A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

Jie Hu, Tao Chen, Moye Wang, Hue Sun Chan and Zhuqing Zhang

Phys. Chem. Chem. Phys., 2017, 19, 13629
DOI: 10.1039/C7CP01532A

The low populated folding intermediate of a mutant of the Fyn SH3 domain identified by a simple model

Jing Wu, Guojun Chen, Zhuqing Zhang, Ping Zhang and Tao Chen

Phys. Chem. Chem. Phys., 2017, 19, 22321
DOI: 10.1039/C7CP04139J

Coarse-grained residue-based models of disordered protein condensates: utility and limitations of simple charge pattern parameters

Suman Das, Alan N. Amin, Yi-Hsuan Lin and Hue Sun Chan

Phys. Chem. Chem. Phys., 2018, 20, 28558
DOI: 10.1039/C8CP05095C

How determinant is N-terminal to C-terminal coupling for protein folding?

Heinrich Krobath, Antonio Rey and Patrícia F. N. Faísca

Phys. Chem. Chem. Phys., 2015, 17, 3512
DOI: 10.1039/C4CP05178E

Benchmarking all-atom simulations using hydrogen exchange

John J. Skinner, Wookyung Yu, Elizabeth K. Gichana, Michael C. Baxa, James R. Hinshaw, Karl F. Freed and Tobin R. Sosnick

Proc. Natl. Acad. Sci. U.S.A., 2014, 111, 15975
DOI: 10.1073/pnas.1404213111

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

Lorenzo Sborgi, Abhinav Verma, Stefano Piana, Kresten Lindorff-Larsen, Michele Cerminara, Clara M. Santiveri, David E. Shaw, Eva de Alba and Victor Muñoz

J. Am. Chem. Soc., 2015, 137, 6506
DOI: 10.1021/jacs.5b02324

Small-Angle X-ray Scattering Signatures of Conformational Heterogeneity and Homogeneity of Disordered Protein Ensembles

Jianhui Song, Jichen Li and Hue Sun Chan

J. Phys. Chem. B, 2021, 125, 6451
DOI: 10.1021/acs.jpcb.1c02453

Analysis of the pH-dependent thermodynamic stability, local motions, and microsecond folding kinetics of carbonmonoxycytochrome c

Rajesh Kumar

Archives of Biochemistry and Biophysics, 2016, 606, 16
DOI: 10.1016/j.abb.2016.07.010

Dispersion Forces and the Molecular Origin of Internal Friction in Protein

Pulikallu Sashi, Dasari Ramakrishna and Abani K. Bhuyan

Biochemistry, 2016, 55, 4595
DOI: 10.1021/acs.biochem.6b00500

Scaling Laws for Protein Folding under Confinement

Bin Zhu, Chenxi Zhang, Jiwei Wang, Chuandong Jia, Teng Lu, Liang Dai and Tao Chen

J. Phys. Chem. Lett., 2024, 15, 10138
DOI: 10.1021/acs.jpclett.4c02098

The role of solvent quality and chain stiffness on the end-to-end contact kinetics of semiflexible polymers

Jing Wu, Yiran Huang, Hongmei Yin and Tao Chen

The Journal of Chemical Physics, 2018, 149
DOI: 10.1063/1.5054829

Folding PDZ2 Domain Using the Molecular Transfer Model

Zhenxing Liu, Govardhan Reddy and D. Thirumalai

J. Phys. Chem. B, 2016, 120, 8090
DOI: 10.1021/acs.jpcb.6b00327

Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches

Tobias Sikosek, Heinrich Krobath, Hue Sun Chan and Robert L Jernigan

PLoS Comput Biol, 2016, 12, e1004960
DOI: 10.1371/journal.pcbi.1004960

Molecular recognition and packing frustration in a helical protein

Loan Huynh, Chris Neale, Régis Pomès, Hue Sun Chan and Tobin Roy Sosnick

PLoS Comput Biol, 2017, 13, e1005909
DOI: 10.1371/journal.pcbi.1005909

Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins

Tao Chen, Hue Sun Chan and Dennis R Livesay

PLoS Comput Biol, 2015, 11, e1004260
DOI: 10.1371/journal.pcbi.1004260

How cooperative are protein folding and unfolding transitions?

Pooja Malhotra and Jayant B. Udgaonkar

Protein Science, 2016, 25, 1924
DOI: 10.1002/pro.3015

The folding pathways and thermodynamics of semiflexible polymers

Jing Wu, Chenqian Cheng, Gaoyuan Liu, Ping Zhang and Tao Chen

The Journal of Chemical Physics, 2018, 148
DOI: 10.1063/1.5018114

Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

Yong Wang, Pengfei Tian, Wouter Boomsma and Kresten Lindorff-Larsen

J. Phys. Chem. B, 2018, 122, 11174
DOI: 10.1021/acs.jpcb.8b06335

Folding of Protein L with Implications for Collapse in the Denatured State Ensemble

Hiranmay Maity and Govardhan Reddy

J. Am. Chem. Soc., 2016, 138, 2609
DOI: 10.1021/jacs.5b11300

Dimensions, energetics, and denaturant effects of the protein unstructured state

Maodong Li and Zhirong Liu

Protein Science, 2016, 25, 734
DOI: 10.1002/pro.2865

Tuning Cooperativity on the Free Energy Landscape of Protein Folding

Pooja Malhotra and Jayant B. Udgaonkar

Biochemistry, 2015, 54, 3431
DOI: 10.1021/acs.biochem.5b00247

Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins

Michiko Kimoto, Hui Pen Tan, Ken-ichiro Matsunaga, Nur Afiqah Binte Mohd Mislan, Gota Kawai and Ichiro Hirao

J. Am. Chem. Soc., 2023, 145, 20432
DOI: 10.1021/jacs.3c06122

Conformational Heterogeneity and FRET Data Interpretation for Dimensions of Unfolded Proteins

Jianhui Song, Gregory-Neal Gomes, Tongfei Shi, Claudiu C. Gradinaru and Hue Sun Chan

Biophysical Journal, 2017, 113, 1012
DOI: 10.1016/j.bpj.2017.07.023

Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding

Tao Chen, Jianhui Song and Hue Sun Chan

Current Opinion in Structural Biology, 2015, 30, 32
DOI: 10.1016/j.sbi.2014.12.002

Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures

Joseph D. Yesselman, Scott Horowitz, Charles L. Brooks and Raymond C. Trievel

Proteins, 2015, 83, 403
DOI: 10.1002/prot.24724

Heterogeneity in Protein Folding and Unfolding Reactions

Sandhya Bhatia and Jayant B. Udgaonkar

Chem. Rev., 2022, 122, 8911
DOI: 10.1021/acs.chemrev.1c00704

Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding

Cristiano L. Dias and Hue Sun Chan

J. Phys. Chem. B, 2014, 118, 7488
DOI: 10.1021/jp501935f

Volumetric Physics of Polypeptide Coil–Helix Transitions

Heinrich Krobath, Tao Chen and Hue Sun Chan

Biochemistry, 2016, 55, 6269
DOI: 10.1021/acs.biochem.6b00802

Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure

Masatake Sugita, Masanari Matsuoka and Takeshi Kikuchi

Proteins, 2015, 83, 1900
DOI: 10.1002/prot.24874