Source: Interfolio F180

Ashok Deniz

Department of Integrative Structural and Computational Biology


Research Focus

Our research is broadly focused around deriving fundamental physical rules governing the properties of complex protein, RNA and other biopolymers at a range of spatial and time scales, with deep implications for biology and disease. We study these fascinating molecular species and tunable materials they can assemble into, and also develop state-of-the-art single-molecule and other biophysical tools for this purpose.

One research focus is on Intrinsically Disordered Proteins (IDPs). While many proteins have well-defined 3-dimensional structures, IDPs have stretches of flexible sequence. IDPs are prevalent in proteomes, and their physics can play key roles in many cellular functions. Our single-molecule studies have shed light on the tunable nature of IDP structural landscapes, with implications for function and diseases such as Parkinson's and Alzheimer's diseases.

We also have a strong interest in understanding the basic biophysics of larger structures that RNA and proteins can assemble into in cells, specifically dynamic structures known as condensates or membraneless organelles. Such structures (well known examples are the nucleolus and stress granules) can have a range of material properties (liquid-like, viscoelastic, solid) as well as complex structural features that are believed to be mechanistically key in the dynamics and functions in cells.

We also develop and use single-molecule fluorescence methods to address key issues in molecular and cell biology. Single-molecule methods provide unprecedented views of structural and dynamic complexity in proteins and other biological macromolecules, allowing us to directly test biological models and theories.

Read News-Medical interview on some of our lab’s emerging research directions, including the effects of 2D-crowding on folding of a Parkinson’s disease-linked IDP.

Scientists "Watch" as Individual Alpha-Synuclein Proteins Change Shape

Researchers Observe Single Protein Dimers Wavering Between Two Symmetrically Opposed Structures

Scripps Research Study Reveals Structural Dynamics of Single Prion Molecules

Scientists Develop Method to Identify Fleetingly Ordered Structures from Intrinsically Disordered Protein


Ph.D. ((Physical Organic) Chemistry), The University of Chicago, 1996
M.S. (Chemistry), University of Chicago, 1994
M.S. (Chemistry), Indian Institute of Technology, 1990
B.S. (Chemistry), St.Xavier's College (University of Bombay), 1988

Professional Experience

2000-2007 Assistant Professor, Scripps Research
2007-2021 Associate Professor, Scripps Research
2021-Present Professor, Scripps Researchw

Awards & Professional Activities

2016 TSRI Outstanding Mentor Award
Meenal Dinkar Rao Mugve Scholarship, Chemistry, St. Xavier's College
1985 Rustomjee Byramjee Jeejeebhoy Colgen Jubilee Prize, Physics, St. Xavier's College

Selected Publications

Banerjee, P. R.; Moosa, M. M.; Deniz, A. A. Two-dimensional crowding uncovers a hidden conformation of a-synuclein. Angewandte Chemie-International Edition 2016, 55, 12789-12792.

Ferreon, A. C.; Ferreon, J. C.; Wright, P. E.; Deniz, A. A. Modulation of allostery by protein intrinsic disorder. Nature 2013, 498, 390-394.

Banerjee, P. R.; Mitrea, D. M.; Kriwacki, R. W.; Deniz, A. A. Asymmetric Modulation of Protein Order-Disorder Transitions by Phosphorylation and Partner Binding. Angewandte Chemie 2015, 55, 1675-1679.

Polinkovsky, M. E.; Gambin, Y.; Banerjee, P. R.; Erickstad, M. J.; Groisman, A.; Deniz, A. A. Ultrafast cooling reveals microsecond-scale biomolecular dynamics. Nature Communications 2014, 5, 5737.

Gambin, Y.; VanDelinder, V.; Ferreon, A. C.; Lemke, E. A.; Groisman, A.; Deniz, A. A. Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. Nature Methods 2011, 8, 239-241.

Mukhopadhyay, S.; Krishnan, R.; Lemke, E. A.; Lindquist, S.; Deniz, A. A. A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proceedings of the National Academy of Sciences of the United States of America 2007, 104, 2649-2654.