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Proton paths in biological systems: Composition, stability, and requirements for transmitting protons

EMSL Project ID


Using structures from known proton transmitters, we will calculate, using DFT, the energy for successive proton positions, the bonding with the protons in these positions, and the charges on the relevant atoms. The calculations will start from plausible proton positions, optimizing these to find local energy minima, to be followed by single point calculations at a high level to obtain the properties of the system with the proton in that local minimum. The aim is to find a path that allows the proton to proceed without a major energy barrier, to find configurations that can be part of such paths, determine whether there are general properties found in configurations in proton paths. For proton paths that contain water as part of the path, hydrogen bonded to protein atoms, determine the stability of the water binding. If there is water solvating the protein, determine the probability of the water exchanging, and the time scale. The latter may have to be found from the energy of activation of a reaction that replaces the exchangeable water. If two water molecules are required to complete a path, determine the same parameters, and determine the fraction of time that the chain would be complete, if the water is not firmly bound. We plan to carry out density functional calculations on a large enough set of hydrogen bonded systems to obtain all this information, including, for example, ion channels, from relevant plants and fungi. Certain bacterial structures are also known, and would also be relevant. We plan to understand the driving forces for proton transport, and the nature of linkages that are required for stability; when water molecules are involved, the fraction of time that the path is in the correct conformation to conduct must be determined; two water molecules can be linked to complete a chain and this will require further study. We will require additional work to determine the activation energy for each step in the path. The activation energy is important to determine the kinetics. While experimental work can give the largest activation energy in a path, it is probably necessary to do a complete calculation to get each step; this in turn is necessary to understand the way in which protons can be transferred. We expect to determine the requirements for a coherent proton path in plants and fungi, and possibly some bacteria. It is necessary to find whether there exists a consistent pattern in all of these paths; our expectation is that there is, but it remains to be proven.

Project Details

Project type
Exploratory Research
Start Date
End Date


Principal Investigator

Michael Green
City College of New York


Alisher Kariev
City College of New York