Members from the group are highlighted in italics

Pre-prints

  1. Zhu H+, Narita M+, Joseph JA+, Krainer G, Arter WE, Saar KL, Ermann N, Espinosa JR, Shen Y, Kuri MA, Qi R, Xu Y, Collepardo-Guevara R*, Narita M*,  Knowles T*. The chromatin regulator HMGA1a undergoes phase separation in the nucleus. bioRxiv: https://doi.org/10.1101/2021.10.14.464384 (2021) *co-correspondence +co-first authors
  2. Garaizar A, Espinosa JR, Joseph JA, Krainer G, Shen Y, Knowles TPJ, Collepardo-Guevara R. Intermolecular reorganisation of single-component condensates during ageing promotes multiphase architectures. bioRxiv: https://doi.org/10.1101/2021.10.09.463670 (2021)

Published

  1. Huertas J, Woods EJ, Collepardo-Guevara R. Multiscale modelling of chromatin organization: resolving nucleosomes at near-atomistic resolution inside genes. Curr Op Cell Biol. In-press (2022)
  2. Garaizar A, Espinosa JR, Joseph JA, Collepardo-Guevara R. Kinetic interplay between droplet maturation and coalescence modulates shape of aged protein condensates. Sci Rep. In-press (2022)
  3. Sanchez-Burgos I, Espinosa JR, Joseph JA, Collepardo-Guevara R. RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins. Plos Comp Biol. In-Press (2022)
  4. Welsh TJ+, Krainer G+, Espinosa JR+, Joseph JA, Sridhar A, Collepardo-Guevara R*, Alberti S*, Knowles TPJ*. Surface Electrostatics Govern the Emulsion Stability of Biomolecular Condensates. Nano Letters (2022) *co-correspondence +co-first authors
  5. Joseph JA, Reinhardt A, Aguirre A, Chew PY, Russell K, Espinosa JR, Garaizar A, Collepardo-Guevara R. Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. Nat Comp Scie (2021) 1(11) https://doi.org/10.1038/s43588-021-00155-3
  6. Itoh Y, Woods EJ, Minami K, Maeshima K, Collepardo-Guevara R. Local chromatin structure and dynamics: What can we learn from imaging and computational modeling? Curr Op Struct Bio (2021) 71:123–135
  7. Lichtinger SM, Garaizar A, Collepardo-Guevara R*, Reinhardt A*. Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence. Plos Comp Biol (2021) 17(8): e1009328 *co-correspondence
  8. Sanchez-Burgos I, Joseph JA, Collepardo-Guevara R, Espinosa JR. Size conservation emerges spontaneously in biomolecular condensates formed by scaffolds and surfactant clients. Sci Rep (2021) 11 15241
  9. Farr SE, Woods EJ, Joseph JA, Garaizar A, Collepardo-Guevara R. Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions. Nat Commun (2021) 12 2883
  10. Joseph JA, Espinosa JR, Sanchez-Burgos I, Garaizar A, Frenkel D, Collepardo-Guevara R. Thermodynamics and kinetics of phase separation of protein–RNA mixtures by a minimal model. Biophys J (2021) 120 1219–1230
  11. Krainer G+, Welsh TJ+, Joseph JA+, Espinosa JR, Wittmann S, de Csilléry E, Sridhar A, Toprakcioglu Z, Gudiškytė G, Czekalska MA, Arter WE, Guillén-Boixet J, Franzmann TM, St George-Hyslop P, Hyman AA*, Collepardo-Guevara R*, Alberti S*, Knowles TPJ*.  Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun (2021) 12 1085 *co-correspondence, +co-first authors
  12. Sanchez-Burgos I, Espinosa JR, Joseph JA, Collepardo-Guevara R. Valency and binding affinity variations can regulate the multilayered organization of protein condensates with many components. Biomolecules (2021) 11 (2) 278.
  13. Garaizar A, Sanchez-Burgos I, Collepardo-Guevara R, Espinosa JR. Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid–Liquid Phase Separation. Molecules (2020) 25 (20) 4705.
  14. Espinosa JE, Joseph JA, Garaizar A, Sanchez-Burgos I, Frenkel D, Collepardo-Guevara R. Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components. Proc Natl Acad Sci USA (2020) 117 (24) 13238-13247.
  15. Sridhar A, Farr SE, Portella G, Schlick T, Orozco M, Collepardo-Guevara R. Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry. Proc Natl Acad Sci USA (2020) 117 (13) 7216-7224.
  16. Sridhar A, Orozco M, Collepardo-Guevara R. Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1. Nucleic Acids Res (2020) 48 (10) 5318–5331.
  17. Sandoval-Perez A, Garaizar A, Farr SE, Berger R, Brehm MA, Konig G, Schneider SW, Huck V, Radler JO, Collepardo-Guevara R, Aponte-Santamarıa C. DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions. Nucleic Acid Res (2020) gkaa466.
  18. Espinosa JR, Garaizar A, Vega C, Frenkel D, Collepardo-Guevara R. Breakdown of the law of rectilinear diameter and related surprises in the liquid-vapor coexistence in systems of patchy particles. J Chem Phys (2019) 150 (22) 224510.

 

 Previous publications

  1. Collepardo-Guevara R, Portella G, Frenkel D, Vendruscolo M, Schlick T, Orozco M. Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study. J Am Chem Soc (2015) 137:10205.
  2. Gungor O, Collepardo-Guevara R, Schlick T. Forced unravelling of chromatin fibers with nonuniform linker DNA lengths. J Phys: Cond Matt (2015) 27:064113.
  3. Collepardo-Guevara R, Schlick T. Chromatin fiber polymorphism triggered by variations of DNA linker lengths. Proc Natl Acad Sci USA (2014) 111:8061.
  4. Chakraborty D, Collepardo-Guevara R, Wales DJ. Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins. J Am Chem Soc (2014) 136:18052.
  5. Arcella A, Portella G, Collepardo-Guevara R, Chakraborty D, Wales DJ, Orozco M. Structure and properties of DNA in apolar solvents. J Phys Chem B (2014) 118:8540.
  6. Luque A, Collepardo-Guevara R, Grigoryev S, Schlick T. Dynamic condensation of linker histone C-terminal domain regulates chromatin structure. Nucleic Acids Res (2014) 42:7553.
  7. Hospital A, Faustino I, Collepardo-Guevara R, González C, Lluís Gelpí J, Orozco M. NAFlex: A web server for the study of nucleic acids flexibility, Nucleic Acids Res (2013) 41:W47.
  8. Collepardo-Guevara R, Schlick T. Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments. Biochem Soc Trans (2013) 41:494.
  9. Collepardo-Guevara R, Schlick T. Crucial role of dynamic linker histone binding for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes. Nucleic Acids Res (2012) 40:8803.
  10. Collepardo-Guevara R, Schlick T. The effect of linker histone’s nucleosome binding affinity on chromatin unfolding mechanisms. Biophys J (2011) 101:1670.
  11. Schlick T, Collepardo-Guevara R. Biomolecular Modeling and Simulation: The Productive Trajectory of a Field. SIAM News (2011) 44:6.
  12. Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X. Biomolecular modelling and simulation: a field coming of age. Quart Rev Biophys (2011) 43:1.
  13. Perisic O+ , Collepardo-Guevara R+, Schlick T. Modelling studies of chromatin fiber structure as a function of DNA linker length. J Mol Bio (2010) 403:777. +co-first author Suleimanov Y, Collepardo-Guevara R, Manolopoulos DE. Bimolecular reaction rates from ring polymer molecular dynamics: application to H + CH4 → H2 + CH3. J Chem Phys (2011) 134:044131.
  14. Collepardo-Guevara R, Suleimanov Y, Manolopoulos DE. Bimolecular chemical reaction rates from ring polymer rate theory. J Chem Phys (2009) 130:174713.
  15. Collepardo-Guevara R, Craig IR, Manolopoulos DE. Proton transfer in a polar solvent from ring polymer molecular dynamics reaction rate theory. J Chem Phys (2008) 128:144502.
  16. Collepardo-Guevara R, Corvera Poiré E. Controlling viscoelastic flow by tuning frequency during occlusions. Phys Review E (2007) 76:026301.
  17. Collepardo-Guevara R, Corvera Poiré E. Maximizing the dynamic permeability during occlusions. Eur. Phys. J. Special Topics (2007) 143:95.
  18. Collepardo-Guevara R, Walter D, Neuhauser D, Baer R. A Hückel study of the effect of a molecular resonance cavity on the quantum conductance of an alkene wire. Chem Phys Lett (2004) 393:367

 

Open-source software from the group

  1. MD_Patchy_model: A fast and computationally cheap implementation of our patchy particle model, along with source code, example input files and a tutorial on how to use it can be found here: https://github.com/CollepardoLab/md_patchy_model
  2. Multiscale_chromatin_model: We are delighted to share with the community our chromatin coarse grained models. Our implementation, source code, example input files, and a demo, can be found here: https://figshare.com/articles/software/CollepardoLab_Chromatin_Model/13663685/1
  3. Mpipi_model: We have developed a sequence-dependent coarse-grained model for biomolecular phase separation in LAMMPS. All input scripts, parameter files and a tutorial can be found in the Figshare data repository at https://doi:10.6084/m9.figshare.16772812