Recently, a series of closely related theoretical constructs termed the “topomer search model” (TSM) has been proposed for the folding mechanism of small, single-domain proteins. A basic...
Knott, Michael, Kaya, Huseyin, Chan, Hue Sun
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric G\=o-like models with a...
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating...
Origins of Chevron Rollovers in Non-Two-State Protein Folding Kinetics (2003)
Chevron rollovers of some proteins imply that their logarithmic folding rates are nonlinear in native stability. This is predicted by lattice and continuum G\=o models to arise from diminished...
Simple Two-State Protein Folding Kinetics Requires Near-Levinthal Thermodynamic Cooperativity (2003)
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium...
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the...
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed...
Harrison, Paul M., Chan, Hue Sun, Prusiner, Stanley B., Cohen, Fred E.
Protein refolding/misfolding to an alternative form plays an aetiologic role in many diseases in humans, including Alzheimer's disease, the systemic amyloidoses, and the prion diseases. Here we have...
Energetic Components of Cooperative Protein Folding (2000)
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials...
Polymer Principles of Protein Calorimetric Two-State Cooperativity (2000)
The experimental calorimetric two-state criterion requires the van't Hoff enthalpy $\Delta H_{\rm vH}$ around the folding/unfolding transition midpoint to be equal or very close to the calorimetric...
Access the most recent version at doi: 10.1110/ps.38701 References (2000)
Paul M. Harrison, Hue Sun Chan, Stanley B. Prusiner, Fred E. Cohen, Email Alerting, Paul M. Harrison, ...
Conformational propagation with prion-like characteristics in a
Designing amino acid sequences to fold with good hydrophobic cores (1995)
Sun, Shaojian, Brem, Rachel, Chan, Hue Sun, Dill, Ken A.
We present two methods for designing amino acid sequences of proteins that will fold to have good hydrophobic cores. Given the coordinates of the desired target protein or polymer structure, the...
Continuum regularization of gauge theory with fermions / (1987)
Thesis (Ph. D. in Physics)--University of California, Berkeley, May 1987.
Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space
Bornberg-Bauer, Erich, Chan, Hue Sun
Random mutations under neutral or near-neutral conditions are studied by considering plausible evolutionary trajectories on “neutral nets”—i.e., collections of sequences (genotypes)...
Cui, Yan, Wong, Wing Hung, Bornberg-Bauer, Erich, Chan, Hue Sun
The role of recombination in evolution is compared with that of point mutations (substitutions) in the context of a simple, polymer physics-based model mapping between sequence (genotype) and...
Ollerenshaw, Jason E., Kaya, Hüseyin, Chan, Hue Sun, Kay, Lewis E.
A complete description of how a protein folds requires the characterization of intermediate conformations traversed during the folding transition. We have calculated dynamics trajectories of a...
Wroe, Richard, Bornberg-Bauer, Erich, Chan, Hue Sun
Understanding the evolution of biopolymers is a key element in rationalizing their structures and functions. Simple exact models (SEMs) are well-positioned to address general principles of evolution...
Kaya, Hüseyin, Liu, Zhirong, Chan, Hue Sun
It has been demonstrated that a “near-Levinthal” cooperative mechanism, whereby the common Gō interaction scheme is augmented by an extra favorability for the native state as a whole, can lead...
Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space
Bornberg-Bauer, Erich, Chan, Hue Sun
Random mutations under neutral or near-neutral conditions are studied by considering plausible evolutionary trajectories on “neutral nets”—i.e., collections of sequences (genotypes)...
Cui, Yan, Wong, Wing Hung, Bornberg-Bauer, Erich, Chan, Hue Sun
The role of recombination in evolution is compared with that of point mutations (substitutions) in the context of a simple, polymer physics-based model mapping between sequence (genotype) and...
Ollerenshaw, Jason E., Kaya, Hüseyin, Chan, Hue Sun, Kay, Lewis E.
A complete description of how a protein folds requires the characterization of intermediate conformations traversed during the folding transition. We have calculated dynamics trajectories of a...
Wroe, Richard, Bornberg-Bauer, Erich, Chan, Hue Sun
Understanding the evolution of biopolymers is a key element in rationalizing their structures and functions. Simple exact models (SEMs) are well-positioned to address general principles of evolution...
Kaya, Hüseyin, Liu, Zhirong, Chan, Hue Sun
It has been demonstrated that a “near-Levinthal” cooperative mechanism, whereby the common Gō interaction scheme is augmented by an extra favorability for the native state as a whole, can lead...
Liu, Zhirong, Zechiedrich, E. Lynn, Chan, Hue Sun
Lattice modeling is applied to investigate how the configurations of local chain juxtapositions may provide information about whether two ring polymers (loops) are topologically linked globally....
Hydrophobic association of α-helices, steric dewetting, and enthalpic barriers to protein folding
MacCallum, Justin L., Moghaddam, Maria Sabaye, Chan, Hue Sun, Tieleman, D. Peter
Efficient protein folding implies a microscopic funnel-like multidimensional free-energy landscape. Macroscopically, conformational entropy reduction can manifest itself as part of an empirical...
Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity
Borg, Mikael, Mittag, Tanja, Pawson, Tony, Tyers, Mike, Forman-Kay, Julie D., Chan, Hue Sun
Regulation of biological processes often involves phosphorylation of intrinsically disordered protein regions, thereby modulating protein interactions. Initiation of DNA replication in yeast requires...
Recently, a series of closely related theoretical constructs termed the “topomer search model” (TSM) has been proposed for the folding mechanism of small, single-domain proteins. A basic...
Conformational propagation with prion-like characteristics in a simple model of protein folding
Harrison, Paul M., Chan, Hue Sun, Prusiner, Stanley B., Cohen, Fred E.
Protein refolding/misfolding to an alternative form plays an aetiologic role in many diseases in humans, including Alzheimer's disease, the systemic amyloidoses, and the prion diseases. Here we have...
Zarrine-Afsar, Arash, Wallin, Stefan, Neculai, A. Mirela, Neudecker, Philipp, Howell, P. Lynne, Davidson, Alan R., ...
Many experimental and theoretical studies have suggested a significant role for nonnative interactions in protein folding pathways, but the energetic contributions of these interactions are not well...
The why and how of DNA unlinking
Liu, Zhirong, Deibler, Richard W., Chan, Hue Sun, Zechiedrich, Lynn
The nucleotide sequence of DNA is the repository of hereditary information. Yet, it is now clear that the DNA itself plays an active role in regulating the ability of the cell to extract its...
A structural model of latent evolutionary potentials underlying neutral networks in proteins
Wroe, Richard, Chan, Hue Sun, Bornberg-Bauer, Erich
A central question in molecular evolution concerns the nature of phenotypic transitions, in particular, if neutral mutations hamper or somehow facilitate adaptability of proteins to new requirements....
Liaison amid disorder: non-native interactions may underpin long-range coupling in proteins
A lattice-model study of double-mutant cycles published in BMC Structural Biology underscores how interactions in non-native conformations can lead to thermodynamic coupling between distant residues...