Now showing 1 - 8 of 8
  • Publication
    SARAH Domain-mediated MST2-RASSF Dimeric Interactions
    We model the conformational changes and protein-protein interactions of enzymes involved in signaling along the Hippo pathwaya key molecular mechanism that controls the process of programmed cell death in eukaryotic cells, including cells affected by cancer. Combining modern computational modeling techniques with experimental information from X-ray crystallography and systems biology studies, can unveil detailed molecular interactions and lead to novel drugs. Here, we study the atomistic mechanisms and interactions between MST2 and RASSF-type kinases, through their respective SARAH domains highly conserved, long, terminal α-helices, which play essential roles in the activation of MST kinases and, therefore, in modulating apoptosis. In spite of their key roles in mediating cell signaling pathways, there is little structural information available for the RASSF SARAH domains and their dimerization with the MST2 SARAH domains. In particular, the RASSF1A crystal structure is not available yet. Here, we model, refine and validate atomistic structural models of dimers of the RASSF1A and MST2 SARAH domains, studying the interaction and the dynamic behavior of these molecular complexes using homology modeling, docking and full atomistic molecular dynamics simulations. Experimentally, we validate our approach by designing a novel peptide that can disrupt effectively MST2 homo and hetero SARAH dimers.
      359Scopus© Citations 14
  • Publication
    Variational Identification of Markovian Transition States
    We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented by using both analytical models and examples from MD simulations of the benchmark system helix-forming peptide Ala5, and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2), the epidermal growth factor receptor (EGFR) protein and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT) quantum mechanics / molecular mechanics (QM/MM) level of theory. In all cases, our method identifies automatically the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy to implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate limiting) conformational pathways occurring in complex dynamical systems such as molecular trajectories.
      391Scopus© Citations 32
  • Publication
    Nanoscale Piezoelectric Properties of Self-Assembled Fmoc-FF Peptide Fibrous Networks
    Fibrous peptide networks, such as the structural framework of self-assembled fluorenylmethyloxycarbonyl diphenylalanine (Fmoc-FF) nanofibrils, have mechanical properties that could successfully mimic natural tissues, making them promising materials for tissue engineering scaffolds. These nanomaterials have been determined to exhibit shear piezoelectricity using piezoresponse force microscopy, as previously reported for FF nanotubes. Structural analyses of Fmoc-FF nanofibrils suggest that the observed piezoelectric response may result from the noncentrosymmetric nature of an underlying β-sheet topology. The observed piezoelectricity of Fmoc-FF fibrous networks is advantageous for a range of biomedical applications where electrical or mechanical stimuli are required.
      465Scopus© Citations 68
  • Publication
    Profiling of a panel of radioresistant prostate cancer cells identifies deregulation of key miRNAs
    miRNAs are increasingly associated with the aggressive phenotype of prostate tumours. Their ability to control radiobiologically-relevant cellular processes strengthens their potential as novel markers of response to radiation therapy. Purpose  To identify miRNAs associated with increased clonogenic survival following radiation exposure. Material and methods  The miRNA expression profiles of a panel of 22RV1 cells with varying levels of radiosensitivities (hypoxic H-22Rv1 cells, RR-22Rv1 cells derived from WT-22Rv1 cells through 2-Gy fractionated repeated exposure, the associated aged matched cells (AMC-22Rv1) and the WT-22Rv1 cell lines) were generated and cross-analysed to identify common miRNAs associated with a radioresistant phenotype. Results  Increased clonogenic survival following irradiation was associated with significant modifications in miRNA expression pattern. miR-221 (up) and miR-4284 (down) in RR-22Rv1 and MiR-31 and miR-200c in AMC-22Rv1 were the most uniquely significantly deregulated miRNAs when compared to WT-22Rv1 cells. miR-200c ranked as the most downregulated miRNAs in hypoxic, when compared to RR-22Rv1 cells. miR-200a was the only differentially expressed miRNA between RR-22Rv1 and AMC-22Rv1 cells. miR-210 yielded the highest fold change in expression in H-22Rv1, when compared to WT-22RV1 cells. Conclusion  This study identifies candidate miRNAs for the development of novel prognostic biomarkers for radiotherapy prostate cancer patients.
    Scopus© Citations 20  458
  • Publication
    Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers
    We characterize the kinetics of dimer formation of the short amyloid microcrystal-forming tetrapeptides NNQQ by constructing coarse master equations for the conformational dynamics of the system, using temperature replica-exchange molecular dynamics (REMD) simulations. We minimize the effects of Kramers-type recrossings by assigning conformational states based on their sequential time evolution. Transition rates are further estimated from short-time state propagators, by maximizing the likelihood that the extracted rates agree with the observed atomistic trajectories without any a priori assumptions about their temperature dependence. Here, we evaluate the rates for both continuous replica trajectories that visit different temperatures, and for discontinuous data corresponding to each REMD temperature. While the binding-unbinding kinetic process is clearly Markovian, the conformational dynamics of the bound NNQQ dimer has a complex character. Our kinetic analysis allows us a quantitative discrimination between short-lived encounter pairs and strongly bound conformational states. The conformational dynamics of NNQQ dimers supports a kinetically driven aggregation mechanism, in agreement with the polymorphic character reported for amyloid aggregates such as microcrystals and fibrils.
      431Scopus© Citations 26
  • Publication
    Note : Network random walk model of two-state protein folding : Test of the theory
    We study two-state protein folding in the framework of a toy model of protein dynamics. This model has an important advantage: it allows for an analytical solution for the sum of folding and unfolding rate constants [A. M. Berezhkovskii, F. Tofoleanu, and N.-V. Buchete, J. Chem. Theory Comput. 7, 2370 (2011)10.1021/ct200281d] and hence for the reactive flux at equilibrium. We use the model to test the Kramers-type formula for the reactive flux, which was derived assuming that the protein dynamics is described by a Markov random walk on a network of complex connectivity [A. Berezhkovskii, G. Hummer, and A. Szabo, J. Chem. Phys. 130, 205102 (2009)10.1063/1.3139063]. It is shown that the Kramers-type formula leads to the same result for the reactive flux as the sum of the rate constants.
      382Scopus© Citations 5
  • Publication
    Thermal and aqueous stability improvement of graphene oxide enhanced diphenylalanine nanocomposites
    Nanocomposites of diphenylalanine (FF) and carbon based materials provide an opportunity to overcome drawbacks associated with using FF micro- and nanostructures in nanobiotechnology applications, in particular, their poor structural stability in liquid solutions. In this study, FF/graphene oxide (GO) composites were found to self-assemble into layered micro- and nanostructures, which exhibited improved thermal and aqueous stability. Dependent on the FF/GO ratio, the solubility of these structures was reduced to 35.65% after 30 min as compared to 92.4% for pure FF samples. Such functional nanocomposites may extend the use of FF structures to, e.g., biosensing, electrochemical, electromechanical or electronic applications.
      499
  • Publication
    Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation
    RAF kinases are key players in the MAPK signaling pathway and are important targets for personalized cancer therapy. RAF dimerization is part of the physiological activation mechanism, together with phosphorylation, and is known to convey resistance to RAF inhibitors. Herein, molecular dynamics simulations are used to show that phosphorylation of a key N-terminal acidic (NtA) motif facilitates RAF dimerization by introducing several interprotomer salt bridges between the αC-helix and charged residues upstream of the NtA motif. Additionally, we show that the R-spine of RAF interacts with a conserved Trp residue in the vicinity of the NtA motif, connecting the active sites of two protomers and thereby modulating the cooperative interactions in the RAF dimer. Our findings provide a first structure-based mechanism for the auto-transactivation of RAF and could be generally applicable to other kinases, opening new pathways for overcoming dimerization-related drug resistance.
      296Scopus© Citations 39