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Comparative Analysis of Protein Surface Hydrophobicity Maps Determined by Sparse Sampling INDUS and Spatial

Imee Sinha¹, Shekhar Garde¹, Steven M Cramer¹

¹Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States of America.

The Journal of Physical Chemistry. B

|November 22, 2023

Summary

Protein surface hydrophobicity is complex, influenced by water

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Area of Science:

Biophysics
Computational Biology
Protein Science

Background:

Protein surface hydrophobicity is critical for biological processes like folding and aggregation.
It also impacts biotherapeutic design and manufacturing.
Previous understanding linked hydrophobicity to residue hydropathies, but water's response is key.

Purpose of the Study:

To map protein surface hydrophobicity using water density perturbations.
To compare a novel sparse indirect umbrella sampling (SSI) method with the spatial aggregation propensity (SAP) technique.
To identify discrepancies between SSI and SAP and understand their causes.

Main Methods:

Employed sparse indirect umbrella sampling (SSI) simulations.
Used water density perturbations to map hydrophobicity.
Compared SSI results with the spatial aggregation propensity (SAP) technique for model proteins.

Main Results:

SSI and SAP methods showed agreement in some cases but significant disagreements in others.
Identified four classes of differing behavior between the two methods.
Found SAP can mask effects of weakly nonpolar or isolated residues, and shift patch position/strength.

Conclusions:

Protein surface hydrophobicity depends on topography and chemical context, not just residue polarity.
Accurate hydrophobicity maps and new descriptors can improve in silico prediction of protein behavior.
Enhanced prediction capabilities benefit protein design, biomanufacturability, and bioprocessing.