Biomaterial Database

Molecular modeling of voltage-gated potassium channel pore. 1997

S R Zhao, and K X Chen, and W Wang, and J D Gu, and Z J Hu, and R Y Ji

Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China.

OBJECTIVE To build a structure model for the pore of voltage-gated Shaker potassium channel and examine its validity. METHODS (1) Structural restraints were derived from experimental and theoretical studies; (2) An initial structural motif satisfying the derived restraints was first constructed, and further refined by restrained molecular mechanics; (3) The quality of the model was judged by the criterion that whether it could clarify molecular mechanisms of channel functions and explain the known experimental facts. RESULTS (1) A computer pore structure was proposed, in which the residues within signature sequence (corresponding to Shaker 439-446) dipped into the membrane and formed the narrow part of the pore in a non-periodic conformation, while the other residues in the P region constituted the outer mouth of the pore; (2) The ion selectivity was achieved through cation-pi orbital interaction mechanism at position 445 and oxygen cage mechanism at position 447; (3) Different binding modes led to different affinity of CTX and AgTx2 to channel; and (4) The inside of pore was dominated by negative electrostatic potential. CONCLUSIONS The model proposed was consistent with the derived restraints from the experimental results.

UI	MeSH Term	Description	Entries
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D004347	Drug Interactions	The action of a drug that may affect the activity, metabolism, or toxicity of another drug.	Drug Interaction,Interaction, Drug,Interactions, Drug
D000595	Amino Acid Sequence	The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.	Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D012604	Scorpion Venoms	Venoms from animals of the order Scorpionida of the class Arachnida. They contain neuro- and hemotoxins, enzymes, and various other factors that may release acetylcholine and catecholamines from nerve endings. Of the several protein toxins that have been characterized, most are immunogenic.	Scorpion Toxin,Scorpion Toxins,Scorpion Venom Peptide,Tityus serrulatus Venom,Scorpion Venom,alpha-Scorpion Toxin,beta-Scorpion Toxin,gamma-Scorpion Toxin,Peptide, Scorpion Venom,Toxin, Scorpion,Toxin, alpha-Scorpion,Toxin, beta-Scorpion,Venom Peptide, Scorpion,Venom, Scorpion,Venom, Tityus serrulatus,alpha Scorpion Toxin,beta Scorpion Toxin,gamma Scorpion Toxin
D015221	Potassium Channels	Cell membrane glycoproteins that are selectively permeable to potassium ions. At least eight major groups of K channels exist and they are made up of dozens of different subunits.	Ion Channels, Potassium,Ion Channel, Potassium,Potassium Channel,Potassium Ion Channels,Channel, Potassium,Channel, Potassium Ion,Channels, Potassium,Channels, Potassium Ion,Potassium Ion Channel
D016415	Sequence Alignment	The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.	Sequence Homology Determination,Determination, Sequence Homology,Alignment, Sequence,Alignments, Sequence,Determinations, Sequence Homology,Sequence Alignments,Sequence Homology Determinations
D051637	Shaker Superfamily of Potassium Channels	Voltage-gated potassium channels whose primary subunits contain six transmembrane segments and form tetramers to create a pore with a voltage sensor. They are related to their founding member, shaker protein, Drosophila.	Kv1 Potassium Channels,Shaker Potassium Channels
D018999	Charybdotoxin	A 37-amino acid residue peptide isolated from the scorpion Leiurus quinquestriatus hebraeus. It is a neurotoxin that inhibits calcium activated potassium channels.	ChTX,CTX Toxin,Quinquestriatus Toxin,Toxin, CTX,Toxin, Quinquestriatus