29 research outputs found
Impact of Ser17 phosphorylation on the conformational dynamics of the oncoprotein MDM2
MDM2 is an important oncoprotein
that downregulates the activity
of the tumor suppressor protein p53 via binding of its N-terminal
domain to the p53 transactivation domain. The first 24 residues of
the MDM2 N-terminal domain form an intrinsically disordered âlidâ
region that interconverts on a millisecond time scale between âopenâ
and âclosedâ states in unliganded MDM2. While the former
conformational state is expected to facilitate p53 binding, the latter
competes in a pseudo-substrate manner with p53 for its binding site.
Phosphorylation of serine 17 in the MDM2 lid region is thought to
modulate the equilibrium between âopenâ and âclosedâ
lid states, but contradictory findings on the favored lid conformational
state upon phosphorylation have been reported. Here, the nature of
the conformational states of MDM2 pSer17 and Ser17Asp variants was
addressed by means of enhanced sampling molecular dynamics simulations.
Detailed analyses of the computed lid conformational ensembles indicate
that both lid variants stabilize a âclosedâ state, with
respect to wild type. Nevertheless, the nature of the closed-state
conformational ensembles differs significantly between the pSer17
and Ser17Asp variants. Thus, care should be applied in the interpretation
of biochemical experiments that use phosphomimetic variants to model
the effects of phosphorylation on the structure and dynamics of this
disordered protein region
Unraveling the Differences of the Hydrolytic Activity of Trypanosoma cruzi trans-Sialidase and Trypanosoma rangeli Sialidase: A Quantum MechanicsâMolecular Mechanics Modeling Study
Chagasâ disease, also known as American trypanosomiasis, is a lethal, chronic disease that currently affects more than 10 million people in Central and South America. The trans-sialidase from Trypanosoma cruzi (T. cruzi, TcTS) is a crucial enzyme for the survival of this parasite: sialic acids from the host are transferred to the cell surface glycoproteins of the trypanosome, thereby evading the hostâs immune system. On the other hand, the sialidase of T. rangeli (TrSA), which shares 70% sequence identity with TcTS, is a strict hydrolase and shows no trans-sialidase activity. Therefore, TcTS and TrSA represent an excellent framework to understand how different catalytic activities can be achieved with extremely similar structures. By means of combined quantum mechanicsâmolecular mechanics (QM/MM, SCC-DFTB/Amberff99SB) calculations and umbrella sampling simulations, we investigated the hydrolysis mechanisms of TcTS and TrSA and computed the free energy profiles of these reactions. The results, together with our previous computational investigations, are able to explain the catalytic mechanism of sialidases and describe how subtle differences in the active site make TrSA a strict hydrolase and TcTS a more efficient trans-sialidase.Fil: Bueren Calabuig, Juan A.. University of Florida; Estados UnidosFil: Pierdominici Sottile, Gustavo. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; ArgentinaFil: Roitberg, AdriĂĄn. University of Florida; Estados Unido
A structural study of the complex between neuroepithelial cell transforming gene 1 (Net1) and RhoA reveals a potential anticancer drug hot spot
XPF-Dependent DNA Breaks and RNA Polymerase II Arrest Induced by Antitumor DNA Interstrand Crosslinking-Mimetic Alkaloids
SummaryTrabectedin and Zalypsis are two potent anticancer tetrahydroisoquinoline alkaloids that can form a covalent bond with the amino group of a guanine in selected triplets of DNA duplexes and eventually give rise to double-strand breaks. Using well-defined in vitro and in vivo assays, we show that the resulting DNA adducts stimulate, in a concentration-dependent manner, cleavage by the XPF/ERCC1 nuclease on the strand opposite to that bonded by the drug. They also inhibit RNA synthesis by: (1) preventing binding of transcription factors like Sp1 to DNA, and (2) arresting elongating RNA polymerase II at the same nucleotide position regardless of the strand they are located on. Structural models provide a rationale for these findings and highlight the similarity between this type of DNA modification and an interstrand crosslink
Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM
Maturation and translation of mRNA in eukaryotes requires the addition of the 7-methylguanosine cap. In vertebrates, the cap methyltransferase, RNA guanine-7 methyltransferase (RNMT), has an activating subunit, RNMT-Activating Miniprotein (RAM). Here we report the first crystal structure of the human RNMT in complex with the activation domain of RAM. A relatively unstructured and negatively charged RAM binds to a positively charged surface groove on RNMT, distal to the active site. This results in stabilisation of a RNMT lobe structure which co-evolved with RAM and is required for RAM binding. Structure-guided mutagenesis and molecular dynamics simulations reveal that RAM stabilises the structure and positioning of the RNMT lobe and the adjacent α-helix hinge, resulting in optimal positioning of helix A which contacts substrates in the active site. Using biophysical and biochemical approaches, we observe that RAM increases the recruitment of the methyl donor, AdoMet (S-adenosyl methionine), to RNMT. Thus we report the mechanism by which RAM allosterically activates RNMT, allowing it to function as a molecular rheostat for mRNA cap methylation
Stepwise Simulation of 3,5-Dihydro-5-methylidene-4H-imidazol-4-one (MIO) Biogenesis in Histidine Ammonia-lyase
The Qi Site of Cytochrome b is a Promiscuous Drug Target in Trypanosoma cruzi and <i>Leishmania donovani</i>:ACS Infectious Diseases
"BioinformĂĄtica con Ă v1.0": a collaborative project of young Spanish scientists to write a complete book about Bioinformatics
Here we present a project aiming to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The idea of writing a book in Spanish language covering the most important topics in the field of Bioinformatics was born in the XIth Spanish Symposium on Bioinformatics in Barcelona two years ago. Different scientists have been involved in the project, from senior scientists to PhD students from different countries. The book intends to be the beginning of an open project, where all the chapters are susceptible of being updated and new topics can be incorporated in future versions. Current book version can be accessed online at http://goo.gl/UYG0o7.Peer Reviewe