On the Folding and Conformation of Peptides and the Development of Novel Methods for Their Study

Proteins are polymers, whose complex chemistry and physics, in the course of evo- lution, permitted their recruitment for immensely diverse functions in the biological machinery. Therefore, the study of protein conformational behavior and interactions of proteins with other entities of the intra- and extra-cellular milieu is of great inter- est. In this Thesis, we do not only quantitatively study the folding of peptide and protein systems using well-established spectroscopic techniques, but also, in recognizing the limits of existing experimental techniques, develop novel methods for studying protein folding, protein-protein and protein-membrane interactions.In the first part of this Thesis, we are concerned with studying the folding process under various conditions using small peptides or proteins as model systems that al- low a tractable, quantitative description of the order-disorder transition. Employing a combined site-directed mutagenesis/temperature-jump kinetics approach, we eluci- dated the folding mechanism of a helical hairpin, which is an important intermediate in protein folding reactions. We further considered how the folding kinetics of such model peptides and proteins are altered in the presence of high concentrations of macromolecular cosolutes, which are thought to provide a simplified model system for the interior of the cellular environment. In another study, we addressed current questions concerning the structural properties of the unfolded state ensemble using a polypeptide that is unstructured by design as a model system. The second part of this Thesis is focused on the development of novel methods to study both protein folding and interactions of proteins with other molecular species. In recent years, the nitrile stretching bands of nitrile-derivatized amino acid side- chains have emerged as attractive probes for monitoring biomolecular processes. In this Thesis, we theoretically and experimentally studied the molecular determinants of the bandwidth of the nitrile stretching band of 5-cyanotryptophan. We further evaluated the feasibility of using light-induced reductive cleavage of disulfide bonds as a means to phototrigger protein folding reactions

Quasiparticle interfacial level alignment of highly hybridized frontier levels: H2_2O on TiO2_2(110)

Knowledge of the frontier levels' alignment prior to photo-irradiation is necessary to achieve a complete quantitative description of H$_2$O photocatalysis on TiO$_2$(110). Although H$_2$O on rutile TiO$_2$(110) has been thoroughly studied both experimentally and theoretically, a quantitative value for the energy of the highest H$_2$O occupied levels is still lacking. For experiment, this is due to the H$_2$O levels being obscured by hybridization with TiO$_2$(110) levels in the difference spectra obtained via ultraviolet photoemission spectroscopy (UPS). For theory, this is due to inherent difficulties in properly describing many-body effects at the H$_2$O-TiO$_2$(110) interface. Using the projected density of states (DOS) from state-of-the-art quasiparticle (QP) $G_0W_0$, we disentangle the adsorbate and surface contributions to the complex UPS spectra of H$_2$O on TiO$_2$(110). We perform this separation as a function of H$_2$O coverage and dissociation on stoichiometric and reduced surfaces. Due to hybridization with the TiO$_2$(110) surface, the H$_2$O 3a$_1$ and 1b$_1$ levels are broadened into several peaks between 5 and 1 eV below the TiO$_2$(110) valence band maximum (VBM). These peaks have both intermolecular and interfacial bonding and antibonding character. We find the highest occupied levels of H$_2$O adsorbed intact and dissociated on stoichiometric TiO$_2$(110) are 1.1 and 0.9 eV below the VBM. We also find a similar energy of 1.1 eV for the highest occupied levels of H$_2$O when adsorbed dissociatively on a bridging O vacancy of the reduced surface. In both cases, these energies are significantly higher (by 0.6 to 2.6 eV) than those estimated from UPS difference spectra, which are inconclusive in this energy region. Finally, we apply self-consistent QP$GW$ (scQP$GW$1) to obtain the ionization potential of the H$_2$O-TiO$_2$(110) interface.Comment: 12 pages, 12 figures, 1 tabl

Towards a multisensor station for automated biodiversity monitoring

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Changes in organismal abundance and diversity are barely documented. Censuses of species are usually fragmentary and inferred by often spatially, temporally and ecologically unsatisfactory simple species lists for individual study sites. Thus, detrimental global processes and their drivers often remain unrevealed. A major impediment to monitoring species diversity is the lack of human taxonomic expertise that is implicitly required for large-scale and fine-grained assessments. Another is the large amount of personnel and associated costs needed to cover large scales, or the inaccessibility of remote but nonetheless affected areas. To overcome these limitations we propose a network of Automated Multisensor stations for Monitoring of species Diversity (AMMODs) to pave the way for a new generation of biodiversity assessment centers. This network combines cutting-edge technologies with biodiversity informatics and expert systems that conserve expert knowledge. Each AMMOD station combines autonomous samplers for insects, pollen and spores, audio recorders for vocalizing animals, sensors for volatile organic compounds emitted by plants (pVOCs) and camera traps for mammals and small invertebrates. AMMODs are largely self-containing and have the ability to pre-process data (e.g. for noise filtering) prior to transmission to receiver stations for storage, integration and analyses. Installation on sites that are difficult to access require a sophisticated and challenging system design with optimum balance between power requirements, bandwidth for data transmission, required service, and operation under all environmental conditions for years. An important prerequisite for automated species identification are databases of DNA barcodes, animal sounds, for pVOCs, and images used as training data for automated species identification. AMMOD stations thus become a key component to advance the field of biodiversity monitoring for research and policy by delivering biodiversity data at an unprecedented spatial and temporal resolution. (C) 2022 Published by Elsevier GmbH on behalf of Gesellschaft fur Okologie

CORUM: the comprehensive resource of mammalian protein complexes

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes. For functional annotation, we use the FunCat catalogue that enables to organize the protein complex space into biologically meaningful subsets. The database contains more than 1750 protein complexes that are built from 2400 different genes, thus representing 12% of the protein-coding genes in human. A web-based system is available to query, view and download the data. CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases. Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes

Current Status and Future Prospects of Next-Generation Data Management and Analytical Decision Support Tools for Enhancing Genetic Gains in Crops

Agricultural disciplines are becoming data intensive and the agricultural research data generation technologies are becoming sophisticated and high throughput. On the one hand, high-throughput genotyping is generating petabytes of data; on the other hand, high-throughput phenotyping platforms are also generating data of similar magnitude. Under modern integrated crop breeding, scientists are working together by integrating genomic and phenomic data sets of huge data volumes on a routine basis. To manage such huge research data sets and use them appropriately in decision making, Data Management Analysis & Decision Support Tools (DMASTs) are a prerequisite. DMASTs are required for a range of operations including generating the correct breeding experiments, maintaining pedigrees, managing phenotypic data, storing and retrieving high-throughput genotypic data, performing analytics, including trial analysis, spatial adjustments, identifications of MTAs, predicting Genomic Breeding Values (GEBVs), and various selection indices. DMASTs are also a prerequisite for understanding trait dynamics, gene action, interactions, biology, GxE, and various other factors contributing to crop improvement programs by integrating data generated from various science streams. These tools have simplified scientists’ lives and empowered them in terms of data storage, data retrieval, data analytics, data visualization, and sharing with other researchers and collaborators. This chapter focuses on availability, uses, and gaps in present-day DMASTs

ESTs in Plants: Where Are We Heading?

Expressed sequence tags (ESTs) are the most important resources for transcriptome exploration. Next-generation sequencing technologies have been generating gigabytes of genetic codes representing genes, partial and whole genomes most of which are EST datasets. Niche of EST in plants for breeding, regulation of gene expression through miRNA studies, and their application for adapting to climatic changes are discussed. Some of the recent tools for analysis of EST exclusive to plants are listed out. Systems biology though in its infancy in plants has influenced EST mapping for unraveling gene regulatory circuits, which is illustrated with a few significant examples. This review throws a glance at the evolving role of ESTs in plants

On the Folding and Conformation of Peptides and the Development of Novel Methods for Their Study

Proteins are polymers, whose complex chemistry and physics, in the course of evo- lution, permitted their recruitment for immensely diverse functions in the biological machinery. Therefore, the study of protein conformational behavior and interactions of proteins with other entities of the intra- and extra-cellular milieu is of great inter- est. In this Thesis, we do not only quantitatively study the folding of peptide and protein systems using well-established spectroscopic techniques, but also, in recognizing the limits of existing experimental techniques, develop novel methods for studying protein folding, protein-protein and protein-membrane interactions.In the first part of this Thesis, we are concerned with studying the folding process under various conditions using small peptides or proteins as model systems that al- low a tractable, quantitative description of the order-disorder transition. Employing a combined site-directed mutagenesis/temperature-jump kinetics approach, we eluci- dated the folding mechanism of a helical hairpin, which is an important intermediate in protein folding reactions. We further considered how the folding kinetics of such model peptides and proteins are altered in the presence of high concentrations of macromolecular cosolutes, which are thought to provide a simplified model system for the interior of the cellular environment. In another study, we addressed current questions concerning the structural properties of the unfolded state ensemble using a polypeptide that is unstructured by design as a model system. The second part of this Thesis is focused on the development of novel methods to study both protein folding and interactions of proteins with other molecular species. In recent years, the nitrile stretching bands of nitrile-derivatized amino acid side- chains have emerged as attractive probes for monitoring biomolecular processes. In this Thesis, we theoretically and experimentally studied the molecular determinants of the bandwidth of the nitrile stretching band of 5-cyanotryptophan. We further evaluated the feasibility of using light-induced reductive cleavage of disulfide bonds as a means to phototrigger protein folding reactions