We have calculated the free energy differences between four conformers of the linear form of the opioid pentapeptide
DPDPE
in aqueous solution. The conformers are Cyc, representing the structure adopted by the linear peptide prior to disulfide bond
formation, β
C
and β
E
, two slightly different β-turns previously identified in unconstrained molecular dynamics simulations, and Ext, an extended
structure. Our simulations indicate that β
E
is the most stable of the studied conformers of linear
DPDPE in aqueous solution, with β
C
, Cyc and Ext having free energies higher by 2.3, 6.3, and 28.2 kcal/mol, respectively. The free energy differences of 4.0 kcal/mol
between β
C
and Cyc, and 6.3 kcal/mol between β
E
and Cyc, reflect the cost of pre-organizing the linear peptide into a conformation conducive for disulfide bond formation.
Such a conformational change is a pre-requisite for the chemical reaction of S–S bond formation to proceed. The relatively
low population of the cyclic-like structure agrees qualitatively with observed lower potency and different receptor specificity
of the linear form relative to the cyclic peptide, and with previous unconstrained simulation results. Free energy component
analysis indicates that the moderate stability difference of 4.0–6.3 kcal/mol between the β-turns and the cyclic-like structure
results from cancellation of two large opposing effects. In accord with intuition, the relaxed β-turns have conformational
strain 43–45 kcal/mol lower than the Cyc structure. However, the cyclic-like conformer interacts with water about 39 kcal/mol
strongly than the open β-turns. Our simulations are the first application of the recently developed multidimensional conformational
free energy thermodynamic integration (CFTI) protocol to a solvated system, with fast convergence of the free energy obtained
by fixing all flexible dihedrals. Additionally, the availability of the CFTI multidimensional free energy gradient leads to
a new decomposition scheme, giving the contribution of each fixed dihedral to the overall free energy change and providing
additional insight into the microscopic mechanisms of the studied processes.
Received: 20 April 1998 / Accepted: 9 September 1998 / Published online: 7 December 1998
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