SynopsisWe present the results of molecular-mechanics studies on base-paired dinucleoside phosphates and hexanucleoside pentaphosphates. Starting from B-DNA-like conformations, we have refined the nucleic acid conformations, allowing all degrees of freedom to relax. 19701. Our calculations appear to reproduce the relative melting temperatures of sequence isomers as well or better than any of the previous calculations which addressed the question of nucleotide stability. We offer a detailed physical explanation of three observa- 19781 and differ by -20" from the B-DNA values. We also see evidence of base tilting and twisting similar to that found by Levitt. The two main differences in the results of our calculations and Levitt's lie in the sugar puckers [we find mainly C(2')endol and in the tendency to stay in local "torsional" minima (we find a number of examples of C(3')endo sugar puckering and w' = trans rather than gauche]. Both of these results are dependent on the nature of the potential function used in our study. However, our finding of movement from local torsional minima is suggestive of the significant flexibility of double-stranded deoxynucleotides.
We have simulated the interaction of L-thyroxine (l), D-thyroxine (2), and their deamino (3) and decarboxy (4) analogues with the human plasma protein prealbumin by using molecular mechanics calculations. Starting geometries were taken from the high-resolution X-ray structure of prealbumin and difference electron density maps of the prealbumin-thyroxine complex. We model the interactions by using the atoms of the thyroxine analogue and approximately 250 atoms within the binding site of prealbumin, minimizing the total energy with respect to all geometric degrees of freedom. Using the molecular mechanics calculated interaction energies and a simple empirical method to estimate the solvation energy differences of 1-4, we qualitatively reproduce the experimentally observed relative free energies of association of these analogues to prealbumin and offer a structural and energetic model to account for the different binding affinities of analogues 1-4 to the protein.
We have simulated the interaction of -chymotrypsin with the substrate L-TV-acetyltryptophanamide (1) and the inhibitor D-W-acetyltryptophanamide (2) as a model for the stereoselective hydrolysis of peptides catalyzed by this enzyme. The noncovalent Michaelis and covalent tetrahedral intermediate complexes of the enzyme active site with each enantiomer were modeled by using molecular mechanics calculations, minimizing the total energy with respect to all geometric degrees of freedom. The lowest energy noncovalent complexes correspond to productive modes of binding that can adopt the geometry of the covalent complexes with some conformational changes; the Michaelis complex for 1 is particularly close to the geometry of the tetrahedral intermediate, while the D complex requires more extensive conformational changes to form the covalent complex. NMR studies have suggested an alternate unproductive mode of noncovalent binding for D-TV-trifluoroacetyltryptophan with the carbonyl oxygen of the -NHCOCF3 group in the "oxyanion hole". Our calculations suggest that this mode of binding would not be favorable for the analogue D-Á-trifluoroacetyltryptophana/M/rfe and predict that this compound should bind to the enzyme in the normal manner.The lowest energy covalent l structure corresponds to the generally accepted model for -chymotrypsin catalyzed hydrolysis: the -hydrogen of the substrate points toward the side chain of Met-192, the O of the CONH2 group is in the oxyanion hóle, and the NH of the A'-acetyl group is hydrogen bonded to the C=0 of Ser-214. Most of the l-d stereoselectivity is due to the poorer interaction of the CONH2 group of the D enantiomer with the enzyme in the tetrahedral intermediate; the A-acetyl group and aromatic side chain also favor the L complex. In particular, the interaction of His-57 with the NH2 leaving group of the substrate is more favorable in the l complex than the D, which stabilizes the tetrahedral intermediate of 1 relative to 2 and facilitates proton transfer from His-57 to the leaving group. The Michaelis complexes of 1 and 2 with -chymotrypsin have similar energies, but the tetrahedral intermediate formed by 1 is calculated to be ~9 kcal mol"1 11more stable than the tetrahedral intermediate formed by 2, consistent with experimental results that show that the stereoselective recognition of the substrate by -chymotrypsin occurs in the transition state (modeled by the tetrahedral intermediate) rather than the initial Michaelis complex. This calculated stereoselectivity only occurs when the protein is allowed to be flexible and "relax"; no stereoselectivity is observed when the protein is constrained to the initial X-ray structure. Our results thus provide a structural and energetic model for stereoselective enzyme-substrate interactions.-Chymotrypsin (CHT) catalyzes the stereoselective hydrolysis of peptides at L-amino acids.1•2 Following the kinetic studies that delineated the functional and steric requirements of substrates for catalysis,3 crystallographic studies have characterized th...
No abstract
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.