Electrostatic polarization is critical for the strong binding in streptavidin-biotin system

Understanding the avidin-biotin binding based on polarized protein-specific charge

In this study, charge updating schemes based on the local polarized protein-specific charge (LPPC) were introduced to vary the atomic charges of the biotin molecule and the residues in close contact during the simulation of the avidin-biotin complexes. The need of the charge variation of the ligand in response to changes in its surroundings was thoroughly studied. The results show that the calculated binding energy difference between biotin (BTN1) and 2'-iminobiotin (BTN2) and avidin is in excellent agreement with the experimental value, thus verifying the feasibility of updating the atomic charges of ligands during the simulation.

Improving the accuracy of predicting protein-ligand binding-free energy with semiempirical quantum chemistry charge

Aim: It is a challenge to predict binding-free energy (ΔG) accurately. Methodology/results: For accurate ΔG prediction, a new strategy combining solvated interaction energy (SIE) or molecular mechanics/generalized Born surface area (MM/GBSA) approach with the Coulson charge of both protein and ligand calculated by semiempirical quantum mechanics (SQM), named SIE-SQMPC or MM/GBSA-SQMPC approach, was developed and tested on 50 protein-ligand complexes. Both approaches achieved higher correlation (R ²) between experimental and predicted ΔG than that with Amber-ff03 charge, even for ligands with highly different scaffolds. But, SIE-SQMPC is computationally much faster than MM/GBSA-SQMPC. Conclusion: SIE-SQMPC provided an effective alternative to predict ΔG of protein-ligand binding (R ² = 0.66-0.94 for SIE-AM1; R ² = 0.59-0.98 for SIE-PM7), which has the potential of high-throughput processing for molecular docking and drug design.

The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force

Classical density functional theory (DFT) can be used to relate the thermodynamic properties of solutions to the indirect solvent mediated part of the solute-solvent potential of mean force (PMF). Standard, but powerful numerical methods can be used to estimate the solute-solvent PMF from which the indirect part can be extracted. In this work we show how knowledge of the direct and indirect parts of the solute-solvent PMF for water at the interface of a protein receptor can be used to gain insights about how to design tighter binding ligands. As we show, the indirect part of the solute-solvent PMF is equal to the sum of the 1-body (energy + entropy) terms in the inhomogeneous solvation theory (IST) expansion of the solvation free energy. To illustrate the effect of displacing interfacial water molecules with particular direct/indirect PMF signatures on the binding of ligands, we carry out simulations of protein binding with several pairs of congeneric ligands. We show that interfacial water locations that contribute favorably or unfavorably at the 1-body level (energy + entropy) to the solvation free energy of the solute can be targeted as part of the ligand design process. Water locations where the indirect PMF is larger in magnitude provide better targets for displacement when adding a functional group to a ligand core.

Improving the Solubility of Artificial Ligands of Streptavidin to Enable More Practical Reversible Switching of Protein Localization in Cells

Chemical inducers that can control target-protein localization in living cells are powerful tools to investigate dynamic biological systems. We recently reported the retention using selective hook or "RUSH" system for reversible localization change of proteins of interest by addition/washout of small-molecule artificial ligands of streptavidin (ALiS). However, the utility of previously developed ALiS was restricted by limited solubility in water. Here, we overcame this problem by X-ray crystal structure-guided design of a more soluble ALiS derivative (ALiS-3), which retains sufficient streptavidin-binding affinity for use in the RUSH system. The ALiS-3-streptavidin interaction was characterized in detail. ALiS-3 is a convenient and effective tool for dynamic control of α-mannosidase II localization between ER and Golgi in living cells.

Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy

Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding.

Accurate Calculation of Electric Fields Inside Enzymes

The specific electric field generated by a protease at its active site is considered as an important source of the catalytic power. Accurate calculation of electric field at the active site of an enzyme has both fundamental and practical importance. Measuring site-specific changes of electric field at internal sites of proteins due to, eg, mutation, has been realized by using molecular probes with CO or CN groups in the context of vibrational Stark effect. However, theoretical prediction of change in electric field inside a protein based on a conventional force field, such as AMBER or OPLS, is often inadequate. For such calculation, quantum chemical approach or quantum-based polarizable or polarized force field is highly preferable. Compared with the result from conventional force field, significant improvement is found in predicting experimentally measured mutation-induced electric field change using quantum-based methods, indicating that quantum effect such as polarization plays an important role in accurate description of electric field inside proteins. In comparison, the best theoretical prediction comes from fully quantum mechanical calculation in which both polarization and inter-residue charge transfer effects are included for accurate prediction of electrostatics in proteins.

The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations

Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.

Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters

The calculation of protein-ligand binding free energy (ΔG) is of great importance for virtual screening and drug design. Molecular dynamics (MD) simulation has been an attractive tool to investigate this scientific problem. However, the reliability of such approach is affected by many factors including electrostatic interaction calculation. Here, we present a practical protocol using quantum mechanics/molecular mechanics (QM/MM) calculations to generate polarizable QM protein charge (QMPC). The calculated QMPC of some atoms in binding pockets was obviously different from that calculated by AMBER ff03, which might significantly affect the calculated ΔG. To evaluate the effect, the MD simulations and MM/GBSA calculation with QMPC for 10 protein-ligand complexes, and the simulation results were then compared to those with the AMBER ff03 force field and experimental results. The correlation coefficient between the calculated ΔΔG using MM/GBSA under QMPC and the experimental data is .92, while that with AMBER ff03 force field is .47 for the complexes formed by streptavidin or its mutants and biotin. Moreover, the calculated ΔΔG with QMPC for the complexes formed by ERβ and five ligands is positively related to experimental result with correlation coefficient of .61, while that with AMBER ff03 charge is negatively related to experimental data with correlation coefficient of .42. The detailed analysis shows that the electrostatic polarization introduced by QMPC affects the electrostatic contribution to the binding affinity and thus, leads to better correlation with experimental data. Therefore, this approach should be useful to virtual screening and drug design.

Functional loop dynamics of the streptavidin-biotin complex

Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop(3-4) in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop(3-4) from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop(3-4) and biotin. (3) The closure of loop(3-4) is concerted to the stable binding of biotin to streptavidin. When the loop(3-4) is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop(3-4) and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop(3-4) in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer.

Molecular dynamics simulation of protein crystal with polarized protein-specific force field

Two 250 ns molecular simulations have been carried out to study the structure and dynamics of crystal toxin protein II from the scorpion Androctonus australis Hector employing the polarized protein-specific charge (PPC), as well as the standard AMBER99SB force field, to investigate the electrostatic polarization on the simulated crystal stability. Results show that under PPC, the monomers in unit cell as well as the lattice in supercell are more stable with smaller root-mean-square deviations and more accurate lattice atomic fluctuations compared with the crystallographic B-factors than under AMBER99SB force field. Most of the interactions at interfaces in the X-ray structure are quite well-preserved, underscoring the important effect of polarization on maintaining the crystal stability. However, the results also show that the hydrogen bond between Asp53 and Gln37 and the cation-π interaction between Arg56 and His64 are not stable, indicating that further optimization of force field, especially the van der Waals interaction parameters, is desired.

Some practical approaches to treating electrostatic polarization of proteins

Conspectus Electrostatic interaction plays a significant role in determining many properties of biomolecules, which exist and function in aqueous solution, a highly polar environment. For example, proteins are composed of amino acids with charged, polar, and nonpolar side chains and their specific electrostatic properties are fundamental to the structure and function of proteins. An important issue that arises in computational study of biomolecular interaction and dynamics based on classical force field is lack of polarization. Polarization is a phenomenon in which the charge distribution of an isolated molecule will be distorted when interacting with another molecule or presented in an external electric field. The distortion of charge distribution is intended to lower the overall energy of the molecular system, which is counter balanced by the increased internal energy of individual molecules due to the distorted charge distributions. The amount of the charge redistribution, which characterizes the polarizability of a molecule, is determined by the level of the charge distortion. Polarization is inherently quantum mechanical, and therefore classical force fields with fixed atomic charges are incapable of capturing this important effect. As a result, simulation studies based on popular force fields, AMBER, CHARMM, etc., lack the polarization effect, which is a widely known deficiency in most computational studies of biomolecules today. Many efforts have been devoted to remedy this deficiency, such as adding additional movable charge on the atom, allowing atomic charges to fluctuate, or including induced multipoles. Although various successes have been achieved and progress at various levels has been reported over the past decades, the issue of lacking polarization in force field based simulations is far from over. For example, some of these methods do not always give converged results, and other methods require huge computational cost. This Account reviews recent work on developing polarized and polarizable force fields based on fragment quantum mechanical calculations for proteins. The methods described here are based on quantum mechanical calculations of proteins in solution, but with a different level of rigor and different computational efficiency for the molecular dynamics applications. In the general approach, a fragment quantum mechanical calculation for protein with implicit solvation is carried out to derive a polarized protein-specific charge (PPC) for any given protein structure. The PPC correctly reflects the polarization state of the protein in a given conformation, and it can also be dynamically changed as the protein changes conformation in dynamics simulations. Another approach that is computationally more efficient is the effective polarizable bond method in which only polar bonds or groups can be polarized and their polarizabilities are predetermined from quantum mechanical calculations of these groups in external electric fields. Both methods can be employed for applications in various situations by taking advantage of their unique features.

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein-ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O-O radial distribution functions similar to TIP4P-EW.

Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis

The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein-specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin and β-secretase binding complexes. This charge fitting scheme, termed delta restrained electrostatic potential, bypasses the prevalent numerical difficulty of rank deficiency in electrostatic-potential-based charge fitting methods via a dual-step fitting strategy. A remarkable consistency between the predicted binding affinities and the experimental measurement has been observed. This work serves as a direct evidence of PPC's applicability in rational drug design.

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect

Recently, Baugh et al. discovered that a distal point mutation (F130L) in streptavidin causes no distinct variation to the structure of the binding pocket but a 1000-fold reduction in biotin binding affinity. In this work, we carry out molecular dynamics simulations and apply an end-state free energy method to calculate the binding free energies of biotin to wild type streptavidin and its F130L mutant. The absolute binding affinities based on AMBER charge are repulsive, and the mutation induced binding loss is underestimated. When using the polarized protein-specific charge, the absolute binding affinities are significantly enhanced. In particular, both the absolute and relative binding affinities are in line with the experimental measurements. Further investigation indicates that polarization effect is indispensable in both the generation of structural ensembles and the calculation of interaction energies. This work verifies Baugh's conjecture that electrostatic polarization effect plays an essential role in modulating the binding affinity of biotin to the streptavidin through F130L mutation.