| 1. |
- Berry, Bruce W., 1974-, et al.
(författare)
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Environmental modulation of protein cation-pi interactions
- 2007
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 129:17, s. 5308+-
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Tidskriftsartikel (refereegranskat)abstract
- Protein cation-pi interactions are frequently found near the protein surface with their interacting residues partly solvent exposed. The structurally characterized alpha W-3 model protein contains the W32/K36 cation-pi interaction which has properties similar to those of naturally occurring protein cation-pi interactions. alpha W-3 was studied with the following results: Cation-pi interactions formed by a buried tryptophan and a partly solvated lysine, arginine, or histidine range from -0.8 to -0.5 kcal mol(-1) and rank as: W32/K36 approximate to W32/R36 > W32/H36. The W32/K36 pair in alpha W-3 represents the first W/K cation-pi interaction for which both the structure and the bond energy have been experimentally determined. Upon increasing the solvent exposure of the cation-pi pair, the W/K interaction energy drops from -0.73 to -0.06 and +0.15 kcal mol(-1). These results suggest that solvent exposure can tune the interaction energy between a tryptophan and a lysine by at least 0.9 kcal mol(-1).
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| 2. |
- Berry, Bruce W., 1974-, et al.
(författare)
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Reversible voltammograms and a Pourbaix diagram for a protein tyrosine radical
- 2012
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:25, s. 9739-9743
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Tidskriftsartikel (refereegranskat)abstract
- Reversible voltammograms and a voltammetry half-wave potential versus solution pH diagram are described for a protein tyrosine radical. This work required a de novo designed tyrosine-radical protein displaying a unique combination of structural and electrochemical properties. The alpha Y-3 protein is structurally stable across a broad pH range. The redox-active tyrosine Y32 resides in a desolvated and well-structured environment. Y32 gives rise to reversible square-wave and differential pulse voltammograms at alkaline pH. The formal potential of the Y32-O-center dot/Y32-OH redox couple is determined to 918 +/- 2 mV versus the normal hydrogen electrode at pH 8.40 +/- 0.01. The observation that Y32 gives rise to fully reversible voltammograms translates into an estimated lifetime of >= 30 ms for the Y32-O-center dot state. This illustrates the range of tyrosine-radical stabilization that a structured protein can offer. Y32 gives rise to quasireversible square-wave and differential pulse voltammograms at acidic pH. These voltammograms represent the Y32 species at the upper edge of the quasirevesible range. The square-wave net potential closely approximates the formal potential of the Y32-O center dot/Y32-OH redox couple to 1,070 +/- 1 mV versus the normal hydrogen electrode at pH 5.52 +/- 0.01. The differential pulse voltammetry half-wave potential of the Y32-O-center dot/Y32-OH redox pair is measured between pH 4.7 and 9.0. These results are described and analyzed.
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| 3. |
- Berry, Bruce W., 1974-
(författare)
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Using de novo design proteins to explore tyrosine radicals and cation-π interactions
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Redox cofactors and amino-acid free radicals play important roles in biology. Although many of the same cofactors and amino acids that form these radicals are found across a broad range of biological systems, identical cofactors can have different reduction potentials. The local environment plays a role in defining these redox potentials. An understanding of this local-environment effect can shed more light on how redox chemistry works in nature. Our laboratory has developed a library of model proteins that are well suited to study amino-acid radicals. a3X is a de novo designed protein that is composed of 67 residues. It forms a three-helix bundle connected by two glycine loops. The radical site is located at position 32 on the central a-helix. The a3X protein is designed to be well-folded and thermodynamically stable across a broad pH range. Paper 1 describes the structural and electrochemical characterization of a3Y, a tyrosine variant of a3X. We were able to obtain a unique Faradaic response from Y32 at both low and high pH, using differential pulse voltammetry. In addition, we successfully redesigned α3Y by introducing a histidine in close proximity to Y32, creating a tyrosine/histidine pair. Our goal in creating this pair was to study proton-coupled electron transfer (PCET) in a well-structured and solvent-sequestered protein environment. In paper 2 we illustrated the redox reversibility of Y32 and produced the first ever Pourbaix diagram for a tyrosine radical in a protein. The formal potential of the Y32-OŸ/Y32-OH redox couple was determined to be 918 ± 2 mV vs. the normal hydrogen electrode (NHE) at pH 8.40. While at pH 5.52, the formal potential of the Y32-OŸ/Y32-OH redox couple was recorded at 1.07 V. Papers 3 and 4 utilize a3W to study cation-π interactions. In paper 3, we showed how solvation can affect the strength of these interactions by -0.9 kcal/mol. In Paper 4, we were able to monitor the disruption of the cation-π interaction with the use of high-pressure fluorescence and were able to calculate the interaction energy for a solvent exposed cation-π. The aim of the work described in this thesis was to use model proteins to study tyrosine radicals to gain a broader perspective and better understanding of the versatility of biological electron transfer and to measure cation-π interactions and how they behave in different environments.
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