Thermodynamics of Nanobody Binding to Lactose Permease

Thermodynamic analysis of an entropically driven, high-affinity nanobody-HIV p24 interaction

Protein-protein interactions are fundamental to life processes. Complementary computational, structural, and biophysical studies of these interactions enable the forces behind their specificity and strength to be understood. Antibody fragments such as single-chain antibodies have the specificity and affinity of full antibodies but a fraction of their size, expediting whole molecule studies and distal effects without exceeding the computational capacity of modeling systems. We previously reported the crystal structure of a high-affinity nanobody 59H10 bound to HIV-1 capsid protein p24 and deduced key interactions using all-atom molecular dynamics simulations. We studied the properties of closely related medium (37E7) and low (48G11) affinity nanobodies, to understand how changes of three (37E7) or one (48G11) amino acids impacted these interactions; however, the contributions of enthalpy and entropy were not quantified. Here, we report the use of qualitative and quantitative experimental and in silico approaches to separate the contributions of enthalpy and entropy. We used complementary circular dichroism spectroscopy and molecular dynamics simulations to qualitatively delineate changes between nanobodies in isolation and complexed with p24. Using quantitative techniques such as isothermal titration calorimetry alongside WaterMap and Free Energy Perturbation protocols, we found the difference between high (59H10) and medium (37E7) affinity nanobodies on binding to HIV-1 p24 is entropically driven, accounted for by the release of unstable waters from the hydrophobic surface of 59H10. Our results provide an exemplar of the utility of parallel in vitro and in silico studies and highlight that differences in entropic interactions between amino acids and water molecules are sufficient to drive orders of magnitude differences in affinity.

It takes two to tango: The dance of the permease

The lactose permease (LacY) of Escherichia coli is the prototype of the major facilitator superfamily, one of the largest families of membrane transport proteins. Structurally, two pseudo-symmetrical six-helix bundles surround a large internal aqueous cavity. Single binding sites for galactoside and H+ are positioned at the approximate center of LacY halfway through the membrane at the apex of the internal cavity. These features enable LacY to function by an alternating-access mechanism that can catalyze galactoside/H+ symport in either direction across the cytoplasmic membrane. The H+-binding site is fully protonated under physiological conditions, and subsequent sugar binding causes transition of the ternary complex to an occluded intermediate that can open to either side of the membrane. We review the structural and functional evidence that has provided new insight into the mechanism by which LacY achieves active transport against a concentration gradient.

Uptake dynamics in the Lactose permease (LacY) membrane protein transporter

The sugar transporter Lactose permease (LacY) of Escherichia coli has become a prototype to understand the underlying molecular details of membrane transport. Crystal structures have trapped the protein in sugar-bound states facing the periplasm, but with narrow openings unable to accommodate sugar. Therefore, the molecular details of sugar uptake remain elusive. In this work, we have used extended simulations and metadynamics sampling to explore a putative sugar-uptake pathway and associated free energy landscape. We found an entrance at helix-pair 2 and 11, which involved lipid head groups and residues Gln 241 and Gln 359. Furthermore, the protein displayed high flexibility on the periplasmic side of Phe 27, which is located at the narrowest section of the pathway. Interactions to Phe 27 enabled passage into the binding site, which was associated with a 24 ± 4 kJ/mol binding free energy in excellent agreement with an independent binding free energy calculation and experimental data. Two free energy minima corresponding to the two possible binding poses of the lactose analog β-D-galactopyranosyl-1-thio-β-D-galactopyranoside (TDG) were aligned with the crystal structure-binding pocket. This work outlines the chemical environment of a putative periplasmic sugar pathway and paves way for understanding substrate affinity and specificity in LacY.

Thermodynamic cooperativity of cosubstrate binding and cation selectivity of Salmonella typhimurium MelB

The melibiose symporter MelB couples melibiose transport to that of cations such as Na⁺. Hariharan and Guan show that the binding of Na⁺ and melibiose is thermodynamically cooperative and that Na⁺ coupling is based on ion concentrations and competitive binding, but not ion selectivity.

The Na⁺-coupled melibiose symporter MelB, which can also be coupled to H⁺ or Li⁺ transport, is a prototype for the glycoside-pentoside-hexuronide:cation symporter family. Although the 3-D x-ray crystal structure of Salmonella typhimurium MelB (MelB_St) has been determined, the symport mechanisms for the obligatory coupled transport are not well understood. Here, we apply isothermal titration calorimetry to determine the energetics of Na⁺ and melibiose binding to MelB_St, as well as protonation of this transporter. Studies of the thermodynamic cycle for the formation of the Na⁺–MelB_St–melibiose ternary complex at pH 7.45 reveal that the binding of Na⁺ and melibiose is cooperative. The binding affinity for one substrate (Na⁺ or melibiose) is increased by the presence of the other by about eightfold. The coupling free energies (ΔΔG) of either substrate binding are ∼5 kJ/mol, and binding of both substrates releases a free energy of ∼35 kJ/mol. Measurements of the Na⁺-binding enthalpy at three different pH values, including the pK_a value of MelB, indicate that the binding of one Na⁺ displaces one H⁺ per MelB_St molecule. In addition, the absolute dissociation constants for Na⁺ and H⁺, determined by competitive binding, show that MelB_St is selective for H⁺ over Na⁺ by ∼1,000-fold at a pK_a of 6.25. Thus, the Na⁺ coupling in MelB_St is based not on ion selectivity but on ion concentrations and competitive binding because of a much higher Na⁺ concentration under physiological conditions. Such a selectivity feature seems to be common for membrane transport proteins that can bind both H⁺ and Na⁺ at a common site.