A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules

Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macromolecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolution single particle analysis of macromolecular complexes with dynamic conformations.

Cloning and expression in Escherichia coli of secondary lymphoid-tissue chemokine (SLC) gene / 生物工程学报

Secondary lymphoid-tissue chemokine (SLC) is a type of CC chemokine identified by searching the Expressed Sequence Tag (EST) database. The full-length SLC gene was synthesized based on human SLC sequence using SOE-PCR. The sequenced SLC gene was cloned into expression vector pTMF and pALM, which used to transform Escherichia coli. Then the E. coli was cultured and induced according to protocol. The expressed target protein was identified by Western blotting. The target protein was expressed as soluble protein as well as inclusion bodies, the ratio of these two forms target protein varied with the difference conditions of culture and induction. The target protein was purified with the methods of nickel-nitrilotriacetic acid (Ni-NTA) metal-affinity chromatography. The results of electrophoresis of the purified target protein showed that the molecular weight was larger than the predicted molecular weight.