213 research outputs found
Development and Characterization of Nonpeptidic Small Molecule Inhibitors of the XIAP/Caspase-3 Interaction
AbstractElevated expression of inhibitor of apoptosis protein (IAP) family members in various types of cancers is thought to provide a survival advantage to these cells. Thus, antiapoptotic functions of IAPs, and their potential as novel anticancer targets have attracted considerable interest. Among the IAPs, the X chromosome-linked inhibitor of apoptosis protein (XIAP) is regarded as the most potent suppressor of mammalian apoptosis through direct binding and inhibition of caspases. A high-throughput biochemical screen of a combinatorial chemical library led to the discovery of a novel nonpeptidic small molecule that has the ability to disrupt the XIAP/caspase-3 interaction. The activity of this nonpeptidic small molecule inhibitor of the XIAP/caspase-3 interaction has been characterized both in vitro and in cells. Molecules of this type can be used to conditionally inhibit the cellular function of XIAP and may provide insights into the development of therapeutic agents that act by modulating apoptotic pathways
Photodissociation of water in crystalline ice: a molecular dynamics study
Ultraviolet irradiation of ice is of great interest for understanding the
chemistry in both atmospheric and astrophysical environments. In interstellar
space, photodissociation of H2O molecules can be a driving force behind the
chemistry on icy dust grains in dense, cold molecular clouds even though the
flux of UV photons is extremely low. The mechanisms of such photoinduced
processes are poorly understood, however. In this work the photodissociation
dynamics of a water molecule in crystalline ice at 10 K is studied
computationally using classical molecular dynamics. Photodissociation in the
first bilayer leads mainly to H atoms desorbing (65%), while in the third
bilayer trapping of H and OH dominates (51%). The kinetic energy distribution
of the desorbing H atoms is much broader than that for the corresponding
gas-phase photodissociation. The H atoms on average move 11 Angstroms before
becoming trapped, while OH radicals typically move 2 Angstroms. In accordance
with experiments a blueshift of the absorption spectrum is obtained relative to
gas-phase water.Comment: 23 pages, 5 figure
Transition states in protein folding kinetics: Modeling Phi-values of small beta-sheet proteins
Small single-domain proteins often exhibit only a single free-energy barrier,
or transition state, between the denatured and the native state. The folding
kinetics of these proteins is usually explored via mutational analysis. A
central question is which structural information on the transition state can be
derived from the mutational data. In this article, we model and structurally
interpret mutational Phi-values for two small beta-sheet proteins, the PIN and
the FBP WW domain. The native structure of these WW domains comprises two
beta-hairpins that form a three-stranded beta-sheet. In our model, we assume
that the transition state consists of two conformations in which either one of
the hairpins is formed. Such a transition state has been recently observed in
Molecular Dynamics folding-unfolding simulations of a small designed
three-stranded beta-sheet protein. We obtain good agreement with the
experimental data (i) by splitting up the mutation-induced free-energy changes
into terms for the two hairpins and for the small hydrophobic core of the
proteins, and (ii) by fitting a single parameter, the relative degree to which
hairpin 1 and 2 are formed in the transition state. The model helps to
understand how mutations affect the folding kinetics of WW domains, and
captures also negative Phi-values that have been difficult to interpret.Comment: 27 pages, 6 pages, 3 tables; to appear in Biophys.
Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes
Orthogonal aminoacyl-tRNA synthetase/tRNA pairs from archaea have been evolved to facilitate site specific in vivo incorporation of unnatural amino acids into proteins in Escherichia coli . Using this approach, unnatural amino acids have been successfully incorporated with high translational efficiency and fidelity. In this study, CHARMM-based molecular docking and free energy calculations were used to evaluate rational design of specific protein–ligand interactions for aminoacyl-tRNA synthetases. A series of novel unnatural amino acid ligands were docked into the p -benzoyl- L -phenylalanine tRNA synthetase, which revealed that the binding pocket of the enzyme does not provide sufficient space for significantly larger ligands. Specific binding site residues were mutated to alanine to create additional space to accommodate larger target ligands, and then mutations were introduced to improve binding free energy. This approach was used to redesign binding sites for several different target ligands, which were then tested against the standard 20 amino acids to verify target specificity. Only the synthetase designed to bind Man-Α-O-Tyr was predicted to be sufficiently selective for the target ligand and also thermodynamically stable. Our study suggests that extensive redesign of the tRNA synthatase binding pocket for large bulky ligands may be quite thermodynamically unfavorable. Proteins 2010. © 2010 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71368/1/22706_ftp.pd
How to do an evaluation: pitfalls and traps
The recent literature is replete with papers evaluating computational tools (often those operating on 3D structures) for their performance in a certain set of tasks. Most commonly these papers compare a number of docking tools for their performance in cognate re-docking (pose prediction) and/or virtual screening. Related papers have been published on ligand-based tools: pose prediction by conformer generators and virtual screening using a variety of ligand-based approaches. The reliability of these comparisons is critically affected by a number of factors usually ignored by the authors, including bias in the datasets used in virtual screening, the metrics used to assess performance in virtual screening and pose prediction and errors in crystal structures used
How to do an evaluation: pitfalls and traps
The recent literature is replete with papers evaluating computational tools (often those operating on 3D structures) for their performance in a certain set of tasks. Most commonly these papers compare a number of docking tools for their performance in cognate re-docking (pose prediction) and/or virtual screening. Related papers have been published on ligand-based tools: pose prediction by conformer generators and virtual screening using a variety of ligand-based approaches. The reliability of these comparisons is critically affected by a number of factors usually ignored by the authors, including bias in the datasets used in virtual screening, the metrics used to assess performance in virtual screening and pose prediction and errors in crystal structures used
Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1
African sleeping sickness is a devastating disease that plagues sub-Saharan Africa. Neglected tropical diseases like African sleeping sickness cause significant death and suffering in the world's poorest countries. Current treatments for African sleeping sickness either have high costs, terrible side effects, or limited effectiveness. Consequently, new medicines are urgently needed. RNA editing ligase 1 is an important protein critical for the survival of Trypanosoma brucei, the unicellular parasite that causes African sleeping sickness. In this paper, we describe our recent efforts to use advanced computer techniques to identify chemicals predicted to prevent RNA editing ligase 1 from functioning properly. We subsequently tested our predicted chemicals and confirmed that a number of them inhibited the protein's function. Additionally, one of the chemicals was effective at stopping the growth of the parasite in culture. Although substantial work remains to be done in order to optimize these chemicals so they are effective and safe to use in human patients, the identification of these parasite-killing compounds is nevertheless a valuable step towards finding a better cure for this devastating disease
Molecular dynamics of ribosomal elongation factors G and Tu
Translation on the ribosome is controlled by external factors. During polypeptide lengthening, elongation factors EF-Tu and EF-G consecutively interact with the bacterial ribosome. EF-Tu binds and delivers an aminoacyl-tRNA to the ribosomal A site and EF-G helps translocate the tRNAs between their binding sites after the peptide bond is formed. These processes occur at the expense of GTP. EF-Tu:tRNA and EF-G are of similar shape, share a common binding site, and undergo large conformational changes on interaction with the ribosome. To characterize the internal motion of these two elongation factors, we used 25 ns long all-atom molecular dynamics simulations. We observed enhanced mobility of EF-G domains III, IV, and V and of tRNA in the EF-Tu:tRNA complex. EF-Tu:GDP complex acquired a configuration different from that found in the crystal structure of EF-Tu with a GTP analogue, showing conformational changes in the switch I and II regions. The calculated electrostatic properties of elongation factors showed no global similarity even though matching electrostatic surface patches were found around the domain I that contacts the ribosome, and in the GDP/GTP binding region
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