Moritz J. Schmidt

A Genetically Encoded Spin Label for Electron Paramagnetic Resonance Distance Measurements

We report the genetic encoding of a noncanonical, spin-labeled amino acid in Escherichia coli. This enables the intracellular biosynthesis of spin-labeled proteins and obviates the need for any chemical labeling step usually required for protein electron paramagnetic resonance (EPR) studies. The amino acid can be introduced at multiple, user-defined sites of a protein and is stable in E. coli even for prolonged expression times. It can report intramolecular distance distributions in proteins by double-electron electron resonance measurements. Moreover, the signal of spin-labeled protein can be selectively detected in cells. This provides elegant new perspectives for in-cell EPR studies of endogenous proteins.

Site-selective time-resolved laser fluorescence spectroscopy of Eu3+ in calcite.

Three samples of calcite homogeneously doped with Eu(3+) were synthesized in a mixed-flow reactor. By means of selective excitation of the 5D0-->7F0 transition at low temperatures (T<20 K), three different Eu(3+) species (species A, B, and C, respectively) could be discriminated. For each one, the emission spectrum and lifetime were obtained after selective excitation of the single species. On the basis of these data, species C could be identified as Eu(3+) incorporated into the calcite lattice on the (nearly) octahedral Ca(2+) site. Species B was also identified as Eu(3+) incorporated into the calcite lattice, but the ligand field shows a much weaker symmetry. Species A, however, is not incorporated into the crystals bulk, having 1-2 H(2)O ligands left in its first coordination sphere and showing very little symmetry, and is considered as Eu(3+) adsorbed onto the calcite surface. The emission spectra of species C for Eu:calcite grown in the presence of Na(+) were found to differ from those of Eu:calcite synthesized in the presence of K(+). The latter revealed a strong distortion in site symmetry, which was not observed in the samples grown in Na(+) solutions. This finding provides spectroscopic evidence in favor of an incorporation mechanism based on the charge-balanced coupled substitution of Na(+)+Eu(3+)<-->2Ca(2+).

Red-Light-Controlled Protein–RNA Crosslinking with a Genetically Encoded Furan†

Well red: A protein-RNA crosslinker has been genetically encoded that can be controlled with red light, thus offering high penetration depths in biological materials. This should enable the discovery and mapping of transient protein-RNA interactions and enable the design of peptide- and protein-based drugs for RNA-targeted photodynamic therapy.

Programmable and Highly Resolved In Vitro Detection of 5‐Methylcytosine by TALEs

Gene expression is extensively regulated by specific patterns of genomic 5-methylcytosine (mC), but the ability to directly detect this modification at user-defined genomic loci is limited. One reason is the lack of molecules that discriminate between mC and cytosine (C) and at the same time provide inherent, programmable sequence-selectivity. Programmable transcription-activator-like effectors (TALEs) have been observed to exhibit mC-sensitivity in vivo, but to only a limited extent in vitro. We report an mC-detection assay based on TALE control of DNA replication that displays unexpectedly strong mC-discrimination ability in vitro. The status and level of mC modification at single positions in oligonucleotides can be determined unambiguously by this assay, independently of the overall target sequence. Moreover, discrimination is reliably observed for positions bound by N-terminal and central regions of TALEs. This indicates the wide scope and robustness of the approach for highly resolved mC detection and enabled the detection of a single mC in a large, eukaryotic genome.

Evolved Sequence Contexts for Highly Efficient Amber Suppression with Noncanonical Amino Acids

The expansion of the genetic code with noncanonical amino acids (ncAA) enables the function of proteins to be tailored with high molecular precision. In this approach, the ncAA is charged to an orthogonal nonsense suppressor tRNA by an aminoacyl-tRNA-synthetase (aaRS) and incorporated into the target protein in vivo by suppression of nonsense codons in the mRNA during ribosomal translation. Compared to sense codon translation, this process occurs with reduced efficiency. However, it is still poorly understood, how the local sequence context of the nonsense codon affects suppression efficiency. Here, we report sequence contexts for highly efficient suppression of the widely used amber codon in E. coli for the orthogonal Methanocaldococcus jannaschii tRNA(Tyr)/TyrRS and Methanosarcina mazei tRNA(Pyl)/PylRS pairs. In vivo selections of sequence context libraries consisting of each two random codons directly up- and downstream of an amber codon afforded contexts with strong preferences for particular mRNA nucleotides and/or amino acids that markedly differed from preferences of contexts obtained in control selections with sense codons. The contexts provided high amber suppression efficiencies with little ncAA-dependence that were transferrable between proteins and resulted in protein expression levels of 70-110% compared to levels of control proteins without amber codon. These sequence contexts represent stable tags for robust and highly efficient incorporation of ncAA into proteins in standard E. coli strains and provide general design rules for the engineering of amber codons into target genes.

EPR Distance Measurements in Native Proteins with Genetically Encoded Spin Labels.

The genetic encoding of nitroxide amino acids in combination with electron paramagnetic resonance (EPR) distance measurements enables precise structural studies of native proteins, i.e. without the need for mutations to create unique reactive sites for chemical labeling and thus with minimal structural perturbation. We here report on in vitro DEER measurements in native E. coli thioredoxin (TRX) that establish the nitroxide amino acid SLK-1 as a spectroscopic probe that reports distances and conformational flexibilities in the enzyme with nonmutated catalytic centers that are not accessible by the use of the traditional methanethiosulfonate spin label (MTSSL). We generated a rotamer library for SLK-1 that in combination with molecular dynamics (MD) simulation enables predictions of distance distributions between two SLK-1 labels incorporated into a target protein. Toward a routine use of SLK-1 for EPR distance measurements in proteins and the advancement of the approach to intracellular environments, we study the stability of SLK-1 in E. coli cultures and lysates and establish guidelines for protein expression and purification that offer maximal nitroxide stability. These advancements and insights provide new perspectives for facile structural studies of native, endogenous proteins by EPR distance measurements.

Structural Basis of Furan-Amino Acid Recognition by a Polyspecific Aminoacyl-tRNA-Synthetase and its Genetic Encoding in Human Cells.

The site‐selective introduction of photo‐crosslinking groups into proteins enables the discovery and mapping of weak and/or transient protein interactions with high spatiotemporal resolution, both in vitro and in vivo. We report the genetic encoding of a furan‐based, photo‐crosslinking amino acid in human cells; it can be activated with red light, thus offering high penetration depths in biological samples. This is achieved by activation of the amino acid and charging to its cognate tRNA by a pyrrolysyl‐tRNA‐synthetase (PylRS) mutant with broad polyspecificity. To gain insights into the recognition of this amino acid and to provide a rationale for its polyspecificity, we solved three crystal structures of the PylRS mutant: in its apo‐form, in complex with adenosine 5′‐(β,γ‐imido)triphosphate (AMP‐PNP) and in complex with the AMP ester of the furan amino acid. These structures provide clues for the observed polyspecificity and represent a promising starting point for the engineering of PylRS mutants with further increased substrate scope.

Genetic code expansion as a tool to study regulatory processes of transcription.

The expansion of the genetic code with non-canonical amino acids (ncAA) enables the chemical and biophysical properties of proteins to be tailored, inside cells, with a previously unattainable level of precision. A wide range of ncAA with functions not found in canonical amino acids have been genetically encoded in recent years and have delivered insights into biological processes that would be difficult to access with traditional approaches of molecular biology. A major field for the development and application of novel ncAA-functions has been transcription and its regulation. This is particularly attractive, since advanced DNA sequencing- and proteomics-techniques continue to deliver vast information on these processes on a global level, but complementing methodologies to study them on a detailed, molecular level and in living cells have been comparably scarce. In a growing number of studies, genetic code expansion has now been applied to precisely control the chemical properties of transcription factors, RNA polymerases and histones, and this has enabled new insights into their interactions, conformational changes, cellular localizations and the functional roles of posttranslational modifications.

Genetically Encoded Spin Labels for In Vitro and In-Cell EPR Studies of Native Proteins

Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a powerful approach to study the structure, dynamics, and interactions of proteins. The genetic encoding of the noncanonical amino acid spin-labeled lysine 1 (SLK-1) eliminates the need for any chemical labeling steps in SDSL-EPR studies and enables the investigation of native, endogenous proteins with minimal structural perturbation, and without the need to create unique reactive sites for chemical labeling. We report detailed experimental procedures for the efficient synthesis of SLK-1, the expression and purification of SLK-1-containing proteins under conditions that ensure maximal integrity of the nitroxide radical moiety, and procedures for intramolecular EPR distance measurements in proteins by double electron-electron resonance.

Structural Characterization of Aluminum (Oxy)hydroxide Films at the Muscovite (001)-Water Interface

The formation of Al (oxy)hydroxide on the basal surface of muscovite mica was investigated to understand how the structure of the substrate controls the nucleation and growth of secondary phases. Atomic force microscopy images showed that solid phases nucleated on the surface initially as two-dimensional islands that were ≤10 Å in height and ≤200 Å in diameter after 16-50 h of reaction in a 100 μM AlCl3 solution at pH 4.2 at room temperature. High-resolution X-ray reflectivity data indicated that these islands were gibbsite layers whose basic unit is composed of a plane of Al ions octahedrally coordinated to oxygen or hydroxyl groups. The formation of gibbsite layers is likely favored because of the structural similarity between its basal plane and the underlying mica surface. After 700-2000 h of reaction, a thicker and continuous film had formed on top of the initial gibbsite layers. X-ray diffraction data showed that this film was composed of diaspore that grew predominantly with its [040] and [140] crystallographic directions oriented along the muscovite [001] direction. These results show the structural characteristics of the muscovite (001) and Al (oxy)hydroxide film interface where presumed epitaxy had facilitated nucleation of metastable gibbsite layers which acted as a structural anchor for the subsequent growth of thermodynamically stable diaspore grown from a mildly acidic and Al-rich solution.