Length Position Research Articles

Mechanism of Inhibition of Glycoside Hydrolases Investigated by Molecular Dynamics Simulations

Biofuels are a well-known alternative to the largely used fossil-derived fuels. One of the main challenges for the production of the second-generation biofuels, produced by enzymatic degradation of agricultural waste, is the inhibition of the glycoside hydrolases enzymes by non-suitable substrates or by their own product. Employing molecular dynamics (MD) simulations, we investigated how two enzymes of the glycoside hydrolases family are affected by a non-suitable substrate (Man5B) or by their own product (CEL7A). Combined with previous experimental results, our simulations reveal that the reduction of Man5B enzymatic efficiency in the presence of a poor substrate (gluco-oligosaccharides) is associated with a loss of the enzyme's flexibility, the latter being required to bind new substrate, while the presence of a more suitable substrate (manno-oligosaccharides) does not pose this problem (1). MD simulations of the glycoside hydrolase enzyme CEL7A interacting with cellulose substrate of different lengths in position −1 to −7 offers a detailed view of its enzymatic mechanism and also on how the enzyme dynamics is affected by substrate. Employing steered molecular dynamics (SMD) we were able to analyze the difference in free-energy when a substrate is moving through CEL7A's catalytic tunnel under different conditions. All together our results are indicating that the inhibition of the CEL7A by its product is directly related to the cellobiose (enzymatic product) that was just cleaved and does not leave the exit pocket because of the already high concentration of cellobiose in solution.

REMARKS ON GENERALIZED UNCERTAINTY PRINCIPLE INDUCED FROM CONSTRAINT SYSTEM

The extended commutation relations for generalized uncertainty principle (GUP) have been based on the assumption of the minimal length in position. Instead of this assumption, we start with a constrained Hamiltonian system described by the conventional Poisson algebra and then impose appropriate second class constraints to this system. Consequently, we can show that the consistent Dirac brackets for this system are nothing, but the extended commutation relations describing the GUP.

Community Leaders’ Characteristic and their Effort in Building Capacity for Tourism Development in Local Communities

Community leaders are an important element of any community and vital to successful community development. In a community capacity approach, community leaders play a vital role in handling the programs and plans towards achieving the goals of the community.This paper investigates relationship between the community leaders’ characteristic and their effort in building capacity for tourism development in local communities of Shiraz, Iran. The results from Pearson correlation showed that there was a significant positive correlation between age, length of residence, length of position held, income with level of community capacity building in tourism development. Spearman rho correlation also found there was a significant positive correlation between educational level, tourism income, extra activities, tourism jobs, and family engaged in tourism activities with level of community capacity building in tourism development.

Physicochemical properties and membrane interactions of anti-apoptotic derivatives 2-(4-fluorophenyl)-3-(pyridin-4-yl)imidazo[1,2- a]pyridine depending on the hydroxyalkylamino side chain length and conformation: An NMR and ESR study

Three imidazo[1,2- a]pyridine derivatives 3a– c have been synthesized from p38 kinase inhibitor structures and evaluated as anti-apoptosis agents. These drugs were designed to interact with nucleic acids and membrane interactions by varying the chain length in position 6, from hydroxyethylamino ( 3a), to hydroxybutylamino ( 3b) and hydroxyhexylamino ( 3c). First experiments showed that 3a and 3b were insoluble in water while 3c could be solubilized in water despite its partition coefficient (log P = 3.2). This latter feature was explained by the formation of a fifth intramolecular cycle thus allowing supramolecular structure formation (NMR and MD calculations). The interactions with membranes have been studied using 1H, 2H, 31P Nuclear Magnetic Resonance (NMR), Electron Spin Resonance (ESR) and High Resolution-Magic Angle Spinning (HR-MAS). Despite the insolubility of 3a and 3b in water, these derivatives could be partially solubilized by synthetic phospholipidic model membranes (small unilamellar vesicles, SUV). 1H NMR paramagnetic broadening experiments performed on the same models showed that 3a was located in the external layer, probably close to the surface while 3b only formed external superficial adducts. Supplementary 31P, 2H NMR and ESR experiments on phospholipid dispersions confirmed the location of 3a close to the polar headgroup of the external layer of the membrane, this resulting in a 2 K lowering of the transition temperature. Moreover, no significant interaction was detected on the deep part of the layer ( 2H NMR and 16NS ESR experiments). This binding was also found in the presence of cell cultures, as revealed by HR-MAS NMR experiments. Conversely, no significant interaction with membranes was found with 3b or 3c. From both the unexpected solubility of 3c and 3a interactions with membranes, further chemical modifications were finally proposed.

Cyclic enkephalin and dermorphin analogues containing a carbonyl bridge

Four cyclic enkephalin analogues and four cyclic dermorphin analogues have been synthesized. Cyclization of linear peptides containing basic amino acid residues of various side chain length in position 2 and 5 (enkephalin analogues) or 2 and 4 (dermorphin analogues) was achieved by treatment with bis-(4-nitrophenyl) carbonate to form a urea unit. The peptides were tested in the guinea-pig ileum (GPI) and mouse vas deferens (MVD) assays. Diverse activity was observed, depending on the size of the ring and the location of the urea unit. The conformation of two dermorphin analogues has been studied: one of high activity (IC(50) = 4.15 nM in the GPI assay) and a second of low activity (IC(50) = 6700 nM in the GPI assay). The conformational space of these peptides was examined using the EDMC method. Using data from the NMR spectra, each peptide was described as an ensemble of conformers. Biological activity was discussed in light of the structural data.

Single particle jumps in a binary Lennard-Jones system below the glass transition.

We study a binary Lennard-Jones system below the glass transition with molecular dynamics simulations. To investigate the dynamics we focus on events (jumps) where a particle escapes the cage formed by its neighbors. Using single particle trajectories we define a jump by comparing for each particle its fluctuations with its changes in average position. We find two kinds of jumps: "reversible jumps," where a particle jumps back and forth between two or more average positions, and "irreversible jumps," where a particle does not return to any of its former average positions, i.e., successfully escapes its cage. For all investigated temperatures both kinds of particles jump and both irreversible and reversible jumps occur. With increasing temperature, relaxation is enhanced by an increasing number of jumps and growing jump lengths in position and potential energy. However, the waiting time between two successive jumps is independent of temperature. This temperature independence might be due to aging, which is present in our system. We therefore also present a comparison of simulation data with three different histories. The ratio of irreversible to reversible jumps is also increasing with increasing temperature, which we interpret as a consequence of the increased likelihood of changes in the cages, i.e., a blocking of the "entrance" back into the previous cage. In accordance with this interpretation, the fluctuations both in position and energy are increasing with increasing temperature. A comparison of the fluctuations of jumping particles and nonjumping particles indicates that jumping particles are more mobile even when not jumping. The jumps in energy normalized by their fluctuations are decreasing with increasing temperature, which is consistent with relaxation being increasingly driven by thermal fluctuations. In accordance with subdiffusive behavior are the distributions of waiting times and jump lengths in position.

C-alkylation of nitriles : a useful route to 2-ethoxyalkyl derivatives of cadaverine planned for enzyme study

The cadaverine derivatives 1–4 containing ethoxyalkyl groups of variable length in position 2, planned as model molecules for the diamine oxidase active site study, were prepared and characterized exploiting as key precursors both 5-(N,N-dimethylamino)pentanonitrile or ethyl 2-cyano-5-(N,N-dimethylamino)pentanoate.

LIPOENKEPHALINS: A STUDY OF THE SURFACE ACTIVE AND PHARMACOLOGICAL PROPERTIES OF THESE NEW MORPHINE-LIKE PEPTIDES∗

ABSTRACT By modifying the physicochemical character of naturally occurring enkephalines, a parallelism between physicochemical behavior and pharmacological activity has been found. This was achieved by introducing alkyl residues of different chain length in position 1 or 5 on the enkephalin sequence. These kinds of substances can be referred to as 1ipoenkephalins and from a physicochemical point of view can be considered as surface active agents. On the other hand, as biological activity is greatly dependent on the conformation or orientation adopted by the molecule, we have also tried to investigate possible conformational or orientation changes when increasing the hydrophobic residue by means of optical rotation measurements and compression isotherm determinations. Finally, as the enkephalin molecule itself suffers an extremely rapid inactivation in brain tissues due to the proteolitic enzyme action, several tests to check the resistance of lipoenkephalins to en zymatic hydrolysis have been carried out,...