The docking accuracy of Glide was evaluated using 16 different docking protocols on 190 protein-fragment complexes representing 78 targets. Standard precision docking (Glide SP) based protocols showed the best performance. The average root-mean-square deviation (rmsd) between the docked and cocrystallized poses achieved by Glide SP with pre- and postprocessing was 1.17 A, and an acceptable binding mode with rmsd < 2 A could be found in 80% of the cases. Comparison of the docking results produced by different protocols suggests that the sampling efficacy of Glide is adequate for fragment docking. The docking accuracy seems to be limited by the performance of scoring schemes, which is supported by the weak correlation between experimental binding affinities and GlideScores. Cross-docking experiments performed on 8 targets represented by 63 complexes revealed that Glide SP gave similar results to that of the computationally more intensive Glide XP. The average rmsd achieved by Glide SP with pre- and postprocessing was 2.06 A, and an acceptable binding mode with rmsd < 2 A could be found in 63% of the cases. These cross-docking results were improved significantly selecting the optimal X-ray structure for each target (average rmsd = 1.3 A, success rate = 77%), indicating the importance of enrichment studies and the use of multiple X-ray structures in virtual fragment screening.

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The dissimilar cytoskeletal architecture in diverse cell types induces a difference in their deformability that presents a viable approach to separate cells in a non-invasive manner. We report on the design and fabrication of a robust and scalable device capable of separating a heterogeneous population of cells with variable degree of deformability into enriched populations with deformability above a certain threshold. The three dimensional device was fabricated in fused silica by femtosecond laser direct writing combined with selective chemical etching. The separator device was evaluated using promyelocytic HL60 cells. Using flow rates as large as 167 μL min(-1), throughputs of up to 2800 cells min(-1) were achieved at the device output. A fluorescence-activated cell sorting (FACS) viability analysis on the cells revealed 81% of the population maintain cellular integrity after passage through the device.

The expansive growth and differentiation potential of human embryonic stem cells (hESCs) make them a promising source of cells for regenerative medicine. However, this promise is off set by the propensity for spontaneous or uncontrolled differentiation to result in heterogeneous cell populations. Cell elasticity has recently been shown to characterize particular cell phenotypes, with undifferentiated and differentiated cells sometimes showing significant differences in their elasticities. In this study, we determined the Young's modulus of hESCs by atomic force microscopy using a pyramidal tip. Using this method we are able to take point measurements of elasticity at multiple locations on a single cell, allowing local variations due to cell structure to be identified. We found considerable differences in the elasticity of the analyzed hESCs, reflected by a broad range of Young's modulus (0.05-10 kPa). This surprisingly high variation suggests that elasticity could serve as the basis of a simple and efficient large scale purification/separation technique to discriminate subpopulations of hESCs.

DJ-1 (PARK7) is a multifunctional protein linked to the onset and progression of a number of diseases, most of which are associated with high oxidative stress. The Cys106 of DJ-1 is unusually reactive and thus sensitive to oxidation, and due to high oxidative stress it was observed to be in various oxidized states in disease condition. The oxidation state of Cys106 of DJ-1 is believed to determine the specific functions of the protein in normal and disease conditions. Here we report molecular dynamics simulation and biophysical experimental studies on DJ-1 in reduced (Cys106, S), oxidized (Cys106, SO), and over-oxidized (Cys106, SO) states. To simulate the different oxidation states of Cys106 in DJ-1, AMBER related force field parameters were developed and reported for 3-sulfinoalanine and cysteine sulfonic acid. Our studies found that the overall structure of DJ-1 in different oxidation states was similar globally, while it differed locally significantly, which have implications on its stability, function and its link to disease on-set. Importantly, the results suggest that over-oxidation may trigger loss of functions due to local structural modification in the Cys106 containing pocket of DJ-1 and structurally destabilize the dimeric state of DJ-1, which is believed to be its bioactive conformation. Such loss of functions would result in reduced ability of DJ-1 to protect from oxidative stress insults and may lead to increased progression of disease.