Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch

Riboswitches are naturally occurring RNA aptamers that control the expression of essential bacterial genes by binding to specific small molecules. The binding with both high affinity and specificity induces conformational changes. Thus, riboswitches were proposed as a possible molecular target for developing antibiotics and chemical tools. The adenine riboswitch can bind not only to purine analogues but also to pyrimidine analogues. Here, long molecular dynamics (MD) simulations and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) computational methodologies were carried out to show the differences in the binding model and the conformational changes upon five ligands binding. The binding free energies of the guanine riboswitch aptamer with C74U mutation complexes were compared to the binding free energies of the adenine riboswitch (AR) aptamer complexes. The calculated results are in agreement with the experimental data. The differences for the same ligand binding to two different aptamers are related to the electrostatic contribution. Binding dynamical analysis suggests a flexible binding pocket for the pyrimidine ligand in comparison with the purine ligand. The 18 μs of MD simulations in total indicate that both ligand-unbound and ligand-bound aptamers transfer their conformation between open and closed states. The ligand binding obviously affects the conformational change. The conformational states of the aptamer are associated with the distance between the mass center of two key nucleotides (U51 and A52) and the mass center of the other two key nucleotides (C74 and C75). The results suggest that the dynamical character of the binding pocket would affect its biofunction. To design new ligands of the adenine riboswitch, it is recommended to consider the binding affinities of the ligand and the conformational change of the ligand binding pocket.

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Sensitivity in binding free energies due to protein reorganization

10.1101/066621 ◽

2016 ◽

Author(s):

Nathan M. Lim ◽

Lingle Wang ◽

Robert Abel ◽

David L. Mobley

Keyword(s):

Ligand Binding ◽

Conformational Changes ◽

Binding Free Energy ◽

Binding Pocket ◽

Free Energy Calculations ◽

Computer Hardware ◽

Sampling Techniques ◽

Free Energies ◽

Sampling Algorithms ◽

Binding Free Energies

AbstractTremendous recent improvements in computer hardware, coupled with advances in sampling techniques and force fields, are now allowing protein-ligand binding free energy calculations to be routinely used to aid pharmaceutical drug discovery projects. However, despite these recent innovations, there are still needs for further improvement in sampling algorithms to more adequately sample protein motion relevant to protein-ligand binding. Here, we report our work identifying and studying such clear and remaining needs in the apolar cavity of T4 Lysozyme L99A. In this study, we model recent experimental results that show the progressive opening of the binding pocket in response to a series of homologous ligands.1 Even while using enhanced sampling techniques, we demonstrate that the predicted relative binding free energies (RBFE) are sensitive to the initial protein conformational state. Particularly, we highlight the importance of sufficient sampling of protein conformational changes and demonstrate how inclusion of three key protein residues in the ‘hot’ region of the FEP/REST simulation improves the sampling and resolves this sensitivity.

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Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.8b00081 ◽

2018 ◽

Vol 14 (6) ◽

pp. 3228-3237 ◽

Cited By ~ 17

Author(s):

Casper Steinmann ◽

Martin A. Olsson ◽

Ulf Ryde

Keyword(s):

Ligand Binding ◽

Md Simulations ◽

Free Energies ◽

Binding Free Energies

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Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

Physical Chemistry Chemical Physics ◽

10.1039/d1cp00206f ◽

2021 ◽

Author(s):

Lennart Gundelach ◽

Christofer S Tautermann ◽

Thomas Fox ◽

Chris-Kriton Skylaris

Keyword(s):

Drug Discovery ◽

Ligand Binding ◽

Dft Calculations ◽

Quantum Mechanical ◽

Free Energies ◽

Ligand Interaction ◽

Exchange Correlation ◽

Ligand Free ◽

Protein Ligand Interaction ◽

Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

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Positive co-operative binding at two weak lysine-binding sites governs the Glu-plasminogen conformational change

Biochemical Journal ◽

10.1042/bj2850419 ◽

1992 ◽

Vol 285 (2) ◽

pp. 419-425 ◽

Cited By ~ 34

Author(s):

U Christensen ◽

L Mølgaard

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Conformational Change ◽

Conformational Changes ◽

Binding Sites ◽

High Specificity ◽

Stopped Flow ◽

Protein Fluorescence ◽

Lysine Residues ◽

Kinetics Of

The kinetics of a series of Glu-plasminogen ligand-binding processes were investigated at pH 7.8 and 25 degrees C (in 0.1 M-NaCl). The ligands include compounds analogous to C-terminal lysine residues and to normal lysine residues. Changes of the Glu-plasminogen protein fluorescence were measured in a stopped-flow instrument as a function of time after rapid mixing of Glu-plasminogen and ligand at various concentrations. Large positive fluorescence changes (approximately 10%) accompany the ligand-induced conformational changes of Glu-plasminogen resulting from binding at weak lysine-binding sites. Detailed studies of the concentration-dependencies of the equilibrium signals and the rate constants of the process induced by various ligands showed the conformational change to involve two sites in a concerted positive co-operative process with three steps: (i) binding of a ligand at a very weak lysine-binding site that preferentially, but not exclusively, binds C-terminal-type lysine ligands, (ii) the rate-determining actual-conformational-change step and (iii) binding of one more lysine ligand at a second weak lysine-binding site that then binds the ligand more tightly. Further, totally independent initial small negative fluorescence changes (approximately 2-4%) corresponding to binding at the strong lysine-binding site of kringle 1 [Sottrup-Jensen, Claeys, Zajdel, Petersen & Magnusson (1978) Prog. Chem. Fibrinolysis Thrombolysis 3, 191-209] were observed for the C-terminal-type ligands. The finding that the conformational change in Glu-plasminogen involves two weak lysine-binding sites indicates that the effect cannot be assigned to any single kringle and that the problem of whether kringle 4 or kringle 5 is responsible for the process resolves itself. Probably kringle 4 and 5 are both participating. The involvement of two lysine binding-sites further makes the high specificity of Glu-plasminogen effectors more conceivable.

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Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Chemical Science ◽

10.1039/d1sc03472c ◽

2021 ◽

Author(s):

Yuriy Khalak ◽

Gary Tresdern ◽

Matteo Aldeghi ◽

Hannah Magdalena Baumann ◽

David L. Mobley ◽

...

Keyword(s):

Free Energy ◽

Drug Discovery ◽

Drug Design ◽

Ligand Binding ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Free Energies ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Binding Free Energies

The recent advances in relative protein-ligand binding free energy calculations have shown the value of alchemical methods in drug discovery. Accurately assessing absolute binding free energies, although highly desired, remains...

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MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies

Molecular Dynamics - Studies of Synthetic and Biological Macromolecules ◽

10.5772/37107 ◽

2012 ◽

Cited By ~ 8

Author(s):

Joseph M. ◽

Georgios Archontis

Keyword(s):

Ligand Binding ◽

Free Energies ◽

Binding Free Energies

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Characterization of the High-Affinity Drug Ligand Binding Site of Mouse Recombinant TSPO

International Journal of Molecular Sciences ◽

10.3390/ijms20061444 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1444 ◽

Cited By ~ 4

Author(s):

Soria Iatmanen-Harbi ◽

lucile Senicourt ◽

Vassilios Papadopoulos ◽

Olivier Lequin ◽

Jean-Jacques Lacapere

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Conformational Changes ◽

Protoporphyrin Ix ◽

Binding Pocket ◽

Site Directed Mutagenesis ◽

Translocator Protein ◽

Binding Affinities ◽

Ligand Selectivity ◽

High Affinity

The optimization of translocator protein (TSPO) ligands for Positron Emission Tomography as well as for the modulation of neurosteroids is a critical necessity for the development of TSPO-based diagnostics and therapeutics of neuropsychiatrics and neurodegenerative disorders. Structural hints on the interaction site and ligand binding mechanism are essential for the development of efficient TSPO ligands. Recently published atomic structures of recombinant mammalian and bacterial TSPO1, bound with either the high-affinity drug ligand PK 11195 or protoporphyrin IX, have revealed the membrane protein topology and the ligand binding pocket. The ligand is surrounded by amino acids from the five transmembrane helices as well as the cytosolic loops. However, the precise mechanism of ligand binding remains unknown. Previous biochemical studies had suggested that ligand selectivity and binding was governed by these loops. We performed site-directed mutagenesis to further test this hypothesis and measured the binding affinities. We show that aromatic residues (Y34 and F100) from the cytosolic loops contribute to PK 11195 access to its binding site. Limited proteolytic digestion, circular dichroism and solution two-dimensional (2-D) NMR using selective amino acid labelling provide information on the intramolecular flexibility and conformational changes in the TSPO structure upon PK 11195 binding. We also discuss the differences in the PK 11195 binding affinities and the primary structure between TSPO (TSPO1) and its paralogous gene product TSPO2.

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