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Serdar Kuyucak

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Cell Membrane

Physiology

Ion Channel Gating

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Publications

TOP 3
Germano Heinzelmann; Turgut Bastug; Serdar Kuyucak
Mechanism and Energetics of Ligand Release in the Aspartate Transporter GltPh.
Emel Durmaz; Serdar Kuyucak; Ugur O Sezerman
Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex.
Somayeh Mahdavi; Serdar Kuyucak
Why the Drosophila Shaker K+ channel is not a good model for ligand binding to voltage-gated Kv1 channels.

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All Publications

2013: Germano Heinzelmann; Turgut Bastug; Serdar Kuyucak
Mechanism and Energetics of Ligand Release in the Aspartate Transporter GltPh.
The journal of physical chemistry. B 2013;117(18):5486-96.
2013: Emel Durmaz; Serdar Kuyucak; Ugur O Sezerman
Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex.
Protein engineering, design & selection : PEDS 2013;26(5):325-33.
2013: Somayeh Mahdavi; Serdar Kuyucak
Why the Drosophila Shaker K+ channel is not a good model for ligand binding to voltage-gated Kv1 channels.
Biochemistry 2013;52(9):1631-40.
2013: M Harunur Rashid; Somayeh Mahdavi; Serdar Kuyucak
Computational studies of marine toxins targeting ion channels.
Marine drugs 2013;11(3):848-69.
2012: Jeff Timko; Serdar Kuyucak
Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.
The Journal of chemical physics 2012;137(20):205106.
2012: Michael Pennington; Rajeev B Tajhya; Christine Beeton; M Harunur Rashid; Serdar Kuyucak; Raymond S Norton
A C-terminally amidated analogue of ShK is a potent and selective blocker of the voltage-gated potassium channel Kv1.3.
FEBS letters 2012;586(22):3996-4001.
2012: Po-Chia Chen; Serdar Kuyucak
Developing a comparative docking protocol for the prediction of peptide selectivity proﬁles: investigation of potassium channel toxins.
Toxins 2012;4(2):110-38.
2012: Turgut Bastug; Germano Heinzelmann; Serdar Kuyucak; Marietta Salim; Robert J Vandenberg; Renae M Ryan
Position of the third Na+ site in the aspartate transporter GltPh and the human glutamate transporter, EAAT1.
PloS one 2012;7(3):e33058.
2011: Germano Heinzelmann; Turgut Baştuğ; Serdar Kuyucak
Free energy simulations of ligand binding to the aspartate transporter Glt(Ph).
Biophysical journal 2011;101(10):2380-8.
2011: Jeff Timko; Alexandra De Castro; Serdar Kuyucak
Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl.
The Journal of chemical physics 2011;134(20):204510.
2011: Po-Chia Chen; Serdar Kuyucak
Accurate determination of the binding free energy for KcsA-charybdotoxin complex from the potential of mean force calculations with restraints.
Biophysical journal 2011;100(10):2466-74.
2011: Turgut Baştuğ; Serdar Kuyucak
Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels.
Biophysical journal 2011;100(3):629-36.
2010: Jeff Timko; Denis Bucher; Serdar Kuyucak
Dissociation of NaCl in water from ab initio molecular dynamics simulations.
The Journal of chemical physics 2010;132(11):114510.
2009: Turgut Baştuğ; Serdar Kuyucak
Importance of the peptide backbone description in modeling the selectivity filter in potassium channels.
Biophysical journal 2009;96(10):4006-12.
2009: Po-Chia Chen; Serdar Kuyucak
Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations.
Biophysical journal 2009;96(7):2577-88.
2009: Pengchu Ju; Guilhem Pages; R Peter Riek; Po-Chia Chen; Allan M Torres; Paramjit S Bansal; Serdar Kuyucak; Philip W Kuchel; Jamie I Vandenberg
The pore domain outer helix contributes to both activation and inactivation of the HERG K+ channel.
The Journal of biological chemistry 2009;284(2):1000-8.
2008: Denis Bucher; Serdar Kuyucak
Polarization of water in the first hydration shell of K+ and Ca2+ ions.
The journal of physical chemistry. B 2008;112(35):10786-90.
2008: Turgut Baştuğ; Po-Chia Chen; Swarna M Patra; Serdar Kuyucak
Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling.
The Journal of chemical physics 2008;128(15):155104.
2007: Rajiv Wijesinghe; Nathan Coorey; Serdar Kuyucak
Charge state of the fast gate in chloride channels: insights from electrostatic calculations in a schematic model.
The Journal of chemical physics 2007;127(19):195102.
2007: Swarna M Patra; Turgut Baştug; Serdar Kuyucak
Binding of organic cations to gramicidin A channel studied with AutoDock and molecular dynamics simulations.
The journal of physical chemistry. B 2007;111(38):11303-11.
2007: Serdar Kuyucak
AIMECS 07 - Sixth AFMC International Medicinal Chemistry Symposium: new therapeutic agents and drug development strategies.
IDrugs : the investigational drugs journal 2007;10(9):618-20.
2007: Turgut Baştuğ; Serdar Kuyucak
Free energy simulations of single and double ion occupancy in gramicidin A.
The Journal of chemical physics 2007;126(10):105103.
2007: Ramzi Kutteh; Jamie I Vandenberg; Serdar Kuyucak
Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel.
The journal of physical chemistry. B 2007;111(5):1090-8.
2006: Turgut Baştuğ; Swarna M Patra; Serdar Kuyucak
Molecular dynamics simulations of gramicidin A in a lipid bilayer: from structure-function relations to force fields.
Chemistry and physics of lipids 2006;141(1-2):197-204.
2006: Turgut Baştuğ; Serdar Kuyucak
Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations.
Biophysical journal 2006;90(11):3941-50.
2006: Turgut Baştuğ; Angus Gray-Weale; Swarna M Patra; Serdar Kuyucak
Role of protein flexibility in ion permeation: a case study in gramicidin A.
Biophysical journal 2006;90(7):2285-96.
2005: Turgut Bastug; Serdar Kuyucak
Test of molecular dynamics force fields in gramicidin A.
European biophysics journal : EBJ 2005;34(5):377-82.
2003: Serdar Kuyucak; Turgut Bastug
Physics of ion channels.
Journal of biological physics 2003;29(4):429-46.
2003: Ben Corry; Serdar Kuyucak; Shin-Ho Chung
Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels.
Biophysical journal 2003;84(6):3594-606.
2003: Turgut Baştuğ; Serdar Kuyucak
Role of the dielectric constants of membrane proteins and channel water in ion permeation.
Biophysical journal 2003;84(5):2871-82.
2003: Takuya Takahashi; Serdar Kuyucak
Functional properties of threefold and fourfold channels in ferritin deduced from electrostatic calculations.
Biophysical journal 2003;84(4):2256-63.
2003: Toby W Allen; Turgut Baştuğ; Serdar Kuyucak; Shin-Ho Chung
Gramicidin A channel as a test ground for molecular dynamics force fields.
Biophysical journal 2003;84(4):2159-68.
2002: Shin Ho Chung; Serdar Kuyucak
Recent advances in ion channel research.
Biochimica et biophysica acta 2002;1565(2):267-86.
2002: Scott Edwards; Ben Corry; Serdar Kuyucak; Shin-Ho Chung
Continuum electrostatics fails to describe ion permeation in the gramicidin channel.
Biophysical journal 2002;83(3):1348-60.
2002: Shin-Ho Chung; Serdar Kuyucak
Ion channels: recent progress and prospects.
European biophysics journal : EBJ 2002;31(4):283-93.
2002: Shin-Ho Chung; Toby W Allen; Serdar Kuyucak
Modeling diverse range of potassium channels with Brownian dynamics.
Biophysical journal 2002;83(1):263-77.
2002: Serdar Kuyucak; Shin-Ho Chung
Permeation models and structure-function relationships in ion channels.
Journal of biological physics 2002;28(2):289-308.
2002: Ben Corry; Matthew Hoyles; Toby W Allen; Michael Walker; Serdar Kuyucak; Shin-Ho Chung
Reservoir boundaries in Brownian dynamics simulations of ion channels.
Biophysical journal 2002;82(4):1975-84.
2002: Shin-Ho Chung; Toby W Allen; Serdar Kuyucak
Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations.
Biophysical journal 2002;82(2):628-45.
2001: Ben Corry; Toby W Allen; Serdar Kuyucak; Shin-Ho Chung
Mechanisms of permeation and selectivity in calcium channels.
Biophysical journal 2001;80(1):195-214.
2001: S H Chung; Serdar Kuyucak
Predicting channel function from channel structure using Brownian dynamics simulations.
Clinical and experimental pharmacology & physiology 2001;28(1-2):89-94.
2000: Ben Corry; Toby W Allen; Serdar Kuyucak; Shin-Ho Chung
A model of calcium channels.
Biochimica et biophysica acta 2000;1509(1-2):1-6.
2000: Toby W Allen; Serdar Kuyucak; Shin-Ho Chung
Molecular dynamics estimates of ion diffusion in model hydrophobic and KcsA potassium channels.
Biophysical chemistry 2000;86(1):1-14.
2000: Ben Corry; Serdar Kuyucak; Shin-Ho Chung
Tests of continuum theories as models of ion channels. II. Poisson-Nernst-Planck theory versus brownian dynamics.
Biophysical journal 2000;78(5):2364-81.
2000: G Moy; Ben Corry; Serdar Kuyucak; Shin-Ho Chung
Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics.
Biophysical journal 2000;78(5):2349-63.
1999: Shin-Ho Chung; Toby W Allen; Matthew Hoyles; Serdar Kuyucak
Permeation of ions across the potassium channel: Brownian dynamics studies.
Biophysical journal 1999;77(5):2517-33.
1999: Toby W Allen; Serdar Kuyucak; Shin-Ho Chung
Molecular dynamics study of the KcsA potassium channel.
Biophysical journal 1999;77(5):2502-16.
1999: Ben Corry; Serdar Kuyucak; Shin-Ho Chung
Test of Poisson-Nernst-Planck theory in ion channels.
The Journal of general physiology 1999;114(4):597-9.
1998: Shin-Ho Chung; Matthew Hoyles; T Allen; Serdar Kuyucak
Study of ionic currents across a model membrane channel using Brownian dynamics.
Biophysical journal 1998;75(2):793-809.
1998: S C Li; Matthew Hoyles; Serdar Kuyucak; Shin-Ho Chung
Brownian dynamics study of ion transport in the vestibule of membrane channels.
Biophysical journal 1998;74(1):37-47.
1998: Serdar Kuyucak; Matthew Hoyles; Shin-Ho Chung
Analytical solutions of Poisson's equation for realistic geometrical shapes of membrane ion channels.
Biophysical journal 1998;74(1):22-36.
1996: Matthew Hoyles; Serdar Kuyucak; Shin-Ho Chung
Energy barrier presented to ions by the vestibule of the biological membrane channel.
Biophysical journal 1996;70(4):1628-42.
1995: Shin-Ho Chung; Serdar Kuyucak
Changes in the kinetics and conductance of N-methyl-D-aspartate (NMDA)-receptor activated single channels with temperature.
Neuroscience letters 1995;187(3):181-4.
1994: Serdar Kuyucak; Shin-Ho Chung
Temperature dependence of conductivity in electrolyte solutions and ionic channels of biological membranes.
Biophysical chemistry 1994;52(1):15-24.