About: Charybdotoxin Unbinding from the mKv1.3 Potassium Channel: A Combined Computational and Experimental Study

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	Charybdotoxin, belonging to the group of so-called scorpiontoxins, is a short peptide able to block many voltage-gated potassium channels, such as mKv1.3, with high affinity. We use a reliable homology model based on the high-resolution crystal structure of the 94% sequence identical homologue Kv1.2 for charybdotoxin docking followed by moleculardynamics simulations to investigate the mechanism and energetics of unbinding, tracing the behavior of the channel protein and charybdotoxin during umbrella-sampling simulations as charybdotoxin is movedaway from the binding site. The potential of mean force is constructed fromthe umbrella sampling simulations and combined with Kd and free energy values gained experimentally using the patch-clamp technique to study the free energy of binding at different ion concentrations andthe mechanism of the charybdotoxin mKv1.3 binding process. A possible charybdotoxin binding mechanism is deduced thatincludes an initial hydrophobic contact followed by stepwise electrostatic interactions and finally optimization of hydrogen bonds and salt bridges. Charybdotoxin, belonging to the group of so-called scorpiontoxins, is a short peptide able to block many voltage-gated potassium channels, such as mKv1.3, with high affinity. We use a reliable homology model based on the high-resolution crystal structure of the 94% sequence identical homologue Kv1.2 for charybdotoxin docking followed by moleculardynamics simulations to investigate the mechanism and energetics of unbinding, tracing the behavior of the channel protein and charybdotoxin during umbrella-sampling simulations as charybdotoxin is movedaway from the binding site. The potential of mean force is constructed fromthe umbrella sampling simulations and combined with Kd and free energy values gained experimentally using the patch-clamp technique to study the free energy of binding at different ion concentrations andthe mechanism of the charybdotoxin mKv1.3 binding process. A possible charybdotoxin binding mechanism is deduced thatincludes an initial hydrophobic contact followed by stepwise electrostatic interactions and finally optimization of hydrogen bonds and salt bridges. (en)
Title	Charybdotoxin Unbinding from the mKv1.3 Potassium Channel: A Combined Computational and Experimental Study Charybdotoxin Unbinding from the mKv1.3 Potassium Channel: A Combined Computational and Experimental Study (en)
skos:prefLabel	Charybdotoxin Unbinding from the mKv1.3 Potassium Channel: A Combined Computational and Experimental Study Charybdotoxin Unbinding from the mKv1.3 Potassium Channel: A Combined Computational and Experimental Study (en)
skos:notation	RIV/67179843:_____/11:00371168!RIV12-AV0-67179843
http://linked.open...avai/predkladatel	Centrum výzkumu globální změny AV ČR v.v.i.
http://linked.open...avai/riv/aktivita	P S Z
http://linked.open...avai/riv/aktivity	P(GA203/08/0114), P(LC06010), S, Z(AV0Z40400503), Z(AV0Z60870520), Z(MSM6007665808)
http://linked.open...iv/cisloPeriodika	39
http://linked.open...vai/riv/dodaniDat	2012
http://linked.open...aciTvurceVysledku	Khabiri, Morteza Ettrich, Rüdiger
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Centrum výzkumu globální změny AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	190094
http://linked.open...ai/riv/idVysledku	RIV/67179843:_____/11:00371168
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	molecular-dynamics simulations; Gated K+ Channels; induced conformational-changes; binding free-energy; C-type inactivation (en)
http://linked.open.../riv/klicoveSlovo	C-type inactivation Gated K+ Channels binding free-energy induced conformational-changes molecular-dynamics simulations
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[8E3FFB7978F6]
http://linked.open...i/riv/nazevZdroje	Journal of Physical Chemistry B
http://linked.open...in/vavai/riv/obor	EH
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Specific ion effects for proteins in solutions and related biologically relevant systems. Center of Biocatalysis and Biotransformation
http://linked.open...UplatneniVysledku	2011
http://linked.open...v/svazekPeriodika	115
http://linked.open...iv/tvurceVysledku	Cwiklik, Lukasz Ettrich, Rüdiger Grissmer, S. Khabiri, Morteza Nikouee, A.
http://linked.open...ain/vavai/riv/wos	000295245400021
http://linked.open...n/vavai/riv/zamer	Struktura, reaktivita a dynamika molekulárních a biomolekulárních systémů: teorie, experiment, aplikace Spatial and functional dynamics of biological, ecological and socio-economic systems interacting with global climatic change Fyzikální biologie -nové přístupy v biologickém výzkumu
issn	1520-6106
number of pages	11 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp2061909
is http://linked.open...avai/riv/vysledek of	Charybdotoxin Unbinding from the mKv1.3 Potassium Channel: A Combined Computational and Experimental Study Charybdotoxin Unbinding from the mKv1.3 Potassium Channel: A Combined Computational and Experimental Study

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