Fig 1.
Breast-cancer-gene 1 (BRCA1) C-terminal (BRCT) binding with a phosphoserine (pSer) peptide.
pSer forms hydrogen bonds with S1655, G1656 and K1702, and the P+3 Phe locates in the hydrophobic packet formed by M1775, N1774 and F1704. The two points of contact (pSer and P+3 Phe) shown in all of our calculations are highlighted by green circles.
Table 1.
Ligand library of BRCT used for binding affinity exploration and study of flexibility of binding site.
Fig 2.
Structures of C1, N1 and D1 that bind to the BRCT domain.
Fig 3.
Ligand L1 is shown in green licorice structure. Only residues within 7 Å of the ligand (live set, labeled in blue) is set flexible in M2 calculations. The rigid set (real set, labeled in yellow) contains the residues within 5 Å of the flexible set; other atoms outside the real set (labeled in pink) were not considered during M2 calculations. Notably, the computed entropy and enthalpy terms from M2 consider the contribution of BRCT (live set) and the ligand.
Fig 4.
Flexibility of active site of BRCT.
(A). Standard deviation of phi and psi angles of the residues of the receptor within 7 Å of ligands during MD simulations. Each residue has one column containing two standard deviation values for the phi angle and psi angle, respectively. (B). Flexible region of the active site. Flexible residues of the protein are shown in a green line representation. Ligand is shown as a blue tube with pSer and Phe (P+3) residues in licorice representation.
Fig 5.
(A, B, C) Three distinct bound conformations of C1 from M2 calculation.
Residues of BRCT are shown in line representation and ligand is shown in licorice representation, hydrogen bonds are drawn in dash lines (free energies of A, B and C bound conformations are -1461.16, -1457.04 and -1453.72 kcal/mol, respectively).
Fig 6.
The rotameric states of selected rotatable bonds of P4 and C1 in both free and bound states.
(A1), (B1). Selected rotatable bonds of ligand P4 and C1 structures, respectively. (A2), (B2). The dihedral angle distribution from 1000 frames collected during 100-ns MD simulations of P4 and C1, respectively. (A3), (B3). The dihedral angle distribution for distinct energy minima found by M2 calculations of P4 and C1, respectively.
Table 2.
BRCT domain−ligand Interaction Energy (kcal/mol) of P1–14 and C1, N1 and D1 calculated by molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA).
Fig 7.
Conformational change of P4 between bent and stretched in free ligand state.
Table 3.
Binding free energy, average binding potential energy, and solvation free energy (kcal/mol) of P1–14, C1, N1 and D1 calculated by M2.
Fig 8.
Calculated versus experimental relative binding free energies ΔΔG (kcal/mol) for P1–P14 and C1.
Fig 9.
Computed configurational entropy contribution, <-TΔS> and energy contribution, Δ<U+W>, for P1–14 and C1, N1 and D1.
<-TΔS> vs Δ<U+W> is plotted using tight peptide binders P1–P12.