Research graph
References from Conformational Landscape of a Marginally Disordered Protein HYPK and its Charge-Variant Mutant in the Context of Folded Domains. Local targets link to admitted publications; unresolved targets remain external evidence.
Natively unfolded proteins: A point where biology waits for physics
10.1110/ps.4210102 · 2002 · External reference
The molten globule concept: 45 years later
10.1134/s0006297918140043 · 2018 · External reference
Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution
10.1002/bip.360281004 · 1989 · External reference
Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators
10.1038/415549a · 2002 · External reference
Role of intrinsic protein disorder in the function and interactions of the transcriptional coactivators CREB-binding protein and p300
10.1074/jbc.r115.692020 · 2016 · External reference
FlgM gains structure in living cells
10.1073/pnas.202331299 · 2002 · External reference
HYPK: A marginally disordered protein sensitive to charge decoration
10.1073/pnas.2316408121 · 2024 · External reference
Cooperativity in protein-folding kinetics
10.1073/pnas.90.5.1942 · 1993 · External reference
Cooperativity in protein folding: from lattice models with sidechains to real proteins
10.1016/s1359-0278(98)00018-2 · 1998 · External reference
Cooperativity and stability in a Langevin model of proteinlike folding
10.1063/1.474039 · 1997 · External reference
Cooperativity principles in protein folding
10.1016/s0076-6879(04)80016-8 · 2004 · External reference
Exploring the effects of hydrogen bonding and hydrophobic interactions on the foldability and cooperativity of helical proteins using a simplified atomic model
10.1016/j.chemphys.2004.06.014 · 2004 · External reference
Theory for protein folding cooperativity: Helix bundles
10.1021/ja808136x · 2009 · External reference
On the role of native contact cooperativity in protein folding
10.1073/pnas.2319249121 · 2024 · External reference
Spatial ranges of driving forces are a key determinant of protein folding cooperativity and rate diversity
10.1103/physreve.88.044701 · 2013 · External reference
All-or-none proteinlike folding transition of a flexible homopolymer chain
10.1103/physreve.79.050801 · 2009 · External reference
An analytical theory to describe sequence-specific inter-residue distance profiles for polyampholytes and intrinsically disordered proteins
10.1063/5.0004619 · 2020 · External reference
Intrinsically disordered regions are poised to act as sensors of cellular chemistry
10.1016/j.tibs.2023.08.001 · 2023 · External reference
Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins
10.1073/pnas.2200559119 · 2022 · External reference
A view of the hydrophobic effect
10.1021/jp015514e · 2002 · External reference
Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy
10.1021/cr400688u · 2014 · External reference
Conformational ensembles of an intrinsically disordered protein consistent with NMR, SAXS, and single-molecule FRET
10.1021/jacs.0c02088 · 2020 · External reference
Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
10.1073/pnas.1207719109 · 2012 · External reference
Developing a molecular dynamics force field for both folded and disordered protein states
10.1073/pnas.1800690115 · 2018 · External reference
A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins
10.1063/1.4929391 · 2015 · External reference
A new continuum solvation model for simulations of polypeptides in aqueous solutions
10.1002/jcc.21005 · 2009 · External reference
Methods for Monte Carlo simulations of biomacromolecules
10.1016/s1574-1400(09)00503-9 · 2009 · External reference
The Amber biomolecular simulation programs
10.1002/jcc.20290 · 2005 · External reference
Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
10.1016/0010-4655(95)00041-d · 1995 · External reference
Improved generalized Born solvent model parameters for protein bimulations
10.1021/ct3010485 · 2013 · External reference
ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB
10.1021/acs.jctc.5b00255 · 2015 · External reference
Critical assessment of self-consistency checks in the all-atom molecular dynamics simulation of intrinsically disordered proteins
10.1021/acs.jctc.2c01140 · 2023 · External reference
Gromacs 4: Algorithms for highly efficient, load balanced, and scalable molecular simulation
10.1021/ct700301q · 2008 · External reference
GROMACS: A message-passing parallel molecular dynamics implementation
10.1016/0010-4655(95)00042-e · 1995 · External reference
A threshold selection method from gray-level histograms
10.1109/tsmc.1979.4310076 · 1979 · External reference
The role of conformational dynamics and allostery in modulating protein evolution
10.1146/annurev-biophys-052118-115517 · 2020 · External reference
Dynamic allostery: Evolution’s double-edged sword in protein function and disease
10.1016/j.jmb.2025.169175 · 2025 · External reference
The role of conformational dynamics and allostery in the disease development of human ferritin
10.1016/j.bpj.2015.06.060 · 2015 · External reference
Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity
10.1038/s41467-021-22089-0 · 2021 · External reference
Ancient thioredoxins evolved to modern-day stability-function requirement by altering native state ensemble
10.1098/rstb.2017.0184 · 2018 · External reference
Mutations utilize dynamic allostery to confer resistance in TEM-1 β-lactamase
10.3390/ijms19123808 · 2018 · External reference
Dynamic allostery highlights the evolutionary differences between the CoV-1 and CoV-2 main proteases
10.1016/j.bpj.2022.03.012 · 2022 · External reference
Structural dynamics flexibility informs function and evolution at a proteome scale
10.1111/eva.12052 · 2013 · External reference
A hinge migration mechanism unlocks the evolution of green-to-red photo conversion in GFP-like proteins
10.1016/j.str.2014.11.011 · 2015 · External reference
Statistical physics-based approaches to model the function and complexation of disordered proteins
10.1021/acs.jpcb.5c05422 · 2025 · External reference
Protein dynamics provide mechanistic insights about epistasis among coming missense polymorphisms
10.1016/j.bpj.2023.01.037 · 2023 · External reference
Folded domain charge properties influence the conformational properties of disordered tails
10.1016/j.crstbi.2021.08.002 · 2021 · External reference
A coarse-grained model for disordered and multi-domain proteins
10.1002/pro.5172 · 2024 · External reference
Effective concentrations enforced by intrinsically disordered linkers are governed by polymer physics
10.1073/pnas.1904813116 · 2019 · External reference
Sequence charge decoration dictates coil-globule transition in Intrinsically Disordered Proteins
10.1063/1.5005821 · 2018 · External reference
Rules of physical mathematics govern intrinsically disordered proteins
10.1146/annurev-biophys-120221-095357 · 2022 · External reference
Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
10.1073/pnas.1304749110 · 2013 · External reference
Intrachain interaction topology can identify functionally similar intrinsically disordered proteins
10.1016/j.bpj.2020.11.2282 · 2021 · External reference
Microsecond folding dynamics of the F13W G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump
10.1073/pnas.0306433101 · 2004 · External reference
Protein design: A hierarchical approach
10.1126/science.270.5238.935 · 1995 · External reference
Modeling competitive substitution in a polyelectrolyte complex
10.1063/1.4936256 · 2015 · External reference
Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes
10.1038/s41467-020-18859-x · 2020 · External reference
Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein
10.1038/s41557-021-00839-3 · 2022 · External reference
Mesoscale properties of biomolecular condensates emerging from chain dynamics
10.1073/pnas.2424135122 · 2025 · External reference
Driving forces of the complex formation between highly charged disordered proteins
10.1073/pnas.2304036120 · 2023 · External reference
Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins
10.1093/pnasnexus/pgae367 · 2024 · External reference
Mapping charge interactions in intrinsically disordered proteins
10.1002/advs.202514056 · 2026 · External reference
ReAsH as a quantitative probe of in-cell protein dynamics
10.1021/acs.biochem.5b01336 · 2016 · External reference
Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs
10.64898/2026.05.21.726897 · 2026 · External reference
Balanced protein-water interactions improve properties of disordered proteins and non-specific protein association
10.1021/ct500569b · 2014 · External reference
Physics-based computational and theoretical approaches to intrinsically disordered proteins
10.1016/j.sbi.2020.12.012 · 2021 · External reference
Ionic strength modulates structural disorder and protein oligomerization in the marginally disordered Phd transcription factor
10.64898/2026.04.15.718675 · 2026 · External reference
Mapping charge interactions in intrinsically disordered proteins
10.1002/advs.202514056 · ExternalCitation · doi-reference
Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution
10.1002/bip.360281004 · ExternalCitation · doi-reference
The Amber biomolecular simulation programs
10.1002/jcc.20290 · ExternalCitation · doi-reference
A new continuum solvation model for simulations of polypeptides in aqueous solutions
10.1002/jcc.21005 · ExternalCitation · doi-reference
A coarse-grained model for disordered and multi-domain proteins
10.1002/pro.5172 · ExternalCitation · doi-reference
Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
10.1016/0010-4655(95)00041-d · ExternalCitation · doi-reference
GROMACS: A message-passing parallel molecular dynamics implementation
10.1016/0010-4655(95)00042-e · ExternalCitation · doi-reference
The role of conformational dynamics and allostery in the disease development of human ferritin
10.1016/j.bpj.2015.06.060 · ExternalCitation · doi-reference
Intrachain interaction topology can identify functionally similar intrinsically disordered proteins
10.1016/j.bpj.2020.11.2282 · ExternalCitation · doi-reference
Dynamic allostery highlights the evolutionary differences between the CoV-1 and CoV-2 main proteases
10.1016/j.bpj.2022.03.012 · ExternalCitation · doi-reference
Protein dynamics provide mechanistic insights about epistasis among coming missense polymorphisms
10.1016/j.bpj.2023.01.037 · ExternalCitation · doi-reference
Exploring the effects of hydrogen bonding and hydrophobic interactions on the foldability and cooperativity of helical proteins using a simplified atomic model
10.1016/j.chemphys.2004.06.014 · ExternalCitation · doi-reference
Folded domain charge properties influence the conformational properties of disordered tails
10.1016/j.crstbi.2021.08.002 · ExternalCitation · doi-reference
Dynamic allostery: Evolution’s double-edged sword in protein function and disease
10.1016/j.jmb.2025.169175 · ExternalCitation · doi-reference
Physics-based computational and theoretical approaches to intrinsically disordered proteins
10.1016/j.sbi.2020.12.012 · ExternalCitation · doi-reference
A hinge migration mechanism unlocks the evolution of green-to-red photo conversion in GFP-like proteins
10.1016/j.str.2014.11.011 · ExternalCitation · doi-reference
Intrinsically disordered regions are poised to act as sensors of cellular chemistry
10.1016/j.tibs.2023.08.001 · ExternalCitation · doi-reference
Cooperativity principles in protein folding
10.1016/s0076-6879(04)80016-8 · ExternalCitation · doi-reference
Cooperativity in protein folding: from lattice models with sidechains to real proteins
10.1016/s1359-0278(98)00018-2 · ExternalCitation · doi-reference
Methods for Monte Carlo simulations of biomacromolecules
10.1016/s1574-1400(09)00503-9 · ExternalCitation · doi-reference
ReAsH as a quantitative probe of in-cell protein dynamics
10.1021/acs.biochem.5b01336 · ExternalCitation · doi-reference
Critical assessment of self-consistency checks in the all-atom molecular dynamics simulation of intrinsically disordered proteins
10.1021/acs.jctc.2c01140 · ExternalCitation · doi-reference
ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB
10.1021/acs.jctc.5b00255 · ExternalCitation · doi-reference
Statistical physics-based approaches to model the function and complexation of disordered proteins
10.1021/acs.jpcb.5c05422 · ExternalCitation · doi-reference
Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy
10.1021/cr400688u · ExternalCitation · doi-reference
Improved generalized Born solvent model parameters for protein bimulations
10.1021/ct3010485 · ExternalCitation · doi-reference
Balanced protein-water interactions improve properties of disordered proteins and non-specific protein association
10.1021/ct500569b · ExternalCitation · doi-reference
Gromacs 4: Algorithms for highly efficient, load balanced, and scalable molecular simulation
10.1021/ct700301q · ExternalCitation · doi-reference
Theory for protein folding cooperativity: Helix bundles
10.1021/ja808136x · ExternalCitation · doi-reference
Conformational ensembles of an intrinsically disordered protein consistent with NMR, SAXS, and single-molecule FRET
10.1021/jacs.0c02088 · ExternalCitation · doi-reference
A view of the hydrophobic effect
10.1021/jp015514e · ExternalCitation · doi-reference
Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators
10.1038/415549a · ExternalCitation · doi-reference
Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes
10.1038/s41467-020-18859-x · ExternalCitation · doi-reference
Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity
10.1038/s41467-021-22089-0 · ExternalCitation · doi-reference
Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein
10.1038/s41557-021-00839-3 · ExternalCitation · doi-reference
Cooperativity and stability in a Langevin model of proteinlike folding
10.1063/1.474039 · ExternalCitation · doi-reference
A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins
10.1063/1.4929391 · ExternalCitation · doi-reference
Modeling competitive substitution in a polyelectrolyte complex
10.1063/1.4936256 · ExternalCitation · doi-reference
Sequence charge decoration dictates coil-globule transition in Intrinsically Disordered Proteins
10.1063/1.5005821 · ExternalCitation · doi-reference
An analytical theory to describe sequence-specific inter-residue distance profiles for polyampholytes and intrinsically disordered proteins
10.1063/5.0004619 · ExternalCitation · doi-reference
Microsecond folding dynamics of the F13W G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump
10.1073/pnas.0306433101 · ExternalCitation · doi-reference
Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
10.1073/pnas.1207719109 · ExternalCitation · doi-reference
Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
10.1073/pnas.1304749110 · ExternalCitation · doi-reference
Developing a molecular dynamics force field for both folded and disordered protein states
10.1073/pnas.1800690115 · ExternalCitation · doi-reference
Effective concentrations enforced by intrinsically disordered linkers are governed by polymer physics
10.1073/pnas.1904813116 · ExternalCitation · doi-reference
FlgM gains structure in living cells
10.1073/pnas.202331299 · ExternalCitation · doi-reference
Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins
10.1073/pnas.2200559119 · ExternalCitation · doi-reference
Driving forces of the complex formation between highly charged disordered proteins
10.1073/pnas.2304036120 · ExternalCitation · doi-reference
HYPK: A marginally disordered protein sensitive to charge decoration
10.1073/pnas.2316408121 · ExternalCitation · doi-reference
On the role of native contact cooperativity in protein folding
10.1073/pnas.2319249121 · ExternalCitation · doi-reference
Mesoscale properties of biomolecular condensates emerging from chain dynamics
10.1073/pnas.2424135122 · ExternalCitation · doi-reference
Cooperativity in protein-folding kinetics
10.1073/pnas.90.5.1942 · ExternalCitation · doi-reference
Role of intrinsic protein disorder in the function and interactions of the transcriptional coactivators CREB-binding protein and p300
10.1074/jbc.r115.692020 · ExternalCitation · doi-reference
Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins
10.1093/pnasnexus/pgae367 · ExternalCitation · doi-reference
Ancient thioredoxins evolved to modern-day stability-function requirement by altering native state ensemble
10.1098/rstb.2017.0184 · ExternalCitation · doi-reference
All-or-none proteinlike folding transition of a flexible homopolymer chain
10.1103/physreve.79.050801 · ExternalCitation · doi-reference
Spatial ranges of driving forces are a key determinant of protein folding cooperativity and rate diversity
10.1103/physreve.88.044701 · ExternalCitation · doi-reference
A threshold selection method from gray-level histograms
10.1109/tsmc.1979.4310076 · ExternalCitation · doi-reference
Natively unfolded proteins: A point where biology waits for physics
10.1110/ps.4210102 · ExternalCitation · doi-reference
Structural dynamics flexibility informs function and evolution at a proteome scale
10.1111/eva.12052 · ExternalCitation · doi-reference
Protein design: A hierarchical approach
10.1126/science.270.5238.935 · ExternalCitation · doi-reference
The molten globule concept: 45 years later
10.1134/s0006297918140043 · ExternalCitation · doi-reference
The role of conformational dynamics and allostery in modulating protein evolution
10.1146/annurev-biophys-052118-115517 · ExternalCitation · doi-reference
Rules of physical mathematics govern intrinsically disordered proteins
10.1146/annurev-biophys-120221-095357 · ExternalCitation · doi-reference
Mutations utilize dynamic allostery to confer resistance in TEM-1 β-lactamase
10.3390/ijms19123808 · ExternalCitation · doi-reference
Ionic strength modulates structural disorder and protein oligomerization in the marginally disordered Phd transcription factor
10.64898/2026.04.15.718675 · ExternalCitation · doi-reference
Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs
10.64898/2026.05.21.726897 · ExternalCitation · doi-reference
