Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics

Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average.

Auditory detection, discrimination and speech processing in ageing, noise-sensitive and hearing-impaired listeners

The aims of this research were to document changes in hearing and speech intelligibility in noise that occur with ageing, noise sensitivity, and progressive bilateral sensorineural hearing loss. Five groups defined by age, clinical complaint and degree of hearing loss were tested. Each of 73 subjects participated in nine different procedures, including detection in quiet and in continuous 90 dB SPL helicopter noise, frequency and duration discrimination, consonant recognition and word identification. The effects of different types of background noise and speech-to-noise ratio were investigated. Ageing, without concomitant hearing loss, resulted in significantly greater DLs both for frequency and for duration with a 20 ms standard at both 500 Hz and 4,000 Hz. Hearing loss, unconfounded by ageing, affected masked detection and frequency discrimination at 4,000 Hz and speech intelligibility in noise. The sole finding for subjects with noise sensitivity was an upward spread of masking for detection. Across tests, the best predictors of speech processing decrements were the detection thresholds for 2,000 Hz and 4,000 Hz in quiet or in noise.

The effect of aging on horizontal plane sound localization

An experiment was conducted to determine the effect of aging on sound localization. Seven groups of 16 subjects, aged 10-81 years, were tested. Sound localization was assessed using six different arrays of four or eight loudspeakers that surrounded the subject in the horizontal plane, at a distance of 1 m. For two 4-speaker arrays, one loudspeaker was positioned in each spatial quadrant, on either side of the midline or the interaural axis, respectively. For four 8-speaker arrays, two loudspeakers were positioned in each quadrant, one close to the midline and the second separated from the first by 15 degrees, 30 degrees, 45 degrees, or 60 degrees. Three different 300-ms stimuli were localized: two one-third-octave noise bands, centered at 0.5 and 4 kHz, and broadband noise. The stimulus level (75 dB SPL) was well above hearing threshold for all subjects tested. Over the age range studied, percent-correct sound-source identification judgments decreased by 12%-15%. Performance decrements were apparent as early as the third decade of life. Broadband noise was easiest to localize (both binaural and spectral cues were available), and the 0.5-kHz noise band, the most difficult to localize (primarily interaural temporal difference cue available). Accuracy was relatively higher in front of than behind the head, and errors were largely front/back mirror image reversals. A left-sided superiority was evident until the fifth decade of life. The results support the conclusions that the processing of spectral information becomes progressively less efficient with aging, and is generally worse for sources on the right side of space.

Sound localization. The interaction of aging, hearing loss and hearing protection

The effect of conventional ear plugs and ear muffs, and muffs with limited dichotic amplification on the ability to localize one-third octave noise bands was investigated under semi-reverberant listening conditions. Forty-eight normal-hearing subjects, half over 40 years of age, and 23 subjects with bilateral sensorineural hearing loss participated. Sound localization was assessed using an array of six loudspeakers surrounding the subject at azimuth angles 60 degrees apart. One block of 120 forced-choice speaker identification trials was presented for each of 16 listening conditions defined by ear condition (unoccluded, E-A-R plug, E-A-R muff, and Bilsom 2392 muff), stimulus frequency (500 Hz and 4000 Hz), and background (quiet and continuous 65 dB SPL-white noise). Plugs and muffs, particularly active muffs, resulted in decrements in right/left judgments based on interaural intensity but not time-of-arrival differences. High-frequency front/back discrimination was affected more by muffs than by plugs. Error patterns for the conventional and active muffs were dissimilar. Aging resulted in a decrement in unoccluded front/back discrimination. Trends for the impaired subjects were the same as those for normal subjects at 500 Hz. Many could not hear 4000 Hz with conventional protectors. Their performance was no different from normal with the active muffs.

Cortisol metabolism by human liver in vitro--I. Metabolite identification and inter-individual variability

The measurement of urinary 6 beta-hydroxycortisol (6 beta-OHF) has been widely used as a non-invasive clinical test to detect cytochrome P450 induction. Although only a minor biotransformation, 6 beta-OHF formation represents a sensitive target for many P450-inducing drugs and environmental chemicals in man. There is good evidence that an isozyme of the P450IIIA subfamily is predominantly responsible for 6 beta-hydroxylase activity and therefore it has been suggested that urinary 6 beta-OHF is a marker of the induction of P450IIIA. The basis of the present study was that in order to realistically assign to 6 beta-OHF the status of a P450IIIA marker we should characterize all the metabolites of cortisol produced by human liver and assess inter-liver variability. Incubations at 37 degrees C for 2 h contained [3H]cortisol (0.1 microCi, 1 or 50 microM), MgCl2 (10 mM), microsomal or cytosolic protein (3 mg), an NADPH-regenerating system and 1/15 M phosphate buffer (pH 7.4) to give a final volume of 0.5 ml. Extraction with ethyl acetate (2 x 2 ml) was followed by radiometric HPLC analysis. Metabolites were identified by co-chromatography with authentic standards and mass spectrometry (electron impact and chemical ionization). All the microsomal incubations (n = 6 livers) produced 6 alpha-hydroxycortisol (6 alpha-OHF), 6 beta-OHF, 20 beta-dihydroxycortisol, 20 beta-dihydroxycortisone, cortisone, and 3 alpha, 5 beta-tetrahydrocortisone (3 alpha, 5 beta-THE), while five produced 6 beta-hydroxycortisone and four produced 3 alpha, 5 beta-tetrahydrocortisol (3 alpha, 5 beta-THF). The cytosolic incubations gave a much simpler metabolic profile, with 3 alpha, 5 beta-THF the major metabolite and 3 alpha, 5 beta-THE a minor metabolite. There was considerable inter-individual variability in metabolite profiles from microsomal incubations. 6 beta-OHF varied from 2.8 to 31.7%. Major metabolites were cortisone and 3 alpha, 5 beta-THE. Inter-liver variability was less for cytosolic incubations, the major metabolite always being 3 alpha, 5 beta-THF. In conclusion we have rigorously identified the hepatic metabolites of cortisol formed in vitro. The highly complex and variable hepatic metabolism of cortisol clearly limits the use of urinary 6 beta-OHF excretion as a marker of baseline P450IIIA activity in man.

Azoles, allylamines and drug metabolism

Four antifungal drugs, the azoles ketoconazole, itraconazole and fluconazole, and the allylamine terbinafine, were studied for their effects on the metabolism of cyclosporin A (CyA) and cortisol by human liver microsomes in vitro (n = 3). Ketoconazole produced marked inhibition of CyA hydroxylase (to metabolites M17 and M1) with IC50 and Ki values of 0.24 +/- 0.01 and 0.022 +/- 0.004 microM, respectively. On the basis of the IC50, itraconazole was 10 times less potent (IC50 of 2.2 +/- 0.2 microM), and fluconazole and terbinafine were each above 100 microM. No kinetic parameters were calculated for terbinafine because of the lack of inhibitory effects. Ketoconazole was the most potent inhibitor of cortisol metabolism (to 6 beta-hydroxycortisol, IC50 = 0.6 microM). Itraconazole produced marked inhibition of cortisol metabolism (IC50 = 2.4 microM), but fluconazole and terbinafine had little effect. These data confirm that ketoconazole is a potent inhibitor of cytochrome P-450-IIIA4, and this has clinical relevance. Although the inhibition with fluconazole was much less than with itraconazole at equimolar concentrations, it should be noted that in-vivo plasma concentrations of fluconazole are much greater than that of itraconazole. Clinical interactions of CyA with both fluconazole and itraconazole have been reported; in contrast to these azoles, terbinafine does not have the same interaction potential.

Sound localization: effects of reverberation time, speaker array, stimulus frequency, and stimulus rise/decay

This research assessed the ability of human listeners to localize one-third octave noise bands in the horizontal plane. The effects of reverberation time (absorbent versus reverberant room), stimulus center frequency (500, 1000, 2000, and 4000 Hz), stimulus rise/decay time (5 vs 200 ms) and speaker array (frontal versus lateral) were investigated for four subjects using a forced-choice speaker-identification paradigm. Sound localization scores were consistently lower in the reverberant room than in the absorbent room. They also revealed strong frequency and azimuthal effects. The benefit of a shorter rise/decay time was small and limited to low frequencies. The identification of a speaker position depended strongly upon the array in which it was embedded, primarily because localization in the lateral array led to frequency-dependent front/back confusions and response bias. The results also illustrated the importance of choosing a coordinate system based on the auditory cone-of-confusion to analyze localization data for speaker arrays spanning the aural axis.

Basic calcium phosphate crystal-induced collagenase production: role of intracellular crystal dissolution

OBJECTIVE

To investigate the potential therapeutic effects of inhibiting intracellular dissolution of basic calcium phosphate (BCP) crystals in tissue culture by raising lysosomal pH using bafilomycin A1, a specific vacuolar pump inhibitor.

DESIGN

45Ca-labeled crystals were used to demonstrate intracellular crystal dissolution in human foreskin fibroblasts (HF). Mitogenesis was evaluated using [3H]thymidine incorporation assays and cell counts. Northern blot and Western blot were used to study collagenase [matrix metalloproteinase-1 (MMP1)] mRNA accumulation and protein secretion, respectively.

RESULTS

Bafilomycin A1 inhibited intracellular dissolution of BCP crystals and caused a concentration-dependent inhibition of BCP crystal-induced mitogenesis. Doses of bafilomycin A1 which inhibited intracellular crystal dissolution and mitogenesis had no effect on BCP crystal-induced MMP1 mRNA accumulation or protein secretion.

CONCLUSION

Raising lysosomal pH to inhibit intracellular BCP crystal dissolution attenuates the proliferative response to BCP crystals in HF but does not prevent metalloprotease synthesis and secretion. The therapeutic potential of lysosomotropic agents for preventing joint destruction in BCP crystal deposition disease is limited.

The membrane environment can promote or suppress bistability in cell signaling networks

Many key biochemical reactions that mediate signal transduction in cells occur at the cell membrane, yet how the two-dimensional membrane environment influences the collective behavior of signaling networks is poorly understood. We study models of two topologically different signaling pathways that exhibit bistability, examining the effects of reduced protein mobility and increased concentration at the membrane, as well as effects due to differences in spatiotemporal correlations between the membrane environment and three-dimensional cytoplasm. The two model networks represent the distributive enzymatic modification of a protein at multiple sites and the positive feedback-mediated activation of a protein. In both cases, we find that confining proteins to a membrane-like environment can markedly alter the emergent dynamics. For the distributive protein modification network, increased concentration promotes bistability through enhanced protein-protein binding, while lower mobility and membrane-enhanced spatiotemporal correlations suppress bistability. For the positive feedback-mediated activation network, confinement to a membrane environment enhances protein activation, which can induce bistability or stabilize a monostable, active state. Importantly, the influence of the membrane environment on signaling dynamics can be qualitatively different for signaling modules with different network topologies.

A novel pH-dependent membrane peptide that binds to EphA2 and inhibits cell migration

Misregulation of the signaling axis formed by the receptor tyrosine kinase (RTK) EphA2 and its ligand, ephrinA1, causes aberrant cell-cell contacts that contribute to metastasis. Solid tumors are characterized by an acidic extracellular medium. We intend to take advantage of this tumor feature to design new molecules that specifically target tumors. We created a novel pH-dependent transmembrane peptide, TYPE7, by altering the sequence of the transmembrane domain of EphA2. TYPE7 is highly soluble and interacts with the surface of lipid membranes at neutral pH, while acidity triggers transmembrane insertion. TYPE7 binds to endogenous EphA2 and reduces Akt phosphorylation and cell migration as effectively as ephrinA1. Interestingly, we found large differences in juxtamembrane tyrosine phosphorylation and the extent of EphA2 clustering when comparing TYPE7 with activation by ephrinA1. This work shows that it is possible to design new pH-triggered membrane peptides to activate RTK and gain insights on its activation mechanism.

Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns

Recent superresolution microscopy studies in E. coli demonstrate that the cytoplasm has highly variable local concentrations where macromolecular crowding plays a central role in establishing membrane-less compartmentalization. This spatial inhomogeneity significantly influences molecular transport and association processes central to gene expression. Yet, little is known about how macromolecular crowding influences gene expression bursting-the episodic process where mRNA and proteins are produced in bursts. Here, we simultaneously measured mRNA and protein reporters in cell-free systems, showing that macromolecular crowding decoupled the well-known relationship between fluctuations in the protein population (noise) and mRNA population statistics. Crowded environments led to a 10-fold increase in protein noise even though there were only modest changes in the mRNA population and fluctuations. Instead, cell-like macromolecular crowding created an inhomogeneous spatial distribution of mRNA ("spatial noise") that led to large variability in the protein production burst size. As a result, the mRNA spatial noise created large temporal fluctuations in the protein population. These results highlight the interplay between macromolecular crowding, spatial inhomogeneities, and the resulting dynamics of gene expression, and provide insights into using these organizational principles in both cell-based and cell-free synthetic biology.

Coreceptor affinity for MHC defines peptide specificity requirements for TCR interaction with coagonist peptide-MHC

The requirement for the TCR to interact with coagonists, endogenous MHC–peptide complexes which do not themselves activate the T cell, decreases as the strength of the CD8–class I interaction increases.

Recent work has demonstrated that nonstimulatory endogenous peptides can enhance T cell recognition of antigen, but MHCI- and MHCII-restricted systems have generated very different results. MHCII-restricted TCRs need to interact with the nonstimulatory peptide–MHC (pMHC), showing peptide specificity for activation enhancers or coagonists. In contrast, the MHCI-restricted cells studied to date show no such peptide specificity for coagonists, suggesting that CD8 binding to noncognate MHCI is more important. Here we show how this dichotomy can be resolved by varying CD8 and TCR binding to agonist and coagonists coupled with computer simulations, and we identify two distinct mechanisms by which CD8 influences the peptide specificity of coagonism. Mechanism 1 identifies the requirement of CD8 binding to noncognate ligand and suggests a direct relationship between the magnitude of coagonism and CD8 affinity for coagonist pMHCI. Mechanism 2 describes how the affinity of CD8 for agonist pMHCI changes the requirement for specific coagonist peptides. MHCs that bind CD8 strongly were tolerant of all or most peptides as coagonists, but weaker CD8-binding MHCs required stronger TCR binding to coagonist, limiting the potential coagonist peptides. These findings in MHCI systems also explain peptide-specific coagonism in MHCII-restricted cells, as CD4–MHCII interaction is generally weaker than CD8–MHCI.

Speech intelligibility in noise: effects of fluency and hearing protector type

This research investigated the effect of car protectors on the intelligibility of speech in noise. Listeners with normal hearing, high-frequency, and flat loss were tested. Half the subjects in each group were fluent in English and half-poorly conversant. Taped lists of 25 words were presented free field under conditions defined by the speech-to-noise ratio, spectrum of noise background, and presence of ear protection. The results showed that intelligibility decreased with speech-to-noise ratio and was poorer in crowd noise than in white noise. The protector had no effect for the normal listener, but caused a substantial decrement in those with impairment. In all groups nonfluency contributed an additional loss of 10% to 20%. Significant differences in performance were noted for different muff and plug types.

Cortisol metabolism in vitro--III. Inhibition of microsomal 6 beta-hydroxylase and cytosolic 4-ene-reductase

The in vitro metabolism of cortisol in human liver fractions is highly complex and variable. Cytosolic metabolism proceeds predominantly via A-ring reduction (to give 3 alpha,5 beta-tetrahydrocortisol; 3 alpha,5 beta-THF), while microsomal incubations generate upto 7 metabolites, including 6 beta-hydroxycortisol (6 beta-OHF), and 6 beta-hydroxycortisone (6 beta-OHE), products of the cytochrome P450 (CYP) 3A subfamily. The aim of the present study was, therefore, to examine two of the main enzymes involved in cortisol metabolism, namely, microsomal 6 beta-hydroxylase and cytosolic 4-ene-reductase. In particular, we wished to assess the substrate specificity of these enzymes and identify compounds with inhibitory potential. Incubations for 30 min containing [3H]cortisol, potential inhibitors, microsomal or cytosolic protein (3 mg), and co-factors were followed by radiometric HPLC analysis. The Km value for 6 beta-OHF and 6 beta-OHE formation was 15.2 +/- 2.1 microM (mean +/- SD; n = 4) and the Vmax value 6.43 +/- 0.45 pmol/min/mg microsomal protein. The most potent inhibitor of cortisol 6 beta-hydroxylase was ketoconazole (Ki = 0.9 +/- 0.4 microM; n = 4), followed by gestodene (Ki = 5.6 +/- 0.6 microM) and cyclosporine (Ki = 6.8 +/- 1.4 microM). Both betamethasone and dexamethasone produced some inhibition (Ki = 31.3 and 54.5 microM, respectively). However, substrates for CYP2C (tolbutamide), CYP2D (quinidine), and CYP1A (theophylline) were essentially non-inhibitory. The Km value for cortisol 4-ene-reductase was 26.5 +/- 11.2 microM (n = 4) and the Vmax value 107.7 +/- 46.0 pmol/min/mg cytosolic protein. The most potent inhibitors were androstendione (Ki = 17.8 +/- 3.3 microM) and gestodene (Ki = 23.8 +/- 3.8 microM). Although both compounds have identical A-rings to cortisol, and undergo reduction, inhibition was non-competitive.

Cortisol metabolism in vitro--II. Species difference

It has been suggested that cortisol 6 beta-hydroxylase activity specifically reflects cytochrome P4503A (CYP3A) levels in the liver. However, we have previously reported that the metabolism of cortisol in human liver fractions in vitro is extremely complex and variable, and therefore complete metabolite analysis must be undertaken if 6 beta-hydroxycortisol is to be used as a marker of CYP3A activity. In the present study, the metabolism of [3H]cortisol by hepatic microsomes from various animal species, and by cytosol from male and female rats, has been defined and compared with metabolites formed by human liver microsomes. Metabolites were characterized by co-chromatography with authentic standards, mass spectrometry, and quantified by radiometric HPLC. The results show that all microsomes prepared from animal species studied (male and female rat, male and female guinea-pig, male hamsters and mice) can metabolize cortisol, although the metabolic profiles are both quantitatively and qualitatively different from that obtained with human microsomes. In general the metabolic profiles for animal microsomes are simpler: hamster, mouse and guinea pig show only 6 beta-hydroxylase and 11 beta-dehydrogenase activity, although male rat shows both of these and 20 beta-reductase activity while the female rat possesses all of the above as well as the ability to reduce the A-ring (delta 4-reductase and 3-oxidoreductase activities). The female rat also produces two metabolites undetected in humans. Incubations with male rat cytosol generated 20 beta-dihydrocortisone as the major metabolite, and several unidentified minor polar metabolites, whereas female cytosolic products were identical to those generated by human cytosol, the major metabolite being 3 alpha,5 beta-tetrahydrocortisol. In conclusion, our studies have shown that hepatic cortisol metabolism is extremely variable amongst the species investigated and that the hamster provides the simplest model with which to explore cortisol 6 beta-hydroxylase activity.

Auditory perception with level-dependent hearing protectors. The effects of age and hearing loss

Auditory perception with hearing protectors was assessed in three groups of subjects, two with normal hearing, but differing in age, and one with moderate bilateral sensorineural hearing loss. Individuals were tested with the ears unoccluded, and fitted with each of two level-dependent ear muffs and their conventional level-independent counterparts. One of the former devices provided limited amplification. In each of these five ear conditions, the threshold of audibility for one-third octave noise bands centered at 500, 1,000, 2,000 and 4,000 Hz, consonant discrimination, and word recognition were measured in quiet and in a continuous impulse noise background. The results showed that the attenuation of sounds (i.e. the difference between protected and unoccluded thresholds) in quiet did not vary as a function of age or hearing loss for any of the four protectors. In noise, the difference between protected and unoccluded listening was close to zero, as long as hearing was normal. With hearing loss as a factor, there was a significant increment in the protected threshold, the amount determined by the device. Word recognition in quiet was adversely affected in normal-hearing listeners by the three attenuating devices but improved in noise relative to unoccluded listening. Amplification had a deleterious effect for both consonant discrimination and word recognition in noise. In hearing-impaired listeners, speech perception was impeded by all four muffs but less so in quiet with limited amplification.

Signal detection in industrial noise: effects of noise exposure history, hearing loss, and the use of ear protection

The detection of one-third octave signals superimposed on backgrounds of steady-state and intermittent industrial noise of 84 dBA was investigated for observers with normal hearing or moderate to severe noise-induced hearing loss (NIHL). Variables included age, noise exposure history, configuration of the audiogram and the wearing of insert hearing protectors. Detection thresholds were obtained binaurally over headphones using a two- interval forced-choice procedure. For unprotected listening all observers showed a masked threshold of about 80 dBA for a one-third octave band cented at 3.15 kHz. Neither variation in noise exposure history nor configuration of the audiogram were significant factors. Using insert protectors in noise, observers with normal hearing showed an advantage on average of 3 dB. Those with NIHL gave masked detection thresholds greater than 100 dBA. Detection of a one-third octave band centred at 1 kHz by hearing-impaired observers with mild to moderate loss at 1 kHz was similar to that for normal observers. A model of the detection process was developed and evaluated.

Nonpalpable occult and metastatic papillary thyroid carcinoma

The results of palpation, ultrasound, and detailed pathology were compared in 50 patients undergoing total thyroidectomy. Of the 211 nodules recognized by pathology, palpation detected 24% and ultrasound detected 43%. There were 14 patients with palpable papillary carcinomas, and 12 of these 14 had metastatic foci in other portions of the gland. Metastatic foci would have been left in 10 patients if only a lobectomy had been performed and would have been left in 6 patients if only a subtotal thyroidectomy (as defined in this report) had been performed. Of the 33 patients with benign palpable nodules, 5 had occult papillary carcinomas. In 2 of those 5 patients, the occult carcinomas would not have been removed if a less-than-total thyroidectomy had been performed. The significance of these occult and metastatic papillary carcinomas is discussed.

First passage of molecular motors on networks of cytoskeletal filaments

Molecular motors facilitate intracellular transport through a combination of passive motion in the cytoplasm and active transport along cytoskeletal filaments. Although the motion of motors on individual filaments is often well characterized, it remains a challenge to understand their transport on networks of filaments. Here we use computer simulations of a stochastic jump process to determine first-passage times (FPTs) of a molecular motor traversing an interval containing randomly distributed filaments of fixed length. We characterize the mean first-passage time (MFPT) as a function of the number and length of filaments. Intervals containing moderate numbers of long filaments lead to the largest MFPTs with the largest relative standard deviation; in this regime, some filament configurations lead to anomalously large FPTs due to spatial regions where motors become trapped for long times. For specific filament configurations, we systematically reverse the directionality of single filaments and determine the MFPT of the perturbed configuration. Surprisingly, altering a single filament can dramatically impact the MFPT, and filaments leading to the largest changes are commonly found in different regions than the traps. We conclude by analyzing the mean square displacement of motors in unconfined systems with a large density of filaments and show that they behave diffusively at times substantially less than the MFPT to traverse the interval. However, the effective diffusion coefficient underestimates the MFPT across the bounded interval, emphasizing the importance of local configurations of filaments on first-passage properties.

Effects of rise/decay time on the lateralization of interaurally delayed 1-kHz tones

Experiments in lateralization were performed to evaluate the relative contribution of onset and phase cues in binaural hearing. A 1-kHz signal was presented with interaural stimulus delays ranging from 0 to 1000 microseconds, corresponding to phase shifts of 0 degree to 360 degrees. For a given value of delay, the leading signal was presented randomly to the right or left ear over a block of 100 trials, and the laterality of the resultant image was judged. The percentage of correct judgments was plotted as a function of delay with rise/decay time as a parameter. Values of rise/decay time ranged from 0 to 500 ms. The results indicated that rise/decay times of at least 200 ms are necessary to avoid contributions from the onset cue to the formation of lateralization judgments. For rise/decay times shorter than 200 ms, a conflict occurs between phase and onset cues in the region of phase shifts from 180 degrees to 360 degrees. At the limit with very short rise/decay times, the onset cue completely overrides the phase cue.

Shaping membrane vesicles by adsorption of a semiflexible polymer

The adsorption of polymers onto fluid membranes is a problem of fundamental interest in biology and soft materials, in part because the flexibility of membranes can lead to nontrivial coupling between polymer and membrane configurations. Here, we use Monte Carlo computer simulations to study the adsorption of a semiflexible polymer onto a fluid membrane vesicle. Polymer adsorption can significantly impact both the vesicle and polymer shapes, and we identify distinct classes of configurations that emerge as a function of polymer persistence length, membrane bending rigidity, adsorption strength, and vesicle size. Large-scale deformations of the vesicle include invaginations of the membrane that internalize the polymer in a membrane bud. The buds range from disk-like shapes surrounding a collapsed polymer to tubular deformations enveloping rod-like polymers. For small vesicles, polymer adsorption also induces dumbbell-like vesicle shapes with a narrow membrane constriction circled by the polymer. Vesicles with sufficiently small or large bending rigidities adopt configurations similar to those without the polymer present. We further characterize statistical properties of the membrane and polymer configurations and identify distinct classes of polymer configurations that emerge within membrane buds. Analysis of idealized polymer-membrane configurations provides additional insight into transitions between bud shapes.

Crowding-induced interactions of ring polymers

Macromolecular crowding and the presence of surfaces can significantly impact the spatial organization of biopolymers. While the importance of crowding-induced depletion interactions in biology has been recognized, much remains to be understood about the effect of crowding on biopolymers such as DNA plasmids. A fundamental problem highlighted by recent experiments is to characterize the impact of crowding on polymer-polymer and polymer-surface interactions. Motivated by the need for quantitative insight, we studied flexible ring polymers in crowded environments using Langevin dynamics simulations. The simulations demonstrated that crowding can lead to compaction of isolated ring polymers and enhanced interactions between two otherwise repulsive polymers. Using umbrella sampling, we determined the potential of mean force (PMF) between two ring polymers as a function of their separation distance at different volume fractions of crowding particles, φ. An effective attraction emerged at φ≈ 0.4, which is similar to the degree of crowding in cells. Analogous simulations showed that crowding can lead to strong adsorption of a ring polymer to a wall, with an effective attraction to the wall emerging at a smaller volume fraction of crowders (φ≈ 0.2). Our results reveal the magnitude of depletion interactions in a biologically-inspired model and highlight how crowding can be used to tune interactions in both cellular and cell-free systems.