# Biomod/2013/NanoUANL/Enzyme

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<html> <!-- MathJax (LaTeX for the web) --> <script type="text/x-mathjax-config"> MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\$','\$']]}}); MathJax.Hub.Config({ TeX: { equationNumbers: { autoNumber: "AMS" } } }); </script> <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> <head> <title></title> </head> <body> <p style="text-align: center;"> <strong><span style="font-size:24px;"><span style="font-family: tahoma,geneva,sans-serif;">&nbsp;&nbsp; ENZYME</span></span></strong></p> <p style="text-align: center;"> &nbsp;</p> <p style="text-align: center;"> <span style="font-size:14px;"><span style="font-family: lucida sans unicode,lucida grande,sans-serif;"><strong><img alt="" src="http://openwetware.org/images/e/e4/UANLEnzyme1.jpg" style="width: 410px; height: 385px;" /></strong></span></span></p> <p style="text-align: justify;"> <span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><strong>Enzyme</strong></span></span></p> <p style="text-align: justify;"> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">In biological systems, chemical transformations are typically accelerated by enzymes, macromolecules capable of turning one or more compounds into others (substrates and products). The activity is determined greatly by their three-dimensional structure. Most enzymes are proteins, although several catalytic RNA molecules have been identified. They may also need to employ organic and inorganic cofactors for the reaction to occur. The process is based upon the diminishment of the activation energy needed for a reaction, greatly increasing its rate of reaction. The rate enhancement provided by these proteins can be as high as 10^19, while maintaining high substrate specificity.</span></span></p> <p style="text-align: justify;"> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Because of this, reaction rates are millions of times faster than un-catalyzed reactions. Enzymes are not consumed by the reactions that they take part in, and they do not alter the equilibrium. Enzyme activity can be affected by a wide variety of factors. Inhibitors and activators intervene directly in the reaction rate, environmental factors like temperature, pressure, pH and substrate concentration also play a part in these kinetics. For temperature and pH, usually exist a range of values for which the enzyme works better (optimal conditions). The enzyme activity lowers dramatically as you get farther away from this range of values. As for concentration, other kind of relationship is observed. With increasing concentration, enzyme activity increases, until we reach the most optimal performance. Further increase of concentration generally won&rsquo;t have an impact on the enzyme activity.</span></span></p> <p style="text-align: justify;"> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Being able to determine these conditions allow us to manipulate the enzyme activity, thus achieving greater control over the reaction.</span></span></p> <p style="text-align: justify;"> <span style="font-size:14px;"><strong><span style="font-family: trebuchet ms,helvetica,sans-serif;">Michaelis-Menten kinetics</span></strong></span></p> <p style="text-align: justify;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Michaelis-Menten kinetics is one of the oldest models for describing the catalytic activity of enzymes. The reaction cycle is divided into two basic steps: the reversible binding between the enzyme and substrate to form an intermediate complex, and the irreversible catalytic step to generate the product and release the enzyme; in which the first step is affected by the constants k<sub>1</sub> and k<sub>-1</sub>, whereas the irreversible step only takes into account&nbsp; k<sub>2</sub>.</span></span></p> $$E + S \leftrightarrow ES \rightarrow E^0 + P$$ <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The rate of consumption can be expressed by the formation of the ES complex in the following equation:</span></span></p> $$\frac{d[ES]}{dt}=k_1[E][S]-k_{-1}[ES]-k_2[ES]$$ <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Using a steady-approximation and rearranging eq. 2 we obtain:</span></span></p> $$[ES]= \frac{[E][S]}{K_M+[S]}$$ <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">where &#39;&#39;K<sub>M</sub>&#39;&#39; is the Michaelis constant defined as </span></span></p> $$K_M= \frac{k_{-1} + k_2}{k_1}$$ <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">As it was mentioned in the introduction, single-enzyme studies have proven that the &quot;traditional&quot; enzyme kinetics do not apply, and a new approach is needed. Enzyme concentration is meaningless in a single-molecule level, so it is more appropriate to consider the probability &#39;&#39;P<sub>E</sub>(t)&#39;&#39; for the enzyme to find a catalytically active enzyme in a time &#39;&#39;t&#39;&#39; in the process. This is because the reaction is a stochastic event.</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Therefore, the rate equations of each species are:</span></span></p> $$\frac{d[E]}{dt}=-k_1[E][S]+k_{-1}[ES]$$ $$\frac{d[ES]}{dt}=k_1[E][S]-(k_{-1}+k_2)[ES]$$ $$\frac{d[E^0]}{dt}=\frac{d[P]}{dt}=k_2[ES]$$ </body> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">where &#39;&#39;t&#39;&#39; is the elapsed time, the initial conditions are [ES]=0 and [E&lt;sup&gt;0&lt;/sup&gt;]=0 at &#39;&#39;t&#39;&#39;=0. To derive the rate equations that describe the corresponding single-molecule Michaelis-Menten kinetics, the concentrations in equations 5-7 are replaced by the probabilities P of finding the single enzyme molecule in the states E, ES, and E&lt;sup&gt;0&lt;/sup&gt; , leading to the equations:</span></span></p> $$\frac{dP_E(t)}{dt}=-k_1^0P_E(t)+k_{-1}P_{ES}(t)$$ $$\frac{dP_{ES}(t)}{dt}=k_1^0P_E(t)-(k_{-1}+k_2)P_{ES}(t)$$ $$\frac{dP_E^0(t)}{dt}=k_2P_{ES}(t)$$ <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">These equations must satisfy the conditions &#39;&#39;P<sub>E</sub>&#39;&#39;(0)=1, &#39;&#39;P<sub>ES</sub>&#39;&#39;(0)=0 and &#39;&#39;P<sub>E<sup>0</sup></sub>&#39;&#39;=0 at &#39;&#39;t&#39;&#39;=0 (start of the reaction). Also, &#39;&#39;P<sub>E</sub>&#39;&#39;(t) + &#39;&#39;P<sub>ES</sub>&#39;&#39;(t) + &#39;&#39;P<sub>E<sup>0</sup></sub>&#39;&#39;(t)=1. The rate constant &#39;&#39;k&#39;&#39;<sub>1</sub><sup>0</sup> can be taken as &#39;&#39;k&#39;&#39;<sub>1</sub><sup>0</sup>=&#39;&#39;k&#39;&#39;<sub>1</sub>[S], assuming [S] is time-independent. Given that a single enzyme is unlikely to deplete all the substrate presence, [S] can be considered constant, virtually being unaffected.</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Equations 8-10 become a system of linear first-order differential equations that can be solved exactly for &#39;&#39;P<sub>E</sub>&#39;&#39;(t), &#39;&#39;P<sub>ES</sub>&#39;&#39;(t) and &#39;&#39;P<sub>E<sup>0</sup></sub>&#39;&#39;(t).</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Knowing &#39;&#39;P<sub>E<sup>0</sup></sub>&#39;&#39;(t), the probability that a turnover occurs between &#39;&#39;t&#39;&#39; and &#39;&#39;t +&#39;&#39; &Delta;&#39;&#39;t&#39;&#39; is &#39;&#39;f(t)&Delta;t, the same as &Delta;&#39;&#39;P<sub>E<sup>0</sup></sub>&#39;&#39;(t). Taking this into account, in the limit of infinitesimal &Delta;&#39;&#39;t&#39;&#39;: </span></span></p> $$f(t)=\frac{dP_E^0(t)}{dt}=k_2P_{ES}(t)$$ <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Solving equations 8-10, and using equation 11: </span></span></p> $$f(t)=\frac{k_1k_2[S]}{2A}[exp(A+B)t-exp(B-A)t]$$ <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">in which:</span></span></p> $$A=\sqrt{(k_1[S]+k_{-1}+k_2)^2/4-k_1k_2[S]}$$ $$B=- \frac{k_1[S]+k_{-1}+k_2}{2}$$ <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">when the substrate concentration dependence [S] has been shown throught the relation &#39;&#39;k<sub>1</sub><sup>0</sup> = k<sub>1</sub>&#39;&#39;[S]. </span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">With these equations, we have used different values for &#39;&#39;k<sub>-1</sub>&#39;&#39; and [S], using values found in literature. </span></span></p> <p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">At the first moment of &#39;&#39;f(t)&#39;&#39;, which would be the mean waiting time for the reaction, &#39;&#39;&lt;t&gt;&#39;&#39;, and its reciprocal can be taken as the average reaction rate.&nbsp; Starting eq. 12:</span></span></p> $$\frac{1}{\langle t \rangle)}=-\frac{(A^2-B^2)^2}{2Bk_1k_2[S]}$$ $$\frac{1}{\langle t \rangle}=\frac{k_2[S]}{[S]+K_M}$$ <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><strong><span style="font-size: 14px;">Randomness parameter</span></strong><br /> <span style="font-size: 12px;">The probability density &#39;&#39;f(t)&#39;&#39; completely characterizes single-enzyme kinetics, with the &#39;&#39;n&#39;&#39;&lt;sup&gt;th&lt;/sup&gt; moment being given by:</span></span></p> $$f(t)= \int_0^\infty dt f(t)t^n$$ <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Although the first moment of &#39;&#39;f(t)&#39;&#39; can be described eq. 11, higher moments of &#39;&#39;f(t)&#39;&#39; are usually calculated along with a &quot;randomness parameter&quot;. Implying no dynamic disorder, &#39;&#39;r&#39;&#39; is given by: </span></span></p> $$r=\frac{(k_1[S]+k_2+k_{-1})^2-2k_1k_2[S]}{(k1[S]+k_2+k_{-1})^2}$$ <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">As substrate concentration increases, ''r'' decreases, indicating the formation of an intermediate enzyme-substrate complex ES. At even higher concentrations, the catalytic step limits the reaction, as is the same when concentration is low and the substrate binding limits the rate. </span></span></p> <p> &nbsp;</p> <p> <strong><span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Enzyme Reaction in a Container</span></span></strong></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Some reactions occur in spaces which have such a small volume that the normal approach to enzyme kinetics does not work. Even when taking into account probability instead of concentration, reaction cannot be modeled by aninfinite volume with a constant density. Examples of these systems include nanoparticles, zeolites or silica gels. In systems containing a small number of interacting species a relatively large fluctuationin the number of reactants is inherent. Therefore, the partitioning of the reagentspecies in small volume and the small number of the species present in eachindividual volume make it difficult to apply classical chemical kinetics to describe individual reactions in the container.</span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">For a spherical system, in which molecules <em>A</em> and <em>B</em> react, the survival probability <em>p(r,t)</em> at the time <em>t </em>when A,B are at a <em>d </em>distance:</span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Enzyme Reaction in a Container</span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Some reactions occur in spaces which have such a small volume that the normal approach to enzyme kinetics does not work. Even when taking into account probability instead of concentration, reaction cannot be modeled by aninfinite volume with a constant density. Examples of these systems include nanoparticles, zeolites or silica gels. In systems containing a small number of interacting species a relatively large fluctuationin the number of reactants is inherent. Therefore, the partitioning of the reagentspecies in small volume and the small number of the species present in eachindividual volume make it difficult to apply classical chemical kinetics to describe individual reactions in the container.</span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">For a spherical system, in which molecules <em>A</em> and <em>B</em> react, the survival probability <em>p(r,t)</em> at the time <em>t </em>when A,B are at a <em>d </em>distance:</span></span></p> $$\frac{δp(r,t)}{δt}=D\bigtriangledown^2p(r,t)$$ $$p(r,0)=1$$ $$p(d,t)=0$$ $$\bigg[ \frac{δp(r,t)}{δr} \bigg]_r=R =0$$ <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">These equations describe the random motion of <em>A</em> with respect to <em>B</em>, the system&rsquo;s initial condition, distance needed to interact, and finally a boundary condition for the sphere.</span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">In a general case where a sphere contains one B molecule and a number N of Amolecules that move mutually independently, the survival probability P(t) can bewritten as a product of the survival probabilities of all (A&hellip;B) pairs:</span></span></p> $$P(t) = \prod_{i=1}^N p(r,t)$$ <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">In this equation, <em>r<sub>i</sub></em>is the initial position of the i<sup>th</sup><em>A </em>molecule. Averaging this last equation over therandom initial distribution of A molecules inside the sphere results in:</span></span></p> $$P(r,t)= \bigg[\sum_{i=1}^\infty H_i•exp(-α_i^2 \frac{Dt}{R^2}\bigg]^N$$ $$H_i=\frac{6\bigg(\frac{d}{R}\bigg)^2}{\alpha_i^2\bigg(1-\frac{d}{R}^2\bigg)\bigg[\frac{\alpha_i^2}{1+\alpha_i^2}-\frac{d}{R}^2\bigg]}$$ <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Thus, <em>P(r,t)</em> decays exponentially, indicating that the contained reaction obeys first-order kinetics.</span></span></p> <p style="text-align: center;"> <span style="font-size:18px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><strong>RESULTS</strong></span></span></p> <p> &nbsp;</p> <p> <strong><span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Single-enzyme Michalis-Menten</span></span></strong></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">After the solution of the differential equations system (eqs. 8-10), the analytical function of waiting time distribution <em>f(t)</em> was obtained. Then we introduced our parameters to understand the behavior of our specific system. The following constants obtained from literature:</span></span></p> $k_1=10^7 M^{-1} s^{-1}$ <p> &nbsp;</p> $k_2=201 s^{-1}$ <p> &nbsp;</p> $k_{-1}=50-250 s^{-1}$ <p> &nbsp;</p> $[S]=0.0001 - 0.1 mM$ <p> &nbsp;</p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Using Matlab for calculating and drawing the plots for this data, we obtained the following figures, varying the values of [S]:</span></span></p> <p style="text-align: center;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/2/2b/Waiting_time.png" style="width: 594px; height: 472px;" /></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Fig.1 Waiting time distribution, as a function of time and [S]</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">At concentrations lower than 0.01 M, we can observe the lowest values of waiting time distributions. With increasing concentrations, the maximum contributions of waiting time distribution were observed around the first 0.02 seconds. After this time, their values drop dramatically, as we expected, because it is less probable to have a reaction after a longer elapsed time (because it must have already happened).</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">The same was done varying the values of k<sub>-1</sub>:</span></span></p> <p style="text-align: center;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/c/c2/Waiting_time_2.png" /></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Fig.2 Waiting time distribution, as a function of time and k<sub>-1</sub></span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">We can observe a change in the height of the curve&acute;s peak aroung 0 and 0.02 seconds, as the values of k<sub>-1</sub> increase. However, the same general behavior is observed for the waiting time distribution. </span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Then, with this function, we obtained the probability of survival (no reaction between the enzyme and the substrate) by the following equation:</span></span></p> $$P(t)= 1- \int f(t) dt$$ <p style="text-align: center;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/7/72/Waiting_prob_2D.png" style="width: 501px; height: 375px;" /></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Fig.3 Probability of survival, as a function of time with varying [S] for the single-enzyme Michaelis-Menten model</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">As expected the probability drops dramatically as time increases, and drops faster for higher [S]. </span></span></p> <p> &nbsp;</p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span style="font-size:14px;"><strong>Confined space model</strong></span></span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">To prove the feasibility of the confined space model, we tested the special case of a container with an infinite radius, which has to behave as the previous model. For this, the probability of survival simplifies as follows:</span></span></p> <p> &nbsp;</p> $$P(t)=exp(-4\pi cdDt)$$ <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">where <em>c </em>is the concentration of the reactive species. During the reaction model, it was found that d = 1.6 x </span>10<sup>12</sup> A<sup>2</sup>s<sup>-1</sup>. <span style="font-family:trebuchet ms,helvetica,sans-serif;">Again, using Matlab to compute these equations, we obtained the following figure:</span></span></p> <p style="text-align: center;"> <span _fck_bookmark="1" style="display: none;">&nbsp;</span><img alt="" src="http://openwetware.org/images/3/3c/Confined_inf.png" /><span _fck_bookmark="1" style="display: none;">&nbsp;</span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Fig.4 Probability of survival, as a function of time with varying [S] for the confined space model</span></span></p> <p style="text-align: justify;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span style="font-size:12px;">The general behavior of this model is very similar to that of the single-enzyme Michaelis-Menten model, although the timescale of the former is in a different order of magnitude. We speculate that this is because the confined space model does is only taking into account geometric considerations (the reaction occurs when the molecules are close enough to each other). This model does not consider many other variables of the phenomenon, such as the location of active sites and substrate specificity, which are taken into account experimentaly by the rate of reaction coefficients in the single-enzyme Michaelis-Menten model. As such, it is apparent that the confined space model is a good model for this phenomenon, but needs to take into account more specific environmental conditions to fit with experimental data before applying it to confined spaces.</span></span></span></p> </html>