Intrinsically Disordered Proteins: Where Computation Meets Experiment

Proteins are heteropolymers that play important roles in virtually every biological reaction. While many proteins have well-defined three-dimensional structures that are inextricably coupled to their function, intrinsically disordered proteins (IDPs) do not have a well-defined structure, and it is this lack of structure that facilitates their function. As many IDPs are involved in essential cellular processes, various diseases have been linked to their malfunction, thereby making them important drug targets. In this review we discuss methods for studying IDPs and provide examples of how computational methods can improve our understanding of IDPs. We focus on two intensely studied IDPs that have been implicated in very different pathologic pathways. The first, p53, has been linked to over 50% of human cancers, and the second, Amyloid-β (Aβ), forms neurotoxic aggregates in the brains of patients with Alzheimer’s disease. We use these representative proteins to illustrate some of the challenges associated with studying IDPs and demonstrate how computational tools can be fruitfully applied to arrive at a more comprehensive understanding of these fascinating heteropolymers.National Science Foundation (U.S.). Directorate for Biological Sciences. Postdoctoral Research Fellowship (Grant 1309247

Biophysical mechanism for Ras-nanocluster formation and signaling in plasma membrane

Ras GTPases are lipid-anchored G proteins which play a fundamental role in cell signaling processes. Electron micrographs of immunogold-labeled Ras have shown that membrane-bound Ras molecules segregate into nanocluster domains. Several models have been developed in attempts to obtain quantitative descriptions of nanocluster formation, but all have relied on assumptions such as a constant, expression-level independent ratio of Ras in clusters to Ras monomers (cluster/monomer ratio). However, this assumption is inconsistent with the law of mass action. Here, we present a biophysical model of Ras clustering based on short-range attraction and long-range repulsion between Ras molecules in the membrane. To test this model, we performed Monte Carlo simulations and compared statistical clustering properties with experimental data. We find that we can recover the experimentally-observed clustering across a range of Ras expression levels, without assuming a constant cluster/monomer ratio or the existence of lipid rafts. In addition, our model makes predictions about the signaling properties of Ras nanoclusters in support of the idea that Ras nanoclusters act as an analog-digital-analog converter for high fidelity signaling.Comment: 8 figures. PLoS ONE, in pres

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a host’s microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patient’s microbiota

Mobile phone based mini-spectrometer for rapid screening of skin cancer

We demonstrate a highly sensitive mobile phone based spectrometer that has potential to detect cancerous skin lesions in a rapid, non-invasive manner. Earlier reports of low cost spectrometers utilize the camera of the mobile phone to image the field after moving through a diffraction grating. These approaches are inherently limited by the closed nature of mobile phone image sensors and built in optical elements. The system presented uses a novel integrated grating and sensor that is compact, accurate and calibrated. Resolutions of about 10 nm can be achieved. Additionally, UV and visible LED excitation sources are built into the device. Data collection and analysis is simplified using the wireless interfaces and logical control on the smart phone. Furthermore, by utilizing an external sensor, the mobile phone camera can be used in conjunction with spectral measurements. We are exploring ways to use this device to measure endogenous fluorescence of skin in order to distinguish cancerous from non-cancerous lesions with a mobile phone based dermatoscope

The ANZUS Treaty during the Cold War: a reinterpretation of U.S. diplomacy in the Southwest Pacific

This article explains the origins of the Australia–New Zealand–United States (ANZUS) Treaty by highlighting U.S. ambitions in the Pacific region after World War II. Three clarifications to the historiography merit attention. First, an alliance with Australia and New Zealand reflected the pursuit of U.S. interests rather than the skill of antipodean diplomacy. Despite initial reservations in Washington, geostrategic anxiety and economic ambition ultimately spurred cooperation. The U.S. government's eventual recourse to coercive diplomacy against the other ANZUS members, and the exclusion of Britain from the alliance, substantiate claims of self-interest. Second, the historiography neglects the economic rationale underlying the U.S. commitment to Pacific security. Regional cooperation ensured the revival of Japan, the avoidance of discriminatory trade policies, and the stability of the Bretton Woods monetary system. Third, scholars have unduly played down and misunderstood the concept of race. U.S. foreign policy elites invoked ideas about a “White Man's Club” in Asia to obscure the pursuit of U.S. interests in the region and to ensure British exclusion from the treaty

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles

Published with license by Taylor & Francis Group, LLC. Several gastrointestinal diseases show a sex imbalance, although the underlying (patho)physiological mechanisms behind this are not well understood. The gut microbiome may be involved in this process, forming a complex interaction with host immune system, sex hormones, medication and other environmental factors. Here we performed sex-specific analyses of fecal microbiota composition in 1135 individuals from a population-based cohort. The overall gut microbiome composition of females and males was significantly different (p = 0.001), with females showing a greater microbial diversity (p = 0.009). After correcting for the effects of intrinsic factors, smoking, diet and medications, female hormonal factors such as the use of oral contraceptives and undergoing an ovariectomy were associated with microbial species and pathways. Females had a higher richness of antibiotic-resistance genes, with the most notable being resistance to the lincosamide nucleotidyltransferase (LNU) gene family. The higher abundance of resistance genes is consistent with the greater prescription of the Macrolide-Lincosamide-Streptogramin classes of antibiotics to females. Furthermore, we observed an increased resistance to aminoglycosides in females with self-reported irritable bowel syndrome. These results throw light upon the effects of common medications that are differentially prescribed between sexes and highlight the importance of sex-specific analysis when studying the gut microbiome and resistome

Order, disorder, and protein aggregation

Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2015.Cataloged from PDF version of thesis.Includes bibliographical references (pages 114-124).Protein aggregation underlies a number of human diseases. Most notably, it occurs widely in neurodegenerative diseases, including Alzheimer's and Parkinson's. At the molecular level, neurotoxicity is thought to originate from toxic gains of function in multimeric aggregates of proteins that are otherwise predominantly monomeric and disordered, fluctuating between a very large number of structurally dissimilar states on nano- and microsecond timescales. These proteins, termed Intrinsically Disordered Proteins (IDPs), are notoriously difficult to probe using traditional biophysical techniques. In order to obtain structural information pertaining to the aggregation of IDPs, it is often necessary to develop computational and modeling tools, both to leverage the full extent of the experimental data, and to generate testable predictions for future experiments. In this thesis, I present three separate computational studies studying the formation of multimeric aggregates in IDPs, spanning different aspects of the aggregation process, from early nucleation events to fibril elongation. In the first study, I present a conformational ensemble of a-synuclein, the culprit protein of Parkinson's disease, constructed using a Variational Bayesian Weighting algorithm in combination with NMR data collected by our collaborators. We find that the data fit a description in which the protein predominantly exists as a disordered monomer but contains small quantities of multimeric states containing both helical and strand-rich conformations. In the second study, I focus on the process of amyloid fibril elongation in the Amyloid-[beta] (A[beta]) peptide of Alzheimer's disease. I compute the free energy surface associated with the fibril elongation reaction, and find that elongation of both A[beta]40 and A[beta]42 experimental fibril structures occurs on a downhill free energy pathway, proceeding via an obligate, fibril-associated hairpin intermediate. The fibril-associated hairpin is significantly more stable (relative to the fibrillar, elongated state) in A[beta]42 compared with A[beta]40, suggesting a potential clinical target of interest. Finally, I present lengthy, all-atom molecular simulations that suggest that nucleation of the minimum aggregating fragment of c-synuclein proceeds via a helical intermediate, requiring a structural conversion into a strand-rich nucleating species via a stochastic process of individual helices unfolding and self-associating via backbone hydrogen bonds.by Thomas Gurry.Ph. D