curp 3.0

Inter-residue Current calculation in Proteins from MD trajectory

CURP permits to compute inter-residue flow of energy or heat and atomic stress tensors(*) in a protein, given atomic coordinates and velocity trajectories obtained through molecular dynamics (MD). Energy flow data permit to picture an inter-residue Energy Exchange Network as a graph.

Within thermally fluctuating protein molecules under physiological conditions, tightly packed amino acid residues interact with each other through heat and energy exchanges. Non-uniform pattern of heat flow in proteins are illustrated and characterized with a theoretical model based on “local heat conductivity” between each residue pair. This model demonstrated characteristic features of “hidden dynamic allostery” in PDZ domain [1] and allosteric transition in the oxygen sensor domain of FixL [2]. Also we applied it to a small protein to understand the features of local thermal transport of protein [3] [4] [5].

Offical website and tutorial can be found at https://curp.jp/.

(*) NOTE: CURP does not support atomic stress calculations on and after version 1.3.

Installation

CURP requires Python3.6 with numpy to work. You can install python here, or anaconda there.

Install CURP via pip

pip install curp

Get CURP from source code

You can get the source code from this repository and build by running following command.

git clone https://github.com/yamatolab/current-calculations-for-proteins.git
cd current-calculations-for-proteins
pip install .

Development

Please read DEVELOP.rst before starting to develop CURP.

References

[1]

Ishikura, T.; Iwata, Y.; Hatano, T.; Yamato, T. Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study. J. Comput. Chem. 2015, 36:1709-1718

[2]

Ota, T.; Yamato, T. Energy Exchange Network Model Demonstrates Protein Allosteric Transition: An Application to an Oxygen Sensor Protein. J. Phys. Chem. B 2019, 123:768-775

[3]

Yamato, T.; Wang, T.; Sugiura, W.; Laprévote, O.; Katagiri, T. Computational study on the thermal conductivity of a protein. J. Phys. Chem. B 2022, 126:3029-3036

[4]

Wang, T.; Yamato, T.; Sugiura, W; Site-selective heat current analysis of α-helical protein with linear-homopolymer-like model. J. Phys. Chem. B 2023, 158

[5]

Wang, T.; Yamato, T.; & Sugiura, W. Thermal Energy Transport through Nonbonded Native Contacts in Protein. J. Phys. Chem. B 2024