Physics-based computational and theoretical approaches to intrinsically disordered proteins

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions

(2020) Jeong-Mo Choi et al.   Annual Review of Biophysics

A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes

(2020) Yi-Hsuan Lin et al.   JOURNAL OF CHEMICAL PHYSICS

TDP-43 α-helical structure tunes liquid–liquid phase separation and function

(2020) Alexander E. Conicella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An analytical theory to describe sequence-specific inter-residue distance profiles for polyampholytes and intrinsically disordered proteins

(2020) Jonathan Huihui et al.   JOURNAL OF CHEMICAL PHYSICS

Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model

(2020) Yani Zhao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hydropathy Patterning Complements Charge Patterning to Describe Conformational Preferences of Disordered Proteins

(2020) Wenwei Zheng et al.   Journal of Physical Chemistry Letters

Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components

(2020) Jorge R. Espinosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior

(2020) Benjamin S. Schuster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analytical Theory for Sequence-Specific Binary Fuzzy Complexes of Charged Intrinsically Disordered Proteins

(2020) Alan N. Amin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Phase transition of RNA−protein complexes into ordered hollow condensates

(2020) Ibraheem Alshareedah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extended experimental inferential structure determination method in determining the structural ensembles of disordered protein states

(2020) James Lincoff et al.   Communications Chemistry

Dehydration entropy drives liquid-liquid phase separation by molecular crowding

(2020) Sohee Park et al.   Communications Chemistry

The proline-rich domain promotes Tau liquid–liquid phase separation in cells

(2020) Xuemei Zhang et al.   JOURNAL OF CELL BIOLOGY

Unraveling Molecular Interactions in Liquid–Liquid Phase Separation of Disordered Proteins by Atomistic Simulations

(2020) Matteo Paloni et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins

(2020) Wai Shing Tang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations

(2020) Wenwei Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations

(2020) Roshan Mammen Regy et al.   NUCLEIC ACIDS RESEARCH

Designing the Morphology of Separated Phases in Multicomponent Liquid Mixtures

(2020) Sheng Mao et al.   PHYSICAL REVIEW LETTERS

Improvements to the ABSINTH forcefield for proteins based on experimentally derived amino-acid specific backbone conformational statistics

(2019) Jeong-Mo Choi et al.   Journal of Chemical Theory and Computation

Complete Phase Diagram for Liquid–Liquid Phase Separation of Intrinsically Disordered Proteins

(2019) James McCarty et al.   Journal of Physical Chemistry Letters

Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins

(2019) Upayan Baul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates

(2019) Ioana M. Ilie et al.   CHEMICAL REVIEWS

Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties

(2019) Gül H. Zerze et al.   Journal of Physical Chemistry Letters

Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions

(2019) Yanxian Lin et al.   eLife

Simulation methods for liquid–liquid phase separation of disordered proteins

(2019) Gregory L Dignon et al.   Current Opinion in Chemical Engineering

Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain

(2019) Anastasia C. Murthy et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

(2019) Utsab R. Shrestha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three archetypical classes of macromolecular regulators of protein liquid–liquid phase separation

(2019) Archishman Ghosh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations

(2019) Lisa M. Pietrek et al.   Journal of Chemical Theory and Computation

Developing a molecular dynamics force field for both folded and disordered protein states

(2018) Paul Robustelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence determinants of protein phase behavior from a coarse-grained model

(2018) Gregory L. Dignon et al.   PLoS Computational Biology

AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins

(2018) Hao Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Relation between single-molecule properties and phase behavior of intrinsically disordered proteins

(2018) Gregory L. Dignon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biophysical experiments and biomolecular simulations: A perfect match?

(2018) Sandro Bottaro et al.   SCIENCE

Molecular Determinants of Aβ42 Adsorption to Amyloid Fibril Surfaces

(2018) Mathias M. J. Bellaiche et al.   Journal of Physical Chemistry Letters

Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations

(2018) Kiersten M Ruff et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

50th Anniversary Perspective: A Perspective on Polyelectrolyte Solutions

(2017) M. Muthukumar   MACROMOLECULES

The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease

(2016) M. Madan Babu   BIOCHEMICAL SOCIETY TRANSACTIONS

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

Recent Developments in Fully Fluctuating Field-Theoretic Simulations of Polymer Melts and Solutions

(2016) Kris T. Delaney et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Advances in the Simulation of Protein Aggregation at the Atomistic Scale

(2016) Martín Carballo-Pacheco et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment

(2016) Wenwei Zheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Vapour–liquid phase equilibrium and surface tension of fully flexible Lennard–Jones chains

(2016) Kevin S. Silmore et al.   MOLECULAR PHYSICS

Computational Studies of Protein Aggregation: Methods and Applications

(2015) Alex Morriss-Andrews et al.   Annual Review of Physical Chemistry

A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins

(2015) Lucas Sawle et al.   JOURNAL OF CHEMICAL PHYSICS

Correction to Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

(2015) Robert B. Best et al.   Journal of Chemical Theory and Computation

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

(2013) R. K. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coarse-grained models for protein aggregation

(2011) Chun Wu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Tuning the Globular Assembly of Hydrophobic/Hydrophilic Heteropolymer Sequences

(2009) Henry S. Ashbaugh   JOURNAL OF PHYSICAL CHEMISTRY B

ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

(2008) Andreas Vitalis et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY