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Aggregation-Fragmentation Models for Protein Polymerization Marie Doumic Journées non linéaires – Journées Venakides Institut de Mathématiques de Jussieu June 24th, 2010 with: V. Calvez, P. Gabriel, T. Goudon, N. Lenuzza, T. Lepoutre, B. Perthame and biologists: F. Mouthon, H. Rezaei. Outline.

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Aggregation-Fragmentation Modelsfor Protein PolymerizationMarie DoumicJournées non linéaires – Journées VenakidesInstitut de Mathématiques de JussieuJune 24th, 2010 with: V. Calvez, P. Gabriel, T. Goudon, N. Lenuzza, T. Lepoutre, B. Perthame and biologists: F. Mouthon, H. Rezaei

Marie DOUMIC Journées Venakides

outline
Marie DOUMIC Journées VenakidesOutline

A (very) little bit about the biology of Prion and Alzheimer

Review on existing mathematical models for prion disease

& previous results

Some recent results:

Link between discrete and continuous modelling

Eigenvalue problem

Parameters dependency

Perspectives

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Marie DOUMIC Journées Venakides
  • What is a common point of
  • Prion (Madcow, Kuru, Creutzfeldt-Jakob disease)
  • Alzheimer
  • Huntington
  • … and some others:
  • Neurodegenerative diseases
  • characterized by abnormal accumulation of
  • insoluble fibrous protein aggregates
  • called AMYLOIDS
where do these fibrils come from
Where do these fibrils come from ?

Healthy state: the considered protein is present

(APP for Alzheimer, PrP for Prion, HTT for Huntington…)

BUT is monomeric (N.B.: mono=1, poly = several)

Disease : Misfolding of the protein, leading to its

polymerization onto long fibrils (monomers attach to one another)

Specificity of Prion disease: transmissible

PRION: PRoteinasceous Infectious Only

(Prusiner 1982, Griffith 1967, Nobel Prize)

slide5
Marie DOUMIC - BONN October, 6th, 2009

i-mer

(i+1)-mer

Polymerization

monomer

+

i+1

slide6

i-mer

j-mer

(i-j)-mer

Fragmentation

+

j monomers if j < i0

slide7

i-mer

j-mer

(i+j)-mer

Coagulation

+

slide8

i-mer

monomer

(i-1)-mer

+

Depolymerization

discrete prion model
Discrete Prion model

Masel, Jansen, Nowak, 1999:

synthesis

fragmentation

Monomer density

degradation

i-polymer

density

polymerization

Size of a nucleus = minimal size of stable polymers

remarks on discrete polymerization models
Remarks on discrete polymerization models

In Biology and Biophysics

  • Huge literature
  • Simulation tools e.g. softwares “PREDICI”, “POLYRED”

(e.g. see articles by Wulkow et al., Choi et al.)

  • Main difficulty: large (infinite…) number of parameters

often drastic simplifying assumptions

In Mathematics

  • Family of coagulation-fragmentation models / Becker-Döring

See e.g. work by Aizenman-Back, 79; Ball, Carr, Penrose1990’s;

Laurençot 02; Jabin-Niethammer, 03; Fournier-Mischler, 04 ;

Dubovski – Stewart ; …

  • Specificity of this model: particular role of monomers V

Coupling v / ui in the “advection” term (replaces coalescence)

discrete model for prion proliferation nowak et al 1998 and masel et al 1999
Discrete model for prion proliferation: Nowak et al, 1998 and Masel et al., 1999

Continuous version: Prüss, Pujo-Menjouet, Webb, Zacher, 2002

Question: is the continuous framework valid ? (Investigated in D, Goudon, Lepoutre, Comm. Math. Sc., 2009)

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Previous works: Laurençot-Mischler, 2007 (coagulation-fragmentation) Collet, Goudon, Poupaud, Vasseur, 2002 (Lifshitz-Slyozov)A- Rescale the equations

Dimensionless parameters appear in the equation:

Mass conservation:

b define a small parameter
B- Define a small parameter

And mass conservation:

Biological interpretation: if and iM typical size

of a polymer

c assumptions on the coefficients
C- Assumptions on the coefficients

Under the following assumption

We set

c assumptions on the coefficients1
C- Assumptions on the coefficients

Assumption on n0 :

Biological interpretation: x0=0 iff n0 << iM

Lemma. Under the previous assumptions + some

compactness, we can define continuous functions m, t, b, k

and extract a subsequence εn such that

d asymptotic result based on moment estimates
Marie DOUMIC Journées VenakidesD- Asymptotic result (based on moment estimates)

Theorem (D, Goudon, Lepoutre). If moreover

We can extract a subsequence εn such that

weak solution of :

d asymptotic result based on moment estimates1
Marie DOUMIC Journées VenakidesD- Asymptotic result (based on moment estimates)

Theorem (D, Goudon, Lepoutre). If moreover

We can extract a subsequence εn such that

weak solution of :

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Marie DOUMIC Journées Venakides

E- What to choose for a boundary condition ?

Discrete model: no boundary condition.

Continuous model: needs one to be well-posed. If:

-> obtained rigorously if

-> obtained only (by formal division by x0) otherwise

We set (in a weak sense):

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Marie DOUMIC Journées Venakides

Some comments

  • Several different possible continuous equations as limits of the discrete one, according to assumptions on the coefficients:

e.g. fragmentation term

Can give depolymerization, a boundary condition or a fragmentation kernel

Necessity to obtain orders of magnitude

  • Coalescence has been neglected but may be added
study of the continuous model
Study of the continuous model

Constant coefficient case (reduces to 3 coupled ODE)

studied by Engl, Prüss, Pujo-Menjouet, Webb, Zacher

Motivation for studying the general case:

- Silveira et al: 2-peak size distributions of polymers

  • Biophysical considerations (Radford et al, PNAS 09)

Density of polymers

“infectious efficiency”:

≈ Polymerization rate

Size of particles

continuous model well posedness
Continuous model – Well-Posedness

A key feature : Mass balance equation:

(Simonnett, Walker, JMAP, 2006

& Laurençot, Walker, J. Evol. Equ. 2007): proved

For positive polymerization rate

  • Existence and uniqueness of classical solutions for regular initial condition and bounded coefficients
  • Existence of weak solutions for L1 initial condition
  • Stability of the disease-free steady state when it is unique
slide22

Continuous model – Steady States

  • Disease-free steady state:
  • Disease steady state:

For x0=0: only possible if

slide23

Continuous model – Disease Steady State

Linked to the following eigenvalue problem:

If : the steady state is for

If the eigenvalue increases with V :

Stability of the disease steady state is possible

continuous model asymptotic behaviour
Marie DOUMIC Journées VenakidesContinuous model – Asymptotic behaviour

(Calvez, Lenuzza, Mouthon, Perthame et al, BMB 08 & JBD 08)

For a polymerization rate possibly vanishing toward zero:

  • Stability or unstability of the zero steady state under 2 conditions:
    • Solution for the eigenvalue problem
    • The eigenvalue increases with V(t)

Tool: General Relative Entropy (see Perthame, Michel, Mischler, etc)

  • Boundedness of the solution
  • Necessary assumptions on t to obtain an eigenvector with two peaks
shape of the eigenvector figures from calvez lenuzza et al 2008
Shape of the eigenvector (figures from Calvez, Lenuzza et al, 2008)

Constant coefficient case

Variable polymerization rate

Question: what conditions to ensure existence and uniqueness of a solution to the eigenvalue problem ?

study of the eigenvalue problem
Study of the eigenvalue problem

(D. Gabriel, M3AS, 2010)

The polymerization rate possibly vanishes toward zero

Rejoin general problems of cell division (see Michel, M3AS, 2006 and Perthame, 2007), and general aggregation/fragmentation models.

Many other possible applications

study of the eigenvalue problem1
Marie DOUMIC Journées VenakidesStudy of the eigenvalue problem

Theorem (D., Gabriel).Under some technical assumptions, there exists a unique solution to the previous eigenvalue problem, and

Application. by General Relative Entropy principle

(work by Michel, Mischler, Perthame, Ryzhik,…)

define

then

assumptions for well posedness of the eigenvalue problem
Assumptions for well-posedness of the eigenvalue problem

Some necessary assumptions for the previous theorem

  • For the kernel k: ,
  • To avoid shattering:
  • Fragmentation and polymerization rates:
well posedness for the eigenvalue problem sketch of the proof
Marie DOUMIC Journées VenakidesWell-posedness for the Eigenvalue problem – sketch of the proof
  • Truncated & regularized problem

-> existence and uniqueness (Krein-Rutman)

  • A priori estimates

(by integration of the equation against proper weights,…)

-> weak compactness in L1 (Dunford Pettis) & convergence of the regularized problem

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Marie DOUMIC Journées Venakides

Eigenvalue problem – Fitness dependency on the coefficients

(Calvez, D., Gabriel, in progress)

Question:

how does the eigenvalue depend on the parameters ?

Application:

  • Asymptotic behaviour (see above: monotonous dependency on V is required)
  • Better understanding of paradoxical biological behaviour

(e.g. : what happens if fragmentation increases ? See Knowles et al, Science 09)

- Improve “PMCA” protocole

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Marie DOUMIC Journées Venakides

Sonication phase: increase of β

Incubation phase: natural coefficients

Some questions:

- Is there an optimal finite λ when β increases ?

  • How to choose an optimal strategy for incubation/sonication times in order to increase the polymer density as fast as possible ?
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Marie DOUMIC Journées Venakides

Eigenvalue problem – Fitness dependency on the coefficients

(Calvez, D., Gabriel, in progress)

Fragmentation dependence:

Proposition. i) If then

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Marie DOUMIC Journées Venakides

Eigenvalue problem – Fitness dependency on the coefficients

(Calvez, D., Gabriel, in progress)

Fragmentation dependence:

Proposition. ii) If then

slide35

Eigenvalue problem – Fitness dependency on the coefficients

Idea: use a self-similar transformation: if

(in the spirit of Escobedo, Mischler, Rodriguez Ricard, 04)

Define

For one has

And

Proving gives the result.

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Marie DOUMIC Journées Venakides

Eigenvalue problem – Fitness dependency on the coefficients

(Calvez, D., Gabriel, in progress)

Polymerization dependency: similarly

Proposition.

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Marie DOUMIC Journées Venakides

Eigenvalue problem – Numerical simulations (P. Gabriel)

perspectives
Perspectives
  • Many open questions concerning the eigenvalue problem / asymptotic behaviour
  • Optimization of the PMCA protocole

(Calvez, Gabriel)

  • Generalize the original model, and justify its use by asymptotic analysis and experiences

(in strong interaction with H. Rezaei)

  • Apply inverse problem techniques to recover the equation parameters from INRA experiments
to be continued thanks to french anr project grant
Marie DOUMIC Journées VenakidesTo be continued…Thanks to French ANR project grant

TOPPAZ

Theory and Observation of Protein polymerization

in Prion and Alzheimer diseases