ICTS

The motor protein cytoplasmic dynein is regulated for its activity in living cells by remaining in an inactive conformation until the formation of a tripartite complex comprising dynein, its regulator, dynactin and a cargo adaptor. Thereupon, dynein processively transports cargo towards the minus ends of microtubules. How this process of dynein activation occurs in living cells is unclear, since this entails the congregation of three kinds of protein complexes inside the crowded environs of cell. Here, we employed high time resolution, single-molecule imaging and tracking techniques to visualize and follow fluorescently-tagged dynein heavy chain in HeLa cells. We observed dynein that bound afresh from the cytoplasm to the microtubule engaged in processive minus end-directed movement only about 30% of the time. Contrary to the existing model of cargo capture by dynein clusters at microtubule plus ends, we discovered that dynein encountered cargo that were anchored all along the length of the microtubule. Taken together, we propose a search strategy that is facilitated by dynein’s frequent microtubule binding-unbinding kinetics: (1) in the event of a futile event when dynein does not encounter cargo anchored to the microtubule, dynein unbinds and diffuses back into the cytoplasm, (2) when dynein encounters cargo upon microtubule binding, it is activated and transports the cargo in a short run towards the minus end. In conclusion, dynein activation and cargo capture are coupled in a step that employs reduction in dimensionality to enable minus-end directed transport in vivo.

 

DNA metabolic processes, such as transcription, repression, replication, and DNA damage repair elicit movement of proteins from one subnuclear location to another. Transport of these DNA binding proteins (DBPs) is amazingly fast and their specific binding to short DNA target sequences in an enormous genomic background containing many alternative sites of similar sequences to that of the specific target site is extremely accurate. In my presentation, I shall discuss the physical basis of such fast and accurate target search mechanism of DNA binding proteins on both single- and double-stranded DNA track.

Cancer metastasis and therapy resistance remain two unsolved clinical challenges for cancer, and cause over 90% of all cancer-related deaths. Despite extensive efforts to identify genomic determinants of metastasis, no unique mutational signature has yet been found. Instead, the ability of cancer cells to adapt and reversibly switch to another state - phenotypic switching - has been identified as a hallmark of metastasis. Phenotypic switching has also been implicated in cancer cells evading attacks by multiple therapies. However, the topological traits and emergent dynamics of regulatory networks enabling phenotypic switching remain elusive. We have investigated the dynamics of multiple regulatory networks enabling phenotypic switching. Discrete and continuous dynamical simulations of these networks reveal their multistable behavior that can explain co-existence of experimentally observed phenotypes and ability to spontaneously switch among them. Analysis of the underlying network topology uncovers that multistability emerges from positive feedback loops embedded in a network, which can often lead to two teams of players that mutually inhibit each other but members of a team activate one another, forming a ‘toggle switch’ between the two teams. Deciphering these topological signatures in these regulatory networks can unravel their ‘latent’ design principles and offer a rational approach to characterize phenotypic switching in a tumor and offer rational and unorthodox ways to inhibit metastasis and the evolution of drug resistance - by reducing the number of positive feedback loops in a network.

The behavior of a cell is controlled by the biochemical reaction network inside it. This reaction pathway is often noisy since various protein levels inside the cell are prone to fluctuations. With the advent of sophisticated techniques to measure single cell response in experiments, an important question has emerged: how pathway noise affects the cell response. In this talk, I will address this question within the framework of E.coli chemotaxis. The chemotaxis describes the migration tendency of  E.coli bacteria towards higher nutrient concentration. The underlying biochemical network has two main modules, sensing and adaptation, which are coupled to each other through the activity of the transmembrane chemoreceptors. The (de)methylation reaction of these receptors is generally believed to be the most important source of noise, since this is the slowest step in the whole pathway. However, recent experiments have shown that even in absence of methylation, large fluctuations are present inside the cell which originate from cooperativity or clustering tendency of the receptors. Using extensive numerical simulations in a detailed theoretical model, we investigate how this newly found noise source is related to the chemotactic performance. We find that there is an optimum size of the receptor cluster at which the chemotactic performance is at its best. We further show that this performance peak results from a competition between sensing and adaptation. 

Hydrolysis (chemical switching of subunits) is a usual process in cytoskeletal filaments like microtubules. In the talk, I will discuss how hydrolysis can make the dynamics of a biofilament non-equilibrium in nature, leading to some collective effects for multiple filaments. Previously, we predicted that when multiple filaments grow against a rigid barrier, forces generated by individual filaments become non-additive in the presence of hydrolysis. Recently, we explored how hydrolysis affects the sizes of microtubules that grow by stochastic assembly and disassembly of subunits in a limiting subunit pool. The length distribution of a single filament is unimodal. In contrast, for multiple filaments, individual filaments toggle stochastically between bigger and smaller lengths, leading to bimodal distributions of individual lengths. Consequently, a limiting subunit pool cannot control filament lengths when the hydrolysis is absent. Thus, we shall discuss how tweaking of an intrinsic parameter (hydrolysis rate) leads to size diversity in an ensemble of microtubules.

Natural environments are seldom static and therefore it is important to ask how a population adapts in a changing environment. I will consider a stochastically evolving population in which the mutant is beneficial during a part of the seasonal cycle and deleterious in another. The chance that the mutant spreads in the population depends on the instant it arose in the population and described by a time-inhomogeneous backward Fokker-Planck equation. I will discuss our analytical results for the first-passage probability and first-passage time, and their relevance to the evolution of genetic dominance.

TBA

Search processes precedes assembly of many functional structures in cell. For instance, during the organization of cellular organelles, division of cells, or finding specific targets on the cell surface, a crucial search is guided by dynamic microtubule. In this talk, I will discuss models that capture the dynamics of a broad class of systems, giving examples of complex search by microtubules while assembling mitotic spindles and interacting with pathogens on the surface of a T cell.

Planar Cell Polarity (PCP), characterized by asymmetric localization of proteins at the cell membrane within the epithelial plane, plays essential roles in embryonic development and physiological functions. The significance of PCP can be appreciated by the outcomes of PCP failure in the form of defects in neural tube formation, tracheal malfunctions, organ shape misregulation, hair follicle misalignment etc. Extensive experimental works on PCP in fruit fly Drosophila melanogaster have classified the proteins involved in PCP into two modules: `core’ module, acting locally by inter-cellular protein interactions, and, `global’ module, responsible for the alignment of cell polarities with that of the tissue axis. Despite the involvement of different molecular players the asymmetric localization of the proteins of the two modules on cell membrane primarily involve inter-cellular dimer formations.

We have developed a continnum model of the localization of PCP proteins on the cell membrane and its regulation via intra- and inter-cellular protein-protein interactions. We have identified the conditions for the asymmetric protein localization, or PCP establishment, for uniform and graded protein expression levels in the tissue. We have found that in the absence of any tissue level expression gradient the polarized state of the tissue is not stable against finite length perturbations which is also a property of the active polar matter. However, in the presence of tissue level expression gradients of proteins the polarized state remains stable. We have also looked at the influence of the loss of PCP proteins from a select regions of the tissue on the polarization of the cells outside of that region. This continuum theory of the planar cell polarity can be coupled with the active matter hydrodynamics to study the cell flows and their regulation by genetic machinery.

DNA is a long polymer that contains the genetic code. Even though different cell types in our body (skin, muscle etc) have exactly the same DNA sequence, these cells function very differently. This functional diversity is thought to be achieved through realizations of different "chromatin states". Chromatin is a three- dimensional assembly of DNA bound by many proteins. Chromatin can be assembled/organized in multiple ways, forming multiple structures, and they eventually result in different function.

In this talk, I will discuss physical models we developed that are useful to understand static and dynamic aspects of chromatin assembly, and copying epigenetic information embedded in folded chromatin. First, we will discuss results from our simulations on 3-dimensional organization of chromatin. We solved an “inverse problem” to reconstruct the 3D organization of chromatin from experimental data that give us contact probabilities between far away segments of chromatin. This helps us to predict various chromatin properties that are consistent with experimentally known constraints. I will also discuss our work trying to understand inheritance of epigenetic information (information beyond the genetic code, embedded in chromatin) during cell division.

The cell is a complex autonomous machine taking in information, performing computations, and responding to the environment. Many of the internal structures and architecture are transient and created through active processes. Recent advances in active matter physics with biological elements are opening new insights into the physics behind how cellular organizations are generated, maintained, and destroyed. I will present two recent stories on two different topics at the interface between biological and soft matter physics. The first will discuss self-organization of microtubules in the presence of “weakly interacting” crosslinkers. The second will discuss possible mechanisms for the cell to mix itself using self-propelled single molecule enzymes. These works illustrate the importance of the fundamental physics to build structures and propel matter inside living cells while informing on new physics we can learn from biological elements and materials.