Articles in 2010

Semisynthetic versions of the small G protein Rab7 in the GDP-bound form have 1,000-fold higher affinity for regulators REP1 and RabGDI because of faster dissociation rates from Rab7-GTP, directly linking nucleotide exchange to Rab membrane targeting.

Crosslinks between the active and inactive M3R and the G-protein G_q to which it couples reveal GPCR-G protein movements that can occur upon agonist binding and define basic architectural features of the interface.

Intein splicing occurs in four steps, but the mechanisms controlling these steps — and thus preventing aberrant splicing — are unknown. Kinetic and NMR analysis of several complex constructs now identifies the rate limiting step as well as the conformational trigger that catalyzes this transformation.

Interaction between HIV-1 integrase and the cellular cofactor LEDGF/p75 is important for viral integration. Newly designed small molecules that block this interaction inhibit HIV replication, illustrating the potential of viral–host protein-protein interaction inhibitors.

Enhancing calnexin function by increasing the ER calcium concentration resculpts the mutant glucocerebrosidase folding free energy diagram in the ER of Gaucher's disease cells, enhancing folding at the expense of the ER-associated degradation pathway.

Synthetic biology enables the reprogramming of cells for useful applications. RNA selection approaches yielded an atrazine-binding riboswitch that was used to engineer Escherichia coli that migrate toward and catabolize this common herbicide.

Metabolomics analysis of stem cells and differentiated cells points to chemical unsaturation as a key feature of stem cell metabolites. Manipulation of these metabolites' concentrations directly influences stem cell behavior, highlighting biological oxidation as a driver for differentiation.

A new pathway screen for small molecules that suppress or enhance an RNAi phenotype in Drosophila cells was used to identify a collection of compounds that perturb different steps in the Rho pathway.

Six new species of electrophilic lipids identified in activated macrophages are derived from COX-2 action on ω-3 fatty acids and mediate anti-inflammatory and anti-oxidant activities.

Reversible palmitoylation controls the localization and signaling of Ras. Development of a potent and specific small molecule inhibitor of the thioesterase APT1 reveals that this enzyme depalmitoylates Ras in cells. Inhibition of APT1 led to redistribution and altered activity of HRas, NRas and an oncogenic mutant Ras.

O-polysaccharide is a major constituent of the bacterial cell wall, yet little mechanistic information is known about its biosynthesis. A reconstruction of this pathway using defined substrates now demonstrates the basis for sugar polymerization and length modulation.

NMR-measured order parameters of methyl groups can be used to quantitate the entropy of protein conformational change associated with calmodulin-peptide ligand interactions. This conformational entropy is a major contributor to the affinity of calmodulin interactions.

Functionally coupled motions between the voltage-sensing and the phosphatidylinositol phosphatase domains of the sea squirt protein Ci-VSP are mediated by PtdIns(4,5)P₂ binding to the segment linking these domains, as shown by electrophysiology and voltage clamp fluorometry.

The detailed characterization of endogenous proteins and use of non-natural amino acid engineering allows the identification and structural and functional analysis of a post-translational modification in regulating ligand binding and enzyme activity.

Elongation factor G (EF-G) is an essential GTPase involved in translation, but how the translocating ribosome activates EF-G remains an open question. Nucleotide functional group mutagenesis implicates A2660 of 23S rRNA as the trigger of GTPase hydrolysis by EF-G.

GlgE is identified as a maltosyltransferase that catalyzes the polymerization step in a previously undescribed pathway in Mycobacterium tuberculosis for converting trehalose to α-glucan. A combination of traditional and chemical genetic strategies suggest GlgE to be a viable therapeutic target.

Glycosylation can affect biological targets transiently and at low levels, making the development of diagnostic tools of critical importance. The application of a new series of antibodies raised against GlcNAc-modified substrates identifies a host of protein targets in normal and traumatized cells.

Asymmetric ADP affinities and dissociation rates as well as optimization of subunit coordination through the long lever arm ensure high processivity under the intramolecular and external off-axis loads that myosin V experiences in vivo.

Profiling of a combinatorial library of post-translationally modified histone H3–based peptides reveals that Thr3 phosphorylation, Arg2 methylation and Thr6 phosphorylation can modulate recognition of Lys4 methylation status by PHD fingers. Additionally, Thr6 phosphorylation, a previously undescribed modification, is shown to exist in native histones.