Free Energy of Binding and Mechanism of Interaction for the MEEVD-TPR2A Peptide-Protein Complex

Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands

The Alchemical Transfer Method (ATM) is herein validated against the relative binding-free energies (RBFEs) of a diverse set of protein-ligand complexes. We employed a streamlined setup workflow, a bespoke force field, and AToM-OpenMM software to compute the RBFEs of the benchmark set prepared by Schindler and collaborators at Merck KGaA. This benchmark set includes examples of standard small R-group ligand modifications as well as more challenging scenarios, such as large R-group changes, scaffold hopping, formal charge changes, and charge-shifting transformations. The novel coordinate perturbation scheme and a dual-topology approach of ATM address some of the challenges of single-topology alchemical RBFE methods. Specifically, ATM eliminates the need for splitting electrostatic and Lennard-Jones interactions, atom mapping, defining ligand regions, and postcorrections for charge-changing perturbations. Thus, ATM is simpler and more broadly applicable than conventional alchemical methods, especially for scaffold-hopping and charge-changing transformations. Here, we performed well over 500 RBFE calculations for eight protein targets and found that ATM achieves accuracy comparable to that of existing state-of-the-art methods, albeit with larger statistical fluctuations. We discuss insights into the specific strengths and weaknesses of the ATM method that will inform future deployments. This study confirms that ATM can be applied as a production tool for RBFE predictions across a wide range of perturbation types within a unified, open-source framework.

Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria

This chapter discusses the theory and application of physics-based free energy methods to estimate protein-peptide binding free energies. It presents a statistical mechanics formulation of molecular binding, which is then specialized in three methodologies: (1) alchemical absolute binding free energy estimation with implicit solvation, (2) alchemical relative binding free energy estimation with explicit solvation, and (3) potential of mean force binding free energy estimation. Case studies of protein-peptide binding application taken from the recent literature are discussed for each method.

A native mass spectrometry platform identifies HOP inhibitors that modulate the HSP90-HOP protein-protein interaction

Herein we describe a native mass spectromery protein-peptide model as a competent surrogate for the HOP-HSP90 protein-protein interaction (PPI), application of which led to the qualititive identification of two new peptides capable of in vitro PPI disruption. This proof of concept study offers a viable alternative for PPI inhibitor screening.

Molecular basis of the interaction of Hsp90 with its co-chaperone Hop

The heat shock protein (Hsp) Hsp90 is one of the most abundant proteins in the cell. It controls the functional turnover of proteins being involved in protein folding, refolding, transport as well as protein degradation. Co-chaperones influence Hsp90's activity in different ways, among which the Hsp organizing protein (Hop) was found to inhibit its ATP hydrolysis upon binding. Despite the availability of a number of studies investigating the Hsp90:Hop complex, several aspects of the Hsp90:Hop interaction have remained unresolved. Here, we employed a combinatory approach comprising native polyacrylamide gel electrophoresis, isothermal titration calorimetry, multiangle light scattering, isothermal titration calorimetry, small-angle X-ray scattering, dynamic light scattering, and nuclear magnetic resonance, spectroscopy to obtain a comprehensive picture about the human Hsp90β:Hop association in solution. Our data show that only one Hop molecule binds the Hsp90β dimer, Hop can interact with the open and closed state of Hsp90β, and Hop's TPR2A-2B domains determine the affinity for Hsp90's C-terminal and middle domain, whereby the interaction with the C-terminal domain of Hsp90β is sufficient to induce an allosteric conformational change between the two Hsp90β monomers in the Hsp90₂ :Hop₁ complex. Together, this study highlights the important role of the co-chaperone Hop in reorganizing Hsp90 for efficient client loading.

Specific Residue Interactions Regulate the Binding of Dengue Antigens to Broadly Neutralizing EDE Antibodies

Antibodies binding to antigens present on the dengue virus (DENV) represent the main defense mechanism of the host organism against the pathogen. Among the antibodies elicited by DENV and that bind to DII of protein E, EDE1-C8 can bind all DENV serotypes. Our analysis reveals the key residues in this interaction as well as structurally conserved hydrogen bonds located at the binding interface. They stabilize the dengue antigen-antibody complex among the EDE1 group of antibodies (Abs). Combining structural alignments with molecular dynamics simulations in the EDE1 Abs, we identified the critical elements that provide a major energetic contribution to the association of antigens from protein E with Abs. We discuss possible molecular insights into the binding mechanism by using a surrogate molecular entity resembling the protein E that forms native salt bridges and hydrogen bonds, including inferences on the light of high-resolution crystal structures of dengue Fab complexes. Finally, the molecular determinants, the free energy profile, and the binding mechanism provide inspiration for potential strategies in protein engineering to design novel immunogens of protein E against DENV.

Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes

The computational modeling of peptide inhibitors to target protein-protein binding interfaces is growing in interest as these are often too large, too shallow, and too feature-less for conventional small molecule compounds. Here, we present a rare successful application of an alchemical binding free energy method for the calculation of converged absolute binding free energies of a series of protein-peptide complexes. Specifically, we report the binding free energies of a series of cyclic peptides derived from the LEDGF/p75 protein to the integrase receptor of the HIV1 virus. The simulations recapitulate the effect of mutations relative to the wild-type binding motif of LEDGF/p75, providing structural, energetic and dynamical interpretations of the observed trends. The equilibration and convergence of the calculations are carefully analyzed. Convergence is aided by the adoption of a single-decoupling alchemical approach with implicit solvation, which circumvents the convergence difficulties of conventional double-decoupling protocols. We hereby present the single-decoupling methodology and critically evaluate its advantages and limitations. We also discuss some of the challenges and potential pitfalls of binding free energy calculations for complex molecular systems which have generally limited their applicability to the quantitative study of protein-peptide binding equilibria.

Theoretical rationalisation of the photophysics of a TICT excited state of cinnamoyl–coumarin derivatives in homogeneous and biological membrane models

Analysis of the potential energy barriers and structural dynamics of a new TICT-probe for monitoring biological environments.