Sandra Luber

S1-State Model of the O2-Evolving Complex of Photosystem II

We introduce a quantum mechanics/molecular mechanics model of the oxygen-evolving complex of photosystem II in the S(1) Mn(4)(IV,III,IV,III) state, where Ca(2+) is bridged to manganese centers by the carboxylate moieties of D170 and A344 on the basis of the new X-ray diffraction (XRD) model recently reported at 1.9 Å resolution. The model is also consistent with high-resolution spectroscopic data, including polarized extended X-ray absorption fine structure data of oriented single crystals. Our results provide refined intermetallic distances within the Mn cluster and suggest that the XRD model most likely corresponds to a mixture of oxidation states, including species more reduced than those observed in the catalytic cycle of water splitting.

Closer to Photosystem II: A Co4O4 Cubane Catalyst with Flexible Ligand Architecture

We introduce the novel Co4O4 complex [Co(II)4(hmp)4(μ-OAc)2(μ2-OAc)2(H2O)2] (1) (hmp = 2-(hydroxymethyl)pyridine) as the first Co(II)-based cubane water oxidation catalyst. Monodentate acetate and aqua ligands lend the flexible environment of 1 closest resemblance to photosystem II among its tetranuclear mimics to date. Visible-light-driven catalytic activity of 1 increases with pH value through aqua ligand deprotonation. The Co(II) core combines robustness and stability with flexibility through a new type of water-oxidation mechanism via mobile ligands.

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression

Eukaryotic cells express a large variety of ribonucleic acid-(RNA)-binding proteins (RBPs) with diverse affinity and specificity towards target RNAs that play a crucial role in almost every aspect of RNA metabolism. In addition, specific domains in RBPs impart catalytic activity or mediate protein-protein interactions, making RBPs versatile regulators of gene expression. In this review, we elaborate on recent experimental and computational approaches that have increased our understanding of RNA-protein interactions and their role in cellular function. We review aspects of gene expression that are modulated post-transcriptionally by RBPs, namely the stability of polymerase II-derived mRNA transcripts and their rate of translation into proteins. We further highlight the extensive regulatory networks of RBPs that implement a combinatorial control of gene expression. Taking cues from the recent development in the field, we argue that understanding spatio-temporal RNA-protein association on a transcriptome level will provide invaluable and unexpected insights into the regulatory codes that define growth, differentiation and disease.

Structural-functional role of chloride in photosystem II.

Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 Å resolution. We find that chloride depletion induces formation of a salt bridge between D2-K317 and D1-D61 that could suppress the transfer of protons to the lumen.

3d–4f {CoII3Ln(OR)4} Cubanes as Bio-Inspired Water Oxidation Catalysts

Although the {CaMn4O5} oxygen evolving complex (OEC) of photosystem II is a major paradigm for water oxidation catalyst (WOC) development, the comprehensive translation of its key features into active molecular WOCs remains challenging. The [Co(II)3Ln(hmp)4(OAc)5H2O] ({Co(II)3Ln(OR)4}; Ln = Ho-Yb, hmp = 2-(hydroxymethyl)pyridine) cubane WOC series is introduced as a new springboard to address crucial design parameters, ranging from nuclearity and redox-inactive promoters to operational stability and ligand exchange properties. The {Co(II)3Ln(OR)4} cubanes promote bioinspired WOC design by newly combining Ln(3+) centers as redox-inactive Ca(2+) analogues with flexible aqua-/acetate ligands into active and stable WOCs (max. TON/TOF values of 211/9 s(-1)). Furthermore, they open up the important family of 3d-4f complexes for photocatalytic applications. The stability of the {Co(II)3Ln(OR)4} WOCs under photocatalytic conditions is demonstrated with a comprehensive analytical strategy including trace metal analyses and solution-based X-ray absorption spectroscopy (XAS) investigations. The productive influence of the Ln(3+) centers is linked to favorable ligand mobility, and the experimental trends are substantiated with Born-Oppenheimer molecular dynamics studies.

Analysis of secondary structure effects on the IR and Raman spectra of polypeptides in terms of localized vibrations.

We demonstrate how the recently developed methodology for the analysis of calculated vibrational spectra in terms of localized modes [J. Chem. Phys. 2009, 130, 084106] can be applied to investigate the influence of the secondary structure on infrared and Raman spectra of polypeptides. As a model system, a polypeptide consisting of 20 (S)-alanine residues in the conformation of an alpha-helix and of a 3(10)-helix is considered. Several features of the calculated spectra are analyzed in detail. First, we show for the amide II band how localized modes facilitate the decomposition of the total Raman intensities into contributions of certain groups of atoms, and how such an analysis can be used to identify the origin of differences in Raman intensity of the two helices. Second, we demonstrate how the shift of the position of the amide I band between the two considered structures can be rationalized and how the observed intensity distribution within the amide I band can be explained by considering the coupling constants between the localized modes. Third, we show how localized modes can be employed to analyze the positions of the bands found in the extended amide III region and how such an analysis makes it possible to gain a better understanding of how structural changes influence the coupling between the amide III and the C(alpha)-H bending modes in this region.

Understanding the Signatures of Secondary‐Structure Elements in Proteins with Raman Optical Activity Spectroscopy

A prerequisite for the understanding of functional molecules like proteins is the elucidation of their structure under reaction conditions. Chiral vibrational spectroscopy is one option for this purpose, but provides only indirect access to this structural information. By first-principles calculations, we investigate how Raman optical activity (ROA) signals in proteins are generated and how signatures of specific secondary-structure elements arise. As a first target we focus on helical motifs and consider polypeptides consisting of twenty alanine residues to represent alpha-helical and 3(10)-helical secondary-structure elements. Although ROA calculations on such large molecules have not been carried out before, our main goal is the stepwise reconstruction of the ROA signals. By analyzing the calculated ROA spectra in terms of rigorously defined localized vibrations, we investigate in detail how total band intensities and band shapes emerge. We find that the total band intensities can be understood in terms of the reconstructed localized vibrations on individual amino acid residues. Two different basic mechanisms determining the total band intensities can be established, and it is explained how structural changes affect the total band intensities. The band shapes can be rationalized in terms of the coupling between the localized vibrations on different residues, and we show how different band shapes arise as a consequence of different coupling patterns. As a result, it is demonstrated for the chiral variant of Raman spectroscopy how collective vibrations in proteins can be understood in terms of well-defined localized vibrations. Based on our calculations, we extract characteristic ROA signatures of alpha helices and of 3(10)-helices, which our analysis directly relates to differences in secondary structure.

Theoretical Raman Optical Activity Study of the β Domain of Rat Metallothionein

We present the calculated vibrational Raman optical activity (ROA) spectrum of the beta domain of rat metallothionein, which is the by far largest molecule for which full ab initio ROA calculations have been performed up to date with more than 400 atoms. While ROA signatures of regular secondary structure elements like beta-sheets and alpha-helices can be conveniently studied in terms of small model structures, this is no longer possible for more irregular proteins like metallothionein. The only secondary structure elements occurring in the molecule are turns, in particular beta turns. Our calculations reveal that especially bands in the wavenumber range from about 1100 to 1400 cm(-1) may be employed as signatures of such beta turns. This is also found in comparison to experimental data. In addition, good agreement between calculated and experimental spectra is found.

Calculated Raman Optical Activity Signatures of Tryptophan Side Chains

Vibrational Raman optical activity (ROA) spectroscopy measures the difference in Raman scattering intensity of chiral molecules in rightand left-polarized incident light, and allows one to determine the structure and absolute configuration of biomolecules in aqueous solution. While most bands in the ROA spectra of proteins are assigned to the peptide backbone and can provide information on secondary structure elements (see, e.g. , ref. [3] for experimental work and refs. [4, 5] for theoretical studies), some bands are related to the conformation of specific side chains. By comparing the ROA backscattering spectra of different viral coat proteins, Blanch et al. suggested that a ROA band at 1550 cm , which is assigned to the W3 vibration of the indole ring in tryptophan, can be used to determine the absolute stereochemistry of the tryptophan side chain. While it had been shown earlier in an analysis of the Raman spectra of different crystalline tryptophan derivatives that the wavenumber of this W3 vibration correlates with the magnitude of the c torsion angle (see Figure 1 for the definition of this angle), they inferred that its sign can be deduced

MOVIPAC: Vibrational spectroscopy with a robust meta‐program for massively parallel standard and inverse calculations

We present the software package MOVIPAC for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. MOVIPAC unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add‐ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta‐program design, MOVIPAC focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode‐ and Intensity‐Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π‐helix consisting of 20 (S)‐alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α‐ and 310‐helical analogs.