In an extension to this framework, we show that a significant thermodynamic partitioning of ribosomes could occur spontaneously in conjunction with phase separation. This would be tantamount to a translation-transcription decoupling, with relevance to cellular evolution.

Miscibility gap in the microbial fitness landscape.

It is shown from molecular statistical considerations that a demixing instability exists in the moment space of a microbial protein expression profile. Although avoidance of demixing is generally requisite for biological function, a comparison with proteomic and genomic data suggests that many microbes lie close to the onset of this instability. Over evolutionary time scales, straying too close or into the immiscible domain may be associated with intracellular compartmentalization.

Effect of director fluctuations on the surface tension of nematic liquid crystals.

We discuss the surface tension of a thermotropic nematic liquid crystal near the nematic-isotropic temperature. We find that certain experimentally observed features of the temperature trend that present difficulties to mean-field theoretical approaches can be attributed to director fluctuations. Our main result is the possibility of a minimum below T(NI) if the anchoring extrapolation length scales with reduced temperature in the spinodal limit as tx, with x<1. We also show in the case of partial nematic wetting that dampening of director fluctuations at the surface by anchoring at the nascent interface can reverse the sign of the surface tension discontinuity at T(NI).

Repeat-modulated population genetic effects in fungal proteins.

A number of fungal lineages, notably N. crassa, have evolved a novel mechanism of processing genomic duplication events known as repeat-induced point (RIP) mutation. This mechanism appears, on the one hand, to act as a conservative genomic safeguard, by introducing stop codons into duplicated nucleotide sequences, thereby preempting consequences such as dosage effects. However, it also typically performs further nonsynonymous (i.e., amino acid-changing) nucleotide substitutions, the significance of which is unclear. We explore here the possibility that RIP-mutated genes which evade silencing may have some microevolutionary impact on functional sequences. Our approach focuses on structurally important hydrophobic/polar (HP) amino-acid substitutions effected by RIP. We exploit a simple generic protein folding model to predict the associated emergence of increased protein-structural stability and variance within a large population.