Biochemically detailed model of LTP and LTD in a cortical spine (Maki-Marttunen et al 2020)

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Accession:260971
"Signalling pathways leading to post-synaptic plasticity have been examined in many types of experimental studies, but a unified picture on how multiple biochemical pathways collectively shape neocortical plasticity is missing. We built a biochemically detailed model of post-synaptic plasticity describing CaMKII, PKA, and PKC pathways and their contribution to synaptic potentiation or depression. We developed a statistical AMPA-receptor-tetramer model, which permits the estimation of the AMPA-receptor-mediated maximal synaptic conductance based on numbers of GluR1s and GluR2s predicted by the biochemical signalling model. We show that our model reproduces neuromodulator-gated spike-timing-dependent plasticity as observed in the visual cortex and can be fit to data from many cortical areas, uncovering the biochemical contributions of the pathways pinpointed by the underlying experimental studies. Our model explains the dependence of different forms of plasticity on the availability of different proteins and can be used for the study of mental disorder-associated impairments of cortical plasticity."
Reference:
1 . Mäki-Marttunen T, Iannella N, Edwards AG, Einevoll GT, Blackwell KT (2020) A unified computational model for cortical post-synaptic plasticity. Elife [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex spiking regular (RS) neuron;
Channel(s): I Calcium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Glutamate; Norephinephrine; Acetylcholine;
Simulation Environment: NEURON; NeuroRD;
Model Concept(s): Long-term Synaptic Plasticity;
Implementer(s): Maki-Marttunen, Tuomo [tuomomm at uio.no];
Search NeuronDB for information about:  I Calcium; Acetylcholine; Norephinephrine; Glutamate;
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synaptic
L23PC
L23_PC_cADpyr229_5
hoc_recordings
mechanisms
morphology
python_recordings
synapses
README *
biophysics.hoc *
cellinfo.json *
CHANGELOG *
constants.hoc *
creategui.hoc *
createsimulation.hoc *
current_amps.dat *
init.hoc *
LICENSE *
morphology.hoc *
mosinit.hoc *
ringplot.hoc *
run.py *
run_hoc.sh *
run_py.sh *
run_RmpRiTau.py *
run_RmpRiTau_py.sh *
template.hoc
VERSION *
                            

/*
Copyright (c) 2015 EPFL-BBP, All rights reserved.

THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJECT
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

This work is licensed under a
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
To view a copy of this license, visit
http://creativecommons.org/licenses/by-nc-sa/4.0/legalcode or send a letter to
Creative Commons,
171 Second Street, Suite 300,
San Francisco, California, 94105, USA.
*/

/*
 * @file biophys.hoc
 * @brief Biophysics
 * @author Etay Hay, Werner Van Geit @ BBP
 * @date 2015
*/
begintemplate cADpyr229_biophys
public biophys, distribute

proc distribute(){local x localobj sl
        strdef stmp,distfunc,mech
        sl = $o1
        mech = $s2
        distfunc = $s3
        sprint(distfunc,"%%s %s(%%f) = %s",mech, distfunc)
        forsec sl for(x) {
            sprint (stmp,distfunc,secname(),x,distance(x))
            execute(stmp)
        }
    }

proc biophys() {
	forsec $o1.basal {
		insert Ih
	}

	forsec $o1.apical {
		insert Im
		insert NaTs2_t
		insert SKv3_1
		insert Ih
	}

	forsec $o1.somatic {
		insert Ca_HVA
		insert SKv3_1
		insert SK_E2
		insert Ca_LVAst
		insert Ih
		insert NaTs2_t
		insert CaDynamics_E2
	}

	forsec $o1.axonal {
		insert Ca_HVA
		insert SKv3_1
		insert SK_E2
		insert CaDynamics_E2
		insert Nap_Et2
		insert K_Pst
		insert K_Tst
		insert Ca_LVAst
		insert NaTa_t
	}

	forsec $o1.all {
		insert pas
	}

	forsec $o1.all {
		e_pas = -75 
	}

	forsec $o1.all {
		Ra = 100 
	}

	forsec $o1.all {
		cm = 1 
	}

	forsec $o1.all {
		g_pas = 3e-5 
	}

	forsec $o1.apical {
		ena = 50 
	}

	forsec $o1.apical {
		ek = -85 
	}

	forsec $o1.apical {
		cm = 2 
	}

	forsec $o1.axonal {
		ena = 50 
	}

	forsec $o1.axonal {
		ek = -85 
	}

	forsec $o1.basal {
		cm = 2 
	}

	forsec $o1.somatic {
		ena = 50 
	}

	forsec $o1.somatic {
		ek = -85 
	}

		distribute($o1.basal,"gIhbar_Ih","(0.0 * %g + 1.0)*0.000080")
		distribute($o1.apical,"gNaTs2_tbar_NaTs2_t","(0.0 * %g + 1.0)*0.012009")
		distribute($o1.apical,"gSKv3_1bar_SKv3_1","(0.0 * %g + 1.0)*0.000513")
		distribute($o1.apical,"gIhbar_Ih","(-0.869600 + 2.087000*exp((%g-0.000000)*0.003100))*0.000080")
		distribute($o1.apical,"gImbar_Im","(0.0 * %g + 1.0)*0.000740")
		distribute($o1.axonal,"gNaTa_tbar_NaTa_t","(0.0 * %g + 1.0)*3.429725")
		distribute($o1.axonal,"gK_Tstbar_K_Tst","(0.0 * %g + 1.0)*0.001035")
		distribute($o1.axonal,"gamma_CaDynamics_E2","(0.0 * %g + 1.0)*0.016713")
		distribute($o1.axonal,"gNap_Et2bar_Nap_Et2","(0.0 * %g + 1.0)*0.009803")
		distribute($o1.axonal,"gSK_E2bar_SK_E2","(0.0 * %g + 1.0)*0.008085")
		distribute($o1.axonal,"gCa_HVAbar_Ca_HVA","(0.0 * %g + 1.0)*0.000306")
		distribute($o1.axonal,"gK_Pstbar_K_Pst","(0.0 * %g + 1.0)*0.959296")
		distribute($o1.axonal,"gSKv3_1bar_SKv3_1","(0.0 * %g + 1.0)*0.094971")
		distribute($o1.axonal,"decay_CaDynamics_E2","(0.0 * %g + 1.0)*384.114655")
		distribute($o1.axonal,"gCa_LVAstbar_Ca_LVAst","(0.0 * %g + 1.0)*0.000050")
		distribute($o1.somatic,"gamma_CaDynamics_E2","(0.0 * %g + 1.0)*0.000533")
		distribute($o1.somatic,"gSKv3_1bar_SKv3_1","(0.0 * %g + 1.0)*0.102517")
		distribute($o1.somatic,"gSK_E2bar_SK_E2","(0.0 * %g + 1.0)*0.099433")
		distribute($o1.somatic,"gCa_HVAbar_Ca_HVA","(0.0 * %g + 1.0)*0.000374")
		distribute($o1.somatic,"gNaTs2_tbar_NaTs2_t","(0.0 * %g + 1.0)*0.926705")
		distribute($o1.somatic,"gIhbar_Ih","(0.0 * %g + 1.0)*0.000080")
		distribute($o1.somatic,"decay_CaDynamics_E2","(0.0 * %g + 1.0)*342.544232")
		distribute($o1.somatic,"gCa_LVAstbar_Ca_LVAst","(0.0 * %g + 1.0)*0.000778")
}

endtemplate cADpyr229_biophys

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