X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-ångström resolutions

Hydrogen atoms are critical to the nature and properties of proteins, and thus deuteration has the potential to influence protein function. In fact, it has been reported that some deuterated proteins show different physical and chemical properties to their protiated counterparts. Consequently, it is important to investigate protonation states around the active site when using deuterated proteins. Here, hydrogen isotope effects on the S65T/F99S/M153T/V163A variant of green fluorescent protein (GFP), in which the deprotonated B form is dominant at pH 8.5, were investigated. The pH/pD dependence of the absorption and fluorescence spectra indicates that the protonation state of the chromophore is the same in protiated GFP in H2O and protiated GFP in D2O at pH/pD 8.5, while the pK a of the chromophore became higher in D2O. Indeed, X-ray crystallographic analyses at sub-ångström resolution revealed no apparent changes in the protonation state of the chromophore between the two samples. However, detailed comparisons of the hydrogen OMIT maps revealed that the protonation state of His148 in the vicinity of the chromophore differed between the two samples. This indicates that protonation states around the active site should be carefully adjusted to be the same as those of the protiated protein when neutron crystallographic analyses of proteins are performed.

Alpha protons as NMR probes in deuterated proteins

We describe a new labeling method that allows for full protonation at the backbone Hα position, maintaining protein side chains with a high level of deuteration. We refer to the method as alpha proton exchange by transamination (α-PET) since it relies on transaminase activity demonstrated here using Escherichia coli expression. We show that α-PET labeling is particularly useful in improving structural characterization of solid proteins by introduction of an additional proton reporter, while eliminating many strong dipolar couplings. The approach benefits from the high sensitivity associated with 1.3 mm samples, more abundant information including Hα resonances, and the narrow proton linewidths encountered for highly deuterated proteins. The labeling strategy solves amide proton exchange problems commonly encountered for membrane proteins when using perdeuteration and backexchange protocols, allowing access to alpha and all amide protons including those in exchange-protected regions. The incorporation of Hα protons provides new insights, as the close Hα–Hα and Hα–HN contacts present in β-sheets become accessible, improving the chance to determine the protein structure as compared with HN–HN contacts alone. Protonation of the Hα position higher than 90% is achieved for Ile, Leu, Phe, Tyr, Met, Val, Ala, Gln, Asn, Thr, Ser, Glu, Asp even though LAAO is only active at this degree for Ile, Leu, Phe, Tyr, Trp, Met. Additionally, the glycine methylene carbon is labeled preferentially with a single deuteron, allowing stereospecific assignment of glycine alpha protons. In solution, we show that the high deuteration level dramatically reduces R2 relaxation rates, which is beneficial for the study of large proteins and protein dynamics. We demonstrate the method using two model systems, as well as a 32 kDa membrane protein, hVDAC1, showing the applicability of the method to study membrane proteins.

Notes On Synthesis Of Perdeutero-5-13C,5,5,5-Trifluoroisoleucine VI

The 13CF3 group is a promising label for heteronuclear (19F,13C) NMR studies of proteins. Desirable locations for this NMR spin label include the branched chain amino acid methyl groups. It is known that replacement of CH3 by CF3 at such locations preserves protein structure and function and enhances stability. In particular, 13CF3 may be introduced at the δ position of isoleucine and incorporated biosynthetically in highly deuterated proteins. This paper reports our work in synthesis and purification of 5,5,5-trifluoroisoleucine, its perdeutero and 5-13C versions and of 2-13C-trifluoroacetate and its utility as a precursor for introduction of the 13CF3 group into proteins.

Backbone assignment for minimal protein amounts of low structural homogeneity in the absence of deuteration

A set of higher-dimensionality 1H-detected experiments is introduced for assigning non-deuterated proteins with low sample homogeneity at fast MAS.

Access to aliphatic protons as reporters in non-deuterated proteins by solid-state NMR

Aliphatic protons as reporters: aliphatic protons are abundant nuclei in biopolymers and rich in spectroscopic, chemical, and biophysical information. Readout of individual proton chemical shifts with a backbone amide resolution via iSOCP enables facilitated access to this information content despite minimal protein amounts without deuteration.