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Päslack C, Das CK, Schlitter J, Schäfer LV. Spectrally Resolved Estimation of Water Entropy in the Active Site of Human Carbonic Anhydrase II. J Chem Theory Comput 2021; 17:5409-5418. [PMID: 34259506 DOI: 10.1021/acs.jctc.1c00554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major challenge in understanding ligand binding to biomacromolecules lies in dissecting the underlying thermodynamic driving forces at the atomic level. Quantifying the contributions of water molecules is often especially demanding, although they can play important roles in biomolecular recognition and binding processes. One example is human carbonic anhydrase II, whose active site harbors a conserved network of structural water molecules that are essential for enzymatic catalysis. Inhibitor binding disrupts this water network and changes the hydrogen-bonding patterns in the active site. Here, we use atomistic molecular dynamics simulations to compute the absolute entropy of the individual water molecules confined in the active site of hCAII using a spectrally resolved estimation (SRE) approach. The entropy decrease of water molecules that remain in the active site upon binding of a dorzolamide inhibitor is caused by changes in hydrogen bonding and stiffening of the hydrogen-bonding network. Overall, this entropy decrease is overcompensated by the gain due to the release of three water molecules from the active site upon inhibitor binding. The spectral density calculations enable the assignment of the changes to certain vibrational modes. In addition, the range of applicability of the SRE approximation is systematically explored by exploiting the gradually changing degree of immobilization of water molecules as a function of the distance to a phospholipid bilayer surface, which defines an "entropy ruler". These results demonstrate the applicability of SRE to biomolecular solvation, and we expect it to become a useful method for entropy calculations in biomolecular systems.
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Affiliation(s)
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | | | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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Päslack C, Schäfer LV, Heyden M. Protein flexibility reduces solvent-mediated friction barriers of ligand binding to a hydrophobic surface patch. Phys Chem Chem Phys 2021; 23:5665-5672. [PMID: 33656505 DOI: 10.1039/d1cp00181g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Solvent fluctuations have been explored in detail for idealized and rigid hydrophobic model systems, but so far it has remained unclear how internal protein motions and their coupling to the surrounding solvent affect the dynamics of ligand binding to biomolecular surfaces. Here, molecular dynamics simulations were used to elucidate the solvent-mediated binding of a model ligand to the hydrophobic surface patch of ubiquitin. The ligand's friction profiles reveal pronounced long-time correlations and enhanced friction in the vicinity of the protein, similar to idealized hydrophobic surfaces. Interestingly, these effects are shaped by internal protein motions. Protein flexibility modulates water density fluctuations near the hydrophobic surface patch and smooths out the friction profile of ligand binding.
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Affiliation(s)
- Christopher Päslack
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Lars V Schäfer
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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Singh H, Vasa SK, Jangra H, Rovó P, Päslack C, Das CK, Zipse H, Schäfer LV, Linser R. Fast Microsecond Dynamics of the Protein–Water Network in the Active Site of Human Carbonic Anhydrase II Studied by Solid-State NMR Spectroscopy. J Am Chem Soc 2019; 141:19276-19288. [DOI: 10.1021/jacs.9b05311] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Himanshu Singh
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Suresh K. Vasa
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Harish Jangra
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Petra Rovó
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Christopher Päslack
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Chandan K. Das
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Hendrik Zipse
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Rasmus Linser
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
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Abstract
Water mediates correlated vibrations of atoms of protein and membrane bilayer surfaces.
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Affiliation(s)
- Christopher Päslack
- Center for Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Lars V. Schäfer
- Center for Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Matthias Heyden
- School of Molecular Sciences
- Arizona State University
- Tempe
- USA
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Päslack C, Smith JC, Heyden M, Schäfer LV. Hydration-mediated stiffening of collective membrane dynamics by cholesterol. Phys Chem Chem Phys 2019; 21:10370-10376. [DOI: 10.1039/c9cp01431d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration water governs the cholesterol-induced changes in collective headgroup dynamics in lipid bilayers.
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Affiliation(s)
- Christopher Päslack
- Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- D-44780 Bochum
- Germany
| | - Jeremy C. Smith
- Center for Molecular Biophysics
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Department of Biochemistry and Cellular and Molecular Biology
| | - Matthias Heyden
- School of Molecular Sciences
- Arizona State University
- Tempe
- USA
| | - Lars V. Schäfer
- Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- D-44780 Bochum
- Germany
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Fisette O, Päslack C, Barnes R, Isas JM, Langen R, Heyden M, Han S, Schäfer LV. Hydration Dynamics of a Peripheral Membrane Protein. J Am Chem Soc 2016; 138:11526-35. [PMID: 27548572 DOI: 10.1021/jacs.6b07005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Water dynamics in the hydration shell of the peripheral membrane protein annexin B12 were studied using MD simulations and Overhauser DNP-enhanced NMR. We show that retardation of water motions near phospholipid bilayers is extended by the presence of a membrane-bound protein, up to around 10 Å above that protein. Near the membrane surface, electrostatic interactions with the lipid head groups strongly slow down water dynamics, whereas protein-induced water retardation is weaker and dominates only at distances beyond 10 Å from the membrane surface. The results can be understood from a simple model based on additive contributions from the membrane and the protein to the activation free energy barriers of water diffusion next to the biomolecular surfaces. Furthermore, analysis of the intermolecular vibrations of the water network reveals that retarded water motions near the membrane shift the vibrational modes to higher frequencies, which we used to identify an entropy gradient from the membrane surface toward the bulk water. Our results have implications for processes that take place at lipid membrane surfaces, including molecular recognition, binding, and protein-protein interactions.
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Affiliation(s)
- Olivier Fisette
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany
| | - Christopher Päslack
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany.,Max-Planck Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Ryan Barnes
- Department of Chemistry and Biochemistry and Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - J Mario Isas
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California 90089, United States
| | - Ralf Langen
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California 90089, United States
| | - Matthias Heyden
- Max-Planck Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Songi Han
- Department of Chemistry and Biochemistry and Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany
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