Person: Wang, Wei
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Wei
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Wang, Wei
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Publication Graphene Hydrate: Theoretical Prediction of a New Insulating Form of Graphene(IOP Publishing, 2010) Wang, Wei; Kaxiras, EfthimiosUsing first-principles calculations, we show that the formation of carbohydrates directly from carbon and water is energetically favored when graphene is subjected to an unequal chemical environment across the two sides, with a difference in the chemical potential of protons and hydroxyl groups. The resultant carbohydrate structure is two-dimensional (2D), with the hydrogen atoms exclusively attached on one side of the graphene and the hydroxyl groups on the other side, the latter forming a herringbone reconstruction that optimizes hydrogen bonding. We show that graphene undergoes a metal–insulator transition upon hydration that is readily detectable from the significant shift in the vibration spectrum. The hydrate form of graphene offers new applications for graphene in electronics, either deposited on a substrate or in solution.Publication Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming(Nature Publishing Group, 2009) Deng, Jie; Shoemaker, Robert; Xie, Bin; Gore, Athurva; LeProust, Emily M; Antosiewicz-Bourget, Jessica; Egli, Dieter; Maherali, Nimet A; Park, In-Hyun; Yu, Junying; Daley, George; Eggan, Kevin; Hochedlinger, Konrad; Thomson, James; Wang, Wei; Gao, Yuan; Zhang, KunCurrent DNA methylation assays are limited in the flexibility and efficiency of characterizing a large number of genomic targets. We report a method to specifically capture an arbitrary subset of genomic targets for single-molecule bisulfite sequencing for digital quantification of DNA methylation at single-nucleotide resolution. A set of ~30,000 padlock probes was designed to assess methylation of ~66,000 CpG sites within 2,020 CpG islands on human chromosome 12, chromosome 20, and 34 selected regions. To investigate epigenetic differences associated with dedifferentiation, we compared methylation in three human fibroblast lines and eight human pluripotent stem cell lines. Chromosome-wide methylation patterns were similar among all lines studied, but cytosine methylation was slightly more prevalent in the pluripotent cells than in the fibroblasts. Induced pluripotent stem (iPS) cells appeared to display more methylation than embryonic stem cells. We found 288 regions methylated differently in fibroblasts and pluripotent cells. This targeted approach should be particularly useful for analyzing DNA methylation in large genomes.Publication Topological Graphene Imaging and Fabrication of Devices(Microscopy Society of America, 2012) Bell, David; Wang, Wei; Bhandari, Sagar; Westervelt, Robert; Kaxiras, EfthimiosPublication Direct Imaging of Atomic-Scale Ripples in Few-Layer Graphene(American Chemical Society, 2012) Wang, Wei; Bhandari, Sagar; Yi, Wei; Bell, David; Westervelt, Robert; Kaxiras, EfthimiosGraphene has been touted as the prototypical two-dimensional solid of extraordinary stability and strength. However, its very existence relies on out-of-plane ripples as predicted by theory and confirmed by experiments. Evidence of the intrinsic ripples has been reported in the form of broadened diffraction spots in reciprocal space, in which all spatial information is lost. Here we show direct real-space images of the ripples in a few-layer graphene (FLG) membrane resolved at the atomic scale using monochromated aberration-corrected transmission electron microscopy (TEM). The thickness of FLG amplifies the weak local effects of the ripples, resulting in spatially varying TEM contrast that is unique up to inversion symmetry. We compare the characteristic TEM contrast with simulated images based on accurate first-principles calculations of the scattering potential. Our results characterize the ripples in real space and suggest that such features are likely common in ultrathin materials, even in the nanometer-thickness range.Publication Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome(Springer Nature, 2018-11-12) Dong, Yuanchen; Zhang, Shuwen; Wu, Zhaolong; Li, Xuemei; Wang, Wei; Zhu, Yanan; Stoilova-McPhie, Svetla; Lu, Ying; Finley, Daniel; Mao, YoudongThe proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven conformational states at 2.8–3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures illuminate a spatiotemporal continuum of dynamic substrate–proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. There are three principal modes of coordinated hydrolysis, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, initiation of translocation and processive unfolding of substrates, respectively. Hydrolysis of ATP powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate.Publication Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome(Nature Publishing Group UK, 2018) Zhu, Yanan; Wang, Wei; Yu, Daqi; Ouyang, Qi; Lu, Ying; Mao, YoudongThe proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all known eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase unfoldase in the regulatory particle (RP) control the gating of the substrate–translocation channel leading to the proteolytic chamber of the core particle (CP). Here we report three alternative states of the ATP-γ-S-bound human proteasome, in which the CP gates are asymmetrically open, visualized by cryo-EM at near-atomic resolutions. At least four nucleotides are bound to the AAA-ATPase ring in these open-gate states. Variation in nucleotide binding gives rise to an axial movement of the pore loops narrowing the substrate-translation channel, which exhibit remarkable structural transitions between the spiral-staircase and saddle-shaped-circle topologies. Gate opening in the CP is thus regulated by nucleotide-driven conformational changes of the AAA-ATPase unfoldase. These findings demonstrate an elegant mechanism of allosteric coordination among sub-machines within the human proteasome holoenzyme.