Predict pKa Values and Protonation States for Dynamical Systems

Protein-inhibitor binding

Henderson JA, Harris RC, Tsai CC, and Shen J*,  

How ligand protonation proton state controls water in protein ligand binding. 

J Phys Chem Lett 9: 5440-5444, 2018.

Harris RC, Tsai CC, Ellis CR, and Shen J*, 

Proton-coupled conformational allostery modulates the inhibitor selectivity for β-secretase. 

J Phys Chem Lett 8: 4832-4837, 2017.

Ellis CR, Tsai CC, Hou XJ, and Shen J*,
Constant pH molecular dynamics reveals pH-modulated binding of two small-molecule BACE1 inhibitors.
J Phys Chem Lett 7: 944-949, 2016.

Protein-protein binding

Wallace JA and Shen JK*,

Unraveling a trap-and-trigger mechanism in the pH-sensitive self-assembly of spider silk proteins.

J Phys Chem Lett 3: 658-662, 2012.

Transmembrane proteins

Chen W, Huang YD and Shen J*,

Conformational activation of a transmembrane proton channel from constant pH molecular dynamics.

J Phys Chem Lett 7: 3961-3966, 2016.

Huang YD, Chen W, Dotson DL, Beckstein O, and Shen J*,

Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA.

Nature Commun 7:12940, 2016.

Soluble proteins and peptides


Huang YD, Yue Z, Tsai CC, Henderson JA, and Shen J*,  

Predicting catalytic proton donors and nucleophiles in enzymes: how adding dynamics helps elucidate the structure-function relationships. 

J Phys Chem Lett 9: 1179-1184, 2018.

Huang YD, Chen W, and Shen J*,

Continuous constant pH molecular dynamics with particle-mesh Ewald and titratabe water.

J Chem Theory Comput. 12: 5411-5421, 2016.

Ellis CR and Shen J*,
pH-dependent population shift regulates BACE1 activity and inhibition.
J Am Chem Soc 137: 9543-9546, 2015.

Shi C, Wallace JA, and Shen JK*,

Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation.

Biophys J. 102: 1590-1597, 2012.


Wallace JA and Shen JK*,

Continuous constant pH molecular dynamics in explicit solvent with pH-based replica exchange.

J Chem Theory Comput 7: 2617-2629, 2011.


Wallace JA, Wang Y, Shi C, Pastoor KJ, Nguyen B-L, Xia K, and Shen JK*,

Towards accurate prediction of pKa values for protein internal residues: the importance of conformational relaxation and desolvation energy.

Proteins 79: 3364-3363, 2011.


Wallace JA and Shen JK*,
Predicting protein pKa’s with continuous constant pH molecular dynamics.
Methods Enzymol 66: 455-475, 2009.

Qian J, Khandogin J, West AH, Cook P*,
Evidence for a catalytic dyad in the active site of homocitrate synthase from saccaromyces cerevisiae.
Biochemistry 47: 6851-6858, 2009.


Khandogin J and Brooks CL III*.
Linking folding with aggregation in Alzheimer’s beta-amyloid peptides.
Proc Natl Acad Sci USA 104: 16880-16885. 2007.


Khandogin J, Raleigh DP, and Brooks CL III*,
Folding intermediate in the villin headpiece domain arises from disruption of an N-terminal hydrogen-bonded network.
J Am Chem Soc 129: 3056-3057, 2007.

Khandogin J, Chen J, and Brooks CL III*,
Exploring atomistic details of pH-dependent peptide folding.
Proc Natl Acad Sci USA 103: 18546-18550, 2006.


Wu S, Yan K, Zhao Y, Tsai CC, Shen J, Bentley WE, Chen Y, Deng H, Du Y, Payne GF* and Shi X*,

Electrical writing onto a dynamically responsive polysaccharide medium: patterning structure and function into a reconfigurable medium. Adv Funct Mater, ASAP, 2018.

Yan K, Liu Y, Zhang J, Correa SO, Shang W, Tsai CC, Bentley WE, Shen J, Scarcelli G, Raub CB, Shi XW, Payne GF*,

Electrical programming of soft matter: using temporally varying electrical inputs to spatially control self assembly. 

Biomacromolecules 19: 364-373, 2018. 

Morrow BH, Payne GF, and Shen J*,
Stimuli-responsive self-assembly of polysaccharide through a rugged energy landscape.
J Am Chem Soc 137: 13024-13030, 2015.


Morrow BH, Eike DM, Murch BP, Koenig PH, and Shen J*,
Predicting proton titration in cationic micelle and bilayer environments.
J Chem Phys 141: 084714, 2014.

Morrow BH, Koenig PH, and Shen JK*,
Self-Assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics.
Langmuir 29: 14823-14830, 2013.


Morrow BH, Koenig PH, and Shen JK*,
Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids.
J Chem Phys 137: 194902, 2012.

Morrow BH, Wang Y, Wallace JA, Koenig PH, and Shen JK*,
Simulating pH titration of a single surfactant in ionic and nonionic micelles.
J Phys Chem B 115: 14980-14990, 2011.


Wang Y, Wallace JA, Koenig PH, and Shen JK*,
Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized Born implicit-solvent model.
J Comput Chem 32: 2358, 2011.