513 citations · 1k across the 21 of their papers we have counts for
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Understanding Protein-Complex Assembly through Grand Canonical Maximum Entropy Modeling
Andrei G. Gasic, Atrayee Sarkar, Margaret S. Cheung
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putativ…
Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif
Pengzhi Zhang, Jaebeom Han, Piotr Cieplak +1
It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding a…
A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior Under High Hydrostatic Pressure
Andrei G. Gasic, Margaret S. Cheung
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from…
Critical phenomena in the temperature-pressure-crowding phase diagram of a protein
Andrei G. Gasic, Mayank M. Boob, Maxim B. Prigozhin +4
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to…
Crowding-induced Elongated Conformation of Urea-unfolded Apoazurin: Investigating the Role of Crowder Shape In Silico
Fabio C. Zegarra, Dirar Homouz, Andrei G. Gasic +4
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present…
The impact of hydrodynamic interactions on protein folding rates depends on temperature
Fabio C. Zegarra, Dirar Homouz, Yossi Eliaz +2
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it acce…