Deprotonated imidodiphosphate in AMPPNP-containing protein structures
Miroslawa Dauter1, Zbigniew Dauter
1Basic Research Program, SAIC-Frederick Inc., Argonne National Laboratory, Argonne, IL 60439, USA. dauter@anl.gov
Acta Crystallographica. Section D, Biological Crystallography
|November 29, 2011
Summary
Adenosine triphosphate (ATP) analogs like AMPPNP are crucial for protein function. Analysis shows the AMPPNP imide group can be deprotonated in protein complexes, challenging typical chemical properties.
Area of Science:
- Biochemistry
- Structural Biology
- Protein Science
Background:
- Proteins harness chemical energy from adenosine triphosphate (ATP) for function.
- Adenosine 5'-(β,γ-imido)triphosphate (AMPPNP) is a non-hydrolyzable ATP analog used in structural studies.
- The imide group in AMPPNP is typically protonated under physiological conditions due to its lack of acidity.
Purpose of the Study:
- To investigate the protonation state of the imide group in AMPPNP within protein complexes.
- To understand the structural and chemical factors influencing AMPPNP's behavior in protein binding sites.
Main Methods:
- Analysis of existing protein structures containing AMPPNP from the Protein Data Bank (PDB).
- Examination of interactions between AMPPNP and surrounding amino acid residues, including metal ions and arginine.
Main Results:
- The imide nitrogen of AMPPNP is found to be deprotonated in specific protein-ligand complexes.
- Deprotonation correlates with the presence of divalent metal ions or arginine residues that neutralize the negative charges of the phosphate groups.
Conclusions:
- The protonation state of AMPPNP is context-dependent within protein structures.
- Protein environments can alter the chemical properties of ATP analogs, influencing their interactions and function.
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