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J. Biochem, 2003, Vol. 133, No. 3 335-342
© 2003 Japanese Biochemical Society

BIOCHEMISTRY

Theoretical Research on Structures of {gamma}-Aminobutyric Acid and Glutamic Acid in Aqueous Conditions

Kei Odai1, Tohru Sugimoto2, Minoru Kubo3 and Etsuro Ito+,3,4

1 Department of Electronics and Informatics, North Shore College, Atsugi 243-8501; 2 Laboratory of Biophysics, School of Engineering, Kanto Gakuin University, Yokohama 236-8501; and 3 Division of Biological Sciences, Graduate School of Science, and 4 Division of Innovative Research, Creative Research Initiative "Sousei", Hokkaido University, Sapporo 060-0810

Even though glutamic acid contains only one more carboxyl group than {gamma}-aminobutyric acid (GABA), these neurotransmitters are recognized by their own specific receptors. To understand the ligand-recognition mechanism of the receptors, we must determine the geometric and electronic structures of GABA and glutamic acid in aqueous conditions using the ab initio calculation. The results of the present study showed that the stable structure of GABA was the extended form, and it attracted both cations and anions. Glutamic acid only attracted cations and was stabilized in four forms in aqueous conditions: Type 1 (an extended form), Type 2 (a rounded form), and Types 3 and 4 (twisted forms of Type 1). The former two types had low energy and the energy barrier between them was estimated to be small. These results showed that most free glutamic acid is present as Type 1, Type 2, and transient forms. The present results therefore suggest that the flexibility of the geometric structures of ligands should be taken into account when we attempt to elucidate the mechanism of recognition between ligands and receptors, in addition to the physicochemical characteristics of ligands and receptors.

+ To whom correspondence should be addressed. Tel: +81-11-706-2615, Fax: +81-11-706-4448, E-mail: eito{at}sci.hokudai.ac.jp


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