Nearest-neighbor-model_2022

Introduction

This is the collections of data fitting scripts in the paper of Li, Weicheng, Norris, Andrew N, et al, Protein science (2022).

It includes the scripts of:

1. Quadratic curve fitting for CD binding data (Fig 3a)
2. One-site binding model fitting for ITC titration data via itcsimlib (Fig 3b)
3. Quadratic curve fitting for concentration correction (Fig S6)
4. NN model simulations of bound population distributions via itcsimlib (Fig 2b)
5. NN model simulations of bound fractional saturations via itcsimlib (Fig 2c)
6. NN model data fitting of native Mass Spectra (nMS) titration via itcsimlib (Fig 4b)
7. NN model predictions of cellular protein saturations via itcsimlib (Fig 5c)

Note: itcsimlib is the python module that helps to fit the thermodynamic binding data via statistical mechanics model. The statistical thermodynamic model can be easily self-designed and automatically computed and displayed in itcsimlib.

More scripts will be updated in the future. Feel free to comment here or contact me.

Requirements

• numpy
• scipy
• matplotlib
• sympy
• pyx
• itcsimlib

Acknowledging

I hope this work could potentially inspire or accelerate your research. If it does, please consider cite the following paper:

1. Li, Weicheng, Norris, Andrew N. et al. "Thermodynamic coupling between neighboring binding sites in homo-oligomeric ligand sensing proteins from mass resolved ligand-dependent population distributions." Protein Science (2022) https://doi.org/10.1002/pro.4424

If itcsimlib was used to help your work efforts, please also consider cite the following paper:

2. Ihms, Elihu C. et al. "Mechanistic models fit to variable temperature calorimetric data provide insights into cooperativity.” Biophysical Journal (2017) https://doi.org/10.1016/j.bpj.2017.02.031