Guanidinium–amino acid hydrogen-bonding interactions in protein crystal structures: implications for guanidinium-induced protein denaturation

Abstract

In the present work, 86 available high resolution X-ray structures of proteins that contain one or more guanidinium ions (Gdm⁺) are analyzed for the distribution and nature of noncovalent interactions between Gdm⁺ and amino-acid residues. A total of 1044 hydrogen-bonding interactions were identified, of which 1039 are N–H⋯O, and five are N–H⋯N. Acidic amino acids are more likely to interact with Gdm⁺ (46% of interactions, 26% Asp and 20% Glu), followed by Pro (19% of interactions). DFT calculations on the identified Gdm⁺–amino acid hydrogen-bonded pairs reveal that although Gdm⁺ interacts primarily with the backbone amides of nonpolar amino acids, Gdm⁺ does interact with the sidechains of polar and acidic amino acids. We classified the optimized Gdm⁺–amino acid pairs into parallel [p], bifurcated [b], single hydrogen bonded [s] and triple hydrogen bonded [t] types. The [p] and [t] type pairs possess higher average interaction strength that is stronger than that of [b] and [s] type pairs. Negatively charged aspartate and glutamate residues interact with Gdm⁺ ion exceptionally tightly (−76 kcal mol⁻¹) in [p] type complexes. This work provides statistical and energetics insights to better describe the observed destabilization or denaturation process of proteins by guanidinium salts.