Steered molecular dynamics (SMD) is used to investigate forced unfolding and spontaneous refolding of immunoglobulin I27, a domain of the muscle protein titin. Previous SMD simulations revealed the events leading to stretch-induced unfolding of I27, the rupture of hydrogen bonds bridging beta-strands A and B, and those bridging beta-strands A' and G, the latter rupture occurring at an extension...

CD83 is an immunoglobulin (Ig) superfamily member that is upregulated during the maturation of dendritic cells (DCs). It has been widely used as a marker for mature DCs, but its function is still unknown. To approach its potential functional role, we have expressed the extracellular Ig domain of human CD83 (hCD83ext) as a soluble protein. Using this tool we could show that immature as well as m...

Large filament proteins in muscle sarcomeres comprise many immunoglobulin-like domains that provide a molecular platform for self-assembly and interactions with heterologous protein partners. We have unravelled the molecular basis for the head-to-tail interaction of the carboxyl terminus of titin and the amino-terminus of obscurin-like-1 by X-ray crystallography. The binary complex is formed by...

The forces developed during stretch of nonactivated muscle consist of velocity-sensitive (viscous/viscoelastic) and velocity-insensitive (elastic) components. At the myofibrillar level, the elastic-force component has been described in terms of the entropic-spring properties of the giant protein titin, but entropic elasticity cannot account for viscoelastic properties, such as stress relaxation...

A nite domain for the abstract interpretation of lazy lists is known, but is not easily generalisable to other lazy data structures. A construction for nite abstract domains is presented which is quite general, based on the notion of a `set of elements'. The abstraction for elements is given, and a new powerdomain is developed. Finally, a means of iterative calculation of the sub-domain which c...

A parametric analysis is an analysis whose input and output are parametrized with a number of parameters which can be instantiated to abstract properties after analysis is completed. This paper proposes to use Cousot and Cousot’s Cardinal power domain to capture functional dependencies of analysis output on its input and obtain a parametric analysis by parametrizing a non-parametric base analys...

Functional transient receptor potential (TRP) channels result from the assembly of four subunits. Here, we show an interaction between the pre-S1, TRP, and the ankyrin repeat domain (ARD)-S1 linker domains of TRPV1 and TRPV4 that is essential for proper channel assembly. Neutralization of TRPV4 pre-S1 K462 resulted in protein retention in the ER, defective glycosylation and trafficking, and unr...

We have identified the yeast and human homologs of the SKP1 gene as a suppressor of cdc4 mutants and as a cyclin F-binding protein. Skp1p indirectly binds cyclin A/Cdk2 through Skp2p, and directly binds Skp2p, cyclin F, and Cdc4p through a novel structural motif called the F-box. SKP1 is required for ubiquitin-mediated proteolysis of Cin2p, Clb5p, and the Cdk inhibitor Sic1p, and provides a lin...

Low-Power Domain-Specific Processors for Digital Signal Processing