Cristian Micheletti

Scuola Internazionale Superiore di Studi Avanzati di Trieste, Trst, Friuli Venezia Giulia, Italy

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Publications (125)558.8 Total impact

  • Antonio Suma · Enzo Orlandini · Cristian Micheletti
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    ABSTRACT: Langevin dynamics simulations are used to characterize the typical mechanisms governing the spontaneous tying, untying and the dynamical evolution of knots in coarse-grained models of DNA chains confined in nanochannels. In particular we focus on how these mechanisms depend on the chain contour length, Lc, at a fixed channel width D = 56 nm corresponding to the onset of the Odijk scaling regime where chain backfoldings and hence knots are disfavoured but not suppressed altogether. We find that the lifetime of knots grows significantly with Lc, while that of unknots varies to a lesser extent. The underlying kinetic mechanisms are clarified by analysing the evolution of the knot position along the chain. At the considered confinement, in fact, knots are typically tied by local backfoldings of the chain termini where they are eventually untied after a stochastic motion along the chain. Consequently, the lifetime of unknots is mostly controlled by backfoldings events at the chain ends, which is largely independent of Lc. The lifetime of knots, instead, increases significantly with Lc because knots can, on average, travel farther along the chain before being untied. The observed interplay of knots and unknots lifetimes underpins the growth of the equilibrium knotting probability of longer and longer chains at fixed channel confinement.
    Journal of Physics Condensed Matter 09/2015; 27(35):354102. DOI:10.1088/0953-8984/27/35/354102 · 2.35 Impact Factor
  • Luca Ponzoni · Guido Polles · Vincenzo Carnevale · Cristian Micheletti
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    ABSTRACT: Identifying dynamical, quasi-rigid domains in proteins provides a powerful means for characterizing functionally oriented structural changes via a parsimonious set of degrees of freedom. In fact, the relative displacements of few dynamical domains usually suffice to rationalize the mechanics underpinning biological functionality in proteins and can even be exploited for structure determination or refinement purposes. Here we present SPECTRUS, a general scheme that, by solely using amino acid distance fluctuations, can pinpoint the innate quasi-rigid domains of single proteins or large complexes in a robust way. Consistent domains are usually obtained by using either a pair of representative structures or thousands of conformers. The functional insights offered by the approach are illustrated for biomolecular systems of very different size and complexity such as kinases, ion channels, and viral capsids. The decomposition tool is available as a software package and web server at spectrus.sissa.it. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Structure 07/2015; DOI:10.1016/j.str.2015.05.022 · 6.79 Impact Factor
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    Giovanni Pinamonti · Sandro Bottaro · Cristian Micheletti · Giovanni Bussi
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    ABSTRACT: Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of RNAs is often linked to their innate internal motions poses the question of whether ENM approaches can be successfully extended to this class of biomolecules. This issue is tackled here by considering various families of elastic networks of increasing complexity applied to a representative set of RNAs. The fluctuations predicted by the alternative ENMs are stringently validated by comparison against extensive molecular dynamics simulations and SHAPE experiments. We find that simulations and experimental data are systematically best reproduced by either an all-atom or a three-beads-per-nucleotide representation (sugar-base-phosphate), with the latter arguably providing the best balance of accuracy and computational complexity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
    Nucleic Acids Research 06/2015; DOI:10.1093/nar/gkv708 · 9.11 Impact Factor
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    ABSTRACT: We study how dispersions of colloidal particles in a cholesteric liquid crystal behave under a time-dependent electric field. By controlling the amplitude and shape of the applied field wave, we show that the system can be reproducibly driven out of equilibrium through different kinetic pathways and navigated through a glassy-like free energy landscape encompassing many competing metastable equilibria. Such states range from simple Saturn rings to complex structures featuring amorphous defect networks, or stacks of disclination loops. A non-equilibrium electric field can also trigger the alignment of particles into columnar arrays, through defect-mediated force impulses, or their repositioning within a plane. Our results are promising in terms of providing new avenues towards controlled patterning and self-assembly of soft colloid-liquid crystal composite materials.
    Physical Review Letters 04/2015; 114(17). DOI:10.1103/PhysRevLett.114.177801 · 7.51 Impact Factor
  • Guido Polles · Davide Marenduzzo · Enzo Orlandini · Cristian Micheletti
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    ABSTRACT: The self-assembly of objects with a set of desired properties is a major goal of material science and physics. A particularly challenging problem is that of self-assembling structures with a target topology. Here we show by computer simulation that one may design the geometry of string-like rigid patchy templates to promote their efficient and reproducible self-assembly into a selected repertoire of non-planar closed folds including several knots. In particular, by controlling the template geometry, we can direct the assembly process so as to strongly favour the formation of constructs tied in trefoil or pentafoil, or even of more exotic torus knots. Polydisperse and racemic mixtures of helical fragments of variable composition add further tunability in the topological self-assembly we discovered. Our results should be relevant to the design of new ways to synthesize molecular knots, which may prove, for instance, to be efficient cargo-carriers due to their mechanical stability.
    Nature Communications 03/2015; 6:6423. DOI:10.1038/ncomms7423 · 10.74 Impact Factor
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    Cristian Micheletti · Marco Di Stefano · Henri Orland
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    ABSTRACT: The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also, abound in viral DNA packaged inside bacteriophages. RNA molecules, however, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the several thousand RNA structures present in the Protein Data Bank (PDB). The search identified no more than three deeply knotted RNA molecules. These entries are rRNAs of about 3,000 nt solved by cryo-EM. Their genuine knotted state is, however, doubtful based on the detailed structural comparison with homologs of higher resolution, which are all unknotted. Compared with the case of proteins and viral DNA, the observed incidence of knots in available RNA structures is, therefore, practically negligible. This fact suggests that either evolutionary selection or thermodynamic and kinetic folding mechanisms act toward minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. A possible general strategy for designing synthetic RNA sequences capable of self-tying in a twist-knot fold is finally proposed.
    Proceedings of the National Academy of Sciences 02/2015; 112(7). DOI:10.1073/pnas.1418445112 · 9.81 Impact Factor
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    ABSTRACT: Recent studies have shown that single-stranded viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison it has been suggested that wild-type viral RNA may have evolved to be atypically compact so as to aid its encapsidation and assist the viral assembly process. In order to further explore the compactness selection hypothesis, we systematically compare the predicted sizes of more than one hundred wild-type viral sequences with those of their mutants, which are evolved in silico and subject to a number of known evolutionary constraints. In particular, we enforce mutation synonynimity, preserve the codon-bias, and leave untranslated regions intact. It is found that progressive accumulation of these restricted mutations still suffices to completely erase the characteristic compactness imprint of the viral RNA genomes, making them in this respect physically indistinguishable from randomly shuffled RNAs. This shows that maintaining the physical compactness of the genome is indeed a primary factor among ssRNA viruses evolutionary constraints, contributing also to the evidence that synonymous mutations in viral ssRNA genomes are not strictly neutral.
    Biophysical Journal 10/2014; 108(1). DOI:10.1016/j.bpj.2014.10.070 · 3.97 Impact Factor
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    ABSTRACT: The HIV-1 Tat protein and several small molecules bind to HIV-1 Trans-Activation Responsive RNA (TAR) by selecting sparsely populated but pre-existing conformations. Thus, a complete characterization of TAR conformational ensemble and dynamics is crucial to understand this paradigmatic system and could facilitate the discovery of new anti-virals targeting this essential regulatory element. We show here that molecular dynamics simulations can be effectively used towards this goal by bridging the gap between functionally-relevant timescales that are inaccessible to current experimental techniques. Specifically, we have performed several independent microsecond long molecular simulations of TAR based on one of the most advanced force fields available for RNA, the parmbsc0 AMBER . Our simulations are first validated against available experimental data, yielding an excellent agreement with measured residual dipolar couplings and order parameter S2. This contrast with previous MD simulations (Salmon et al., J. Am. Chem. Soc. 2013 135, 5457-5466) based on the CHARMM36 force field, which could achieve only modest accord with the experimental RDC values. Next, we direct the computation towards characterizing the internal dynamics of TAR over the microsecond timescale. We show that the conformational fluctuations observed over this previously-elusive timescale have a strong functionally-oriented character in that they are primed to sustain and assist ligand binding.
    Journal of the American Chemical Society 10/2014; 136(44). DOI:10.1021/ja507812v · 11.44 Impact Factor
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    Cristian Micheletti · Marco Di Stefano · Henri Orland
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    ABSTRACT: The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the other hand, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the ~6,000 RNA structures present in the protein data bank. The search identified no more than three deeply-knotted RNA molecules. These are ribosomal RNAs solved by cryo-em and consist of about 3,000 nucleotides. Compared to the case of proteins and viral DNA, the observed incidence of RNA knots is therefore practically negligible. This suggests that either evolutionary selection, or thermodynamic and kinetic folding mechanisms act towards minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. The properties of the three observed RNA knotting patterns provide valuable clues for designing RNA sequences capable of self-tying in a twist-knot fold.
  • Cristian Micheletti · Enzo Orlandini
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    ABSTRACT: The self-knotting dynamics of DNA strands confined in nanochannels is studied with Brownian simulations. The model DNA chains are several microns long and placed inside channels that are 50300 nm wide. This width range covers the transition between different metric scaling regimes and the concomitant drop of DNA knotting probability for channel widths below similar to 75 nm. We find that knots typically originate from deep looping and backfoldings of the chain ends. Upon lowering the channel width, backfoldings become shallower and rarer and the lifetime of knots decreases while that of unknots increases. This lifetimes interplay causes the dramatic reduction of knots incidence for increasing confinement. The results can aid the design of nanochannels capable of harnessing the self-knotting dynamics to quench or relax the DNA topological state as desired.
    ACS Macro Letters 09/2014; 3(9):876-880. DOI:10.1021/mz500402s · 5.24 Impact Factor
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    ABSTRACT: The dynamical properties of entangled polyelectrolytes are investigated theoretically and computationally for a proposed novel micromanipulation setup. Specifically, we investigate the effects of DC and AC electric fields acting longitudinally on knotted DNA chains, modelled as semiflexible chains of charged beads, under mechanical tension. We consider various experimentally accessible values of the field amplitude and frequency as well as several of the simplest knot types. In particular, we consider both torus and twist knots because they are respectively known to be able or unable to slide along macroscopic threads and ropes. Strikingly, this qualitative distinction disappears in this microscopic context because all the considered knot types acquire a systematic drift in the direction of the electric force. Notably, the knot drift velocity and diffusion coefficient in zero field (both measurable also experimentally) can be used to define a characteristic "frictional" lengthscale for the various knot types. This previously unexplored length provides valuable information on the extent of self-interactions in the nominal knotted region. It is finally observed that the motion of a knot can effectively follow the AC field only if the driving period is larger than the knot relaxation time (for which the self-diffusion time provides an upper bound). These results suggest that salient aspects of the intrinsic dynamics of knots in DNA chains could be probed experimentally by means of external, time-dependent electric fields.
    Soft Matter 07/2014; 10(34). DOI:10.1039/c4sm00160e · 4.15 Impact Factor
  • Davide Marenduzzo · Cristian Micheletti · Enzo Orlandini · De Witt Sumners
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    ABSTRACT: Bacteriophages initiate infection by releasing their double-stranded DNA into the cytosol of their bacterial host. However, what controls and sets the timescales of DNA ejection? Here we provide evidence from stochastic simulations which shows that the topology and organization of DNA packed inside the capsid plays a key role in determining these properties. Even with similar osmotic pressure pushing out the DNA, we find that spatially ordered DNA spools have a much lower effective friction than disordered entangled states. Such spools are only found when the tendency of nearby DNA strands to align locally is accounted for. This topological or conformational friction also depends on DNA knot type in the packing geometry and slows down or arrests the ejection of twist knots and very complex knots. We also find that the family of (2, 2k+1) torus knots unravel gradually by simplifying their topology in a stepwise fashion. Finally, an analysis of DNA trajectories inside the capsid shows that the knots formed throughout the ejection process mirror those found in gel electrophoresis experiments for viral DNA molecules extracted from the capsids.
    Proceedings of the National Academy of Sciences 11/2013; DOI:10.1073/pnas.1306601110 · 9.81 Impact Factor
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    ABSTRACT: Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available.
    PLoS Computational Biology 11/2013; 9(11):e1003331. DOI:10.1371/journal.pcbi.1003331 · 4.83 Impact Factor
  • Journal of Molecular Graphics and Modelling 08/2013; 18(s 4–5):549. DOI:10.1016/S1093-3263(00)80108-4 · 2.02 Impact Factor
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    L. Tubiana · A. Rosa · F. Fragiacomo · C. Micheletti
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    ABSTRACT: We report on a computational study of the statics and dynamics of long flexible linear polymers that spontaneously knot and unknot. Specifically, the equilibrium self-entanglement properties, such as the knotting probability, knot length and position, are investigated with extensive Monte Carlo sampling of chains of up to 15,000 beads. Tens of such equilibrated chains of up to 4, 096 beads are next used as starting points for Langevin dynamics simulations. The complex interplay of chain dynamics and self-knotting is addressed by monitoring the time evolution of various metric and entanglement properties. In particular, the extensive duration of the simulations allows for observing the spontaneous formation and disappearance of prime and composite physical knots in linear chains. Notably, a sizeable fraction of self-knotting and unknotting events is found to involve regions that are far away from the chain termini. To the best of our knowledge this represents the first instance where spontaneous changes in knotting for linear homopolymers are systematically characterized using unbiased dynamics simulations.
    Macromolecules 05/2013; 46(9):3669-3678. DOI:10.1021/ma4002963 · 5.93 Impact Factor
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    ABSTRACT: UreG are small GTP-binding (G) proteins that catalyse the hydrolysis of GTP necessary for the maturation of urease, a virulence factor in bacterial pathogenesis. UreG proteins are the first documented cases of intrinsically disordered enzymes. The comprehension of the dynamics of folding/unfolding events occurring in this protein could shed light on the enzymatic mechanism of UreG. Here, we used the recently developed replica exchange with solute tempering (REST2) computational methodology to explore the conformational space of UreG from Helicobacter pylori (HpUreG) and to identify its structural fluctuations. The same simulation and analysis protocol has been also applied to HypB from Methanocaldococcus jannaschii (MjHypB), which is closely related to UreG for both sequence and function, even though it is not intrinsically disordered. A comparison of the two systems reveals that both HpUreG and MjHypB feature a substantial rigidity of the protein regions involved in catalysis, justifying its residual catalytic activity. On the other hand, HpUreG tends to unfold more than MjHypB in portions involved in protein-protein interactions with metallo-chaperones necessary for the formation of multi-protein complexes known to be involved in urease activation.
    Biochemistry 04/2013; 52(17). DOI:10.1021/bi4001744 · 3.01 Impact Factor
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    ABSTRACT: For several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins motivated researchers to look into the physico-chemical mechanisms governing the concerted sequence of folding steps leading to the consistent formation of the same knot type in the same protein location. Besides experiments, computational studies are providing considerable insight into these mechanisms. Here, we revisit a number of such recent investigations within a common conceptual and methodological framework. By considering studies employing protein models with different structural resolution (coarse-grained or atomistic) and various force fields (from pure native-centric to realistic atomistic ones), we focus on the role of native and non-native interactions. For various unrelated instances of knotted proteins, non-native interactions are shown to be very important for favoring the emergence of conformations primed for successful self-knotting events.
    03/2013; 4(1):1-19. DOI:10.3390/biom4010001
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    ABSTRACT: We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native [Formula: see text]-sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting.
    PLoS Computational Biology 03/2013; 9(3):e1003002. DOI:10.1371/journal.pcbi.1003002 · 4.83 Impact Factor
  • Cristian Micheletti
    Physics of Life Reviews 03/2013; 10(1):39-40. DOI:10.1016/j.plrev.2012.11.001 · 9.48 Impact Factor
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    Journal of Biological Physics 03/2013; 39(2):161-2. DOI:10.1007/s10867-013-9320-1 · 1.15 Impact Factor

Publication Stats

3k Citations
558.80 Total Impact Points

Institutions

  • 1998–2015
    • Scuola Internazionale Superiore di Studi Avanzati di Trieste
      • Neurobiology Group
      Trst, Friuli Venezia Giulia, Italy
  • 2008–2012
    • Istituto Italiano di Tecnologia
      Genova, Liguria, Italy
  • 2010
    • Brandeis University
      Волтам, Massachusetts, United States
  • 2005–2006
    • The University of Warwick
      • Warwick Mathematics Institute
      Coventry, ENG, United Kingdom
  • 1970–2003
    • Abdus Salam International Centre for Theoretical Physics
      Trst, Friuli Venezia Giulia, Italy
  • 1995–1998
    • University of Oxford
      • Department of Physics
      Oxford, England, United Kingdom
  • 1997
    • University of Padova
      • Department of Physics and Astronomy "Galileo Galilei"
      Padua, Veneto, Italy