3-Hydroxy-5,5-dimethylhexanoic acid (HDH) is an analogue of carnitine which differs only in the substitution of a quaternary carbon atom for the quaternary ammonium nitrogen. Thus HDH is isosteric with carnitine but lacks the quaternary ammonium positive charge. Racemic HDH, each of its enantiomers, and the O-acetyl derivative (Ac-HDR) were evaluated as alternate substrates and inhibitors for several carnitine acyltransferases. HDH and Ac-HDH are not substrates for carnitine acetyltransferase (CAT) at concentrations up to 10 mM, suggesting that the positive quaternary ammonium charge on carnitine is essential for CAT catalysis. However, HDH competitively inhibits CAT (Ki = 8.3 mM), carnitine palmitoyltransferase-I (C PT-I) (Ki = 3.6 mM), and CPT-II (Ki = 2.8 mM). Ac-HDH is also a competitive inhibitor of CAT when assayed in the reverse direction (Ki = 4.1 mM). Similarly, R-(+)-HDH and S-(-)-HDH are not substrates for CAT, but they are stereoselective competitive inhibitors (Ki = 20.3 and 7.5 mM for the R and S enantiomers, respectively). Stereoselective inhibition by RDR is even more dramatic with CPT-I, since S-(-)-HDH inhibits CPT-I (Ki = 1.4 mM) but R-(+)-HDH has no effect in concentrations up to 5 mM. As with CAT, HDH is a stereoselective inhibitor of CPT-II, and the Ki values for S-(-)- and R-(+)-HDH are 2.2 and 6.7 mM, respectively. Since the observed Ki values are significantly larger than the Km for carnitine, the positive charge on carnitine must also be important, but not essential, for binding to the carnitine site on carnitine acyltransferases. © 1993 Academic Press. All rights reserved.