To calculate RMSd we used PTRAJ from the AMBER package and then we compared the conformation of the enzyme after the simulations at the 0.1 ps interval. [7]
2.8.2. The Hydrogen Bond Analysis
Hydrogen bonds formed between residues of the protease and between residues and water molecules, were analyzed using PTRAJ. Only bonds with a distance less than 3.5 Å with the angle of interaction greater than 140 ° were considered. The output file gave us the results which hydrogen bonds were formed, with which occupancy, distance and angle. The occupancy is the ratio of the time in which the bond is formed and the total simulation time.
2.8.3. The Radial Distribution Function
The radial distribution function is a quantitative measure for the evaluation
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water molecule). We can define the density of the water molecules at a given distance from the central atom and define solvation beads.
We used PTRAJ to run the analysis for Glu21, Leu19, Asp25 and Asp29 residues of both chains. Number of water molecules is obtained by defining spheres of increasing rays centered on the atom, and counting the total encircled molecules for each sphere regarding the central atom. The calculation is repeated for 0.1 ps interval and at the end divided the number of atoms present in each sphere by the volume of the sphere and by the density of those atoms in the system.
2.8.4. The Distance Analysis
Using PTRAJ we determined distances between some atoms and how they vary with the simulation. It was carried out for the distances between oxygen atoms of the carboxyl groups of the Asp25 residue and the oxygen group of the hydroxyl group of the Nelfinavir.
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3. Results And Disscusion
3.1. Visualisation of Results
Using the VMD software it was possible to study what changes happened in terms of the HIV-1 protease and inhibitor during the processes of solvation, minimization, equilibration and production. The results showed that the addition of the solvent (water), the hydrogen atoms, the chloride ions (added to
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(a) (b)
Figure 16. Graphical representation of the temperature as the function of time for the production dynamics in 10 ps (a) and 12,09 ns (b). The temperature reached 310,15 K.
Due to smaller dimensions of the system, pressure tends to oscilate between a previously established equilibrium value. The pressure oscilated in the range of
-250 to 250 bars and in the first 20 ps of each dynamics simulation there is no data as the pressure is set to 0 bar due to software settings in the equilibration phase
(Figure 17.)
(a) (b)
Figure 17. Graphical representation of variation of pressure as a function of time for simulation of 100 ps of production (a) and 12.09 ns of production (b).
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Volume was kept constant during the equilibration step so there is no data for the first 20 ps. The number of atoms was constant during the whole simulation, the density varies inversely of volume. At the beginning of the production phase, pressure becomes constant and volume decreases during the first 40 ps. After 40 ps, volume is constant (Figure 18.).
(a) (b)
Figure 18. Graphical representation of variation of volume as a function of time for simulation
Introduction The purpose of this Lab was to identify the density of the unidentified object and determine what substance the unidentified object given by the teacher was. The density calculated in the experiment will stay the same because the density of the unidentified object will stay constant. The Independent Variable of this experiment was the calculated density and the unidentified object given. The Dependant Variable for this experiment was the density.
Dalia El-Desoky Organic Chemistry II Lab 05 8 February 2017 Dehydration of 2-methylcyclohexanol Introduction: Dehydration is a common reaction in Organic Chemistry used to produce carbon-carbon double bonds. The dehydration mechanism involves the removal of water from an alcohol to form an alkene. In this experiment, 2-methylcyclohexanol will undergo acid catalyzed dehydration in heat to form three products: 1-methylcyclohexene, 3-methylcyclohexene, and methylenecyclohexane [1]. The reaction is carried out in a Hickman still filled with Drierite, a drying agent composed of CaSO4 which absorbs water.
The enzymeʼs have an active site that allows only certain substances to bind, they do this by having an enzyme and substrate that fit together perfectly. If the enzyme shape is changed then the binding
It was hypothesized that the optimal pH for the enzyme was pH 7 while the 1.0 ml peroxidase would have the best reaction rate. At the end of the experiment the results prove the hypothesis to be incorrect. INTRODUCTION Enzymes are proteins that allow a reaction to speed up. These proteins are made up of monomers known as amino acids.
The competitive inhibitor that was added was lactose. We predicted this because competitive inhibitors block and bind to the active site so it will slow down the binding of the desired substrate. An alternative hypothesis that came up was that the reaction of substrate would stay consistent as if no inhibitor was added. The enzyme could reject the inhibitor if it does not fit in the active site, causing the substrate to bind as it normally would. Our results showed that with the addition of lactose, the reaction did slow down a considerably
The topic of research is, “how fast does an Alka-Seltzer tablet make gas?”. In the experiment, the scientists will be measuring the chemical reaction rates that occur, when 1 Alka-Seltzer tablet is placed in a specific temperature of water. The independent variable during the experiment will be the temperature of the water (degrees Celsius). The dependent variable during the experiment will be, the rate in which gas is produced (in seconds). The constants of the experiment, will be the amount of water used and the Alka Selter compound.
Bio Chem lab Report 04 Enzyme Biochemistry Group Member: Chan Man Jeun Duncan (16002621) Law Sze Man (16000478) Introduction Enzyme is a protein base structure substance in our body. It works at a biocatalyst that will catalyzing the chemical reaction, which helps to speed up the chemical reaction. Enzyme could only function in specific shape, and the shape of enzyme is depending on the environment, therefore it is hard for an enzyme to function well in an extreme environment. The aim of this experiment is to see can the enzyme functions normally in different environment(pH, temperature and salt concentration) via using starch solution, amylase from saliva, 0.5M HCl solution, 0.5M NaOH solution and NaCl solution, and using iodine solution
Introduction 1.1 Aim: To determine the kinetic parameters, Vmax and Km, of the alkaline phosphatase enzyme through the determination of the optimum pH and temperature. 1.2 Theory and Principles (General Background): Enzymes are highly specific protein catalysts that are utilised in chemical reactions in biological systems.1 Enzymes, being catalysts, decrease the activation energy required to convert substrates to products. They do this by attaching to the substrate to form an intermediate; the substrate binds to the active site of the enzyme. Then, another or the same enzyme reacts with the intermediate to form the final product.2 The rate of enzyme-catalysed reactions is influenced by different environmental conditions, such as: concentration
By observing figure 3, the more enzyme that is available, the faster the reaction rate is. The optimal enzyme concentration was chosen based on the R2 values from figure 2. The highest observable rate also had the best R2 number, which was closest to one. This enzyme concentration was used in part 2.
Aim: To find out the relationship between the greater concentration of sodium thiosulfate when mixed with hydrochloric acid and the time it takes for the reaction (the time it takes for the solution to turn cloudy) to take place and to show the effect on the rate of reaction when the concentration of one of the reactants change. Introduction: The theory of this experiment is that sodium thiosulfate and hydrochloric acid reach together to produce sulfur as one of its products. Sulfur is a yellow precipitate so, the solution will turn to yellow color while the reaction is occurring and it will continue until it will slowly turn completely opaque. The reaction of the experiment happens with this formula: “Na2 S2 O3 + HCL =
ABSTRACT: The purpose of the experiments for week 5 and week 6 support each other in the further understanding of enzyme reactions. During week 5, the effects of a substrate and enzyme concentration on enzyme reaction rate was observed. Week 6, the effects of temperature and inhibitor on a reaction rate were monitored. For testing the effects of concentrations, we needed to use the table that was used in week 3, Cells.
The graph shows the average volume of hydrogen that was produced from the 3 trials and the average volume of oxygen that was produced from the 3 trials across the voltage. I added the volumes of hydrogen in each trial and I divided them by 3 to get the average and I made the same thing for the volume of oxygen. The graph shows that the volume of hydrogen produced during the experiment is twice as much as the volume of oxygen. For example using the third data when I used 11 volts the average volume of hydrogen that was produced was 5.8 cm3 and the average volume of oxygen produced was 2.9 cm3
Introduction The term chromatography actually means colour writing, and signifies a technique by which the substance to be examined is placed in a vertical glass tube containing an adsorbent, the different segments of the substance traveling through the adsorbent at distinctive rates of velocity, according to their degree of attraction to it, and producing bands of colour at different levels of the adsorption column. The substances least absorbed emerge earliest; those more strongly absorbed emerge later. (Wixom et al., 2011) In chromatography of all types, there is a mobile phase and a stationary phase.
Introduction Strong acids and strong acids both dissociate completely in water forming ions. However, strong acids donate a proton to form H3O+ along with a conjugate base and strong bases accept a proton to form OH- along with a conjugate acid. The chemical behavior of acids and bases are opposite. When they are together, their ions cancel out and form a neutral solution. In this experiment, HCl and NaOH will react to form NaOH and H2O with these two steps: The overall reaction is: Both Na+ and Cl- ions combine to form NaCl.
The Env in post-translation step is cleaved by the cellular protease to produce