Identification of rare inherited variants associated with ASD and 16 new ASD risk genes d Inherited risk reveals both new biological pathways and shared PPI with known genes d We develop and validate a machine learning algorithm (ARC) to remove WGS artifacts d NR3C2 mutations define a novel syndromic form of ASD, which we model in zebrafish

SummaryDrugs and certain proteins are transported across the membranes of Gram-negative bacteria by energy-activated pumps. The outer membrane component of these pumps is a channel that opens from a sealed resting state during the transport process. We describe two crystal structures of the Escherichia coli outer membrane protein TolC in its partially open state. Opening is accompanied by the exposure of three shallow intraprotomer grooves in the TolC trimer, where our mutagenesis data identify a contact point with the periplasmic component of a drug efflux pump, AcrA. We suggest that the assembly of multidrug efflux pumps is accompanied by induced fit of TolC driven mainly by accommodation of the periplasmic component.

Heteromeric amino acid transporters (HATs) are the unique example, known in all kingdoms of life, of solute transporters composed of two subunits linked by a conserved disulfide bridge. In metazoans, the heavy subunit is responsible for the trafficking of the heterodimer to the plasma membrane, and the light subunit is the transporter. HATs are involved in human pathologies such as amino acidurias, tumor growth and invasion, viral infection and cocaine addiction. However structural information about interactions between the heavy and light subunits of HATs is scarce. In this work, transmission electron microscopy and single-particle analysis of purified human 4F2hc/L-type amino acid transporter 2 (LAT2) heterodimers overexpressed in the yeast Pichia pastoris, together with docking analysis and crosslinking experiments, reveal that the extracellular domain of 4F2hc interacts with LAT2, almost completely covering the extracellular face of the transporter. 4F2hc increases the stability of the light subunit LAT2 in detergent-solubilized Pichia membranes, allowing functional reconstitution of the heterodimer into proteoliposomes. Moreover, the extracellular domain of 4F2hc suffices to stabilize solubilized LAT2. The interaction of 4F2hc with LAT2 gives insights into the structural bases for light subunit recognition and the stabilizing role of the ancillary protein in HATs.CD98hc | 4F2hc ectodomain H eteromeric amino acid transporters (HATs) are composed of two subunits, a heavy (SLC3 family) and a light subunit [SLC7 or L-type amino acid transporter (LAT) family] linked by a conserved disulfide bridge (1). HATs are amino acid exchangers (1), and this transport activity resides in the light subunit (2). The heavy subunit (either 4F2hc or rBAT) is essential for trafficking of the holotransporter to the plasma membrane (3, 4). In mammals, six transporters heterodimerize with 4F2hc, and only one heterodimerizes with rBAT. The rBAT/b 0,+ AT complex is a dimer of heterodimers in which the light subunit is required for proper rBAT folding and stability (5, 6). In contrast, 4F2hc-associated transporters are simple heterodimers (6), and possible stabilizing roles of the two subunits in the biogenesis of the heterodimer have not been described.HATs have major impacts on human health and are involved directly in amino acidurias (cystinuria and lysinuric protein intolerance), tumor cell growth, glioma invasion, Kaposi's sarcomaassociated herpesvirus infection, and cocaine relapse (1). In addition to the role of HATs in amino acid transport, 4F2hc heterodimers mediate β1-and β3-integrin signaling (7).Structural information about HATs is scarce (1). The heavy subunits are type II membrane N-glycoproteins with a single transmembrane domain (TMD), an intracellular N terminus, and a large extracellular C terminus with sequence homology with bacterial α-amylases. Indeed, the atomic structure of the extracellular domain (ED) of human 4F2hc (4F2hc-ED) is similar to that of bacterial glucosidases [i.e., a triose phosphate isomerase barr...

The CAPRI and CASP prediction experiments have demonstrated the power of community wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting there may be important physical chemistry missing in the energy calculations. 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the non-polar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were on average structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a non-binder.

Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side chain sampling and backbone relaxation, and evaluated packing, electrostatic and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of methodological improvement.