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The thermodynamic influence of trapped water molecules on a protein-ligand interaction.

Stegmann CM, Seeliger D, Sheldrick GM, de Groot BL, Wahl MC
Angew Chem Int Ed Engl 48 5207-10 (2009)
Cited: 16 times
EuropePMC logo PMID: 19499554

Abstract

Water molecules doing time: Atomic-resolution crystal structures of the PPIase domain of cyclophilin G, alone and in complex with cyclosporin A, and together with MD simulations and calorimetry, reveal how trapped water molecules influence the thermodynamic profile of a protein-ligand interaction.

Reviews - 2wfj mentioned but not cited (1)

  1. Structural and Functional Insights into Human Nuclear Cyclophilins. Rajiv C, Davis TL. Biomolecules 8 (2018)

Articles - 2wfj mentioned but not cited (4)

  1. Some B(eq) are more equivalent than others. Merritt EA. Acta Crystallogr A 67 512-516 (2011)
  2. A backbone-dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations. Mortensen JC, Damjanovic J, Miao J, Hui T, Lin YS. Protein Sci 31 e4491 (2022)
  3. GISA: using Gauss Integrals to identify rare conformations in protein structures. Grønbæk C, Hamelryck T, Røgen P. PeerJ 8 e9159 (2020)
  4. The oxygen-oxygen distance of water in crystallographic data sets. Palese LL. Data Brief 28 105076 (2020)


Reviews citing this publication (2)

  1. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Spyrakis F, Cavasotto CN. Arch. Biochem. Biophys. 583 105-119 (2015)
  2. Thermodynamics and solvent linkage of macromolecule-ligand interactions. Duff MR, Howell EE. Methods 76 51-60 (2015)

Articles citing this publication (9)

  1. Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains. Vollmuth F, Geyer M. Angew Chem Int Ed Engl 49 6768-6772 (2010)
  2. The crystal structure of PPIL1 bound to cyclosporine A suggests a binding mode for a linear epitope of the SKIP protein. Stegmann CM, Lührmann R, Wahl MC. PLoS ONE 5 e10013 (2010)
  3. Multiple protein-protein interactions converging on the Prp38 protein during activation of the human spliceosome. Schütze T, Ulrich AK, Apelt L, Will CL, Bartlick N, Seeger M, Weber G, Lührmann R, Stelzl U, Wahl MC. RNA 22 265-277 (2016)
  4. Structural-thermodynamic relationships of interactions in the N-terminal ATP-binding domain of Hsp90. Nilapwar S, Williams E, Fu C, Prodromou C, Pearl LH, Williams MA, Ladbury JE. J. Mol. Biol. 392 923-936 (2009)
  5. Pushing the Limits of Detection of Weak Binding Using Fragment-Based Drug Discovery: Identification of New Cyclophilin Binders. Georgiou C, McNae I, Wear M, Ioannidis H, Michel J, Walkinshaw M. J. Mol. Biol. 429 2556-2570 (2017)
  6. The intervening domain from MeCP2 enhances the DNA affinity of the methyl binding domain and provides an independent DNA interaction site. Claveria-Gimeno R, Lanuza PM, Morales-Chueca I, Jorge-Torres OC, Vega S, Abian O, Esteller M, Velazquez-Campoy A. Sci Rep 7 41635 (2017)
  7. Against the odds? De novo structure determination of a pilin with two cysteine residues by sulfur SAD. Gorgel M, Bøggild A, Ulstrup JJ, Weiss MS, Müller U, Nissen P, Boesen T. Acta Crystallogr. D Biol. Crystallogr. 71 1095-1101 (2015)
  8. Multiple helical conformations of the helix-turn-helix region revealed by NOE-restrained MD simulations of tryptophan aporepressor, TrpR. Harish B, Swapna GV, Kornhaber GJ, Montelione GT, Carey J. Proteins 85 731-740 (2017)
  9. Sub-Atomic Resolution Crystal Structures Reveal Conserved Geometric Outliers at Functional Sites. Laulumaa S, Kursula P. Molecules 24 (2019)


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