<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article  PUBLIC "-//NLM//DTD Journal Publishing DTD v3.0 20080202//EN" "http://dtd.nlm.nih.gov/publishing/3.0/journalpublishing3.dtd"><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="3.0" xml:lang="en" article-type="research article"><front><journal-meta><journal-id journal-id-type="publisher-id">JBiSE</journal-id><journal-title-group><journal-title>Journal of Biomedical Science and Engineering</journal-title></journal-title-group><issn pub-type="epub">1937-6871</issn><publisher><publisher-name>Scientific Research Publishing</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.4236/jbise.2016.92009</article-id><article-id pub-id-type="publisher-id">JBiSE-64009</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biomedical&amp;Life Sciences</subject></subj-group></article-categories><title-group><article-title>
 
 
  Closed and Open Metabolic Cycles: Transition Time
 
</article-title></title-group><contrib-group><contrib contrib-type="author" xlink:type="simple"><name name-style="western"><surname>ntonio</surname><given-names>Sillero</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author" xlink:type="simple"><name name-style="western"><surname>Víctor</surname><given-names>García-Herrero</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib></contrib-group><aff id="aff1"><addr-line>Departamento de Bioquímica, Facultad de Medicina, Instituto de Investigaciones Biomédicas Alberto Sols, UAM/CSIC, Madrid, Spain</addr-line></aff><author-notes><corresp id="cor1">* E-mail:<email>antonio.sillero@uam.es(NS)</email>;</corresp></author-notes><pub-date pub-type="epub"><day>24</day><month>02</month><year>2016</year></pub-date><volume>09</volume><issue>02</issue><fpage>127</fpage><lpage>140</lpage><history><date date-type="received"><day>25</day>	<month>January</month>	<year>2016</year></date><date date-type="rev-recd"><day>accepted</day>	<month>26</month>	<year>February</year>	</date><date date-type="accepted"><day>29</day>	<month>February</month>	<year>2016</year></date></history><permissions><copyright-statement>&#169; Copyright  2014 by authors and Scientific Research Publishing Inc. </copyright-statement><copyright-year>2014</copyright-year><license><license-p>This work is licensed under the Creative Commons Attribution International License (CC BY). http://creativecommons.org/licenses/by/4.0/</license-p></license></permissions><abstract><p>
 
 
  A metabolic cycle can be viewed as a central core and its branches. The central core is here firstly considered as a pre-closed metabolic cycle (CMC), with a unique first substrate, but with no input or output of other components. By contrast, the metabolic cycles in nature are open metabolic cycles (OMC) with output and input of external substrates (through “metabolic branches”), modulating continuously the enzyme activities and the total concentration of their substrates thorough complex regulatory phenomena. In this work, the transition from a Closed to an Open metabolic cycle has been simulated by a consecutive entry and exit of two components through the catalytic action of two enzymes. It is known that after any alteration of the initial conditions, the cycles need a time to reach new equilibrium. We have measured the changes of transition time (T.T.) values in 81 models of CMC differing in Km or 
  Vmax values. In general, the T.T. tends to be shorter in cycles with preponderant lower Km and higher 
  Vmax values. Further, 
  Mathematica refinement for the estimation of transition time from the data previously calculated can be obtained with the use of the command 
  Interpolating Function.
 
</p></abstract><kwd-group><kwd>Metabolic Cycles</kwd><kwd> Equilibration Times</kwd><kwd> Kinetic Constants</kwd><kwd> Differential Equations</kwd><kwd> Mathematica</kwd></kwd-group></article-meta></front><body><sec id="s1"><title>1. Introduction</title><p>The open metabolic cycles (OMC) can be considered as systems, with a permanent entry and exit of substrates (metabolites); in spite of this dynamic state they tend to maintain, between physiological ranges, the concentration of their components. The OMC cycles can be studied with different and complementary approaches, among others by measuring the level of their components and analyzing potential changes in their concentration in different metabolic or nutritional conditions. However, these are cumbersome procedures and sometimes difficult to be implemented [<xref ref-type="bibr" rid="scirp.64009-ref1">1</xref>] - [<xref ref-type="bibr" rid="scirp.64009-ref3">3</xref>] . The advances in computational techniques have allowed a more comprehensive understanding of open metabolic cycles [<xref ref-type="bibr" rid="scirp.64009-ref1">1</xref>] [<xref ref-type="bibr" rid="scirp.64009-ref4">4</xref>] - [<xref ref-type="bibr" rid="scirp.64009-ref7">7</xref>] .</p><p>Part of the experimental work from our laboratory had been lately centered on the mechanism of action of enzymes ligases [<xref ref-type="bibr" rid="scirp.64009-ref8">8</xref>] , and more particularly on the ubiquitin-activating enzyme. In this last case, experimental and theoretical aspects were carried out in parallel, with the help of the Mathematica Program [<xref ref-type="bibr" rid="scirp.64009-ref9">9</xref>] ; the occurrence of 19 hypothetical intermediate enzyme forms (EFs) and 22 different reactions were then contemplated [<xref ref-type="bibr" rid="scirp.64009-ref9">9</xref>] .</p><p>These previous studies directed us to apply the Mathematica Program to the analysis of several biochemical processes, such as:</p><p>a) Simulation of linear pathways exploring the effect of changing Vmax and/or Km values of one or more enzymes of the pathway; the reservoir model for enzyme kinetics previously developed in our laboratory was adapted to visualize the effect of the retro-inhibition of the first enzyme of the pathway by the final product; the time needed to achieve half of the total synthesis of the final product was also addressed [<xref ref-type="bibr" rid="scirp.64009-ref10">10</xref>] ;</p><p>b) Simulation of metabolic cycles, usually composed of a number of interconnected substrates and the same number of enzymes. Two different types of cycles can be theoretically considered, depending on whether i) substrates and enzymes form a separate entity in itself, with no entry or exit of material (a closed metabolic cycle, or CMC) or ii) a continuous interchange of material (input and/or output) between the substrates of the inner core cycle and other related metabolites takes place (open metabolic cycles, or OMC). For reasons of simplicity we have firstly approached a peculiar type of closed metabolic cycle (or pre-CMC) which reaches equilibrium, starting from a unique initial substrate [<xref ref-type="bibr" rid="scirp.64009-ref9">9</xref>] - [<xref ref-type="bibr" rid="scirp.64009-ref13">13</xref>] .</p><p>In this work, the changes in the substrate profiles of a closed metabolic cycle (CMC) promoted by the input and/or output of material are shown, and a new correlation between CMC and OMC is obtained. Although by definition the metabolic cycles tend permanently to equilibrium, the time needed to get that situation has been mathematically explored in theoretical situations in which the time needed to get the equilibrium was measured in cycles starting with only one of its substrates(a) at a fixed concentration (of 12 mM or 1 mM).</p></sec><sec id="s2"><title>2. Materials and Methods</title><sec id="s2_1"><title>2.1. Nomenclature</title><p>The close metabolic cycle (CMC) here considered contains 6 substrates and 6 enzymes, with Michaelis-Menten kinetics (<xref ref-type="fig" rid="fig1">Figure 1</xref>). The substrates of CMC are named as (a), (b), (c), (d), (e) and (f); for convenience, (a) and (f), were considered located in the first and last position. The enzymes are named with the letter E sub indexed with both, their position in the cycle and the name of the substrate (E1a, E2b, E3c, E4d, E5e, E6f); the actual equation velocities of the enzymes of the CMC are named from v1 to v6. In order to facilitate computer calculation and writing, the kinetic constants (Vmax and Km) of those enzymes are named simply as (Va to Vf) and (Ka to Kf), i.e. with the letters V and K sub indexed with the name of the corresponding substrate.</p><p>The closed metabolic cycle (CMC) is transformed into an open metabolic cycle (OMC) (<xref ref-type="fig" rid="fig1">Figure 1</xref>) by: i) the input of an external substrate (xc), at a fixed concentration(in this case ((xc), 3 mM) which is transformed into substrate (c) of the CMC by the enzyme E7xc with the following nomenclature and values: actual velocity (v7); Vmax (Vxc = 1) and Km (Kxc = 1); ii) the output of a substrate (e) of the CMC which is transformed into an external substrate (ew) by the enzyme E8ew with the following nomenclature and values for its kinetic constants: actual velocity (v8); V8max (Vew = 1) and Km (Kew = 1).</p></sec>
<sec id="s2_2"><title>2.2. General Mathematica Treatment</title>
<p>Part of this treatment is similar to that previously followed in other works from this laboratory [<xref ref-type="bibr" rid="scirp.64009-ref10">10</xref>] - [<xref ref-type="bibr" rid="scirp.64009-ref12">12</xref>] .</p><p>The general procedure is outlined in <xref ref-type="table" rid="table1">Table 1</xref>.</p>
<p>Part A of <xref ref-type="table" rid="table1">Table 1</xref> contains the actual equation velocity of the 8 enzymes involved (<xref ref-type="fig" rid="fig1">Figure 1</xref>): the six enzymes of the CMC (v1 to v6) plus the enzyme (E7xc) catalyzing the input of (c) from an external fixed source (xc, 3 mM), and the enzyme (E8ew) catalyzing the output of (e) to an different external substrate (ew).</p><p>Part B of <xref ref-type="table" rid="table1">Table 1</xref> contains the Vmax and Km values of all the enzymes of the ensemble (<xref ref-type="fig" rid="fig1">Figure 1</xref>) Note as the Vmax values of the CMC start with a Va = 1.02 with increments of 0.08 units up to a value of Vf = 1.42; all enzymes present a Km value = 1. The enzymes E7xc and E8ew, catalyzing the input and output of substrates (c)</p></sec></sec></body>
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