1
|
Robalo JR, Streacker LM, Mendes de Oliveira D, Imhof P, Ben-Amotz D, Verde AV. Hydrophobic but Water-Friendly: Favorable Water–Perfluoromethyl Interactions Promote Hydration Shell Defects. J Am Chem Soc 2019; 141:15856-15868. [DOI: 10.1021/jacs.9b06862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- João R. Robalo
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany
| | - Louis M. Streacker
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Petra Imhof
- Institute for Theoretical Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ana Vila Verde
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany
| |
Collapse
|
2
|
TOMITA S, YOSHIMOTO K, NIWA O, KURITA R. Protein Sensing Based on Cross-reactive Optical Fingerprinting. BUNSEKI KAGAKU 2017. [DOI: 10.2116/bunsekikagaku.66.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Shunsuke TOMITA
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | | | - Osamu NIWA
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Advanced Science Research Laboratory, Saitama Institute of Technology
| | - Ryoji KURITA
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| |
Collapse
|
3
|
Tomita S, Niwa O, Kurita R. Artificial Modification of an Enzyme for Construction of Cross-Reactive Polyion Complexes To Fingerprint Signatures of Proteins and Mammalian Cells. Anal Chem 2016; 88:9079-86. [DOI: 10.1021/acs.analchem.6b02010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Shunsuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Osamu Niwa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Advanced
Science Research Laboratory, Saitama Institute of Technology, 1690 Fusaiji, Fukaya, Saitama 369-0293, Japan
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| |
Collapse
|
4
|
Clark GA, Baleja JD, Kumar K. Cross-strand interactions of fluorinated amino acids in β-hairpin constructs. J Am Chem Soc 2012; 134:17912-21. [PMID: 23078597 DOI: 10.1021/ja212080f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We describe herein the design, synthesis, and thermodynamic characterization of fluorinated β-hairpin constructs. Introduction of hexafluoroleucine (Hfl) did not perturb β-hairpin formation, as judged by (1)H NMR structures of four peptides determined to <1 Å backbone RMSDs, allowing direct comparison of thermodynamic stabilities of fluorinated peptides to their hydrocarbon counterparts. Judicious fluorination of peptides often results in increased thermal and chemical stability of the resultant folded structures. However, we found that when cross-strand residue partners were varied, the side-chain interaction energies followed the order Leu-Leu > Hfl-Leu > Hfl-Hfl. All peptides were more structured in 90% MeOH than in aqueous buffers. The peptides with Hfl-Leu or Hfl-Hfl cross-strand partners showed increased interaction energies in this solvent compared to those in water, in contrast to the insignificant effect on Leu-Leu. Our results inform the binding and assembly of peptides containing Hfl in the context of β-sheet structures and may be useful in interpreting binding of fluorinated ligands and peptides to biological targets.
Collapse
Affiliation(s)
- Ginevra A Clark
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, USA
| | | | | |
Collapse
|
5
|
Mecinović J, Snyder PW, Mirica KA, Bai S, Mack ET, Kwant RL, Moustakas DT, Heroux A, Whitesides GM. Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase. J Am Chem Soc 2011; 133:14017-26. [PMID: 21790183 PMCID: PMC3171206 DOI: 10.1021/ja2045293] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The hydrophobic effect, the free-energetically favorable association of nonpolar solutes in water, makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different but structurally similar hydrophobic groups, aliphatic hydrocarbons and aliphatic fluorocarbons, and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H(2)NSO(2)C(6)H(4)-CONHCH(2)(CX(2))(n)CX(3), n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of nonoptimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks of hydrogen bonds among molecules of water) and entropy (from release of water from configurationally restricted positions).
Collapse
Affiliation(s)
- Jasmin Mecinović
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Phillip W. Snyder
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Katherine A. Mirica
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Serena Bai
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Eric T. Mack
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Richard L. Kwant
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Demetri T. Moustakas
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Annie Heroux
- National Synchrotron Light Source, Brookhaven National Laboratory, 725 Brookhaven Avenue, Upton, NY 11973-5000
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
- Wyss Institute for Biologically Inspired Engineering, 725 Brookhaven Avenue, Upton, NY 11973-5000
| |
Collapse
|