Tertiary structure is a principal determinant to protein deamidation

Area of Science:

• Protein chemistry and structural biology
• Biochemical modifications and post-translational modifications

Background:

• Protein deamidation involves converting asparagine and glutamine amide side chains to carboxyl groups.
• This modification is an intramolecular reaction requiring specific residue proximity.
• Previous studies suggested residue flanking influenced deamidation, but lacked direct structural evidence.

Purpose of the Study:

• To investigate the stereochemical factors governing protein deamidation.
• To identify specific structural features of deamidated residues using high-resolution structural data.
• To determine if flanking residue character correlates with deamidation propensity.

Main Methods:

• Utilized neutron crystallography of trypsin to obtain high-resolution structural data.
• Leveraged the distinct neutron scattering properties of amide groups and oxygen for unambiguous differentiation.
• Analyzed the local conformation and hydrogen-bonding patterns of asparagine residues.

Main Results:

• Identified 3 out of 13 asparagine residues in trypsin as deamidated.
• Deamidated asparagine residues exhibited distinct local conformations and hydrogen-bonding structures compared to unmodified ones.
• No correlation was found between deamidation preference and the chemical nature of adjacent residues.

Conclusions:

• Protein deamidation is associated with specific local structural and hydrogen-bonding environments.
• The stereochemistry and local conformation, rather than flanking residue character, appear critical for deamidation.
• Neutron crystallography provides a powerful tool for studying subtle protein modifications like deamidation.