Systems explorations of substrate modification systems

Abstract: The post-translational modification of proteins is a basic way of establishing protein functionality. There are many examples of classes of reversible modification (phosphorylation, ubiquination, acetylation). Typically proteins are reversibly modified at multiple site by associated enzymes. In some instances, the same enzymes can perform multiple modifications or demodifications. In such cases, different types of chemical mechanisms are possible: distributive, wherein each modification is associated with the enzyme binding to the substrate, and then dissociating after the modification, and processive wherein the enzyme is bound to the substrate as multiple modifications are effected. Substrate modifications could also occur in a particular sequence (ordered), or could occur in any order (random).

Interest in substrate modification systems arises from the fact that they are fundamental ingredients of cellular networks on one hand, while also being complex molecular information processors in their own right. In this talk, we discuss various aspects of the information processing characteristics of substrate modification systems. We first discuss some aspects of the intrinsic behaviour of these substrate modification systems and connect them to basic ingredients (eg. chemical mechanism, substrate modification ordering, commonality of enzymes). Following this, we discuss how such substrate modification systems may behave as part of networks. We discuss the relevance of the results and insights for both systems and synthetic biology

(Joint work with Vaidhiswaran Ramesh and Thapanar Suwanmajo).

algebraic geometrydynamical systemsprobability

Audience: researchers in the topic

( video )

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Seminar on the Mathematics of Reaction Networks

Series comments: Subscription link: list.ku.dk/postorius/lists/morn.list.ku.dk/

This seminar series focuses on progress in mathematical theory for the study of reaction networks, mainly in biology and chemistry. The scope is broad and accommodates works arising from dynamical systems, stochastics, algebra, topology and beyond.

We aim at providing a common forum for sharing knowledge and encouraging discussion across subfields. In particular we aim at facilitating interactions between junior and established researchers. These considerations will be represented in the choice of invited speakers and we will strive to create an excellent, exciting and diverse schedule.

The seminar runs twice a month, typically on the 2nd and 4th Thursday of the month, at 17:00 Brussels time (observe that this webpage shows the schedule in your current time zone). Each session consists of two 25-minute talks followed by 5-minute questions. After the two talks, longer discussions will take place for those interested. To this end, we will use breakout rooms. For this to work well, you need to have the latest version of Zoom installed (version 5.3.0 or higher), and use the desktop client or mobile app (not supported on ChromeOS).

We look forward hearing about new work and meeting many of you over zoom! Many of the talks are recorded; to see the recording, from Past Talks, open details of the listed talk for a video link.

The organizers.

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