Selective molecular recognition of arginine by anionic salt bridge formation with bis-phosphate crown ethers: implications for gas phase peptide acidity from adduct dissociation

Abstract

Arginine forms a stable noncovalent anionic salt bridge complex with DP (a crown ether which contains two endocyclic dialkylhydrogenphosphate esters). Abundant adduct formation with DP is observed for complexes with arginine, YAKR, HPPGFSPFR, AAKRKAA, RR, RPPGF-SPFR, RYLGYL, RGDS, and YGGFMRGL in electrospray ionization mass spectrometry (ESI-MS) experiments. DFT calculations predict a hydrogen bonded salt bridge structure with a protonated guanidinium flanked by two deprotonated phosphates to be the lowest energy structure. Dissociation of DP/peptide adducts reveals that, in general, the relative gas phase acidity of a peptide is dependent on peptide length, with longer peptides being more acidic. In particular, peptides that are six residues or more in length can stabilize the deprotonated C-terminus by extensive hydrogen bonding with the peptide backbone. Dissociation of DP/peptide complexes often yields the deprotonated peptide, allowing for the facile formation of anionic peptides that otherwise would be difficult to generate in high abundance. Although DP has a preference for binding to arginine residues in peptides, DP is also observed to form less abundant complexes with peptides containing multiple lysines. Lys-Xxx-Lys and Lys-Lys sequences form low abundance anionic adducts with DP. For example, KKKK exclusively forms a double adduct with one net negative charge on the complex. T he development of methods that enable the rapid identification and characterization of proteins, especially those providing information relating to sequence, structure, and function, will facilitate new discoveries in the emerging field of proteomics [1,2,3]. Toward this goal, we have undertaken the development and systematic study of reagents that will selectively bind to peptides and proteins though specific noncovalent complexation of targeted amino acids both in solution and in the gas phase. For example, electrospray ionization (ESI) experiments employing 18-crown-6 ether (18C6) to form noncovalent complexes with lysine containing peptides and proteins have yielded valuable information about sequence and structure [4]. In these experiments, attachment of 18C6 to peptides yields quantitative information about the number of lysines present, whereas complexation with proteins reveals information about the tertiary structure and surface availability of lysine residues [4]. In a related work, 18C6 serves as a molecular scaffold for the attachment of a diazo functional group, yielding a reagent known as a "molecular mousetrap" because of its ability to convert noncovalent complexes into covalently bound molecules following appropriate activation to form a reactive carbene [5].Similar recognition of the side chain of arginine has been accomplished with larger crown ethers such as dibenzo-30-crown-10, which forms extensive hydrogen bonds with the protonated alkyl-guanidinium side chain of arginine [6]. Recognition of arginine can also be accomplished through the formation of salt bridges. A variety of solution phase reagents such...

A Simple and Robust Method for Determining the Number of Basic Sites in Peptides and Proteins Using Electrospray Ionization Mass Spectrometry

“…18-22,32 Addition of 18-crown-6-ether to solutions containing peptides and proteins results in preferential adduction to lysine although some binding to histidine, arginine, and the N-terminus also occurs. 20-22 Information about the number of lysine residues can be obtained for small peptides, but not all lysine residues are adducted with larger proteins, a result that has been attributed to solvent inaccessible residues.…”

Crown ethers attenuate aggregation of amyloid beta of Alzheimer's disease

“…Apart from their high affinities for alkali ions, crown ethers also could form stable complexes with protonated amines through hydrogen bonds, a property that has been adapted for various applications of crown ethers. Beauchamp et al, Julian et al, and others developed the SNAPP (selective non-covalent adduct protein probing) technique using crown ether to probe protein sequences, which is based on the selectivity of crown ethers towards basic amino acids such as lysine, arginine, and histidine [4] . Using theoretical electronic structure calculations, Chen et al recently demonstrated that crown ethers could form non-covalent complexes with lysine, arginine and histidine [5] .…”

How Important Is Molecular Rigidity for the Complex Stability of Artificial Host–Guest Systems? A Theoretical Study on Self‐Assembly of Gas‐Phase Arginine

“…The stronger stabilization of the MMFF structures does not only result from the differences in the bonding network between the guanidinium and carboxylate moieties, but also (8) 1.67 O(1)···HN (7), O(3)···HN (5) 2.12 N(10)···HN (9), N(11)···HN (12) 1.92 C(13)···C (14), C(15)···C (16) 3.22 MMFF2 O(1)···HN (5) 1.77 O(2)···HN (6) 1.68 O(1)···HN (7) 2.10 N(10)···HN (9) 1.91 C(13)···C (14) 3.26 O(3)···HN (7) 1.86 O(4)···HN (8) 1.63 O(3)···HN (5) 1.97 N(11)···HN (12) 1.86 C(15)···C (16) 3.57 MMFF4 O(1)···HN (5), O(3)···HN (7) 1.82 O(2)···HN(6), O(4)···HN (8) 1.66 O(1)···HN (7), O(3)···HN (5) 1.98 N(10)···HN (9), N(11)···HN (12) 1.86 C(13)···C (14), C(15)···C (16) 3.56 OPLS-AA1 O(1)···HN (5), O(3)···HN (7) 1.71 O(2)···HN(6), O(4)···HN (8) 1.67 O(1)···HN (7), O(3)···HN (5) 1.80 DZ1 O(1)···HN (5), O(3)···HN (7) 1.69 O(2)···HN(6), O(4)···HN (8) 1.71 O(1)···HN (7), O(3)···HN (5) 1.77 Figure 5. RI-MP2/TZVP optimised structures of zwitterionic arginine dimers.…”