Integrated model description - Revision history

Akberdinir@gmail.com: /* Gene expression level */

2021-03-06T12:37:16Z

‎Gene expression level

Akberdinir@gmail.com: /* References */

2021-03-06T12:36:52Z

‎References

Akberdinir@gmail.com: /* Gene expression level */

2021-03-06T12:32:27Z

‎Gene expression level

Akberdinir@gmail.com: /* References */

2021-03-06T12:30:32Z

‎References

Akberdinir@gmail.com: /* Signaling level */

2021-03-06T12:27:28Z

‎Signaling level

Akberdinir@gmail.com: /* References */

2021-03-06T12:15:24Z

‎References

Akberdinir@gmail.com: /* Signaling level */

2021-03-06T12:13:08Z

‎Signaling level

Akberdinir@gmail.com: /* Signaling level */

2021-03-06T12:08:09Z

‎Signaling level

Akberdinir@gmail.com: /* Upgrade of the model (metabolic level) */

2021-03-06T12:04:03Z

‎Upgrade of the model (metabolic level)

Akberdinir@gmail.com: /* References */

2021-03-06T12:03:53Z

‎References

@@ Line 52: / Line 52: @@
 <p align=justify> An aerobic exercise induces expression of several hundreds of genes regulating many cell functions: energy metabolism, transport of various substances, angiogenesis, mitochondrial biogenesis. Regulation of the transcriptomic response to acute exercise includes dozens of transcription regulators (Popov et al., 2019)<cite>33</cite> and seems to be extremely complex. Therefore to consider the response on gene expression level we exemplify the regulation of some genes encoding a transcription co-activator PGC-1α (encoded by PPARGC1A gene) and nuclear receptors NR4As  -  key exercise-induced regulators of the angiogenesis, mitochondrial biogenesis, fat and carbohydrate metabolism in skeletal muscle (Lira et al., 2010, Pearen&Muscat, 2018)<cite>44</cite><cite>45</cite>.
-Expression of NR4A2, NR4A3 mRNA rapidly increases during the first hour after an aerobic exercise (early response genes) due to activation of Ca<sup>2+</sup>\calcineurin-dependent signaling (Stienen et al., 1996, He et al., 2000, Szentesi  et al., 2001, Pearen&Muscat 2018, Popov et al., 2019, Coccimiglio&Clarke, 2020)<cite>6</cite><cite>7</cite><cite>8</cite><cite>45</cite><cite>33</cite><cite>46</cite>. We included in our model the Ca<sup>2+</sup>-dependent regulation (Ca<sup>2+</sup>\calcineurin-CaMKII-CREB1) of NR4As genes using data of contractile activity-specific mRNA response of these genes (Popov et al., 2019)<cite>33</cite>. Expression of PPARGC1A mRNA rises 3 to 4 h after an exercise (late response gene) (Popov et al., 2019)<cite>33</cite>. The transcription regulation of PPARGC1A via the canonical (proximal) and inducible (distal) promoters is very complicated, and includes Ca<sup>2+</sup>- and AMPK-dependent signalling, as well as CREB1 and its co-activator CRTC (Popov et al., 2015, Popov, 2018)<cite>47</cite><cite>48</cite>. The phosphorylation level of many signalling kinases drops to basal levels within the first hour after an aerobic exercise. Moreover, in a genome-wide study on various human tissues, it was shown that the phosphorylation level of CREB Ser133 does not always correlate with its transcriptional activity (Broxterman et al., 2017)<cite>13</cite>. Therefore, we suggested the expression of late response genes (including PPARGC1A) is regulated by increasing the expression of one of the early response genes encoding transcription factors leading to a rapid increase of corresponding protein (see Fig. 5 in Akberdin et al., 2020)<cite>5</cite>. Analysis of contractile activity-specific transcriptomic data (Popov et al., 2019)<cite>32</cite> showed that a rapid increase in the expression of genes encoding various TFs is observed already in the first hour after an exercise. It turned out that the binding motifs of some TFs (CREB-like proteins, as well as proteins of the AP-1 family: FOS and JUN) are located and intersected with each other both in the alternative and in the canonical promoters of the PPARGC1A gene (Akberdin et al., 2020)<cite>5</cite>, i.e. these TFs can act as potential regulators of this gene. This is consistent with the fact that these TFs can bind to DNA and regulate the expression of target genes as homo- and heterodimers (Barclay, 2017, Parolin et al., 1999)<cite>9</cite><cite>10</cite>. Based on these considerations, we included in the model the regulation of gene expression of early (NR4A2, NR4A3) and delayed (PPARGC1A) genes: early response genes are regulated via the activation of existent TFs (e.g. CREB1) and their co-activators (e.g. CRTC), while delayed response genes - via an increase in the expression of early response genes encoding transcription factors (transcription factor X in our model)</p>.
+Expression of NR4A2, NR4A3 mRNA rapidly increases during the first hour after an aerobic exercise (early response genes) due to activation of Ca<sup>2+</sup>\calcineurin-dependent signaling (Stienen et al., 1996, He et al., 2000, Szentesi  et al., 2001, Pearen&Muscat 2018, Popov et al., 2019, Coccimiglio&Clarke, 2020)<cite>6</cite><cite>7</cite><cite>8</cite><cite>45</cite><cite>33</cite><cite>46</cite>. We included in our model the Ca<sup>2+</sup>-dependent regulation (Ca<sup>2+</sup>\calcineurin-CaMKII-CREB1) of NR4As genes using data of contractile activity-specific mRNA response of these genes (Popov et al., 2019)<cite>33</cite>. Expression of PPARGC1A mRNA rises 3 to 4 h after an exercise (late response gene) (Popov et al., 2019)<cite>33</cite>. The transcription regulation of PPARGC1A via the canonical (proximal) and inducible (distal) promoters is very complicated, and includes Ca<sup>2+</sup>- and AMPK-dependent signalling, as well as CREB1 and its co-activator CRTC (Popov et al., 2015, Popov, 2018)<cite>47</cite><cite>48</cite>. The phosphorylation level of many signalling kinases drops to basal levels within the first hour after an aerobic exercise. Moreover, in a genome-wide study on various human tissues, it was shown that the phosphorylation level of CREB Ser133 does not always correlate with its transcriptional activity (Broxterman et al., 2017)<cite>13</cite>. Therefore, we suggested the expression of late response genes (including PPARGC1A) is regulated by increasing the expression of one of the early response genes encoding transcription factors leading to a rapid increase of corresponding protein (see Fig. 5 in Akberdin et al., 2020)<cite>5</cite>. Analysis of contractile activity-specific transcriptomic data (Popov et al., 2019)<cite>33</cite> showed that a rapid increase in the expression of genes encoding various TFs is observed already in the first hour after an exercise. It turned out that the binding motifs of some TFs (CREB-like proteins, as well as proteins of the AP-1 family: FOS and JUN) are located and intersected with each other both in the alternative and in the canonical promoters of the PPARGC1A gene (Akberdin et al., 2020)<cite>5</cite>, i.e. these TFs can act as potential regulators of this gene. This is consistent with the fact that these TFs can bind to DNA and regulate the expression of target genes as homo- and heterodimers (Barclay, 2017, Parolin et al., 1999)<cite>9</cite><cite>10</cite>. Based on these considerations, we included in the model the regulation of gene expression of early (NR4A2, NR4A3) and delayed (PPARGC1A) genes: early response genes are regulated via the activation of existent TFs (e.g. CREB1) and their co-activators (e.g. CRTC), while delayed response genes - via an increase in the expression of early response genes encoding transcription factors (transcription factor X in our model)</p>.
 ===References===

@@ Line 99: / Line 99: @@
 #42 pmid=26616193        <!-- Hardie et al 2016 -->
 #43 pmid=27809416        <!-- Li et al 2017 -->
 </biblio>

@@ Line 51: / Line 51: @@
 ===Gene expression level===
-<p align=justify> An aerobic exercise induces expression of several hundreds of genes regulating many cell functions: energy metabolism, transport of various substances, angiogenesis, mitochondrial biogenesis. Regulation of the transcriptomic response to acute exercise includes dozens of transcription regulators (Popov et al., 2019)cite>32</cite> and seems to be extremely complex. Therefore to consider the response on gene expression level we exemplify the regulation of some genes encoding a transcription co-activator PGC-1α (encoded by PPARGC1A gene) and nuclear receptors NR4As  -  key exercise-induced regulators of the angiogenesis, mitochondrial biogenesis, fat and carbohydrate metabolism in skeletal muscle (Lira et al., 2010, Pearen&Muscat, 2018)<cite>43</cite><cite>44</cite>.
+<p align=justify> An aerobic exercise induces expression of several hundreds of genes regulating many cell functions: energy metabolism, transport of various substances, angiogenesis, mitochondrial biogenesis. Regulation of the transcriptomic response to acute exercise includes dozens of transcription regulators (Popov et al., 2019)<cite>33</cite> and seems to be extremely complex. Therefore to consider the response on gene expression level we exemplify the regulation of some genes encoding a transcription co-activator PGC-1α (encoded by PPARGC1A gene) and nuclear receptors NR4As  -  key exercise-induced regulators of the angiogenesis, mitochondrial biogenesis, fat and carbohydrate metabolism in skeletal muscle (Lira et al., 2010, Pearen&Muscat, 2018)<cite>44</cite><cite>45</cite>.
-Expression of NR4A2, NR4A3 mRNA rapidly increases during the first hour after an aerobic exercise (early response genes) due to activation of Ca<sup>2+</sup>\calcineurin-dependent signaling (Stienen et al., 1996, He et al., 2000, Szentesi  et al., 2001, Pearen&Muscat 2018, Popov et al., 2019, Coccimiglio&Clarke, 2020)<cite>6</cite><cite>7</cite><cite>8</cite><cite>44</cite><cite>32</cite><cite>45</cite>. We included in our model the Ca<sup>2+</sup>-dependent regulation (Ca<sup>2+</sup>\calcineurin-CaMKII-CREB1) of NR4As genes using data of contractile activity-specific mRNA response of these genes (Popov et al., 2019)<cite>32</cite>. Expression of PPARGC1A mRNA rises 3 to 4 h after an exercise (late response gene) (Popov et al., 2019)<cite>32</cite>. The transcription regulation of PPARGC1A via the canonical (proximal) and inducible (distal) promoters is very complicated, and includes Ca<sup>2+</sup>- and AMPK-dependent signalling, as well as CREB1 and its co-activator CRTC (Popov et al., 2015, Popov, 2018)<cite>46</cite><cite>47</cite>. The phosphorylation level of many signalling kinases drops to basal levels within the first hour after an aerobic exercise. Moreover, in a genome-wide study on various human tissues, it was shown that the phosphorylation level of CREB Ser133 does not always correlate with its transcriptional activity (Broxterman et al., 2017)<cite>13</cite>. Therefore, we suggested the expression of late response genes (including PPARGC1A) is regulated by increasing the expression of one of the early response genes encoding transcription factors leading to a rapid increase of corresponding protein (see Fig. 5 in Akberdin et al., 2020)<cite>5</cite>. Analysis of contractile activity-specific transcriptomic data (Popov et al., 2019)<cite>32</cite> showed that a rapid increase in the expression of genes encoding various TFs is observed already in the first hour after an exercise. It turned out that the binding motifs of some TFs (CREB-like proteins, as well as proteins of the AP-1 family: FOS and JUN) are located and intersected with each other both in the alternative and in the canonical promoters of the PPARGC1A gene (Akberdin et al., 2020)<cite>5</cite>, i.e. these TFs can act as potential regulators of this gene. This is consistent with the fact that these TFs can bind to DNA and regulate the expression of target genes as homo- and heterodimers (Barclay, 2017, Parolin et al., 1999)<cite>9</cite><cite>10</cite>. Based on these considerations, we included in the model the regulation of gene expression of early (NR4A2, NR4A3) and delayed (PPARGC1A) genes: early response genes are regulated via the activation of existent TFs (e.g. CREB1) and their co-activators (e.g. CRTC), while delayed response genes - via an increase in the expression of early response genes encoding transcription factors (transcription factor X in our model)</p>.
+Expression of NR4A2, NR4A3 mRNA rapidly increases during the first hour after an aerobic exercise (early response genes) due to activation of Ca<sup>2+</sup>\calcineurin-dependent signaling (Stienen et al., 1996, He et al., 2000, Szentesi  et al., 2001, Pearen&Muscat 2018, Popov et al., 2019, Coccimiglio&Clarke, 2020)<cite>6</cite><cite>7</cite><cite>8</cite><cite>45</cite><cite>33</cite><cite>46</cite>. We included in our model the Ca<sup>2+</sup>-dependent regulation (Ca<sup>2+</sup>\calcineurin-CaMKII-CREB1) of NR4As genes using data of contractile activity-specific mRNA response of these genes (Popov et al., 2019)<cite>33</cite>. Expression of PPARGC1A mRNA rises 3 to 4 h after an exercise (late response gene) (Popov et al., 2019)<cite>33</cite>. The transcription regulation of PPARGC1A via the canonical (proximal) and inducible (distal) promoters is very complicated, and includes Ca<sup>2+</sup>- and AMPK-dependent signalling, as well as CREB1 and its co-activator CRTC (Popov et al., 2015, Popov, 2018)<cite>47</cite><cite>48</cite>. The phosphorylation level of many signalling kinases drops to basal levels within the first hour after an aerobic exercise. Moreover, in a genome-wide study on various human tissues, it was shown that the phosphorylation level of CREB Ser133 does not always correlate with its transcriptional activity (Broxterman et al., 2017)<cite>13</cite>. Therefore, we suggested the expression of late response genes (including PPARGC1A) is regulated by increasing the expression of one of the early response genes encoding transcription factors leading to a rapid increase of corresponding protein (see Fig. 5 in Akberdin et al., 2020)<cite>5</cite>. Analysis of contractile activity-specific transcriptomic data (Popov et al., 2019)<cite>32</cite> showed that a rapid increase in the expression of genes encoding various TFs is observed already in the first hour after an exercise. It turned out that the binding motifs of some TFs (CREB-like proteins, as well as proteins of the AP-1 family: FOS and JUN) are located and intersected with each other both in the alternative and in the canonical promoters of the PPARGC1A gene (Akberdin et al., 2020)<cite>5</cite>, i.e. these TFs can act as potential regulators of this gene. This is consistent with the fact that these TFs can bind to DNA and regulate the expression of target genes as homo- and heterodimers (Barclay, 2017, Parolin et al., 1999)<cite>9</cite><cite>10</cite>. Based on these considerations, we included in the model the regulation of gene expression of early (NR4A2, NR4A3) and delayed (PPARGC1A) genes: early response genes are regulated via the activation of existent TFs (e.g. CREB1) and their co-activators (e.g. CRTC), while delayed response genes - via an increase in the expression of early response genes encoding transcription factors (transcription factor X in our model)</p>.
 ===References===

@@ Line 86: / Line 86: @@
 #29 pmid=21346730        <!-- Altarejos&Montminy 2011 -->
 #30 pmid=19812359        <!-- Abbott et al 2009 -->
+#31 pmid=18063805        <!-- Thomson et al 2008 -->
 </biblio>

@@ Line 43: / Line 43: @@
 <p align=justify> The concentration of Ca<sup>2+</sup> ions in the myoplasm increases in proportion to the intensity of exercise. Ca<sup>2+</sup> binds to calmodulin, thereby activating CaMKs and phosphatase calcineurin (Gehlert et al., 2015)<cite>25</cite>. CaMKII is the most abundant isoform in the human skeletal muscle, whereas CaMKI and CaMKIV are not expressed at detectable levels (Rose et al., 2006)<cite>26</cite>. An increase in CaMKII activity results in CREB1 Ser133 phosphorylation leading to activation of the transcription factor (Johannessen&Moens, 2007, Olesen et al., 2010) <cite>27</cite><cite>28</cite>. Calcineurin can dephosphorylate (and activate) CRTCs at Ser171 (CREB-regulated transcription coactivators) playing a key role in regulating the transcriptional activity of CREB1 (Altarejos&Montminy, 2011)<cite>29</cite>. Another target of calmodulin is calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) that phosphorylates AMPK Thr172 thereby activating the kinase (Abbott et al., 2009)<cite>30</cite>. In turn, activated AMPK can phosphorylate CREB1 Ser133 (Thomson et al., 2008)<cite>31</cite>. Collectively, these findings drove us to include in our model the Ca<sup>2+</sup>-dependent regulation of calmodulin, CREB1 (via CaMKII), CRTC (via calcineurin), and AMPK (via CaMKK2) (Figure 3). The amount of these proteins in human skeletal muscle was estimated using published proteomics and transcriptomics data (Murgia et al., 2017, Popov et al., 2019)<cite>32</cite><cite>33</cite> (see Supplementary data in Akberdin et al., 2020<cite>5</cite>).
-There are three different heterotrimeric complexes in the human skeletal muscles: α2β2γ1, α2β2γ3, and α1β2γ1 (Wojtaszewski et al., 2005)<cite>34</cite>. Distinct kinetic properties (an intrinsic enzyme activity,  binding affinities of AMP, ADP and ATP to the specific isoform, sensitivity to de- and phosphorylation of AMPK heterotrimers) (Rajamohan et al., 2016, Ross et al., 2016)<cite>35</cite><cite>36</cite> and their subcellular localization (Pinter et al., 2013)<cite>37</cite> cause a differential regulation of the AMPK heterotrimers ''in vivo''. The α2β2γ3 complex is phosphorylated and activated during moderate- to high-intensity exercise, while the activity associated with the other two AMPK heterotrimers is almost unchanged (Birk et al., 2006)<cite>38</cite>. However, the basal activity of α2β2γ3 complex is significantly lower than others. Taking into account the general AMPK basal and exercise-induced activity is considered as a sum of isoforms activities,  all isoforms in the corresponding module was considered to quantitatively fit an experimental data obtained at baseline and after an exercise  (Birk et al., 2006, Willows et al., 2017)<cite>38</cite><cite>39</cite>. AMPK is regulated by various ways: an up-stream kinase LKB1 can phosphorylate AMPK at Thr172 (Lizcano et al., 2004, Jansen et al., 2009)<cite>40</cite><cite>41</cite>. On the other hand, both ATP and AMP allosterically regulate AMPK: an exercise-induced decrease in intramuscular ATP increases its activity, while an increase in AMP activates it (Hardie et al., 2016, Li et al., 2017)<cite>42</cite><cite>43</cite>. Hence, in our model the AMPK is regulated via AMP, ATP, and LKB1, as well as CaMKK2 (as mentioned above).</p>
+There are three different heterotrimeric complexes in the human skeletal muscles: α2β2γ1, α2β2γ3, and α1β2γ1 (Wojtaszewski et al., 2005)<cite>34</cite>. Distinct kinetic properties (an intrinsic enzyme activity,  binding affinities of AMP, ADP and ATP to the specific isoform, sensitivity to de- and phosphorylation of AMPK heterotrimers) (Rajamohan et al., 2016, Ross et al., 2016)<cite>35</cite><cite>36</cite> and their subcellular localization (Pinter et al., 2013)<cite>37</cite> cause a differential regulation of the AMPK heterotrimers ''in vivo''. The α2β2γ3 complex is phosphorylated and activated during moderate- to high-intensity exercise, while the activity associated with the other two AMPK heterotrimers is almost unchanged (Birk&Wojtaszewski, 2006)<cite>38</cite>. However, the basal activity of α2β2γ3 complex is significantly lower than others. Taking into account the general AMPK basal and exercise-induced activity is considered as a sum of isoforms activities,  all isoforms in the corresponding module was considered to quantitatively fit an experimental data obtained at baseline and after an exercise  (Birk&Wojtaszewski, 2006, Willows et al., 2017)<cite>38</cite><cite>39</cite>. AMPK is regulated by various ways: an up-stream kinase LKB1 can phosphorylate AMPK at Thr172 (Lizcano et al., 2004, Jansen et al., 2009)<cite>40</cite><cite>41</cite>. On the other hand, both ATP and AMP allosterically regulate AMPK: an exercise-induced decrease in intramuscular ATP increases its activity, while an increase in AMP activates it (Hardie et al., 2016, Li et al., 2017)<cite>42</cite><cite>43</cite>. Hence, in our model the AMPK is regulated via AMP, ATP, and LKB1, as well as CaMKK2 (as mentioned above).</p>
 [[File:Fig3 Signaling.png|center]]

← Older revision		Revision as of 12:15, 6 March 2021
Line 80:		Line 80:
	#23 pmid=8226558 <!-- Mannion et al 1993 -->		#23 pmid=8226558 <!-- Mannion et al 1993 -->
	#24 pmid=22942911 <!-- Li et al 2012 -->		#24 pmid=22942911 <!-- Li et al 2012 -->
		+	#25 pmid=25569087 <!-- Gehlert et al 2015) -->
		+	#26 pmid=16690701 <!-- Rose et al 2006 -->
		+	#27 pmid=17127423 <!-- Johannessen&Moens 2007 -->
		+	#28 pmid=20401754 <!-- Olesen et al 2010 -->
		+	#29 pmid=21346730 <!-- Altarejos&Montminy 2011 -->
		+	#30 pmid=19812359 <!-- Abbott et al 2009 -->

@@ Line 42: / Line 42: @@
 ===Signaling level===
-<p align=justify> The concentration of Ca<sup>2+</sup> ions in the myoplasm increases in proportion to the intensity of exercise. Ca<sup>2+</sup> binds to calmodulin, thereby activating CaMKs and phosphatase calcineurin (Gehlert et al., 2015)<cite>25</cite>. CaMKII is the most abundant isoform in the human skeletal muscle, whereas CaMKI and CaMKIV are not expressed at detectable levels (Rose et al., 2006)<cite>26</cite>. An increase in CaMKII activity results in CREB1 Ser133 phosphorylation leading to activation of the transcription factor (Johannessen&Moens, 2007, Olesen et al., 2010) <cite>27</cite><cite>28</cite>. Calcineurin can dephosphorylate (and activate) CRTCs at Ser171 (CREB-regulated transcription coactivators) playing a key role in regulating the transcriptional activity of CREB1 (Altarejos et al., 2011)<cite>29</cite>. Another target of calmodulin is calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) that phosphorylates AMPK Thr172 thereby activating the kinase (Abbott et al., 2009)<cite>30</cite>. In turn, activated AMPK can phosphorylate CREB1 Ser133 (Thomson et al., 2008)<cite>31</cite>. Collectively, these findings drove us to include in our model the Ca<sup>2+</sup>-dependent regulation of calmodulin, CREB1 (via CaMKII), CRTC (via calcineurin), and AMPK (via CaMKK2) (Figure 3). The amount of these proteins in human skeletal muscle was estimated using published proteomics and transcriptomics data (Murgia et al., 2017, Popov et al., 2019)<cite>32</cite><cite>33</cite> (see Supplementary data in Akberdin et al., 2020<cite>5</cite>).
+<p align=justify> The concentration of Ca<sup>2+</sup> ions in the myoplasm increases in proportion to the intensity of exercise. Ca<sup>2+</sup> binds to calmodulin, thereby activating CaMKs and phosphatase calcineurin (Gehlert et al., 2015)<cite>25</cite>. CaMKII is the most abundant isoform in the human skeletal muscle, whereas CaMKI and CaMKIV are not expressed at detectable levels (Rose et al., 2006)<cite>26</cite>. An increase in CaMKII activity results in CREB1 Ser133 phosphorylation leading to activation of the transcription factor (Johannessen&Moens, 2007, Olesen et al., 2010) <cite>27</cite><cite>28</cite>. Calcineurin can dephosphorylate (and activate) CRTCs at Ser171 (CREB-regulated transcription coactivators) playing a key role in regulating the transcriptional activity of CREB1 (Altarejos&Montminy, 2011)<cite>29</cite>. Another target of calmodulin is calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) that phosphorylates AMPK Thr172 thereby activating the kinase (Abbott et al., 2009)<cite>30</cite>. In turn, activated AMPK can phosphorylate CREB1 Ser133 (Thomson et al., 2008)<cite>31</cite>. Collectively, these findings drove us to include in our model the Ca<sup>2+</sup>-dependent regulation of calmodulin, CREB1 (via CaMKII), CRTC (via calcineurin), and AMPK (via CaMKK2) (Figure 3). The amount of these proteins in human skeletal muscle was estimated using published proteomics and transcriptomics data (Murgia et al., 2017, Popov et al., 2019)<cite>32</cite><cite>33</cite> (see Supplementary data in Akberdin et al., 2020<cite>5</cite>).
 There are three different heterotrimeric complexes in the human skeletal muscles: α2β2γ1, α2β2γ3, and α1β2γ1 (Wojtaszewski et al., 2005)<cite>34</cite>. Distinct kinetic properties (an intrinsic enzyme activity,  binding affinities of AMP, ADP and ATP to the specific isoform, sensitivity to de- and phosphorylation of AMPK heterotrimers) (Rajamohan et al., 2016, Ross et al., 2016)<cite>35</cite><cite>36</cite> and their subcellular localization (Pinter et al., 2013)<cite>37</cite> cause a differential regulation of the AMPK heterotrimers ''in vivo''. The α2β2γ3 complex is phosphorylated and activated during moderate- to high-intensity exercise, while the activity associated with the other two AMPK heterotrimers is almost unchanged (Birk et al., 2006)<cite>38</cite>. However, the basal activity of α2β2γ3 complex is significantly lower than others. Taking into account the general AMPK basal and exercise-induced activity is considered as a sum of isoforms activities,  all isoforms in the corresponding module was considered to quantitatively fit an experimental data obtained at baseline and after an exercise  (Birk et al., 2006, Willows et al., 2017)<cite>38</cite><cite>39</cite>. AMPK is regulated by various ways: an up-stream kinase LKB1 can phosphorylate AMPK at Thr172 (Lizcano et al., 2004, Jansen et al., 2009)<cite>40</cite><cite>41</cite>. On the other hand, both ATP and AMP allosterically regulate AMPK: an exercise-induced decrease in intramuscular ATP increases its activity, while an increase in AMP activates it (Hardie et al., 2016, Li et al., 2017)<cite>42</cite><cite>43</cite>. Hence, in our model the AMPK is regulated via AMP, ATP, and LKB1, as well as CaMKK2 (as mentioned above).</p>

@@ Line 30: / Line 30: @@
 <p align=justify> It is worth to note that values of activation coefficients associated with ATPase (Stienen et al., 1996, He et al., 2000, Szentesi  et al., 2001, Barclay, 2017)<cite>6</cite><cite>7</cite><cite>8</cite><cite>9</cite> and pyruvate dehydrogenase reaction fluxes for type I and type II fibers (Parolin et al., 1999, Kiilerich et al., 2008, Albers et al., 2015)<cite>10</cite><cite>11</cite><cite>12</cite> as well as time constant of ATPase flux rate coefficient in response to exercise were modified according to recently published data and estimations (Broxterman et al., 2017, Bartlett et al., 2020)<cite>13</cite><cite>14</cite>.
 Despite overall net glycogen breakdowns during muscle contraction, exercise also increases the activity of glycogen synthase (GS) (Wojtaszewski et al., 2001, Nielsen&Richter, 2003, Jensen&Lai, 2009, Jensen&Richter, 2012)<cite>15</cite><cite>16</cite><cite>17</cite><cite>18</cite>. The GS reaction results in ATP consumption, therefore GS reaction fluxes were modified according to (Wojtaszewski et al., 2001, Jensen et al., 2009, Jensen  et al., 2012b)<cite>15</cite><cite>17</cite><cite>19</cite>. The rates of muscle glycogen synthesis during exercise assumed to be equal in type I and type II fibres and were estimated from average post-exercise glycogen synthesis data (Casey et al., 1995)<cite>20</cite>.
-To consider the allosteric regulation of AMPK activity (in corresponding modules) concentrations of free ADP and AMP in the cytosol were calculated using intracellular Cr, PCr, ATP and H+ concentrations as well as the equilibrium constants for creatine phosphokinase and adenylate kinases in each fiber type as described previously (Lawson&Veech, 1979, Dudley et al., 1985, Mannion et al., 1993)<cite>21</cite><cite>22</cite><cite>23</cite> (Figure 3).</p>
+To consider the allosteric regulation of AMPK activity (in corresponding modules) concentrations of free ADP and AMP in the cytosol were calculated using intracellular Cr, PCr, ATP and H+ concentrations as well as the equilibrium constants for creatine phosphokinase and adenylate kinases in each fiber type as described previously (Lawson&Veech, 1979, Dudley&Terjung, 1985, Mannion et al., 1993)<cite>21</cite><cite>22</cite><cite>23</cite> (Figure 3).</p>

@@ Line 77: / Line 77: @@
 #20 pmid=7776237         <!-- Casey et al 1995 -->
 #21 pmid=36398           <!-- Lawson&Veech 1979 -->
 </biblio>