Replication Data for: Short- and long-range crowding effects on water’s hydrogen bond networks

Data for manuscript: Short- and long-range crowding effects on water’s hydrogen bond networks, Cell Reports Physical Science.

Authors: Xiao You, Joseph C. Shirley, Euihyun Lee, Carlos R. Baiz
Department of Chemistry, University of Texas at Austin, Austin, TX 78757, USA
email: [e-mail]

Intracellular water is highly confined with approximately 40% of the cell volume occupied by biomolecules. Crowding alters water dynamics and interactions with biomolecules. In biochemical experiments, artificial crowders are commonly used to mimic intracellular environments, but their effects on biomolecules remain elusive. Here, we investigate the crowding effects by directly accessing the picosecond hydrogen-bond dynamics in crowded solutions using ultrafast two-dimensional infrared spectroscopy and all-atom molecular dynamics simulations. We quantify the effects of different crowding agents: small sugars, polysaccharides, and polyethylene glycol (PEG). Our results show that crowders introduce disorder within the first two solvation shells but stabilize ice-like order in water >1 nm from the crowder. The results show that accounting for crowder chemical structure, conformation, and crowder-solvent interactions is a key step towards a complete description of crowded solutions for in vitro for biomolecular studies.

Main folder contains the following subfolders:
.\NaSCN_H2O_2DIR_anisotropy
.\NaSCN_Dextrose_2DIR_anisotropy
.\NaSCN_Sucrose_2DIR_anisotropy
.\NaSCN_Dextran_2DIR_anisotropy
.\NaSCN_Ficoll70_2DIR_anisotropy
.\NaSCN_PEG600_2DIR_anisotropy
.\NaSCN_PEG1500_2DIR_anisotropy
.\NaSCN_H2O_reproduce_2DIR_anisotropy
Each of them contains the raw data in .mat format, such as 'NaSCN in H2O.mat'
Each folder contains the NLS analysis of each data set, such as 'NaSCN in H2O_NLS.mat'
The plots generated from Matlab analysis are also included in each folder.

Folder MD simulation contains four subfolders:
.\MD_raw_data contains all the pdb files from MD simulation
As described in '_naming.txt':
AGLC0_4PEW... represents water
AGLC160_4PEW... represents glucose water solution
SUCR84_4PEW... represents sucrose water solution
LINDEX9_4PEW... represents dextran water solution
SwiFC15_4PEW... represents Ficoll water solution
PEG1063_4PEW... represents PEG n = 10 water solution
PEG3518 _4PEW... represents PEG n =35 water solution

.\Hbond_Analysis contains all the data analysis that results in the plots of H-bond population, order parameters and their distributions in each system
- Data type is .mat and .fig files for use with matlab

.\FFCF stands for frquency-frequency-correlation-function, contains all the data analysis that results in the simulated dacay time
- Data type is .mat and .fig files for use with matlab
-'_description.txt' contains the data analysis inputs and parameters

.\Mean_Square_Displacement contains the data for calculating Mean Square Displacement.
- Data type is .mat files for use with matlab
-'_description.txt' includes the data analysis inputs and parameters