Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software

Hédi Soula,Sébastien Gripon,Céline Robardet,Guillaume Beslon,François Perrin,Olivier Gandrillon

doi:10.1186/1471-2105-6-228

Abstract

BackgroundThere is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have been proposed as good candidates to achieve this goal.ResultsWe have created 3DSpi, a multi-agent based software that we used to explore the generation of multi-protein dynamic structures. Being based on a very restricted set of parameters, it is perfectly suited for exploring the minimal set of rules needed to generate large multi-protein structures. It can therefore be used to test the hypothesis that such structures are formed and maintained by principles of self-organization. We observed that multi-protein structures emerge and that the system behavior is very robust, in terms of the number and size of the structures generated. Furthermore, the generated structures very closely mimic spatial organization of real life multi-protein structures.ConclusionThe behavior of 3DSpi confirms the considerable potential of MAS for modeling subcellular structures. It demonstrates that robust multi-protein structures can emerge using a restricted set of parameters and allows the exploration of the dynamics of such structures. A number of easy-to-implement modifications should make 3DSpi the virtual simulator of choice for scientists wishing to explore how topology interacts with time, to regulate the function of interacting proteins in living cells.

Highlights

There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells
One important lesson from these studies is that, various nuclear structures appear to be stable, their components are permanently engaged in an extraordinarily dynamic process: proteins are exchanged between nuclear structures and the nucleoplasm at a rate that makes the stability of the structures really astonishing
This provocative and speculative model raises the question of the stability of the nuclear structures: how do such structures reconcile the extensive material exchange with their environment and the global stability that we observe at a macroscopic level? Computer-based simulations can help to answer this question

Summary

Introduction

There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. The possibility of probing the biophysical properties of fluorescent proteins in intact living cells by using confocal microscopy has led to a major step forward in contemporary biology This technical advance has allowed biologists to obtain a new perception of different biological structures. This was shown to be especially important in studies of the nuclear architecture [1]. It has been proposed that multi-protein dynamic structures are formed and maintained by principles of self-organization [1] This provocative and speculative model raises the question of the stability of the nuclear structures: how do such structures reconcile the extensive material exchange with their environment and the global stability that we observe at a macroscopic level? If the selforganization hypothesis is true, one should be able to virtually reconstruct computer-based model structures using a very restricted set of simple local interaction rules

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