Predicting protein-ligand affinity with a random matrix framework

Rapid determination of whether a candidate compound will bind to a particular target receptor remains a stumbling block in drug discovery. We use an approach inspired by random matrix theory to decompose the known ligand set of a target in terms of orthogonal "signals" of salient chemical features, and distinguish these from the much larger set of ligand chemical features that are not relevant for binding to that particular target receptor. After removing the noise caused by finite sampling, we show that the similarity of an unknown ligand to the remaining, cleaned chemical features is a robust predictor of ligand-target affinity, performing as well or better than any algorithm in the published literature. We interpret our algorithm as deriving a model for the binding energy between a target receptor and the set of known ligands, where the underlying binding energy model is related to the classic Ising model in statistical physics.This research was funded by a grant from Roche Pharmaceuticals. A.A.L. acknowledges the support of a Fulbright Fellowship. L.J.C. was supported by a Next Generation Fellowship, and a Marie Curie Career Integration Grant (Evo-Couplings, Grant 631609). M.P.B. is an investigator of the Simons Foundation, and also acknowledges support from the National Science Foundation through DMS-1411694

Modifying one’s hand’s trajectory when a moving target’s orientation changes

The path that the hand takes to intercept an elongated moving target depends on the target’s orientation. How quickly do people respond to changes in the moving target’s orientation? In the present study, participants were asked to intercept moving targets that sometimes abruptly changed orientation shortly after they started moving. It took the participants slightly more than 150 ms to adjust their hands’ paths to a change in target orientation. This is about 50 ms longer than it took them to respond to a 5-mm jump in the moving target’s position. It is only slightly shorter than it took them to initiate the movement. We propose that responses to changes in visually perceived orientation are not exceptionally fast, because there is no relationship between target orientation and direction of hand movement that is sufficiently general in everyday life for one to risk making an inappropriate response in order to respond faster

Self-Organization, Layered Structure, and Aggregation Enhance Persistence of a Synthetic Biofilm Consortium

Microbial consortia constitute a majority of the earth’s biomass, but little is known about how these cooperating communities persist despite competition among community members. Theory suggests that non-random spatial structures contribute to the persistence of mixed communities; when particular structures form, they may provide associated community members with a growth advantage over unassociated members. If true, this has implications for the rise and persistence of multi-cellular organisms. However, this theory is difficult to study because we rarely observe initial instances of non-random physical structure in natural populations. Using two engineered strains of Escherichia coli that constitute a synthetic symbiotic microbial consortium, we fortuitously observed such spatial self-organization. This consortium forms a biofilm and, after several days, adopts a defined layered structure that is associated with two unexpected, measurable growth advantages. First, the consortium cannot successfully colonize a new, downstream environment until it selforganizes in the initial environment; in other words, the structure enhances the ability of the consortium to survive environmental disruptions. Second, when the layered structure forms in downstream environments the consortium accumulates significantly more biomass than it did in the initial environment; in other words, the structure enhances the global productivity of the consortium. We also observed that the layered structure only assembles in downstream environments that are colonized by aggregates from a previous, structured community. These results demonstrate roles for self-organization and aggregation in persistence of multi-cellular communities, and also illustrate a role for the techniques of synthetic biology in elucidating fundamental biological principles

Predicted trends in long-term breast cancer survival in England and Wales

Trends in long-term relative survival from breast cancer are examined for women diagnosed in England and Wales up to 2001, using both period and hybrid approaches. Large improvements in long-term survival are predicted. Women with breast cancer still experience persistent excess mortality up to at least 20 years after diagnosis