Research Description

Theoretical and Computational Investigations of Protein Folding, Interactions, and Evolution

Protein folding and interactions are physico-chemical processes. Our group’s overall research goal is to elucidate their underlying energetics. To this end, a main emphasis of our effort is to develop proteinlike heteropolymer models with coarse-grained interactions and simplified representations of chain geometries. The rationale of these approaches is to capture the essential physics and at the same time allow for a broad coverage of the protein conformational space — and also a broad coverage of the sequence space for evolutionary studies — that is not readily achievable currently in higher-resolution models.

Enthalpy-entropy compensation at the desolvation barrier to folding (Chan et al., Annu Rev Phys Chem 2011).

Molecular dynamics simulations using common atomic forcefields and explicit water models are used in our work as well, especially for deciphering subtle properties of solvent-mediated interactions. Various combinations of coarse-grained and atomic methods are being used to gain physical insights into general principles of folding, protein interactions, and evolution. The topics we address including folding cooperativity, origin of enthalpic and volumetric folding barriers, nonnative effects in folding, formation of functional and disease-causing  dynamic, “fuzzy” complexes involving intrinsically disordered proteins, and conformational switching in protein evolution. Some of these efforts are highlighted below.

Cooperativity and nonnative interactions in folding

Comparing the simulated folding thermodynamic free energy profiles (top) and kinetic chevron plots (bottom) of the proteins Top7 (left) and S6 (right) (Zhang & Chan, PNAS 2010).

The Levinthal paradox of protein folding is commonly perceived as a statement about the impossibility of folding by a completely random conformational search. Often missed in such narratives is that the question raised by Levinthal was in response to the experimental discovery of two-state, switch-like cooperative folding by calorimetry in the late 1960s, rather than to the issue of conformational search per se. Two-state folding is expected to serve biological functions such as avoidance of aggregation. Folding cooperativity likely emerges from a coupling between local structural preferences and nonlocal packing interactions. To elucidate this local-nonlocal coupling  mechanism and other folding properties, we develop native-centric as well as “hybrid” models in which nonnative effects are treated perturbatively. Many-body interactions, hydrogen bonding, sidechain packing and solvation are now being examined for their impact on folding cooperativity.

Intrinsically disordered proteins

Polyelectrostatic (left) and polycation-π (right) interactions can facilitate intrinsically disordered protein binding in fuzzy complexes (Borg et al., PNAS 2007; Song et al., PLoS Comput Biol 2013).

While many proteins function in their folded states, it is now clear that intrinsically disordered proteins (IDPs) perform critical functions in transcription, translation and cell cycle regulation. Altering the functions of these IDPs can lead to cancer and other diseases. Molecular recognition by IDPs often involves target-induced folding. However, certain IDPs interact with other proteins without coupled folding-binding. Those cases entail dynamic, “fuzzy” complexes in which the bound IDPs remain largely disordered. In collaboration with experimentalist colleagues, we are developing biophysical models of IDP conformational ensembles. A main focus of our effort is to decipher the role of multisite electrostatic and aromatic interactions in IDP function and malfunction.

Atomic simulations of solvent-mediated interactions

Entropic, enthalpic, and volumetric effects of hydrophobic association (MacCallum et al., PNAS 2007; Dias & Chan, J Phys Chem B 2014).

As part of our effort to understand protein energetics, we conduct atomic simulations of aqueous solvation. Comparisons between theory and experiment indicate a prominent role of desolvation barriers in cooperative folding. Desolvation effects are key to resolving an apparent inconsistency between experimentally observed enthalpic barriers and the funnel picture of folding. They also provide novel insights into volumetric barriers to folding. Results from these atomic studies — which are not always obvious a priori — are being used to build physically more accurate coarse-grained models.

Biophysical models of protein evolution

Supernets, inter-connecting neutral nets, superfunnels and conformational switches between superfunnels (Sikosek & Chan, J R Soc Interface 2014).

The study of protein evolution requires a model of the mapping between amino acid sequences and the conformational ensembles they encode. Because of their computational tractability, lattice models with biophysics-based interaction schemes are useful for addressing large-scale evolution across many different protein folds. Together with collaborators, we have applied this approach to several fundamental aspects of protein evolution. Our effort has led to the recognition that neutral nets of globular proteins are likely organized as superfunnels, and that sequence-space topology or mutational robustness can have significant impact on evolutionary population and thus can help resolve adaptive conflict.

Mathematical basis of type-2 topoisomerase action

Writhe compensation in small DNA circles with a hook-like juxtaposition (Liu et al., J Mol Biol 2010).

Type-2 topoisomerases (topoIIs) are enzymes that unknot and decatenate DNA circles and reduce the variance of linking number Lk of supercoiled DNA. Given that a topoII is much smaller than the DNA it acts upon, how does a topoII discern the global DNA topology from the limited, local DNA conformational information it can access? To answer this question, we focus on DNA rather than protein conformations. Working with collaborators, we address the hypothesis that  topological simplification by topoII is achieved by performing DNA segment passage and re-sealing only at hook-like DNA juxtapositions. To test this “hook juxtaposition hypothesis”, we use exact enumeration and Monte Carlo sampling of conformations with various preformed juxtaposition geometries. Results from cubic-lattice and worm-like chain models indicate that the hypothesis is likely valid because it consistently accounts for a wide range of experimental data.

Publications

View all publications on PubMed

Comparative Roles of Charge, π, and Hydrophobic Interactions in Sequence-Dependent Phase Separation of Intrinsically Disordered Proteins.
S. Das, Y.-H. Lin, R.M. Vernon, J.D. Forman-Kay and H.S. Chan
Proceedings of the National Academy of Sciences, USA 117, 28795-28805 (2020).  Read

Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid-Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications.
H. Cinar, Z. Fetahaj, S. Cinar, R. M. Vernon, H.S. Chan and R. Winter
Chemistry, A European Journal (Chem. Eur. J.) 25, 13049-13069 (2019).  Read

Theories for Sequence-Dependent Phase Behaviors of Biomolecular Condensates.
Y.-H. Lin, J.D. Forman-Kay and H.S. Chan
Biochemistry 57, 2499-2508 (2018).  Read

Charge Pattern Matching as a "Fuzzy" Mode of Molecular Recognition for the Functional Phase Separations of Intrinsically Disordered Proteins.
Y.-H. Lin, J.P. Brady, J.D. Forman-Kay and H.S. Chan
New Journal of Physics 19, 115003 (2017).  Read

Sequence-Specific Polyampholyte Phase Separation in Membraneless Organelles.
Y.-H. Lin, J. D. Forman-Kay and H.S. Chan
Physical Review Letters 117:178101 (2016).  Read

Theoretical Insights into the Biophysics of Protein Bi-Stability and Evolutionary Switches.
T. Sikosek, H. Krobath and H.S. Chan
PLoS Computational Biology 12(6):e1004960 (2016)  Read

Theoretical Perspectives on Nonnative Interactions and Intrinsic Disorder in Protein Folding and Binding.
T. Chen, J. Song and H.S. Chan
Current Opinion in Structural Biology 30, 32-42 (2015).  Read

Biophysics of Protein Evolution and Evolutionary Protein Biophysics.
T. Sikosek and H.S. Chan
Journal of the Royal Society Interface 11, 20140419 (2014).  Read

Polycation-π Interactions are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family.
J. Song, S.C. Ng, P. Tompa, K.A.W. Lee and H.S. Chan
PLoS Computational Biology 9(9): e1003239 (2013).  Read

Transition Paths, Diffusive Processes, and Preequilibria of Protein Folding.
Z. Zhang and H.S. Chan
Proceedings of the National Academy of Sciences, USA 109, 20919-20924 (2012).  Read

Escape from Adaptive Conflict Follows from Weak Functional Trade-Offs and Mutational Robustness.
T. Sikosek, H.S. Chan and E. Bornberg-Bauer
Proceedings of the National Academy of Sciences, USA 109, 14888-14893 (2012).  Read

Cooperativity, Local-Nonlocal Coupling, and Nonnative Interactions: Principles of Protein Folding from Coarse-Grained Models.
H.S. Chan, Z. Zhang, S. Wallin and Z. Liu
Annual Review of Physical Chemistry 62, 301-326 (2011).  Read

Action at Hooked or Twisted-Hooked DNA Juxtapositions Rationalizes Unlinking Preference of Type-2 Topoisomerases.
Z. Liu, L. Zechiedrich and H.S. Chan
Journal of Molecular Biology 400, 963-982 (2010).  Read

Competition Between Native Topology and Nonnative Interactions in Simple and Complex Folding Kinetics of Natural and Designed Proteins.
Z. Zhang and H.S. Chan
Proceedings of the National Academy of Sciences, USA 107, 2920-2925 (2010).  Read

Theoretical and Experimental Demonstration of the Importance of Specific Nonnative Interactions in Protein Folding.
A. Zarrine-Afsar, S. Wallin, A.M. Neculai, P. Neudecker, P.L. Howell, A.R. Davidson and H.S. Chan
Proceedings of the National Academy of Sciences, USA 105, 9999-10004 (2008).  Read

Polyelectrostatic Interactions of Disordered Ligands Suggest a Physical Basis for Ultrasensitivity.
M. Borg, T. Mittag, T. Pawson, M. Tyers, J.D. Forman-Kay and H.S. Chan
Proceedings of the National Academy of Sciences, USA 104, 9650-9655 (2007).  Read

Hydrophobic Association of α-Helices, Steric Dewetting and Enthalpic Barriers to Protein Folding.
J. L. MacCallum, M. Sabaye Moghaddam, H.S. Chan and D.P. Tieleman
Proceedings of the National Academy of Sciences, USA 104, 6206-6210 (2007).  Read

From Levinthal to Pathways to Funnels.
K.A. Dill and H.S. Chan
Nature Structural Biology 4, 10-19 (1997).  Read