A new way to see RNA.

Unlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced the RNA backbone torsion angles to two (η and θ, analogous to φ and ψ in proteins).

RosettaBackrub--a web server for flexible backbone protein structure modeling and design.

The RosettaBackrub server (http://kortemmelab.ucsf.edu/backrub) implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling.

Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design.

A major challenge in computational protein design is to identify functional sequences as top predictions. One reason for design failures is conformational plasticity, as proteins frequently change their conformation in response to mutations. To advance protein design, here we describe a method employing flexible backbone ensembles to predict sequences tolerated for a protein-protein interface.

Design of multi-specificity in protein interfaces.

Interactions in protein networks may place constraints on protein interface sequences to maintain correct and avoid unwanted interactions. Here we describe a "multi-constraint" protein design protocol to predict sequences optimized for multiple criteria, such as maintaining sets of interactions, and apply it to characterize the mechanism and extent to which 20 multi-specific proteins are constrained by binding to multiple partners. We find that multi-specific binding is accommodated by at least two distinct patterns.

Structural and mechanistic exploration of acid resistance: kinetic stability facilitates evolution of extremophilic behavior.

Kinetically stable proteins are unique in that their stability is determined solely by kinetic barriers rather than by thermodynamic equilibria. To better understand how kinetic stability promotes protein survival under extreme environmental conditions, we analyzed the unfolding behavior and determined the structure of Nocardiopsis alba Protease A (NAPase), an acid-resistant, kinetically stable protease, and compared these results with a neutrophilic homolog, alpha-lytic protease (alphaLP). Although NAPase and alphaLP have the same number of acid-titratable residues, kinetic studies revealed that the height of the unfolding free energy barrier for NAPase is less sensitive to acid than that of alphaLP, thereby accounting for NAPase's improved tolerance of low pH.

Role of toll-like receptors in changes in gene expression and NF-kappa B activation in mouse hepatocytes stimulated with lipopolysaccharide.

The liver is an important site of host-microbe interaction. Although hepatocytes have been reported to be responsive to lipopolysaccharide (LPS), the global gene expression changes by LPS and mechanism(s) by which LPS stimulates cultured hepatocytes remain uncertain. Cultures of primary mouse hepatocytes were incubated with LPS to assess its effects on the global gene expression, hepatic transcription factors, and mitogen-activated protein (MAP) kinase activation.