Publications

Complete list of publications of people in the group can be found in their home pages.
Here we list some recent publications (2000- ) with links to the pdf files.

Invalidity of continuum theories of electrolytes in nanopores.
B. Corry, S. Kuyucak and S.H. Chung, Chem. Phys. Lett. 320 (2000) 35-41.

Tests of continuum theories as models of ion channels: I. Poisson-Boltzmann theory versus Brownian Dynamics.
G. Moy, B. Corry, S. Kuyucak and S.H. Chung, Biophys. J. 78 (2000) 2349-2363.

Tests of continuum theories as models of ion channels: II. Poisson-Nernst-Planck theory versus Brownian Dynamics.
B. Corry, S. Kuyucak and S.H. Chung, Biophys. J. 78 (2000) 2364-2381.

Molecular  dynamics estimates of ion diffusion in model hydrophobic and the KcsA potassium channels.
T.W. Allen, S. Kuyucak and S.H. Chung, Biophys. Chem. 86 (2000) 1-14.

The potassium channel:  structure, selectivity and diffusion.
T.W. Allen, A. Bliznyuk, A.P. Rendell, S. Kuyucak and S.H. Chung, J. Chem. Phys. 112 (2000) 8191-8204.

A model of calcium channels.
B. Corry, T.W. Allen, S. Kuyucak and S.H. Chung, Biochim. Biophys. Acta,  Rapid report 1509 (2000) 1-6.

Predicting channel function from channel structure using Brownian Dynamics simulations.
S.H. Chung and S. Kuyucak, Clinical & Exp. Physiology & Pharmacology 28 (2001) 89-94.

Mechanisms of permeation and selectivity in calcium channels.
B. Corry, T.W. Allen, S. Kuyucak and S.H. Chung, Biophys. J. 80 (2001) 195-214.

Models of permeation in ion channels.
S. Kuyucak, O.A. Andersen and S.H. Chung, Rep. Prog. Phys. 64 (2001) 1427-1472.

Conducting-state properties of the KcsA potassium channel from molecular and Brownian Dynamics simulations.
S.H. Chung, T.W. Allen and S. Kuyucak, Biophys. J. 82 (2002) 628-645.

Permeation models and structure-function relationships in ion channels.
S. Kuyucak and S.H. Chung, J. Biol. Phys. 28 (2002) 289-308.

Reservoir boundaries in Brownian Dynamics simulations of ion channels.
B. Corry, M. Hoyles, T.W. Allen, M. Walker, S. Kuyucak and S.H. Chung, Biophys. J. 82 (2002) 1975-1984.

Modeling diverse range of potassium channels with Brownian Dynamics.
S.H. Chung, T.W. Allen and S. Kuyucak, Biophys. J. 83 (2002) 263-277.

Ion channels: recent progress and prospects.
S.H. Chung and S. Kuyucak, Eur. Biophys. J. 31 (2002) 283-293.

Continuum electrostatics fails to describe ion permeation in the gramicidin A channel.
S. Edwards, B. Corry, S. Kuyucak and S.H. Chung, Biophys. J. 83 (2002) 1348-1360.

Recent advances in ion channels research.
S.H. Chung and S. Kuyucak, Biochim. Biophys. Acta - Reviews 1565 (2002) 267-286.

Gramicidin A channel as a test ground for molecular dynamics force fields.
T.W. Allen, T. Bastug, S. Kuyucak and S.H. Chung, Biophys. J. 84 (2003) 2159-2168.

Functional properties of 3-fold and 4-fold channels in Ferritin deduced from electrostatic calculations.
T. Takahashi and S. Kuyucak, Biophys. J. 84 (2003) 2256-2263.

Role of the dielectric constants of membrane proteins and channel water in ion permeation.
T. Bastug and S. Kuyucak, Biophys. J. 84 (2003) 2871-2882.

Dielectric self energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels.
B. Corry, S. Kuyucak and S.H. Chung, Biophys. J. 84 (2003) 3594-3606.

Physics of ion channels.
S. Kuyucak and T. Bastug, J. Biol. Phys. 29 (2003) 429-446.

Memory effects in Brownian dynamics simulations of ion transport.
T. Bastug and S. Kuyucak, Chem. Phys. Lett.  401 (2005) 175-179. 

Temperature dependence of the transport coefficients of ions from molecular dynamics simulations.
T. Bastug and S. Kuyucak, Chem. Phys. Lett.  408 (2005) 84-88.

Test of molecular dynamics force fields in gramicidin A.
T. Bastug and S. Kuyucak, Eur. Biophys. J. 34 (2005) 377-382.

Role of protein flexibility in ion permeation: a case study in gramicidin A.
T. Bastug, A. Gray-Weale, S.M. Patra and S. Kuyucak, Biophys. J. 90 (2006) 2285-2296.

Energetics of ion permeation, rejection, binding and block in gramicidin A from free energy simulations.
T. Bastug and S. Kuyucak, Biophys. J. 90 (2006) 3941-3950.

Molecular dynamics simulations of calcium binding in gramicidin A.
T. Bastug and S. Kuyucak, Chem. Phys. Lett. 424 (2006) 82-85.

Molecular dynamics simulations of gramicidin A in a lipid bilayer: from structure-function relations to force fields.

T. Bastug, S.M. Patra and S. Kuyucak, Chem. Phys. Lipids 141 (2006) 197-204.

Finite system and periodicity effects in free energy simulations of membrane proteins.
T. Bastug, S.M. Patra and S. Kuyucak,
Chem. Phys. Lett. 425 (2006) 320-323.

Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel.
R. Kutteh, J.I. Vandenberg and S. Kuyucak,
J. Phys. Chem. B 111 (2007) 1090-1098.

Free energy simulations of single and double ion occupancy in gramicidin A.
T. Bastug and S. Kuyucak,
J. Chem. Phys. 126 (2007) #105103 (12 pages).

Application of Jarzynski's equality in simple versus complex systems.
T. Bastug and S. Kuyucak,
Chem. Phys. Lett. 436 (2007) 383-387.

Binding of organic cations to gramicidin A channel studied with Autodock and molecular dynamics simulations.
S.M. Patra, T. Bastug and S. Kuyucak, J. Phys. Chem. B 111 (2007) 11303-11311.


Charge state of the fast gate in chloride channels: electrostatic calculations in a schematic model.
R. Wijesinghe, N. Coorey, and S.Kuyucak, J. Chem. Phys. 127 (2007) #195102 (9 pages).


Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling.
T. Bastug, P. C. Chen, S. M. Patra and S. Kuyucak, J. Chem. Phys. 128 (2008) #155104 (12 pages).


Response to Comment on "Free energy simulations of single and double ion occupancy in gramicidin A".
T. Bastug and S. Kuyucak, J. Chem. Phys. 128 (2008) #227102 (2 pages)


Polarization of water in the first hydration shell of K+ and Ca2+ ions
D. Bucher and S. Kuyucak, J. Phys. Chem. B (Letters), 112 (2008) 10786-10790.


The pore domain outer helix contributes to both activation and inactivation of the hERG K+ channel.
P. Ju, G. Pages, R.P. Riek, P.C. Chen, A.M. Torres, P.S. Bansal, S.Kuyucak, P.W. Kuchel, and J.I. Vandenberg, J. Biol. Chem. 284 (2009) 1000-1008.


Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations.
P.C. Chen and S. Kuyucak, Biophys. J. 96 (2009) 2577-2588.


Importance of the peptide backbone description in modeling the selectivity filter in potassium channels.
T. Bastug and S. Kuyucak, Biophys. J. 96 (2009) 4006-4012.


Importance of water polarization for ion permeation in narrow pores.
D. Bucher and S. Kuyucak, Chem. Phys. Lett. 477 (2009) 207-210.


Dissociation of NaCl in water from ab initio molecular dynamics simulations.
J. Timko, D. Bucher and S. Kuyucak, J. Chem. Phys. 132 (2010) #114510 (8 pages).


Ab initio study of water polarization in the hydration shell of aqueous hydroxide: comparison between polarizable and nonpolarizable water models.
D. Bucher, A. Gray-Weale, and S. Kuyucak, J. Chem. Theory Comput. 6 (2010) 2888-2895.


Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels.
T. Bastug and S. Kuyucak, Biophys. J. 100 (2011) 629-636.


Accurate determination of the binding free energy for KcsA-Charybdotoxin complex from the potential of mean force calculations with restraints.
P.C. Chen and S. Kuyucak, Biophys. J. 100 (2011) 2466-2474.


Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl.
J. Timko, A. De Castro, and S. Kuyucak, J. Chem. Phys. 134 (2011) #204510 (9 pages).


Free energy simulations of ligand binding to the aspartate transporter GltPh.
G. Heinzelmann, T. Bastug, and S. Kuyucak, (2011). Biophys. J. 101 (2011) 2380-2388.


Position of the third Na+ site in the aspartate transporter GltPh and the human glutamate transporter EAAT1.
T. Bastug, G. Heinzelmann, S. Kuyucak, M. Salim, R.J. Vandenberg, and R.M. Ryan (2012), PLoS One 7 (2012) e33058.


Developing a comparative docking protocol for the prediction of peptide selectivity profiles: investigation of potassium channel toxins.
P.C. Chen and S. Kuyucak, Toxins 4 (2012) 110-138.


Affinity and selectivity of ShK toxin for the Kv1 potassium channels from free energy simulations.
M.H. Rashid and S. Kuyucak, J. Phys. Chem. B 116 (2012) 4812-4822.


Molecular dynamics simulations of membrane proteins.
T. Bastug and S. Kuyucak, Biophys. Rev. 4 (2012) 271-282.


A C-terminally amidated analogue of ShK is a potent and selective blocker of the voltage-gated potassium channel Kv1.3.
M.W. Pennington, M.H. Rashid, R.B. Tajhya, C. Beeton, S. Kuyucak, and R.S. Norton, FEBS Lett. 586 (2012) 3996-4001.


Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.
J. Timko and S. Kuyucak, J. Chem. Phys. 137 (2012) #205106 (11 pages).


Why the Drosophila Shaker K+ Channel Is Not a Good Model for Ligand Binding to Voltage-Gated Kv1 Channels.
S. Mahdavi and S. Kuyucak, Biochemistry 52 (2013) 1631-1640.


Computational Studies of Marine Toxins Targeting Ion Channels.
M.H. Rashid, S. Mahdavi, and S. Kuyucak, Marine Drugs 11 (2013) 848-869.


Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme–substrate complex.
E. Durmaz, S. Kuyucak, and U.O. Sezerman, Protein Engineering, Design and Selection 26 (2013) 325-333.


Mechanism and Energetics of Ligand Release in the Aspartate Transporter GltPh.
G. Heinzelmann, T. Bastug, and S. Kuyucak, J. Phys. Chem. B 117 (2013) 5486-5496.


A potent and selective peptide blocker of the Kv1.3 channel: prediction from free-energy simulations and experimental confirmation.
M.H. Rashid, G. Heinzelmann, R. Huq, R.B. Tajhya, S.C. Chang, S. Chhabra, M.W. Pennington, C. Beeton, R.S. Norton, and S. Kuyucak, PLoS One 8 (2013) e78712.


Free energy simulations of binding of HsTx1 toxin to Kv1 potassium channels:the basis of Kv1.3/Kv1.1 selectivity.
M.H. Rashid and S. Kuyucak, J. Phys. Chem. B 118 (2014) 707-716.


Computation of standard binding free energies of polar and charged ligands to the glutamate receptor GluA2.
G. Heinzelmann, P.C. Chen, and S. Kuyucak, J. Phys. Chem. B 118 (2014) 1813-1824.


Molecular dynamics simulations of the mammalian glutamate transporter EAAT3
G. Heinzelmann and S. Kuyucak, PLoS One 9 (2014) e92089.


A potent and Kv1.3-selective analogue of the scorpion toxin HsTX1 as a potential therapeutic for autoimmune diseases.
M.H. Rashid, R. Huq, M.R. Tanner, S. Chhabra, K.K. Khoo, R. Estrada, V. Dhawan, S. Chauhan, M.W. Pennington, C. Beeton, S. Kuyucak, and R.S. Norton, Sci. Reps. 4 (2014) 4509.


Molecular dynamics simulations elucidate the mechanism of proton transport in the glutamate transporter EAAT3.
G. Heinzelmann and S. Kuyucak, Biophys. J. 106 (2014) 2675-2683.


Na+ interactions with the neutral amino acid transporter ASCT1.
A.J. Scopelliti, G. Heinzelmann, S. Kuyucak, R.M. Ryan, and R.J. Vandenberg, J. Biol. Chem. 289 (2014) 17468-17479.


Molecular dynamics study of binding of mu-conotoxin GIIIA to the voltage-gated sodium channel Nav1.4
S. Mahdavi and S. Kuyucak, PLoS One 9 (2014) e105300.


Systematic study of binding of mu-conotoxins to the sodium channel Nav1.4.
S. Mahdavi and S. Kuyucak, Toxins 6 (2014) 3454-3470.


Computational approaches for designing potent and selective analogs of peptide toxins as novel therapeutics.
S. Kuyucak and R.S. Norton, Future Med. Chem. 6 (2014) 1645-1658.


Calculation of free energy changes due to mutations from alchemical free energy simulations.
M.H. Rashid, G. Heinzelmann, and S. Kuyucak, J. Theor. Comput. Chem. 14 (2015) 1550023 (19 pages).


Mechanism of ion permeation in mammalian voltage-gated sodium channels.
S. Mahdavi and S. Kuyucak, PLoS One 10 (2015) e0133000 (16 pages).


Computational studies of glutamate transporters.
J. Setiadi, G. Heinzelmann, and S. Kuyucak, Biomolecules 5 (2015) 3067-3086.


Molecular dynamics simulations of insulin: Elucidating the conformational changes that enable its binding.
A. Papaioannou, S. Kuyucak, and Z. Kuncic, PLoS One 10 (2015) e0144058 (18 pages).


Force fields for simulating the interaction of surfaces with biological molecules.
L. Martin, M.M. Bilek, A.S. Weiss, and S. Kuyucak, Interface Focus 6 (2016) 20150045 (10 pages).