Psychoactive Plant Database - Neuroactive Phytochemical Collection

1. J Mol Biol. 2007 May 25;369(1):198-209. doi: 10.1016/j.jmb.2007.03.023. Epub 
2007 Mar 15.

Thermodynamic and structural basis for transition-state stabilization in 
antibody-catalyzed hydrolysis.

Oda M(1), Ito N, Tsumuraya T, Suzuki K, Sakakura M, Fujii I.

Author information:
(1)Graduate School of Agriculture, Kyoto Prefectural University, 1-5 Hangi-cho, 
Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.

Catalytic antibodies 6D9 and 9C10, which were induced by immunization with a 
haptenic transition-state analog (TSA), catalyze the hydrolysis of a 
nonbioactive chloramphenicol monoester derivative to generate a bioactive 
chloramphenicol. These antibodies stabilize the transition state to catalyze the 
hydrolysis reaction, strictly according to the theoretical relationship: for 
6D9, k(cat)/k(uncat)=895 and K(S)/K(TSA)=900, and for 9C10, k(cat)/k(uncat)=56 
and K(S)/K(TSA)=60. To elucidate the molecular basis of the antibody-catalyzed 
reaction, the crystal structure of 6D9 was determined, and the binding 
thermodynamics of 6D9 and 9C10 with both the substrate and the TSA were analyzed 
using isothermal titration calorimetry. The crystal structure of the unliganded 
6D9 Fab was determined at 2.25 A resolution and compared with that of the 
TSA-liganded 6D9 Fab reported previously, showing that the TSA is bound into the 
hydrophobic pocket of the antigen-combining site in an "induced fit" manner, 
especially at the L1 and H3 CDR loops. Thermodynamic analyses showed that 6D9 
binds the substrate of the TSA with a positive DeltaS, differing from general 
thermodynamic characteristics of antigen-antibody interactions. This positive 
DeltaS could be due to the hydrophobic interactions between 6D9 and the 
substrate or the TSA mediated by Trp H100i. The difference in DeltaG between 
substrate and TSA-binding to 6D9 was larger than that to 9C10, which is in good 
correlation with the larger k(cat) value of 6D9. Interestingly, the DeltaDeltaG 
was mainly because of the DeltaDeltaH. The correlation between k(cat) and 
DeltaDeltaH is suggestive of "enthalpic strain" leading to destabilization of 
antibody-substrate complexes. Together with X-ray structural analyses, the 
thermodynamic analyses suggest that upon binding the substrate, the antibody 
alters the conformation of the ester moiety in the substrate from the planar Z 
form to a thermodynamically unstable twisted conformation, followed by 
conversion into the transition state. Enthalpic strain also contributes to the 
transition-state stabilization by destabilizing the ground state, and its degree 
is much larger for the more efficient catalytic antibody, 6D9.

DOI: 10.1016/j.jmb.2007.03.023
PMID: 17428500 [Indexed for MEDLINE]


2. J Biomol Struct Dyn. 1996 Aug;14(1):25-30. doi:
10.1080/07391102.1996.10508926.

Tryptophan intercalation in G, C containing polynucleotides: Z to B conversion 
of poly [d(G-5M C)] in low salt induced by a tetra peptide.

Rajeswari MR(1).

Author information:
(1)Department of Biochemistry, All India Institute of Medical Sciences, New 
Delhi, India. raji@aiims.ernet.in

Binding of a tetra peptide, lysyl tryptophenyl glycyl lysine O-ter butyl ester 
(KWGK) with duplex forms of G, C containing polynucleotides, Poly [d(G-C)], Poly 
[d(G-5M C)], Poly (dG), Poly (dC) and E.coli DNA were studied under low salt 
conditions using UV absorption, fluorescence, and circular dichroic (C.D) 
spectroscopy. On addition of the peptide (upto a P/N mole ratio of 0.5), the 
Poly [d(G-5M C)] under low salt (1 mM Na Cl) conditions, was converted from Z to 
B-form as shown by the inversion of C.D spectra. The two binding constants (K1 
and K2) were determined from fluorescence spectroscopy of which K2 estimates the 
intercalation of the tryptophenyl side chain between the base pairs of DNA and 
K1 estimates the electrostatic interactions between the lysyl side chains and 
phosphate groups. The strength of intercalation is: Z-form of Poly [d(G-5M C)] 
>> B form of Poly [d(G-5M C)] >> E.Coli DNA > Poly (dG).Poly (dC). This means 
that peptide seems to have strong preference for Z compared to B-form and for 
alternating over non-alternating G, C Sequences. This suggests that tryptophan 
intercalation may act as a discriminating factor in recognizing Z and B-forms 
and may have a potential role in Protein-Nucleic acid interactions that are 
important for transcription.

DOI: 10.1080/07391102.1996.10508926
PMID: 8877559 [Indexed for MEDLINE]


3. Drug Metab Dispos. 1984 Jan-Feb;12(1):82-92.

Fluvoxamine: metabolic fate in animals.

Ruijten HM, de Bree H, Borst AJ, de Lange N, Scherpenisse PM, Vincent WR, Post 
LC.

The metabolic fate in animals of the antidepressant compound fluvoxamine was 
investigated. The 14C-labeled drug was administered orally to dogs, rats, 
hamsters, and mice, and excretion in urine and feces was measured. 
Chromatographic patterns of the urines were developed by high performance liquid 
chromatography. These patterns were used as guides in the isolation of the 
metabolites, its initial step consisting of concentration of the radioactivity 
in the urine pools in a conical precolumn, followed by separation in the same 
HPLC system as used for the metabolite patterns. Altogether, 32 radioactive 
substances were isolated from the urine pools of the four animal species. They 
were all identified by the combined use of proton nuclear magnetic resonance and 
mass spectrometry, and by information obtained from chromatographic behavior and 
color reactions. Several of the 32 compounds were identical, leaving a total of 
11 different metabolites in the four species. In all the animal species, the 
main focus of fluvoxamine degradation was its aliphatic methoxyl group. In three 
species, this resulted in the corresponding carboxylic acid as the main 
metabolite, but in the mouse the corresponding alcohol, in glucuronidated form, 
was at least as important. In mouse and hamster, the methyl ester was a minor 
metabolite. Products of acetylation or oxidative removal of the primary amino 
group accounted for only minor proportions of the metabolite patterns. While 
fluvoxamine itself has the (E)-configuration, several metabolites occurred both 
in the (E)- and the (Z)-form. The parent compound was isolated only from the 
urine of dogs, it accounted for less than 10% of the urinary radioactivity.

PMID: 6141918 [Indexed for MEDLINE]


4. Biochem Biophys Res Commun. 1983 Oct 31;116(2):682-8. doi: 
10.1016/0006-291x(83)90579-x.

Enzymatic methylation of chemically alkylated DNA and poly(dG-dC) X poly(dG-dC) 
in B and Z forms.

Pfohl-Leszkowicz A, Boiteux S, Laval J, Keith G, Dirheimer G.

The enzymatic methylation of chemically alkylated DNA and of poly(dG-dC) X 
poly(dG-dC) by beef brain DNA(cytosine-5-)-methyltransferase have been tested. 
The alkylation by dimethylsulfate, which yields mostly 7 methylguanine (m7G) and 
3 methyladenine (m3A) do not affect the enzymatic methylation. The 
dimethylsulfate alkylated poly(dG-dC) X poly(dG-dC) converted into the Z-form in 
the presence of MgCl2, is just as well methylated as the native or the alkylated 
polynucleotide in the B-form. The alkylation of DNA or of poly(dG-dC) X 
poly(dG-dC) by methylnitrosourea yields, in addition to the above base 
modifications described for dimethylsulfate, methylphosphotriesters and 
O6-methylguanine. The enzymatic methylation of these substrates modified by 
methylnitrosourea is decreased. This decrease is proportional to the extent of 
the chemical alkylation of the substrate.

DOI: 10.1016/0006-291x(83)90579-x
PMID: 6651830 [Indexed for MEDLINE]