Ligand‐induced transition in conformations of vicinal cysteine disulfides in proteins

Abstract

Vicinal cysteine disulfides are thought to be associated with specific conformations of cysteine disulfides due to the restricted rotation of single bonds in an eightmembered cyclic disulfide loop. Conformations of vicinal cysteine disulfides are analyzed using χ 1 , χ 2 , χ 3 , χ 2 ', χ 1 ' torsion angles in the crystal structures of proteins retrieved from Protein Data Bank (PDB). 85% of vicinal disulfides have (+, −)LHStaple conformation with trans configuration of the peptide bond and 9% have (−, −) RHStaple conformation with cis configured peptide bond. Conformational analysis of dipeptide Cys-Cys vicinal disulfide by density functional theory (DFT) further supported (+, −)LHStaple, (−, −)RHStaple, and (+, +)RHStaple as the preferred conformations of vicinal disulfides. Interestingly, the rare conformations of vicinal disulfides are observed in the ligand-bound forms of proteins and have higher disulfide strain energy. Conformations of vicinal disulfides in palmitoyl protein thioesterase 1, AChBP, and α7 nicotinic receptor are changed from preferred (+, −)LHStaple to rare (+, −)AntiLHHook/(+, −)AntiRHHook/(+, +)RHStaple conformation due to binding of ligands. Surprisingly, ligands are proximal to the vicinal disulfides in protein complexes that exhibited rare conformations of vicinal disulfides. The report has identified (+, −) LHStaple/(−, −) RHStaple as the hallmark conformations of vicinal disulfides and unraveled ligand-induced transition in conformations of vicinal cysteine disulfides in proteins. K E Y W O R D S conformation, crystal structure of proteins, ligand, Protein Data Bank, vicinal cysteine disulfide | INTRODUCTIONVicinal cysteine disulfide is the smallest intramolecular disulfide loop in proteins with a cyclic eight-membered ring containing either cis (or) trans configured peptide bond. [1][2][3][4] The formation of the disulfide bond between adjacent cysteine residues in the sequence results in a vicinal disulfide which is a rare, hydrophobic, and unique structural motif in polypeptide. [5][6][7][8] The constrain imposed due to ring size may restrict free rotation of side-chain single bonds of vicinal disulfide limiting their conformational space. 4,9 The restricted rotations may enforce vicinal disulfide to accommodate specific conformations of disulfides which may serve as hallmark conformations of vicinal cysteine disulfides. Structural disulfides are associated with -LHSpiral, catalytic disulfides with +/-RHHook and allosteric disulfide with -RHStaple/-LHStaple conformation. [10][11][12] Similarly, vicinal cysteine disulfides can also be mapped with the specific conformations of Abbreviations: +/−, positive/negative torsion angle; AChBP, acetyl choline binding protein; DSE, disulfide strain energy (or) dihedral strain energy; LH/RH, left-handed/right-handed; PDB, Protein Data Bank.

Accurate Free Energies for Complex Condensed-Phase Reactions Using an Artificial Neural Network Corrected DFTB/MM Methodology

“…The higher values correspond to the two reactions that lead to a vicinal disulfide bond between the adjacent cysteines S78 and S79. Vicinal disulfides constitute the smallest possible intramolecular disulfide loops, which experience a high steric strain due to their small ring size. , Thus, a higher barrier has to be overcome to form the bond S78–S79, which also lies higher in energy than the other two disulfide bonds, S36–S78 and S79–S36. All other investigated thiol–disulfide exchange reactions have barriers around 9 kcal/mol.…”

Complete amide cis–trans switching synchronized with disulfide bond formation and cleavage in a proline-mimicking system

“…3(c) box). 6,[17][18][19] We have found that the amide in the fused bicyclic pyrrolidine ring (5), that is, a bicyclic proline skeleton bearing a bridgehead substituent, forms exclusively a trans-amide structure, despite being a tertiary amide (Fig. 1(d)).…”

“…However, the vicinal disulfide ring conformations in proteins often undergo conformational change in response to nearby ligand binding, and this can generate rare and highly strained conformations such as trans-(+, -)AntiRHHook, which has (χ 1 , χ 2 , χ 3 , χ 2' , χ 1' ) = (+,-,+,+,-) (see Figure 3c box). 6,17,18,19 We have found that the amide in the fused bicyclic pyrrolidine ring (5), that is, a bicyclic proline skeleton bearing a bridgehead substituent, takes exclusively trans-amide structure, despite being a tertiary amide (Figure 1d). 20,21 These results inspired us to consider molecules with a similar bicyclic skeleton, in which the amide isomerism might be switched from exclusively trans to exclusively cis and vice versa, concomitantly with disulfide ring formation and cleavage, respectively.…”

“…In particular, the formation and cleavage of a disulfide bond between the side-chains of two cysteine residues in a peptide or protein are considered to synchronize with the trans-cis conversion of amides in the main-chain, which would cause conformational switching of the whole molecule. [6][7][8][9][10] However, this is not the case (see below).…”

“…residues (1), generating an 8-membered lactam ring (2) called a vicinal disulfide ring (VDR), upon oxidative disulfide bond formation (Figure 1a). 6,7,9,11,12 While 1 has trans-amide structure, the Cys-Cys disulfide (2) has various conformers with respect to the amide trans-cis isomerism as well as disulfide ring conformations, due to ring strains arising from the long C-S (1.8Å) and S-S (2.0Å) bonds and acute dihedral angle (∠CSSC: 85°). 13 14 Indeed, the Cys-Cys disulfide ( 2) is known to change its conformation depending on the protein environment.…”