<< Welcome >>
Namaste, and welcome to our website. We do research to understand how very small things move over very small distances inside the cells of our body. Our work spans the traditionally defined disciplines of Biology, Physics, Chemistry and Computation. You can explore our website using the links above. If you want to know why we are excited about what we do, read on below…
<< Motivation >>
Some of the most insightful research in biology has come by applying ideas and tools from the physical sciences on biological systems. Quantitative answers have been obtained through novel techniques, such as those invented to measure function of a single biological molecule (for example, a protein). Such “single molecule” experiments are technically challenging, and are typically done with the molecule placed in an artificial (in vitro) environment. While these experiments are pioneering in their own right, it is often not possible to relate their results to real-world biology. This is because inside a cell (in vivo), there is almost never anything like a “single molecule”. Biological molecules usually work as part of a larger complex, where many of them come together to achieve a common function. It is the NET function of this complex that is relevant, and not just that of the single constituent proteins. Our goal is to extend the precision of single-molecule techniques inside living cells, and directly measure function of a protein-complex in real-time in a cellular environment.
<< Focus >>
The living cell is an assembly of specialized factories with a constant give-and-take of material occurring within them. Nanoscale proteins called Molecular motors (Ref 1,2,3) carry cellular material as cargo from one factory to the other (e.g. mRNA, vesicles, endosomes). This transport of material is essential for the cell and its factories to function. A heavy traffic of cargoes different size and shapes can be observed under the microscope. To achieve this transport, the cell uses a network of roadways that are actually polymerized protein filaments. The motors attach to specific cargo, and walk in a step-like manner on these roads inside the cell. In order to walk, the motors generate forces about a million-million times smaller than what we use in our day-to-day life (Ref 4,5). Thus, most of the action happens at the nanoscale.
Different motors with inclination to walk in different directions may be simultaneously present as a protein complex on a given cargo, along with a host of other non-motor proteins (Ref 6,7). It is this protein complex that we are probing with biophysical assays. The big questions that drive our research are
? All molecular motors are not designed the same, and therefore do not have similar capabilities. Yet, they work together on a single cargo. What is the advantage of this heterogeneity? What are the specific adaptations that allow a particular motor to work with another class of motors, and do something useful in the cell
? How is the relative activity of antagonistic motors regulated to achieve directed transport
? Many non-motor proteins interact with the motors. What are these proteins doing to the motors
<< Importance >>
To the Biologist
How motors achieve organized transport provides some answers to a fundamental biological question: How does organization and structure arise from microscopic complexity in the living animal? Transport driven by Molecular motors is crucial for almost every conceivable cellular process, and how the activity of motors is regulated directly impacts all these processes.
To the Physicist and Engineer
Understanding the architecture and function of molecular motors can elucidate basic design mechanisms in nature to build machines at the size of nanometers (for example, see Ref 5). Biophysical measurements like what we do are unique in that they directly measure biological function in real-time in an in vivo context.
Molecular motors are essential proteins, critically important for a myriad biological processes. Motors are involved in Golgi positioning, chromosomal segregation, mRNA and protein transport, neuronal transport, development of the central nervous system, localization of cytoplasmic determinants to establish embryonic body axis etc. For all the above processes to occur normally, regulation of the relative activity of different motors is essential. Dysfunctional molecular motors result in numerous diseases (Cancer, Alzheimers, Motor neuron degeneration etc; see Ref 9).
<< How we do our Research >> Summary of our recent papers is available on the Publications page …
The obvious, yet most remarkable thing about molecular motors is that they actually move !! This motion can be directly observed under a microscope, and interpreted in terms of the motor’s function. We record and analyze this motion, measure the forces generated during motion using optical tweezers, try to identify the molecules driving such motion using protein biochemistry, and also interfere with the motion using genetic/biochemical techniques. We use the microtubule-motor dependent motion of endosomes, phagosomes and lipid droplets as our model systems, and interrogate these systems at multiple levels of complexity:-
− Directly inside living cells.
− Semi in vitro experiments in cell extracts.
− With purified single motor proteins coated on sub-micron plastic beads.
− Computer simulations using parameters directly obtained from the above experiments.
<< Snapshots >>
The schematic below shows how Dynein motors cluster into cholesterol rich domains on the lipid membrane of a phagosome as this phagosome matures inside a cell. A pathogen is shown surviving happily inside the phagosome (on the left). However, once the dynein clusters on the phagosome membrane, this pathogen is rapidly transported to its death in a Lysosome. For more details, see (Rai et al, Cell 2016)
The cartoon below shows how the weak and erratic Dynein motor could generate large collective forces as a team (Rai et al, Cell 2013). The illustration is courtesy Precision Graphics. Reprinted with permission. Original appeared in "Sharing the Load" (The Scientist, May 2013).
The figure below shows dynein and kinesin motors in a tug-of-war on single endosomes inside the cell. The motors function very differently at the single-molecule level, and this difference may help in regulating endosome biogenesis (Soppina et al, PNAS 2009)
<< Further Reading >>
1. Vale RD: The molecular motor toolbox for intracellular transport. Cell 2003, 112:467-480.
2. Vale RD, Milligan RA: The way things move: looking under the hood of molecular motor proteins. Science 2000, 288:88-95.
3. Schliwa M, Woehlke G: Molecular motors. Nature 2003, 422:759-765.
4. Visscher K, Schnitzer MJ, Block SM: Single kinesin molecules studied with a molecular force clamp. Nature 1999, 400:184-189.
5. Mallik R, Carter BC, Lex SA, King SJ, Gross SP: Cytoplasmic dynein functions as a gear in response to load. Nature 2004, 427:649-652.
6. Mallik R, Gross SP: Molecular motors: strategies to get along. Curr Biol 2004, 14:R971-982.
7. M. Welte. Bidirectional transport along microtubules Current Biology, Vol 14, R525-37 (2004)
8. S.P. Gross. Hither and yon: a review of bi-directional microtubule-based transport Physical Biology, Vol 1, R1-11 (2004)
9. Hirokawa N, Takemura R: Biochemical and molecular characterization of diseases linked to motor proteins. Trends in Biochemical Sciences 2003, 28: 558