Biopolymers exhibit structure and function at the individual protein level and at the scale of assemblies such as filaments and assemblies of filaments. We are interested in how (i) intrinsic disorder (ii) chirality and (iii) surface interactions are responsible for function in protein biopolymers.
At the molecular level, we have studied, for example, using explicit atomically detailed computer simulations protein filaments such as FtsZ which aid in bacterial cell division and we have shown that flexibility in the protein can produce mechanical forces. Geometric incompatibility between such filaments and the surfaces to which they bind can also result in novel physics including geometry controlled switching of protein filament conformations .
Intrinsically disordered proteins can extract function from entropy. Entropically driven processes such as translocation are important for disordered proteins and are sensitive to the surrounding geometry and crowding. Intrinsic disorder also plays a role in events at the cellular level such as the transport of cargo from the nucleus to cytoplasm and vice versa through the nuclear pore complex - one of the biggest macromolecular gates in your bodies made of hundreds of proteins. We have shown, using appropriately coarse-grained simulations and analytical theory that interactions between the cargo and a higher order organization of the proteins in the pore can lead to the opening and closing of the pore, pointing to a novel way of gating channels.
Representative papers on some of these topics are below:
"Cooperative interactions between different classes of disordered proteins play a functional role in the nuclear pore complex of Baker’s yeast", D. Ando, A. Gopinathan, PLoS ONE 12(1): e0169455 (2017)
"Shape selection of surface-bound helical filaments: biopolymers on curved membranes" D. A. Quint, A. Gopinathan and G. M. Grason, Biophysical Journal 111, 1575 (2016).
"Nuclear Pore Complex Protein Sequences Determine Overall Copolymer Brush Structure and Function",D Ando, R Zandi, YW Kim, M Colvin, M Rexach, A Gopinathan, Biophysical Journal 106 (9), 1997 (2014)
"Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features", D Ando, M Colvin, M Rexach, A Gopinathan, PloS one 8 (9), e73831 (2013)
"Mechanical Consequences of Cell-Wall Turnover in the Elongation of a Gram-Positive Bacterium", G Misra, ER Rojas, A Gopinathan, KC Huang, Biophysical journal 104 (11), 2342-2352 (2013)
"Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations" , Jen Hsin, Ajay Gopinathan and K.C. Huang, Proc. Natl. Acad. Sci. USA, 109 (24): 9432 (2012)
"Conformational collapse of surface-bound helical filaments" David Quint, Ajay Gopinathan and Greg Grason, Soft Matter 8 (36), 9460-9468 (2012)
"Modeling the formation of in vitro filopodia", K.-C. Lee, Ajay Gopinathan, J. M. Schwarz, Journal of Mathematical Biology 63(2), 229 (2011)
“A Bimodal Distribution of Two Distinct Categories of Natively Unfolded Structures with Separate Functions in FG Nucleoporins”, Justin Yamada; Joshua L Phillips; Samir Patel; Gabriel Goldfien; Alison Calestagne-Morelli; Hans Huang; Ryan Reza; Justin Acheson; Viswanathan Krishnan; Shawn Newsam; Ajay Gopinathan; Edmond Y Lau; Michael Colvin; Vladimir N Uversky; Michael F Rexach, Molecular and Cellular Proteomics (2010) doi:10.1074/mcp.M000035-MCP201
“Polymer Translocation in Crowded Environments”, Ajay Gopinathan and Y.W. Kim, Phys. Rev. Lett., 99, 228106 (2007)
“Branching, Capping, and Severing in Dynamic Actin Structures”, Ajay Gopinathan, J. Schwarz, K.C. Lee and A.J. Liu, Phys. Rev. Lett., 99, 058103 (2007)
“Dynamics of Membranes Driven by Actin Polymerization”, Nir Gov, and Ajay Gopinathan, Biophys .J , 90(2), 454 (2006)