420 research outputs found
Crystallization and preliminary X-ray analysis of human platelet profilin complexed with an oligo proline peptide
No full textProfilin is an actin-monomer binding protein that regulates the distribution and dynamics of the actin cytoskeleton. Profilin binds poly-L-proline and proline-rich peptides in vitro and co-localizes with proline-rich proteins in focal adhesions and at the site of actin tail assembly on the surface of intracellular parasites such as Listeria monocytogenes. The crystallization of the complex between human platelet profilin (HPP) and an L-proline decamer [(Pro)10] is reported here. Diffraction from these crystals is consistent with the space group P21212 with unit-cell constants a = 68.25, b = 97.64, c = 39.10 Å. The crystals contain two HPP molecules per asymmetric unit and diffract to 2.2 Å.</jats:p
Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC
No full textTransition state energy decomposition study of acetate-assisted and internal electrophilic substitution C−H bond activation by (acac-O,O)_2Ir(X) complexes (X = CH_3COO, OH)
No full textChelate-assisted and internal electrophilic substitution type transition states were studied using a DFT-based energy decomposition method. Interaction energies for benzene and methane C−H bond activation by (acac-O,O)_2Ir(X) complexes (X = CH_3COO and OH) were evaluated using the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA). A ratio of ~1.5:1 for forward to reverse charge-transfer between (acac-O,O)_2Ir(X) and benzene or methane transition state fragments confirms “ambiphilic” bonding, the result of an interplay between the electrophilic iridium center and the internal base component. This analysis also revealed that polarization effects account for a significant amount of transition state stabilization. The energy penalty to deform reactants into their transition state geometry, distortion energy, was also used to understand the large activation energy difference between six-membered and four-membered acetate-assisted transition states and help explain why these complexes do not activate the methane C−H bond
General principles of binding between cell surface receptors and multi-specific ligands: A computational study.
No full textThe interactions between membrane receptors and extracellular ligands control cell-cell and cell-substrate adhesion, and environmental responsiveness by representing the initial steps of cell signaling pathways. These interactions can be spatial-temporally regulated when different extracellular ligands are tethered. The detailed mechanisms of this spatial-temporal regulation, including the competition between distinct ligands with overlapping binding sites and the conformational flexibility in multi-specific ligand assemblies have not been quantitatively evaluated. We present a new coarse-grained model to realistically simulate the binding process between multi-specific ligands and membrane receptors on cell surfaces. The model simplifies each receptor and each binding site in a multi-specific ligand as a rigid body. Different numbers or types of ligands are spatially organized together in the simulation. These designs were used to test the relation between the overall binding of a multi-specific ligand and the affinity of its cognate binding site. When a variety of ligands are exposed to cells expressing different densities of surface receptors, we demonstrated that ligands with reduced affinities have higher specificity to distinguish cells based on the relative concentrations of their receptors. Finally, modification of intramolecular flexibility was shown to play a role in optimizing the binding between receptors and ligands. In summary, our studies bring new insights to the general principles of ligand-receptor interactions. Future applications of our method will pave the way for new strategies to generate next-generation biologics
General principles of binding between cell surface receptors and multi-specific ligands: A computational study
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Recent advances in mammalian protein production
No full textAbstractMammalian protein production platforms have had a profound impact in many areas of basic and applied research, and an increasing number of blockbuster drugs are recombinant mammalian proteins. With global sales of these drugs exceeding US$120 billion per year, both industry and academic research groups continue to develop cost effective methods for producing mammalian proteins to support pre-clinical and clinical evaluations of potential therapeutics. While a wide range of platforms have been successfully exploited for laboratory use, the bulk of recent biologics have been produced in mammalian cell lines due to the requirement for post translational modification and the biosynthetic complexity of the target proteins. In this review we highlight the range of mammalian expression platforms available for recombinant protein production, as well as advances in technologies for the rapid and efficient selection of highly productive clones
Transition State Energy Decomposition Study of Acetate-Assisted and Internal Electrophilic Substitution C−H Bond Activation by (acac-O,O)<sub>2</sub>Ir(X) Complexes (X = CH<sub>3</sub>COO, OH)
No full textChelate-assisted and internal electrophilic substitution type transition states were studied using a DFT-based energy decomposition method. Interaction energies for benzene and methane C−H bond activation by (acac-O,O)2Ir(X) complexes (X = CH3COO and OH) were evaluated using the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA). A ratio of ∼1.5:1 for forward to reverse charge-transfer between (acac-O,O)2Ir(X) and benzene or methane transition state fragments confirms “ambiphilic” bonding, the result of an interplay between the electrophilic iridium center and the internal base component. This analysis also revealed that polarization effects account for a significant amount of transition state stabilization. The energy penalty to deform reactants into their transition state geometry, distortion energy, was also used to understand the large activation energy difference between six-membered and four-membered acetate-assisted transition states and help explain why these complexes do not activate the methane C−H bond
Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density
No full textEfforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy (CryoEM) has assumed an increasingly important role in determining the structures of these large macromolecular assemblies to intermediate resolutions (6-10 A). While these structures provide a snapshot of the assembly and its components in well-defined functional states, the resolution limits the ability to build accurate structural models. In contrast, sequence-based modeling techniques are capable of producing relatively robust structural models for isolated proteins or domains. In this work, we developed and applied a hybrid modeling approach, utilizing CryoEM density and ab initio modeling to produce a structural model for the core domain of a herpesvirus structural protein, VP26. Specifically, this method, first tested on simulated data, utilizes the CryoEM density map as a geometrical constraint in identifying the most native-like models from a gallery of models generated by ab initio modeling. The resulting model for the core domain of VP26, based on the 8.5-A resolution herpes simplex virus type 1 (HSV-1) capsid cryoEM structure and mutational data, exhibited a novel fold. Additionally, the core domain of VP26 appeared to have a complementary interface to the known upper-domain structure of VP5, its cognate binding partner. While this new model provides for a better understanding of the assembly and interactions of VP26 in HSV-1, the approach itself may have broader applications in modeling the components of large macromolecular assemblies
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