QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer.

The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2' migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN + DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10(11) difference in rate strongly supporting the less accepted triester mechanism.

Theoretical investigation of the enzymatic phosphoryl transfer of ß-phosphoglucomutase: revisiting both steps of the catalytic cycle.

Enzyme catalyzed phosphate transfer is a part of almost all metabolic processes. Such reactions are of central importance for the energy balance in all organisms and play important roles in cellular control at all levels. Mutases transfer a phosphoryl group while nucleases cleave the phosphodiester linkages between two nucleotides. The subject of our present study is the Lactococcus lactis ß-phosphoglucomutase (ß-PGM), which effectively catalyzes the interconversion of ß-D-glucose-1-phosphate (ß-G1P) to ß-D-glucose-6-phosphate (ß-G6P) and vice versa via stabile intermediate ß-D-glucose-1,6-(bis)phosphate (ß-G1,6diP) in the presence of Mg(2+). In this paper we revisited the reaction mechanism of the phosphoryl transfer starting from the bisphosphate ß-G1,6diP in both directions (toward ß-G1P and ß-G6P) combining docking techniques and QM/MM theoretical method at the DFT/PBE0 level of theory. In addition we performed NEB (nudged elastic band) and free energy calculations to optimize the path and to identify the transition states and the energies involved in the catalytic cycle. Our calculations reveal that both steps proceed via dissociative pentacoordinated phosphorane, which is not a stabile intermediate but rather a transition state. In addition to the Mg(2+) ion, Ser114 and Lys145 also play important roles in stabilizing the large negative charge on the phosphate through strong coordination with the phosphate oxygens and guiding the phosphate group throughout the catalytic process. The calculated energy barrier of the reaction for the ß-G1P to ß-G1,6diP step is only slightly higher than for the ß-G1,6diP to ß-G6P step (16.10 kcal mol(-1) versus 15.10 kcal mol(-1)) and is in excellent agreement with experimental findings (14.65 kcal mol(-1)).

Structural Stability of V-Amylose Helices in Water-DMSO Mixtures Analyzed by Molecular Dynamics.

Computational techniques have been employed to fundamentally understand the behavior of helically structured amylose in water/DMSO mixtures. Using a computationally generated amylose helix of 55 glucose residues, we have investigated the time-dependent behavior of intra- and intermolecular hydrogen bonds, particularly between O2 and O3 of adjacent glucose molecules and between O6 and neighboring O2 and O3 groups. The helix character was defined by the total number of residually existing hydrogen bonds. Our results parallel the experimental finding that increasing the percentage of DMSO results in increasing helical stability. It can be shown that O6-O2/O3 hydrogen bonds are preferentially lost when the helix starts to unfold to a finally resulting random coil structure. While water is small enough to interact with every hydroxyl group at the helix surface and finally penetrate the helix coil, DMSO can initially only form single hydrogen bonds to part of the OH groups of the amylose molecule, thereby allowing a longer conservation of intramolecular hydrogen bonds that are necessary to maintain the helix. However, given a long enough time for interaction, the helical structure of amylose is lost in water as well as in DMSO, yielding a random orientation of the glucose strand.

Nucleotide docking: prediction of reactant state complexes for ribonuclease enzymes.

Ribonuclease enzymes (RNases) play key roles in the maturation and metabolism of all RNA molecules. Computational simulations of the processes involved can help to elucidate the underlying enzymatic mechanism and is often employed in a synergistic approach together with biochemical experiments. Theoretical calculations require atomistic details regarding the starting geometries of the molecules involved, which, in the absence of crystallographic data, can only be achieved from computational docking studies. Fortunately, docking algorithms have improved tremendously in recent years, so that reliable structures of enzyme-ligand complexes can now be successfully obtained from computation. However, most docking programs are not particularly optimized for nucleotide docking. In order to assist our studies on the cleavage of RNA by the two most important ribonuclease enzymes, RNase A and RNase H, we evaluated four docking tools-MOE2009, Glide 5.5, QXP-Flo+0802, and Autodock 4.0-for their ability to simulate complexes between these enzymes and RNA oligomers. To validate our results, we analyzed the docking results with respect to the known key interactions between the protein and the nucleotide. In addition, we compared the predicted complexes with X-ray structures of the mutated enzyme as well as with structures obtained from previous calculations. In this manner, we were able to prepare the desired reaction state complex so that it could be used as the starting structure for further DFT/B3LYP QM/MM reaction mechanism studies.

Localization by site-directed mutagenesis of a galantamine binding site on α7 nicotinic acetylcholine receptor extracellular domain.

Galantamine is an approved drug treatment for Alzheimer's disease. Initially identified as a weak cholinesterase inhibitor, we have established that galantamine mainly acts as an 'allosterically potentiating ligand (APL)' of nicotinic acetylcholine receptors (nAChR). Meanwhile other 'positive allosteric modulators (PAM)' of nAChR channel activity have been discovered, and for one of them a binding site within the transmembrane domain has been proposed. Here we show, by performing site-directed mutagenesis studies of ectopically expressed chimeric chicken α7/mouse 5-hydroxytryptamine 3 receptor-channel complex, in combination with whole-cell current measurements, in the presence and absence of galantamine, that the APL binding site is different from the proposed PAM binding site. We demonstrate that residues T197, I196, and F198 of ß-strand 10 represent major elements of the galantamine binding site. Residue K123, earlier suggested as being 'close to' the APL binding site, is not part of this site but rather appears to play a role in coupling of agonist binding to channel opening and closing. Our data confirm our earlier results that the galantamine binding site is different from the ACh binding site. Both sites are in close proximity and hence may influence each other in a synergistic fashion. Other interesting areas identified in the present study are a 'hinge' region around and containing residues F122, K123, and K143 possibly being involved in relaying the signal of agonist binding to gating of the transmembrane channel, and a 'folding centre', with P119 as the dominating residue, that crucially positions the agonist binding site with respect to the hinge region.

Atomistic details of the associative phosphodiester cleavage in human ribonuclease H.

During translation of the genetic information of DNA into proteins, mRNA is synthesized by RNA polymerase and after the transcription process degraded by RNase H. The endoribonuclease RNase H is a member of the nucleotidyl-transferase (NT) superfamily and is known to hydrolyze the phosphodiester bonds of RNA which is hybridized to DNA. Retroviral RNase H is part of the viral reverse transcriptase enzyme that is indispensable for the proliferation of retroviruses, such as HIV. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. In our study we investigated the molecular mechanism of RNA cleavage by human RNase H using a comprehensive high level DFT/B3LYP QM/MM theoretical method for the calculation of the stationary points and nudged elastic band (NEB) and free energy calculations to identify the transition state structures, the rate limiting step and the reaction barrier. Our calculations reveal that the catalytic mechanism proceeds in two steps and that the nature of the nucleophile is a water molecule. In the first step, the water attack on the scissile phosphorous is followed by a proton transfer from the water to the O2P oxygen and a trigonal bipyramidal pentacoordinated phosphorane is formed. Subsequently, in the second step the proton is shuttled to the O3' oxygen to generate the product state. During the reaction mechanism two Mg(2+) ions support the formation of a stable associated in-line S(N)2-type phosphorane intermediate. Our calculated energy barrier of 19.3 kcal mol(-1) is in excellent agreement with experimental findings (20.5 kcal mol(-1)). These results may contribute to the clarification and understanding of the RNase H reaction mechanism and of further enzymes from the RNase family.

Probing Torpedo californica acetylcholinesterase catalytic gorge with two novel bis-functional galanthamine derivatives.

N-Piperidinopropyl-galanthamine (2) and N-saccharinohexyl-galanthamine (3) were used to investigate interaction sites along the active site gorge of Torpedo californica actylcholinesterase (TcAChE). The crystal structure of TcAChE-2 solved at 2.3 A showed that the N-piperidinopropyl group in 2 is not stretched along the gorge but is folded over the galanthamine moiety. This result was unexpected because the three carbon alkyl chain is just long enough for the bulky piperidine group to be placed above the bottleneck (Tyr121, Phe330) midway down the gorge. The crystal structure of TcAChE-3 at 2.2 A confirmed that a dual interaction with the sites at the bottom, and at the entrance of the gorge, enhances inhibitory activity: a chain of six carbon atoms has, in this class of derivatives, the correct length for optimal interactions with the peripheral anionic site (PAS).

Structural model for the binding sites of allosterically potentiating ligands on nicotinic acetylcholine receptors.

Current treatments of Alzheimer's disease include the allosteric potentiation of nicotinic acetylcholine receptor (nAChR) response. The location of the binding site for allosteric potentiating ligands (APLs) within the receptor is not yet fully understood. Based on homology models for the ligand binding domain of human alpha7, human alpha4beta2, and chicken alpha7 receptors, as well as blind docking experiments with galanthamine, physostigmine, codeine, and 5HT, we identified T197 as an essential element of the APL binding site at the outer surface of the ligand binding domain (LBD) of nAChR. We also found the previously known galanthamine binding site in the region of K123 at the inside of the receptor funnel, which, however, was shown to not be part of the APL site. Our results are verified by site-directed mutagenesis and electrophysiological experiments, and suggest that APL and ACh bind to different sites on nicotinic receptors and that allosteric potentiation may arise from a direct interplay between both these sites.

Time resolved structure analysis of growing beta-amyloid fibers.

Formation of beta-amyloid plaques is a crucial feature of Alzheimer's disease. In the present work time resolved static light scattering was applied to investigate the size and shape of growing beta-amyloid aggregates preceding plaque formation. The beta-amyloid protein with 40 amino acid residues was used. Salt free buffer solutions and solutions with 0.15M NaCl at 37 degrees C served as the aggregation medium. The focus lay on the first 2h following initiation of the aggregation process which corresponds to the protofibril phase. Addition of the NaCl accelerated the aggregation process considerably. Scattering data from aggregation in saline solutions indicated formation of long fibers which suggest interpretation of data with the worm-like chain model. Two important results were revealed: (i) At the end of the time resolved recordings, the worm-like chain model provided a fully adequate picture for the growing aggregates. Chain stiffness is characterised in terms of the persistence length, which is close to 50 nm. The linear mass density of the growing fibers approached a value of two monomers per nm corresponding to single stranded fibers, which is in accordance with presently existing models for the aggregation of beta-amyloid. The fibers finally reached contour lengths of several thousand nanometers. (ii) The plateau values for the persistence length and linear mass density observed in the final regime are gradually approached from higher values. This observation is inconsistent with simple worm-like chains. Rather does it indicate existence of another species during the initial phase of the aggregation, in addition to monomers and fibers. Aside from further insight into fundamental aspects of beta-amyloid aggregation, time resolved static light scattering provides an appropriate tool for assay tests with drugs designed to interfere with the aggregation process.

Combined biological-chemical procedure for the mineralization of TNT.

Contamination of ground and surface water with 2,4,6-trinitrotoluene (TNT) and its biological and chemical transformation products are a persisting problem at former TNT production sites. We have investigated the photochemical degradation of TNT and its aminodinitro-(ADNT) and diaminonitrotoluene (DANT) metabolites using OH-radical generating systems like Fenton and hydrogen peroxide irradiated with UV, in order to compare the degradation and mineralization rate of ADNT- and DANT-isomers with TNT itself. As a result, we find that the aminoderivatives were mineralized much faster than TNT. Consequently, as ADNTs and DANTs are the known dead-end products of biological TNT degradations, we have combined our photochemical procedure with a preceding biological treatment of TNT by a mixed culture from sludge of a sewage plant. This consecutive degradation procedure, however, shows a reduced mineralization rate of the ADNTa and DANTs in the biologically derived supernatant as compared to the pure substances, suggesting that during the biological TNT treatment by sludge competing substrates are released into the solution, and that a more defined biological procedure would be necessary in order to achieve an effective, ecologically and economically acceptable mineralization of TNT from aqueous systems.

TNT transformation products are affected by the growth conditions of Raoultella terrigena.

High concentrations of 2,4,6-trinitrotoluene (TNT) and related nitroaromatic compounds are commonly found in soil and groundwater at former explosive plants. The bacterium, Raoultella terrigena strain HB, isolated from a contaminated site, converts TNT into the corresponding amino products. Radio-HPLC analysis with [(14)C]TNT identified aminodinitrotoluene, diaminonitrotoluene and azoxy-dimers as the main metabolites. Transformation rate and the type of metabolites that predominated in the culture medium and within the cells were significantly influenced by the culture conditions. The NAD(P)H-dependent enzymatic reduction of nitro-substituted compounds by cell-free extracts of R. terrigena was evaluated in vitro.

A QXP-based multistep docking procedure for accurate prediction of protein-ligand complexes.

The two great challenges of the docking process are the prediction of ligand poses in a protein binding site and the scoring of the docked poses. Ligands that are composed of extended chains in their molecular structure display the most difficulties, predominantly because of the torsional flexibility. On the basis of the molecular docking program QXP-Flo+0802, we have developed a procedure particularly for ligands with a high degree of rotational freedom that allows the accurate prediction of the orientation and conformation of ligands in protein binding sites. Starting from an initial full Monte Carlo docking experiment, this was achieved by performing a series of successive multistep docking runs using a local Monte Carlo search with a restricted rotational angle, by which the conformational search space is limited. The method was established by using a highly flexible acetylcholinesterase inhibitor and has been applied to a number of challenging protein-ligand complexes known from the literature.

Molecular docking study on the "back door" hypothesis for product clearance in acetylcholinesterase.

Acetylcholinesterase (AChE) is one of the fastest enzymes known, even though the active site is buried inside the protein at the end of a 20-A deep narrow gorge. Among the great variety of crystal structures of this enzyme, both in the absence and presence of various ligands and proteins, the structure of a complex of AChE with the pseudo-irreversible inhibitor Mf268 is of particular interest, as it assists in the proposal of a back door for product clearance from the active site. Binding of Mf268 to AChE results in the carbamoylation of Ser200 and liberation of an eseroline-fragment as the leaving group. The crystal structure of the AChE-Mf268 complex, however, proves that eseroline has escaped from the enzyme, despite the fact that the Ser-bound inhibitor fragment blocks the gorge entrance. The existence of alternative routes other than through the gorge for product clearance has been postulated but is still controversially discussed in the literature, as an experimental proof for such a back door is still missing. We have used Monte Carlo-based molecular docking methods in order to examine possible alternative pathways that could allow eseroline to be released from the protein after being cleaved from the substrate by Ser200. Based on our results, a short channel at the bottom of the gorge seems to be the most probable back-door site, which begins at amino acid Trp84 and ends at the enzyme surface in a cavity close to amino acid Glu445. [Figure: see text].

Biological reduction of TNT as part of a combined biological-chemical procedure for mineralization.

The explosive 2,4,6-trinitrotoluene (TNT), one of the most abundant and persistent contaminants at former armament factories and military sites, was cometabolically reduced by sludge (mixed culture) from a sewage plant in order to facilitate mineralization in a subsequent photochemical treatment. Under aerobic conditions, the main reduction products were aminodinitrotoluenes (ADNTs). A greater amount of the nitroaromatics (ca. 30%) was adsorbed by the sludge as was shown by a complete balance of the process using 14C-TNT. Under anaerobic conditions, TNT was further converted into ADNTs and diaminonitrotoluenes (DANTs) while only negligible adsorption to the sludge occured.

Galanthamine as bis-functional ligand for the acetylcholinesterase.

Acetylcholinesterase plays a key role in the development of Alzheimer's disease as this enzyme is responsible for cleavage of the neurotransmitter acetylcholine, and, according to recent investigations, also promotes aggregation of beta-amyloid peptides, which causes plaque formation in synaptic areas. We have performed a molecular modeling study to investigate bis-galanthamine derivatives connected by a methylene spacer of varying length as dual acting acetylcholinesterase ligands. Our results suggest that such ligands indeed can interact simultaneously with both biological functions of the enzyme and should therefore serve as the basis for a further development of bis-functional Alzheimer drugs.