Projects / Programmes
Reliable first arrivals and their importance for cellular signaling
| Code |
Science |
Field |
Subfield |
| 1.02.07 |
Natural sciences and mathematics |
Physics |
Biophysics |
| Code |
Science |
Field |
| P002 |
Natural sciences and mathematics |
Physics |
| Code |
Science |
Field |
| 1.03 |
Natural Sciences |
Physical sciences |
the first passage problem, statistical physics, fluctuations, linear response theory, cellular signaling, molecular transport, biding to a receptor
Researchers (1)
| no. |
Code |
Name and surname |
Research area |
Role |
Period |
No. of publicationsNo. of publications |
| 1. |
29487 |
PhD Aljaž Godec |
Physics |
Head |
2016 - 2017 |
80 |
Organisations (1)
| no. |
Code |
Research organisation |
City |
Registration number |
No. of publicationsNo. of publications |
| 1. |
0104 |
National Institute of Chemistry |
Ljubljana |
5051592000 |
21,023 |
Abstract
An intact biochemical signaling machinery is vital for cellular function. It encompasses numerous coupled processes consisting of transport-coupled binding to a target. Signaling often occurs at extremely low concentrations, which inevitably leads to appreciable fluctuations in the dynamics and precision of signaling pathways. Nevertheless, intracellular signaling evolves with remarkable precision. Modern single-particle tracking methods inside living cells revealed striking differences in intracellular transport as compared to transport in solution, as the former is often spatially or mechanistically heterogeneous. Spatial heterogeneity is a consequence of a heterogeneous cellular composition, whereas mechanistic heterogeneity occurs due to the transient binding to static or mobile cellular structures (e.g. molecular motors and/or other macromolecules and organelles). The latter leads to stochastic switching between different transport modes, i.e. between diffusion and active directed transport or between diffusion and phases of immobilization. The role and consequences of dynamical heterogeneity of intracellular transport for the speed and precision of cellular signaling, however, remain elusive.
Within the scope of the project we will therefore analyze the speed and precision of simple, generic but representative models of cellular signaling pathways including heterogeneous transport of signal molecules. The purpose of the research is to obtain a fundamental physical understanding of dynamics of transport-coupled binding to a target. Our goal are analytical results identifying and quantifying the physical parameters determining and limiting the speed and precision of simple generic models of cellular signaling pathways. We will address the speed and precision of both effectively reversible as well as effectively irreversible signaling pathways, the former in form of a first passage time analysis and the latter by analyzing fluctuations in target occupancy at equilibrium. We are also interested in the optimization of transport to achieve maximal speed versus minimal fluctuations. From a mathematical point of view the project involves the analysis of systems of coupled partial differential and partial integro-differential equations, methods of asymptotic analysis and linear response theory for relaxational dynamics. The analytical approaches will be complemented and tested by numerical simulations.
The basic questions addressed in the project are: In what circumstances does spatially/temporally heterogeneous transport allow for faster and more precise signaling? Can receptors indeed count molecules more precisely if their motion is spatially/temporally heterogeneous? Is the theoretically predicted optimal transport compatible with experimental observations? In addressing those questions we will also develop new mathematical-physical approaches, which will be useful also in other branches of statistical, chemical and/or mathematical physics. Our results will also provide, for the first time, an estimate for the capability of state-of-the-art molecular diagnostic methods based on active transport mediated by molecular motors. Such methods are expected to revolutionize molecular diagnostics but have not succeeded to do so to date. Our preliminary results already confirmed that a markedly improved capability of the mentioned diagnostic devices is indeed possible from a physical point of view. A deep physical understanding of complex transport coupled with interactions with biochemical receptors hence represents a solid theoretical basis for targeted development and optimization of next generation molecular diagnostic devices.
Significance for science
State-of-the-art experimental single-molecule methods nowadays allow us to track individual molecules inside living cells and thus follow molecular processes in vivo. These methods reveal striking sample-to-sample fluctuations in the motion of signaling molecules, yet cellular signaling appears to be exceptionally precise. It is therefore timely to extend the classical mean-rate approaches to biochemical kinetics and consider the full distribution of first passage times. The theoretical results derived within the project will be a quantitative basis for the development and analysis of massive single-molecule experiments for first passage time dynamics in living cells or chemical reactions in micro- and nano-containers. The few-encounter limit introduced here, together with the proximity effect, complements the many-encounter regime associated with the standard mean first passage time theory. Our results have grave consequences for the interpretation of single-molecule reaction or binding experiments that nowadays allow one to directly visualize the few-encounter regime. Namely, the quantification of reaction kinetics is paradigmatically reduced to the mean, which is meaningful if we are interested in systems in which most of the molecules are required to react. In contrast, when only a small number of reactive encounters are required, e.g., the binding of a few transcription factors to their targets deciding the regulatory pathway of a cell or phosphorylation cascades in cellular signal transduction propagating towards the nucleus, our results show that typical and direct realizations are essential. In this few-encounter regime, mean first passage time-based concepts grossly underestimate the speed and precision of experimentally observed signaling kinetics and would thus lead to severe parameter misjudgments. These would deteriorate further for first passage time cascades. In other words, the notion of a kinetic rate in the traditional bulk sense ceases to exist in the few-encounter regime. The universality of the proximity effect in target search kinetics enabling temporal signal focusing, and related results uncovered within the project, therefore challenge traditional views on biochemical reactions in cells and provide the basis for new models for molecular regulatory kinetics in the few-encounter regime.
Significance for the country
Our results provide an unprecedented estimate for the capabilities of state-of-the-art molecular diagnostic methods utilizing active intermittent transport. These methods are expected to revolutionize molecular diagnostic yet have failed to do so at present. A deep physical understanding of complex transport-coupled interactions with biochemical receptors represents a solid basis for a targeted knowledge-based development and optimization of next generation molecular diagnostic methods. Since members of the Laboratory for molecular modeling cooperate with the Slovene pharmaceutical industry (e.g. Lek (Sandoz) and Krka), we anticipate that the results might also be interesting for the pharmaceutical industry.
Most important scientific results
Final report
Most important socioeconomically and culturally relevant results
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