Nanoformulations that can respond to the specific tumor microenvironment (TME), such as a weakly acidic pH, low oxygen, and high glutathione (GSH), show promise for killing cancer cells with minimal invasiveness and high specificity. In this study, we demonstrate self-assembled copper−amino acid mercaptide nanoparticles (Cu-Cys NPs) for in situ glutathione-activated and H 2 O 2 -reinforced chemodynamic therapy for drugresistant breast cancer. After endocytosis into tumor cells, the Cu-Cys NPs could first react with local GSH, induce GSH depletion, and reduce Cu 2+ to Cu + . Subsequently, the generated Cu + would react with local H 2 O 2 to generate toxic hydroxyl radicals (•OH) via a Fenton-like reaction, which has a fast reaction rate in the weakly acidic TME, that are responsible for tumor-cell apoptosis. Due to the high GSH and H 2 O 2 concentration in tumor cells, which sequentially triggers the redox reactions, Cu-Cys NPs exhibited relatively high cytotoxicity to cancer cells, whereas normal cells were left alive. The in vivo results also proved that Cu-Cys NPs efficiently inhibited drug-resistant breast cancer without causing obvious systemic toxicity. As a novel copper mercaptide nanoformulation responsive to the TME, these Cu-Cys NPs may have great potential in chemodynamic cancer therapy.

PDZ domains are found in many signaling proteins. One of their functions is to provide scaffolds for forming membrane-associated protein complexes by binding to the carboxyl termini of its partners. PDZ domains are thought to play a signal transduction role by propagating the information that binding has occurred to remote sites. In the current study, a molecular dynamics simulation based approach, referred to an interaction correlation analysis, is applied to the PDZ2 domain to identity the possible signal transduction pathways. A residue correlation matrix is constructed from the interaction energy correlation between all residue pairs obtained from the molecular dynamics simulations. Two continuous interaction pathways, starting at the ligand binding pocket, are identified by a hierarchical clustering analysis of the residue correlation matrix. One pathway is mainly localized at the N terminal side of helix α1 and the adjacent C terminus of loop β1–β2. The other pathway is perpendicular to the central β sheet toward the side of PDZ2 domain opposite to the ligand binding pocket. The present results extend previous studies based on multiple sequence analysis, NMR and molecular dynamics simulations. Importantly, they reveal the energetic origin of the long-range coupling. The PDZ2 results, as well as the earlier rhodopsin analysis, show that the interaction correlation analysis is a robust approach for determining pathways of intramolecular signal transduction.

This paper reports a computational method, the quantized elastic deformational model, that can reliably describe the conformational flexibility of a protein in the absence of the amino acid sequence and atomic coordinates. The essence of this method lies in the fact that, in modeling the functionally important conformational changes such as domain movements, it is possible to abandon the traditional concepts of protein structure (bonds, angles, dihedrals, etc.) and treat the protein as an elastic object. The shape and mass distribution of the object are described by the electron density maps, at various resolutions, from methods such as x-ray diffraction or cryo-electron microscopy. The amplitudes and directionality of the elastic deformational modes of a protein, whose patterns match the biologically relevant conformational changes, can then be derived solely based on the electron density map. The method yields an accurate description of protein dynamics over a wide range of resolutions even as low as 15-20 Å at which there is nearly no visually distinguishable internal structures. Therefore, this method dramatically enhances the capability of studying protein motions in structural biology. It is also expected to have ample applications in related fields such as bioinformatics, structural genomics, and proteomics, in which one's ability to extract functional information from the not-so-well-defined structural models is vitally important.conformational flexibility ͉ elastic deformation ͉ large conformational change ͉ elastic network ͉ normal mode analysis C omputational simulations of protein dynamics (1, 2) play an important role in deciphering protein functions in modern structural biology. To date, all the procedures for describing the motions of a protein require the knowledge of the atomic coordinates-i.e., the precise locations of the atoms. However, as the field of structural biology moves into an era of supermolecular complexes and membrane-bound proteins, there have been an increasing number of cases in which one can only obtain fuzzy images of the molecules by means of, for example, cryoelectron microscopy (cryo-EM). The knowledge of structures in these cases is not much more than the rough shapes of the molecules. Therefore, a challenging question is whether one can describe the motions of a protein, at least the gross features, based on its fuzzy image. The success of such a method would not only advance one's ability to model protein motions to a completely new level in structure biology, but it will also profoundly inf luence broader fields such as bioinformatics, structural genomics, and proteomics, in which one's ability to extract functional information from the not-so-well-defined structural models is vitally important.In the light of such a challenge, we developed a computational method, the quantized elastic deformational model (QEDM), by combining and extending several existing methods that were developed for related, but different, purposes. The results clearly demonstrate that, without the...

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The crystal structures of lactose repressor protein (LacI) provide static endpoint views of the allosteric transition between DNA-and IPTG-bound states. To obtain an atom-by-atom description of the pathway between these two conformations, motions were simulated with targeted molecular dynamics (TMD). Strikingly, this homodimer exhibited asymmetric dynamics. All asymmetries observed in this simulation are reproducible and can begin on either of the two monomers. Asymmetry in the simulation originates around D149 and was traced back to the pre-TMD equilibrations of both conformations. In particular, hydrogen bonds between D149 and S193 adopt a variety of configurations during repetitions of this process. Changes in this region propagate through the structure via noncovalent interactions of three interconnected pathways. The changes of pathway 1 occur first on one monomer. Alterations move from the inducer-binding pocket, through the N-subdomain ␤-sheet, to a hydrophobic cluster at the top of this region and then to the same cluster on the second monomer. These motions result in changes at (1) side chains that form an interface with the DNA-binding domains and (2) K84 and K84Ј, which participate in the monomer-monomer interface. Pathway 2 reflects consequent reorganization across this subunit interface, most notably formation of a H74-H74Ј -stacking intermediate. Pathway 3 extends from the rear of the inducer-binding pocket, across a hydrogen-bond network at the bottom of the pocket, and transverses the monomer-monomer interface via changes in H74 and H74Ј. In general, intermediates detected in this study are not apparent in the crystal structures. Observations from the simulations are in good agreement with biochemical data and provide a spatial and sequential framework for interpreting existing genetic data.Keywords: Gene regulation; allosteric mechanism; structural flexibility; conformational transition pathway; targeted molecular dynamics Supplemental material: See www.proteinscience.org Since its discovery in 1961, the lactose (lac) operon has been the prototypic model for studying genetic and allosteric regulation (Jacob and Monod 1961;Monod et al. 1965;Matthews and Nichols 1998;Matthews et al. 2000). The central component of this regulatory system-lactose repressor protein (LacI)-binds to three operator sites within the lac operon to repress gene transcription (Matthews 1992). Inducer sugars, such as allolactose (Jobe and Bourgeois 1972) These authors made equal contributions to this work. Article and publication are at http://www.proteinscience.org/cgi

Ribonuclease-A (RNase-A) encapsulated PbS quantum dots (RNase-A@PbS Qdots) which emit in the second near-infrared biological window (NIR-II, ca. 1000–1400 nm) are rapidly synthesized under microwave heating. Photoluminescence (PL) spectra of the Qdots can be tuned across the entire NIR-II range by simply controlling synthesis temperature. The size and morphology of the Qdots are examined by transmission electron microscopy (TEM), atomic force microscopy (AFM), and dynamic light scattering (DLS). Quantum yield (Φf) measurement confirms that the prepared Qdots are one of the brightest water-soluble NIR-II emitters for in vivo imaging. Their high Φf (∼17.3%) and peak emission at ∼1300 nm ensure deep optical penetration to muscle tissues (up to 1.5 cm) and excellent imaging contrast at an extremely low threshold dose of ∼5.2 pmol (∼1 μg) per mouse. Importantly, this protein coated Qdot displays no signs of toxicity toward model neuron, normal, and cancer cells in vitro. In addition, the animal’s metabolism results in thorough elimination of intravenously injected Qdots from the body within several days via the reticuloendothelial system (RES), which minimizes potential long-term toxicity in vivo from possible release of lead content. With a combination of attractive properties of high brightness, robust photostability, and excellent biocompatibility, this new NIR-II emitting Qdot is highly promising in accurate disease screening and diagnostic applications.