We have been running on Anton 2 2023-2024: Interrogating transcription factor and enzyme translocation along DNA using all-atom computational microscope
We were on Summit 2020-2021: DISSECTING INHIBITOR IMPACTS ON VIRAL RNA POLYMERASE AND FIDELITY CONTROL OF RNA SYNTHESIS IN SARS-COV-2
Research highlight (New & Notable in BPS 2022) Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY domain protein along DNA How transcription factors search for target genes impact on how quickly and accurately the genes are transcribed and expressed. To locate target sufficiently fast, 1D diffusion of the protein along DNA appears essential. Experimentally, it remains challenging to determine diffusional steps of protein on DNA. Here, we report all-atom equilibrium simulations of a WRKY protein binding and diffusing on DNA, revealing structural dynamics details which have not been identified previously. We unprecedently demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic stepping or sliding, directional switching and strand crossing. Additionally, we have found preferential DNA strand association of WRKY. These suggest how protein factors approach toward target DNA sequences (Poster).
Transcription protein machines and genome wide functions
We studied nucleic acid motor proteins such as DNA/RNA helicase, polymerase, packaging motor (see previous reviews in 2014 and 2016) to understand mechanical, energetic, and informational regulation in genomic processes.
Recently, we have systematically investigated elongation mechanisms of a viral transcription machine, an RNA polymerase (RNAP) from bacteriophage T7, as a model system to reveal mechano-chemical coupling and fidelity control in gene transcription (see our recent min review in 2019 and movies made from simulations of PPi release (steered),RNAP translocation (distributed equilibrium samplings), and cognate NTP incorporation (umbrella samplings)). Ongoing research includes studying DNA supercoiling as a feedback control in transcription.
We are further interested in comparatively studying DNA polymerases in replication (and in sequencing and synthetic approaches), the more complex and regulated transcription machine in higher organisms (e.g. RNAP II in front of nucleosome barrier) , and probing diverse protein machinery in genetic and epigenetic regulation.
Molecular coordination and cooperativity
In macromolecular assembly, coordination and cooperativity usually arise from local/ neighbor-neighbor interaction, e.g. via protein/DNA allostery or inter-subunit coupling. Long range correlation and impact may also reveal via large conformation rearrangements (e.g DNA looping or supercoiling) or inter-molecular movements (e.g. protein diffusion or shuffling).
We had studied ring-shaped protein machines such as F1-ATPase (Dai et al Biophys J 2017 ; see a movie of product Pi release in F1 upon neighbor-site ATP hydrolysis simulated in this study) and viral DNA packaging motor (Yu et al JMB 2010) that require multiple subunits to work sequentially to perform enzymatic and mechanical functions. It would be valuable to examine a variety of multi-subunit protein machinery and large protein-DNA assemblies to probe on multiple levels of molecular association, conformation propagation, and intracellular communication with hierarchical physical principles.
Protein search and recognition on DNA
The central dogma of molecular biology requires genetic information to be read out to propagate, with sufficiently high fidelity. Protein factors and machinery have accordingly evolved to achieve efficient sequence recognition via search and coordination along DNA, which is vital to maintain genome stability, integrity and heredity.
On top of existing theories and quantitative studies, we want to probe underlying physics of protein search and recognition on DNA by employing structure-based simulations and physical modeling. Ongoing and planned research include: all-atom simulation of a small transcription factor (TF) in diffusion, an RNAP at promotor initiation, and a Cas enzyme in foreign DNA capture; coarse-grained simulation on dimeric protein Myc-Max (or a recent publication), on large protein-DNA complexes and clustering of TFs; quantitative modeling that also incorporate experimental information from single molecule measurement, genome profiling, and lab directed evolution.