Biology subjects

Yap, G. P. A.

Publications and source records attributed to Yap, G. P. A..

3 recordsLinked to original sources

bioRxiv2025

Structural Basis for HIV-1 Maturation Inhibition by PF-46396 Determined by MAS NMR

Among the different types of HIV-1 maturation inhibitors, those that stabilize the junction between the capsid protein C-terminal domain (CACTD) and the spacer peptide 1 (SP1) within the immature Gag lattice are promising candidates for antiretroviral therapies. Here, we report the atomic- resolution structure of CACTD-SP1 assemblies with the small-molecule maturation inhibitor PF- 46396 and the assembly cofactor inositol hexakisphosphate (IP6), determined by magic angle spinning (MAS) NMR spectroscopy. Our results reveal that although the two PF-46396 enantiomers exhibit distinct binding modes, they both possess similar anti-HIV potency. PF-46396 binding arrests IP6 dynamics in the six-helix bundle pore, and the two enantiomers induce unique IP6 orientations in the pore. Importantly, our data suggest the presence of monoanionic IP6 form IP6 in the complex. Our study establishes the structural basis for PF-46396 action and suggests a mechanistic model for drug resistance.

biophysics↗

bioRxiv2024

Helical Twists and beta-Turns in Structures at Serine-Proline Sequences: Stabilization of cis-Proline and type VI beta-turns via C-H/O interactions

Structures at serine-proline sites in proteins were analyzed using a combination of peptide synthesis with structural methods and bioinformatics analysis of the PDB. Dipeptides were synthesized with the proline derivative (2S,4S)-(4-iodophenyl)hydroxyproline [hyp(4-I-Ph)]. The crystal structure of Boc-Ser-hyp(4-I-Ph)-OMe had two molecules in the unit cell. One molecule exhibited cis-proline and a type VIa2 {beta}-turn (BcisD). The cis-proline conformation was stabilized by a C-H/O interaction between Pro C-H and the Ser side-chain oxygen. NMR data were consistent with stabilization of cis-proline by a C-H/O interaction in solution. The other crystallographically observed molecule had trans-Pro and both residues in the PPII conformation. Two conformations were observed in the crystal structure of Ac-Ser-hyp(4-I-Ph)-OMe, with Ser adopting PPII in one and the {beta} conformation in the other, each with Pro in the {delta} conformation and trans-Pro. Structures at Ser-Pro sequences were further examined via bioinformatics analysis of the PDB and via DFT calculations. Ser-Pro versus Ala-Pro sequences were compared to identify bases for Ser stabilization of local structures. C-H/O interactions between the Ser side-chain O{gamma} and Pro C-H were observed in 45% of structures with Ser-cis- Pro in the PDB, with nearly all Ser-cis-Pro structures adopting a type VI {beta}-turn. 53% of Ser- trans-Pro sequences exhibited main-chain C=Oi***H-Ni+3 or C=Oi***H-Ni+4 hydrogen bonds, with Ser as the i residue and Pro as the i+1 residue. These structures were overwhelmingly either type I {beta}-turns or N-terminal capping motifs on -helices or a 310-helices. These results indicate that Ser-Pro sequences are particularly potent in favoring these structures. In each, Ser is in either the PPII or {beta} conformation, with the Ser O{gamma} capable of engaging in a hydrogen bond with the amide N-H of the i+2 (type I {beta}-turn or 3 -helix; Ser{chi} 1 t) or i+3 (-helix; Ser{chi} 1 g+) residue. Non-proline cis amide bonds can also be stabilized by C-H/O interactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/585129v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1b84fdorg.highwire.dtl.DTLVardef@b81090org.highwire.dtl.DTLVardef@47636forg.highwire.dtl.DTLVardef@d12a4d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Table of ContentsC_FLOATNO C_FIG

biophysics↗

bioRxiv2020

An Inherent Structural Difference Between Serine and Threonine Phosphorylation: Phosphothreonine Prefers an Ordered, Compact, Cyclic Conformation

Phosphorylation and dephosphorylation of proteins by kinases and phosphatases are central to cellular responses and function. The structural effects of serine and threonine phosphorylation were examined in peptides and in proteins, by circular dichroism, NMR spectroscopy, bioinformatics analysis of the PDB, small-molecule X-ray crystallography, and computational investigations. Phosphorylation of both serine and threonine residues induces substantial conformational restriction in their physiologically more important dianionic forms. Threonine exhibits a particularly strong disorder-to-order transition upon phosphorylation, with dianionic phosphothreonine preferentially adopting a cyclic conformation with restricted{phi} ({phi} [~] -60{degrees}) stabilized by three noncovalent interactions: a strong intraresidue phosphate-amide hydrogen bond, an n[->]{pi}* interaction between consecutive carbonyls, and an n[->]{sigma}* interaction between the phosphate O{gamma} lone pair and the antibonding orbital of C-H{beta} that restricts the{chi} 2 side chain conformation. Proline is unique among the canonical amino acids for its covalent cyclization on the backbone. Phosphothreonine can mimic prolines backbone cyclization via noncovalent interactions. The preferred torsions of dianionic phosphothreonine are{phi} ,{psi} = polyproline helix or -helix ({phi} [~] -60{degrees});{chi} 1 = g-;{chi} 2 = eclipsed C-H/O-P bonds. This structural signature is observed in diverse proteins, including the activation loops of protein kinases and protein-protein interactions. In total, these results suggest a structural basis for the differential use and evolution of threonine versus serine phosphorylation sites in proteins, with serine phosphorylation typically inducing smaller, rheostat-like changes, versus threonine phosphorylation promoting larger, step function-like switches, in proteins.

biophysics↗