Theses Doctoral

A Computational Approach to Rational Engineering of Protein Crystallization

Banayan, Nooriel Elan

X-ray crystallography is a popular method for resolving protein structures. Protein crystals need to be used for X-ray crystallography, but most naturally occurring proteins do not readily crystallize. The Hunt lab performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization.

To test this hypothesis, we developed software that ranks lysine sites in a target protein based on the redundancy-corrected KR substitution frequency in homologs. We demonstrate that three unrelated single-domain proteins can tolerate 5-11 KR substitutions with at most minor destabilization and that these substitutions consistently enhance crystallization propensity. This approach rapidly produced a 1.9 Å crystal structure of a human protein domain refractory to crystallization with its native sequence. Structures from bulk-KR-substituted domains show the engineered arginine residues frequently make high-quality hydrogen-bonds across crystal-packing interfaces.

We thus demonstrate that bulk KR substitution represents a rational and efficient method for probabilistic engineering of protein surface properties to improve protein crystallization. This stands in direct contrast to earlier work and dogmas that posited that surface entropy reduction was the clear path forward to crystallzing proteins. Arginine is a high-entropy sidechain, yet it helps drive protein crystallization.

To understand which structure and dynamical features of arginine give rise to crystal packing propensity, we performed 60 Molecular Dynamics (MD) simulations to measure the sidechain order parameter of arginine and compare it against crystal packing propensity. This work found that surface-exposed arginines with low order parameters are most likely to participate in crystal packing interactions. This is evidence against earlier thinking that high entropy surface sidechains oppose crystallization. Entropic barriers to protein crystallization can be enthalpically overcome.


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More About This Work

Academic Units
Biological Sciences
Thesis Advisors
Hunt, John F.
Ph.D., Columbia University
Published Here
September 27, 2023