2 research outputs found
Orchestration of Structural, Stereoelectronic, and Hydrogen-Bonding Effects in Stabilizing Triplexes from Engineered Chimeric Collagen Peptides (Pro<sup>X</sup>âPro<sup>Y</sup>âGly)<sub>6</sub> Incorporating 4(<i>R</i>/<i>S</i>)âAminoproline
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
analoguesî¸chimeric cationic collagensî¸wherein both X-
and Y-sites in collagen triad are simultaneously substituted by a
combination of 4Â(<i>R</i>/<i>S</i>)-(OH/NH<sub>2</sub>/NH<sub>3</sub><sup>+</sup>/NHCHO)-prolyl units and triplex
stabilities measured at different pHs and in EG:H<sub>2</sub>O. 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 â
Ď* interactions in dictating the triplex strength. The ionizable
NH<sub>2</sub> 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 HIVâ1 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 âF43
pocketâ of gp120 in a bridging sheet naiĚve gp120 conformation
of the glycoprotein led to a stable complex. This pose prevents formation
of the bridging sheet minidomain, which is required for receptorâcoreceptor
binding, providing a mechanistic basis for dual-site antagonism of
this class of inhibitors. Burial of the peptide triazole at the gp120
inner domainâouter 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)Âpyrrolidine]
tripartite hydrophobic motif in the peptide is the major contributor
of contacts at the gp120âPT interface. Because the model predicts
that the peptide Trp side chain hydrogen bonding with gp120 S375 contributes
to the stability of the PTâgp120 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 PTâgp120 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