Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.     

Visualizing dislocation nucleation by indenting colloidal crystals

The formation of dislocations is central to our understanding of yield, work hardening, fracture, and fatigue of crystalline materials. While dislocations have been studied extensively in conventional materials, recent results have shown that colloidal crystals offer a potential model system for visualizing their structure and dynamics directly in real space. Although thermal fluctuations are thought to play a critical role in the nucleation of these defects, it is difficult to observe them directly. Nano-indentation, during which a small tip deforms a crystalline film, is a common tool for introducing dislocations into a small volume that is initially defect-free. Here, we show that an analogue of nano-indentation performed on a colloidal crystal provides direct images of defect formation in real time and on the single particle level, allowing us to probe the effects of thermal fluctuations. We implement a new method to determine the strain tensor of a distorted crystal lattice and we measure the critical dislocation loop size and the rate of dislocation nucleation directly. Using continuum models, we elucidate the relation between thermal fluctuations and the applied strain that governs defect nucleation. Moreover, we estimate that although bond energies between particles are about fifty times larger in atomic systems, the difference in attempt frequencies makes the effects of thermal fluctuations remarkably similar, so that our results are also relevant for atomic crystals.     

The cargo-binding domain regulates structure and activity of myosin 5

Myosin 5 is a two-headed motor protein that moves cargoes along actin filaments. Its tail ends in paired globular tail domains (GTDs) thought to bind cargo. At nanomolar calcium levels, actin-activated ATPase is low and the molecule is folded. Micromolar calcium concentrations activate ATPase and the molecule unfolds. Here we describe the structure of folded myosin and the GTD's role in regulating activity. Electron microscopy shows that the two heads lie either side of the tail, contacting the GTDs at a lobe of the motor domain (approximately Pro 117-Pro 137) that contains conserved acidic side chains, suggesting ionic interactions between motor domain and GTD. Myosin 5 heavy meromyosin, a constitutively active fragment lacking the GTDs, is inhibited and folded by a dimeric GST-GTD fusion protein. Motility assays reveal that at nanomolar calcium levels heavy meromyosin moves robustly on actin filaments whereas few myosins bind or move. These results combine to show that with no cargo, the GTDs bind in an intramolecular manner to the motor domains, producing an inhibited and compact structure that binds weakly to actin and allows the molecule to recycle towards new cargoes.     

Optical monitoring of activity of many neurons in invertebrate ganglia during behaviors

Summary Optical methods for monitoring neuron activity were developed because these methods lend themselves to simultaneous multiple-site measurements. With the use of new voltage-sensitive dyes, the dye-related pharmacology and photodynamic damage appear to be relatively unimportant. Using multiple-site measurements made with a 124-element photodiode array, we estimated that approximately 30 of the 200 neurons present in theNavanax buccal ganglion make action potentials during feeding and that approximately 300 of the 1100 neurons present in theNavanax buccal ganglion make are active during the gill-withdrawal reflex. The fact that a light mechanical touch to the siphon skin activated such a large number of neurons in the abdominal ganglion suggests that understanding the neuronal basis of the gill-withdrawal reflex and its behavioral plasticity may be forbiddingly difficult.     

On characterizing optimization-based clustering methods

This paper suggests a simplification of a recent approach suggested by Windham to characterizing optimization-based clustering methods. The simplification is based on noting an analogy between certain quantities in Windham's formulation and corresponding quantities in mathematical statistics, particularly sufficient statistics and the exponential family of densities.He thanks an anonymous referee for several helpful comments.     

Large-sample results for optimization-based clustering methods

Many common (nonhierarchical) clustering and classification methods are optimization-based methods, in the sense described by Windham (1987) in this Journal. This paper gives some large sample properties for estimates derived by such methods. Under appropriate conditions, such estimates converge with probability one to a limit, and are asymptotically normally distributed around that limiting value. The conditions are satisfied by most of the common examples of optimization-based methods. Prepared for the 2nd International Conference, International Federation of Classification Societies, Charlottesville, VA, 1989. Supported in part by summer research funds, Graduate School of Business Administration, University of Colorado at Denver.     

Evidence for an activating effect of tabernanthine on rat brain catecholamine synthesis and elimination

Tabernanthine increased the synthesis and elimination of catecholamines (CA) in the striatum and the rest of the brain, but not in the hypothalamus. These data provide evidence that tabernanthine may activate CA turnover of some brain structures by acting at 2 steps of the metabolic pathway. The results are discussed in relation to a central stimulating action and a hypoxia antagonistic effect of this drug.