A new structural arrangement in proteins involving lysine NH3+ group and carbonyl.

ABSTRACT: Screening of the Protein Data Bank led to identification of a recurring structural motif where lysine NH3+ group interacts with backbone carbonyl. This interaction is characterized by linear atom arrangement, with carbonyl O atom positioned on the three-fold symmetry axis of the NH3+ group (angle C?-N?-O close to 180°, distance N?-O ca. 2.7-3.0?Å). Typically, this linear arrangement coexists with three regular hydrogen bonds formed by lysine NH3+ group (angle C?-N?-acceptor atom close to 109°, distance N?-acceptor atom ca. 2.7-3.0?Å). Our DFT calculations using polarizable continuum environment suggest that this newly identified linear interaction makes an appreciable contribution to protein's energy balance, up to 2?kcal/mol. In the context of protein structure, linear interactions play a role in capping the C-termini of ?-helices and 310-helices. Of note, linear interaction involving conserved lysine is consistently found in the P-loop of numerous NTPase domains, where it stabilizes the substrate-binding conformation of the P-loop. Linear interaction NH3+ - carbonyl represents an interesting example of ion-dipole interactions that has so far received little attention compared to ion-ion interactions (salt bridges) and dipole-dipole interactions (hydrogen bonds), but nevertheless represents a distinctive element of protein architecture.

SUBMITTER: Rogacheva ON 

PROVIDER: S-EPMC5704018 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature