With the rapid development of sequencing technologies towards higher throughput and lower cost, sequence data are generated at an unprecedentedly explosive rate. To provide an efficient and easy-to-use platform for managing huge sequence data, here we present Genome Sequence Archive (GSA; http://bigd.big.ac.cn/gsa or http://gsa.big.ac.cn), a data repository for archiving raw sequence data. In compliance with data standards and structures of the International Nucleotide Sequence Database Collaboration (INSDC), GSA adopts four data objects (BioProject, BioSample, Experiment, and Run) for data organization, accepts raw sequence reads produced by a variety of sequencing platforms, stores both sequence reads and metadata submitted from all over the world, and makes all these data publicly available to worldwide scientific communities. In the era of big data, GSA is not only an important complement to existing INSDC members by alleviating the increasing burdens of handling sequence data deluge, but also takes the significant responsibility for global big data archive and provides free unrestricted access to all publicly available data in support of research activities throughout the world.

High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C␣-rmsd from the x-ray structure was 0.46 Å, and the C␣-rmsd of the center of the most populated cluster was 1. Despite decades of effort, high-accuracy ab initio protein folding has remained elusive to the simulation community. Most existing ab initio protein folding simulations have typically been at the 3-4 Å level based on the best C ␣ -rmsd compared with the experimental structures. When heavy-atom rmsd is used, a much larger rmsd (Ͼ5 Å) would be common. Yet, crystals of small proteins that can diffract only at 5-Å resolution are not considered of acceptable quality. Thus, most of the ab initio folding simulations have never reached the native states despite the enormous effort, underscoring the challenge. Because of the lack of accuracy in those simulations, it is impossible to obtain the crucial information on the folding pathways to the native states. This renders great ambiguity to the interpretation of the folding mechanisms. In this work, we demonstrate consistent ab initio protein folding to the native state of HP35.Villin headpiece is an F actin-binding domain that resides in the far C terminal of the super villin (1, 2). The 35-residue C-terminal subdomain HP35 can fold autonomously without the assistance of disulfide bonds or metal ions and has a melting temperature of T m ϭ 342 K, which is surprisingly high for a protein of its size (3-5). HP35 is arguably the smallest native occurring protein with the features of much bigger proteins, where multiple secondary structures (three helices) are bound together by a well packed hydrophobic core (three phenylalanine residues and other hydrophobic residues). As such, unveiling the folding mechanism of HP35 will augment our understanding of protein folding.The unique structural architecture of HP35 was revealed by using both NMR and x-ray crystallography (5, 6). However, the elucidation of the folding mechanism of HP35, remains a long-standing endeavor. In a laser-induced temperature-jump experiment, the quenching of Trp 23 by the engineered His 27 revealed a 4.3-s fast folding (4), which was later confirmed by NMR line-shape analysis (7) and loop-formation dynamics (8).Two kinetic phases, with the time constant of 70 ns and 5 s, were observed experimentally (4), indicating hidden complexities in the folding process. Mutagenesis experiments on the three core phenylalanine residues (9) and the Pro 21 -X 22 -Trp 23 motif (10) demonstrated the contribution from interior and surface residues to the stability. Studies of the HP35 fragments showed that the individual helices are largely unstructured, whereas the frag...

Congo red has been used to identify amyloid fibrils in tissues for more than 80 years and is also a weak inhibitor to both amyloid-beta fibril formation and toxicity. However, the specificity of the binding and its inhibition mechanism remain unclear. Using all-atom molecular dynamics simulations with the explicit solvent model, we have identified and characterized two specific binding modes of Congo red molecules to a protofibril formed by an amyloidogenic fragment (GNNQQNY) of the yeast prion protein Sup35. The observation of dual-mode was consistent with the experimentally observed dual-mode binding to Abeta fibrils by a series of compounds similar to Congo red. In the primary mode, Congo red bound to a regular groove formed by the first three residues (GNN) of the beta-strands along the beta-sheet extension direction. Comparative simulations demonstrated that Thioflavin T also bound to the grooves on KLVFFAE protofibril surface. Because of the ubiquitous long grooves on the amyloid fibril surface, we propose that this binding interaction could be a general recognition mode of amyloid fibrils by Congo red, Thioflavin T, and other long flat molecules. In the secondary mode, Congo red bound parallel to the beta-strands on the edge or in the middle of a beta-sheet. The primary binding mode of Congo red and GNNQQNY protofibril was more stable than the secondary mode by -5.7 kcal/mol as estimated by the MM-GBSA method. Detailed analysis suggests that the hydrophobic interactions play important roles for burial of the hydrophobic part of the Congo red molecules. Two potential inhibition mechanisms of disrupting beta-sheet stacking were inferred from the primary mode, which could be exploited for the development of non-peptidic amyloid-specific inhibitors.

The phytochrome family of red/far-red photoreceptors has been optimized to support photochemical isomerization of a bound bilin chromophore, a process that triggers a conformational change and modulates biochemical output from the surrounding protein scaffold. Recent studies have established that the efficiency of this photochemical process is profoundly altered by mutation of a conserved tyrosine residue (Tyr176) within the bilin-binding GAF domain of the cyanobacterial phytochrome Cph1 [Fischer, A. J., and Lagarias, J. C. (2004) Harnessing phytochrome's glowing potential, Proc. Natl. Acad. Sci. U.S.A. 101, 17334-17339]. Here, we show that the equivalent mutation in plant phytochromes behaves similarly, indicating that the function of this tyrosine in the primary photochemical mechanism is conserved. Saturation mutagenesis of Tyr176 in Cph1 establishes that no other residue can support comparably efficient photoisomerization. The spectroscopic consequences of Tyr176 mutations also reveal that Tyr176 regulates the conversion of the porphyrin-like conformation of the bilin precursor to a more extended conformation. The porphyrin-binding ability of the Tyr176Arg mutant protein indicates that Tyr176 also regulates the ligand-binding specificity of apophytochrome. On the basis of the hydrogen-bonding ability of Tyr176 substitutions that support the nonphotochemical C15-Z,syn to C15-Z,anti interconversion, we propose that Tyr176 orients the carboxyl side chain of a conserved acidic residue to stabilize protonation of the bilin chromophore. A homology model of the GAF domain of Cph1 predicts a C5-Z,syn, C10-Z,syn, C15-Z,anti configuration for the chromophore and implicates Glu189 as the proposed acidic residue stabilizing the extended conformation, an interpretation consistent with site-directed mutagenesis of this conserved acidic residue.