Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions

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

Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning

(2020) Alex S. Holehouse et al.   Journal of Chemical Theory and Computation

Elastin-Like Polypeptides for Biomedical Applications

(2020) Anastasia K. Varanko et al.   Annual Review of Biomedical Engineering

RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation

(2020) Jordina Guillén-Boixet et al.   CELL

Single-Protein Collapse Determines Phase Equilibria of a Biological Condensate

(2020) Han-Yi Chou et al.   Journal of Physical Chemistry Letters

Liquid-liquid phase separation drives skin barrier formation

(2020) Felipe Garcia Quiroz et al.   SCIENCE

Making the Case for Disordered Proteins and Biomolecular Condensates in Bacteria

(2020) Megan C. Cohan et al.   TRENDS IN BIOCHEMICAL SCIENCES

Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins

(2020) Xiangze Zeng et al.   BIOPHYSICAL JOURNAL

Simulations of activities, solubilities, transport properties, and nucleation rates for aqueous electrolyte solutions

(2020) Athanassios Z. Panagiotopoulos   JOURNAL OF CHEMICAL PHYSICS

De novo engineering of intracellular condensates using artificial disordered proteins

(2020) Michael Dzuricky et al.   Nature Chemistry

Liquid Phase Separation Controlled by pH

(2020) Omar Adame-Arana et al.   BIOPHYSICAL JOURNAL

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

Protein Solubility Predictions Using the CamSol Method in the Study of Protein Homeostasis

(2019) Pietro Sormanni et al.   Cold Spring Harbor Perspectives in Biology

Temperature-Controlled Liquid–Liquid Phase Separation of Disordered Proteins

(2019) Gregory L. Dignon et al.   ACS Central Science

New frontiers for the materials genome initiative

(2019) Juan J. de Pablo et al.   npj Computational Materials

q-Canonical Monte Carlo Sampling for Modeling the Linkage Between Charge Regulation and Conformational Equilibria of Peptides

(2019) Martin J Fossat et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Engineered Ribonucleoprotein Granules Inhibit Translation in Protocells

(2019) Joseph R. Simon et al.   MOLECULAR CELL

LASSI: A lattice model for simulating phase transitions of multivalent proteins

(2019) Jeong-Mo Choi et al.   PLoS Computational Biology

Intrinsically disordered proteins access a range of hysteretic phase separation behaviors

(2019) Felipe Garcia Quiroz et al.   Science Advances

Engineering of silk proteins for materials applications

(2019) Merisa Saric et al.   CURRENT OPINION IN BIOTECHNOLOGY

Structural Regulation of a Neurofilament-Inspired Intrinsically Disordered Protein Brush by Multisite Phosphorylation

(2018) Ruoxing Lei et al.   BIOCHEMISTRY

Convergence of Artificial Protein Polymers and Intrinsically Disordered Proteins

(2018) Michael Dzuricky et al.   BIOCHEMISTRY

Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers

(2018) Kiersten M. Ruff et al.   JOURNAL OF MOLECULAR BIOLOGY

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Studies on the phase transition of hydrogels and aqueous solutions of thermosensitive polymers

(2018) Hiroyuki Kojima   POLYMER JOURNAL

Tinker 8: Software Tools for Molecular Design

(2018) Joshua A. Rackers et al.   Journal of Chemical Theory and Computation

Many-body effect determines the selectivity for Ca2+and Mg2+in proteins

(2018) Zhifeng Jing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

All-Atom Simulations Reveal Protein Charge Decoration in the Folded and Unfolded Ensemble Is Key in Thermophilic Adaptation

(2017) Lucas Sawle et al.   Journal of Chemical Theory and Computation

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

(2017) Matthew Harger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

(2017) Joseph R. Simon et al.   Nature Chemistry

GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins

(2016) Tyler S. Harmon et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Relating sequence encoded information to form and function of intrinsically disordered proteins

(2015) Rahul K Das et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

(2015) Felipe García Quiroz et al.   NATURE MATERIALS

Conserved interdomain linker promotes phase separation of the multivalent adaptor protein Nck

(2015) Sudeep Banjade et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temperature-dependent solvation modulates the dimensions of disordered proteins

(2014) R. Wuttke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Improved Atomistic Monte Carlo Simulations Demonstrate That Poly-l-Proline Adopts Heterogeneous Ensembles of Conformations of Semi-Rigid Segments Interrupted by Kinks

(2012) Aditya Radhakrishnan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automation of AMOEBA polarizable force field parameterization for small molecules

(2012) Johnny C. Wu et al.   THEORETICAL CHEMISTRY ACCOUNTS

Molecular Origin of the Hierarchical Elasticity of Titin: Simulation, Experiment, and Theory

(2011) Jen Hsin et al.   Annual Review of Biophysics

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

(2011) Pengyu Ren et al.   Journal of Chemical Theory and Computation

Hydration, phase separation and nonlinear rheology of temperature-sensitive water-soluble polymers

(2011) Fumihiko Tanaka et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

A highly parallel method for synthesizing DNA repeats enables the discovery of ‘smart’ protein polymers

(2011) Miriam Amiram et al.   NATURE MATERIALS

Multipole electrostatics in hydration free energy calculations

(2010) Yue Shi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

New Estimators for Calculating Solvation Entropy and Enthalpy and Comparative Assessments of Their Accuracy and Precision

(2010) Matthew A. Wyczalkowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cooperative Hydration Induces Discontinuous Volume Phase Transition of Cross-Linked Poly(N-isopropylacrylamide) Gels in Water

(2010) Hiroyuki Kojima et al.   MACROMOLECULES

Molecular origin of the negative heat capacity of hydrophilic hydration

(2009) Masahiro Kinoshita et al.   JOURNAL OF CHEMICAL PHYSICS

Isothermal-isobaric molecular dynamics using stochastic velocity rescaling

(2009) Giovanni Bussi et al.   JOURNAL OF CHEMICAL PHYSICS

Systematic optimization of long-range corrected hybrid density functionals

(2008) Jeng-Da Chai et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water

(2008) Omer Markovitch et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculation of protein-ligand binding free energy by using a polarizable potential

(2008) D. Jiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsic disorder in scaffold proteins: Getting more from less

(2008) Marc S. Cortese et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY