Robosample: A rigid-body molecular simulation program based on robot mechanics

H-Bonds in Crambin: Coherence in an α-Helix

We applied coherence analysis-used by engineers to identify linear interactions in stochastic systems-to molecular dynamics simulations of crambin, a thionin storage protein found in Abyssinian cabbage. A key advantage of coherence over other analyses is that it is robust, independent of the properties, or even the existence of probability distributions often relied on in statistical mechanics. For frequencies between 0.391 and 5.08 GHz (corresponding reciprocally to times of 2.56 and 0.197 ns), the displacements of oxygen and nitrogen atoms across α-helix H-bonds are strongly correlated, with a coherence greater than 0.9; the secondary structure causes the H-bonds to effectively act as a spring. Similar coherence behavior is observed for covalent bonds and other noncovalent interactions including H-bonds in β-sheets and salt bridges. In contrast, arbitrary pairs of atoms that are physically distant have uncorrelated motions and negligible coherence. These results suggest that coherence may be used to objectively identify atomic interactions without subjective thresholds such as H-bond lengths angles and angles. Strong coherence is also observed between the average position of adjacent leaves (groups of atoms) in an α-helix, suggesting that the harmonic analysis of classical molecular dynamics can successfully describe the propagation of allosteric interactions through the structure.

EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning

EDEM3 recognizes and directs misfolded proteins to the ER-associated protein degradation (ERAD) process. EDEM3 was predicted to act as lectin or as a mannosidase because of its homology with the GH47 catalytic domain of the Man1B1, but the contribution of the other regions remained unresolved. Here, we dissect the molecular determinants governing EDEM3 function and its cellular interactions. LC/MS analysis indicates very few stable ER interactors, suggesting EDEM3 availability for transient substrate interactions. Sequence analysis reveals that EDEM3 consists of four consecutive modules defined as GH47, intermediate (IMD), protease-associated (PA), and intrinsically disordered (IDD) domain. Using an EDEM3 knock-out cell line, we expressed EDEM3 and domain deletion mutants to address EDEM3 function. We find that the mannosidase domain provides substrate binding even in the absence of mannose trimming and requires the IMD domain for folding. The PA and IDD domains deletions do not impair the trimming, but specifically modulate the turnover of two misfolded proteins, NHK and the soluble tyrosinase mutant. Hence, we demonstrate that EDEM3 provides a unique ERAD timing to misfolded glycoproteins, not only by its mannose trimming activity, but also by the positive and negative feedback modulated by the protease-associated and intrinsically disordered domain, respectively.