Cargando…

Entropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C

[Image: see text] Molecular recognition is fundamental to biological signaling. A central question is how individual interactions between molecular moieties affect the thermodynamics of ligand binding to proteins and how these effects might propagate beyond the immediate neighborhood of the binding...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wallerstein, Johan, Ekberg, Vilhelm, Ignjatović, Majda Misini, Kumar, Rohit, Caldararu, Octav, Peterson, Kristoffer, Wernersson, Sven, Brath, Ulrika, Leffler, Hakon, Oksanen, Esko, Logan, Derek T., Nilsson, Ulf J., Ryde, Ulf, Akke, Mikael
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	American Chemical Society 2021
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8395690/ https://www.ncbi.nlm.nih.gov/pubmed/34467311 http://dx.doi.org/10.1021/jacsau.0c00094

Ejemplares similares

Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures
por: Caldararu, Octav, et al.
Publicado: (2020)

Exploring ligand dynamics in protein crystal structures with ensemble refinement
por: Caldararu, Octav, et al.
Publicado: (2021)

Structure and Energetics of Ligand–Fluorine Interactions with Galectin‐3 Backbone and Side‐Chain Amides: Insight into Solvation Effects and Multipolar Interactions
por: Kumar, Rohit, et al.
Publicado: (2019)

On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies
por: Ekberg, Vilhelm, et al.
Publicado: (2021)

Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3
por: Diehl, Carl, et al.
Publicado: (2010)

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
por: Misini Ignjatović, Majda, et al.
Publicado: (2016)

Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks
por: Ekberg, Vilhelm, et al.
Publicado: (2022)

Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase
por: Caldararu, Octav, et al.
Publicado: (2018)

Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data
por: Caldararu, Octav, et al.
Publicado: (2019)

Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Corrigendum
por: Caldararu, Octav, et al.
Publicado: (2020)

Critical evaluation of a crystal structure of nitrogenase with bound N(2) ligands
por: Bergmann, Justin, et al.
Publicado: (2021)

Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement
por: Cao, Lili, et al.
Publicado: (2020)

Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps
por: Kelpšas, Vinardas, et al.
Publicado: (2021)

Binding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD(T)
por: Caldararu, Octav, et al.
Publicado: (2016)

Ligand Induced Galectin-3 Protein Self-association
por: Lepur, Adriana, et al.
Publicado: (2012)

Can the results of quantum refinement be improved with a continuum-solvation model?
por: Bergmann, Justin, et al.
Publicado: (2021)

Cosolvent Dimethyl Sulfoxide Influences Protein–Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein–Ligand Encounter
por: Wernersson, Sven, et al.
Publicado: (2022)

Ligand Sulfur Oxidation State Progressively Alters Galectin-3-Ligand Complex Conformations To Induce Affinity-Influencing Hydrogen Bonds
por: Mahanti, Mukul, et al.
Publicado: (2023)

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
por: Genheden, Samuel, et al.
Publicado: (2015)

Entropy gain due to water release upon ligand binding
por: Ahmad, Mazen, et al.
Publicado: (2014)

Enthalpy–entropy compensation in the binding of peptide ligands to human Arc
por: Kang, Jonghoon, et al.
Publicado: (2021)

Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand
por: Jiang, Hao, et al.
Publicado: (2022)

Improved Estimation of Protein-Ligand Binding Free Energy by Using the Ligand-Entropy and Mobility of Water Molecules
por: Fukunishi, Yoshifumi, et al.
Publicado: (2013)

Aromatic heterocycle galectin-1 interactions for selective single-digit nM affinity ligands
por: Peterson, Kristoffer, et al.
Publicado: (2018)

The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics
por: Saraboji, Kadhirvel, et al.
Publicado: (2011)

fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins
por: Bergmann, Justin, et al.
Publicado: (2020)

QM/MM study of the reaction mechanism of sulfite oxidase
por: Caldararu, Octav, et al.
Publicado: (2018)

Combinatorial entropy behaviour leads to range selective binding in ligand-receptor interactions
por: Liu, Meng, et al.
Publicado: (2020)

Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level
por: Olsson, Martin A., et al.
Publicado: (2016)

Entropy of Branching Out: Linear versus Branched Alkylthiols Ligands on CdSe Nanocrystals
por: Elimelech, Orian, et al.
Publicado: (2022)

Paramagnetic Ligand Tagging To Identify Protein Binding Sites
por: Brath, Ulrika, et al.
Publicado: (2015)

The Neutron Structure of Urate Oxidase Resolves a Long-Standing Mechanistic Conundrum and Reveals Unexpected Changes in Protonation
por: Oksanen, Esko, et al.
Publicado: (2014)

Superior hydrogen storage in high entropy alloys
por: Sahlberg, Martin, et al.
Publicado: (2016)

Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study
por: Ryde, Ulf, et al.
Publicado: (2009)

Entropy predicts sensitivity of pseudorandom seeds
por: Maier, Benjamin Dominik, et al.
Publicado: (2023)

BiEntropy, TriEntropy and Primality
por: Croll, Grenville J.
Publicado: (2020)

Digital self-management of hip and knee osteoarthritis and trajectories of work and activity impairments
por: Kiadaliri, Ali, et al.
Publicado: (2023)

CHANGES IN PAIN AND DISABILITY IN PATIENTS WITH SHOULDER PAIN AFTER THREE MONTHS OF DIGITALLY DELIVERED EXERCISE AND PATIENT EDUCATION
por: WÖRNER, Tobias, et al.
Publicado: (2023)

Designing interactions by control of protein–ligand complex conformation: tuning arginine–arene interaction geometry for enhanced electrostatic protein–ligand interactions
por: Noresson, A.-L., et al.
Publicado: (2017)

Auditory environment diversity quantified using entropy from real-world hearing aid data
por: Jorgensen, Erik, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_4ml9oqtjj590o6vg6c0onaeoko