Orchestration of Structural, Stereoelectronic, and Hydrogen-Bonding Effects in Stabilizing Triplexes from Engineered Chimeric Collagen Peptides (Pro^X‑Pro^Y‑Gly)₆ Incorporating 4(<i>R</i>/<i>S</i>)‑Aminoproline

Collagens are an important family of structural proteins found in the extracellular matrix with triple helix as the characteristic structural motif. The collagen triplex is made of three left-handed polyproline II (PPII) helices with each PPII strand consisting of repetitive units of the tripeptide motif X-Y-Gly, where the amino acids X and Y are most commonly proline (Pro) and 4<i>R</i>-hydroxyproline (Hyp), respectively. A C4-<i>endo</i> pucker at X-site and C4-<i>exo</i> pucker at Y-site have been proposed to be the key for formation of triplex, and the nature of pucker is dependent on both the electronegativity and stereochemistry of the substituent. The present manuscript describes a new class of collagen analogueschimeric cationic collagenswherein both X- and Y-sites in collagen triad are simultaneously substituted by a combination of 4­(<i>R</i>/<i>S</i>)-(OH/NH₂/NH₃⁺/NHCHO)-prolyl units and triplex stabilities measured at different pHs and in EG:H₂O. Based on the results a model has been proposed with the premise that any factors which specifically favor the ring puckers of C4-<i>endo</i> at X-site and C4-<i>exo</i> at Y-site stabilize the PPII conformation and hence the derived triplexes. The pH-dependent triplex stability uniquely observed with ionizable 4-amino substituent on proline enables one to define the critical combination of factors C4-(<i>exo</i>/<i>endo</i>), intraresidue H-bonding, stereoelectronic (<i>R</i>/<i>S</i>) and n → π* interactions in dictating the triplex strength. The ionizable NH₂ substituent at C4 in <i>R</i>/<i>S</i> configuration is thus a versatile probe for delineating the triplex stabilizing factors and the results have potential for designing of collagen analogues with customized properties for material and biological applications

A Model of Peptide Triazole Entry Inhibitor Binding to HIV‑1 gp120 and the Mechanism of Bridging Sheet Disruption

Peptide triazole (PT) entry inhibitors prevent HIV-1 infection by blocking the binding of viral gp120 to both the HIV-1 receptor and the coreceptor on target cells. Here, we used all-atom explicit solvent molecular dynamics (MD) to propose a model for the encounter complex of the peptide triazoles with gp120. Saturation transfer difference nuclear magnetic resonance (STD NMR) and single-site mutagenesis experiments were performed to test the simulation results. We found that docking of the peptide to a conserved patch of residues lining the “F43 pocket” of gp120 in a bridging sheet naïve gp120 conformation of the glycoprotein led to a stable complex. This pose prevents formation of the bridging sheet minidomain, which is required for receptor–coreceptor binding, providing a mechanistic basis for dual-site antagonism of this class of inhibitors. Burial of the peptide triazole at the gp120 inner domain–outer domain interface significantly contributed to complex stability and rationalizes the significant contribution of hydrophobic triazole groups to peptide potency. Both the simulation model and STD NMR experiments suggest that the I-X-W [where X is (2<i>S</i>,4<i>S</i>)-4-(4-phenyl-1<i>H</i>-1,2,3-triazol-1-yl)­pyrrolidine] tripartite hydrophobic motif in the peptide is the major contributor of contacts at the gp120–PT interface. Because the model predicts that the peptide Trp side chain hydrogen bonding with gp120 S375 contributes to the stability of the PT–gp120 complex, we tested this prediction through analysis of peptide binding to gp120 mutant S375A. The results showed that a peptide triazole KR21 inhibits S375A with 20-fold less potency than WT, consistent with predictions of the model. Overall, the PT–gp120 model provides a starting point for both the rational design of higher-affinity peptide triazoles and the development of structure-minimized entry inhibitors that can trap gp120 into an inactive conformation and prevent infection