title: Slow dissociation of a charged ligand: analysis of the primary quinone Q(A) site of photosynthetic bacterial reaction centers.
abstract: Reaction centers (RCs) are integral membrane proteins that undergo a series of electron transfer reactions during the process of photosynthesis. In the Q(A) site of RCs from Rhodobacter sphaeroides, ubiquinone-10 is reduced, by a single electron transfer, to its semiquinone. The neutral quinone and anionic semiquinone have similar affinities, which is required for correct in situ reaction thermodynamics. A previous study showed that despite similar affinities, anionic quinones associate and dissociate from the Q(A) site at rates ≈10(4) times slower than neutral quinones indicating that anionic quinones encounter larger binding barriers (Madeo, J.; Gunner, M. R. Modeling binding kinetics at the Q(A) site in bacterial reaction centers. Biochemistry 2005, 44, 10994-11004). The present study investigates these barriers computationally, using steered molecular dynamics (SMD) to model the unbinding of neutral ground state ubiquinone (UQ) and its reduced anionic semiquinone (SQ(-)) from the Q(A) site. In agreement with experiment, the SMD unbinding barrier for SQ(-) is larger than for UQ. Multi Conformational Continuum Electrostatics (MCCE), used here to calculate the binding energy, shows that SQ(-) and UQ have comparable affinities. In the Q(A) site, there are stronger binding interactions for SQ(-) compared to UQ, especially electrostatic attraction to a bound non-heme Fe(2+). These interactions compensate for the higher SQ(-) desolvation penalty, allowing both redox states to have similar affinities. These additional interactions also increase the dissociation barrier for SQ(-) relative to UQ. Thus, the slower SQ(-) dissociation rate is a direct physical consequence of the additional binding interactions required to achieve a Q(A) site affinity similar to that of UQ. By a similar mechanism, the slower association rate is caused by stronger interactions between SQ(-) and the polar solvent. Thus, stronger interactions for both the unbound and bound states of charged and highly polar ligands can slow their binding kinetics without a conformational gate. Implications of this for other systems are discussed.
authors.affiliation: Department of Physics, City College of New York, New York, New York 10031, USA. jen_madeo@yahoo.com
authors.forename: Jennifer
authors.initials: J
authors.lastname: Madeo
authors.forename: Maja
authors.initials: M
authors.lastname: Mihajlovic
authors.forename: Themis
authors.initials: T
authors.lastname: Lazaridis
authors.forename: M R
authors.initials: MR
authors.lastname: Gunner
mesh_terms: D018360:Crystallography, X-Ray; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D045322:Photosynthetic Reaction Center Complex Proteins / Q000737:chemistry / Q000378:metabolism*; D011809:Quinones / Q000737:chemistry / Q000378:metabolism*; D012242:Rhodobacter sphaeroides / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D008024:Ligands; D045322:Photosynthetic Reaction Center Complex Proteins; D011809:Quinones