@article{HornemannEichertHoehletal.2022,
  author    = {Hornemann, Andrea and Eichert, Diane Madeleine and Hoehl, Arne and Tiersch, Brigitte and Ulm, Gerhard and Ryadnov, Maxim G. and Beckhoff, Burkhard},
  title     = {Investigating Membrane-Mediated Antimicrobial Peptide Interactions with Synchrotron Radiation Far-Infrared Spectroscopy},
  series = {ChemPhysChem : a European journal of chemical physics and physical chemistry},
  volume    = {23},
  journal   = {ChemPhysChem : a European journal of chemical physics and physical chemistry},
  number    = {4},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1439-4235},
  doi       = {10.1002/cphc.202100815},
  pages     = {11},
  year      = {2022},
  abstract  = {Synchrotron radiation-based Fourier transform infrared spectroscopy enables access to vibrational information from mid over far infrared to even terahertz domains. This information may prove critical for the elucidation of fundamental bio-molecular phenomena including folding-mediated innate host defence mechanisms. Antimicrobial peptides (AMPs) represent one of such phenomena. These are major effector molecules of the innate immune system, which favour attack on microbial membranes. AMPs recognise and bind to the membranes whereupon they assemble into pores or channels destabilising the membranes leading to cell death. However, specific molecular interactions responsible for antimicrobial activities have yet to be fully understood. Herein we probe such interactions by assessing molecular specific variations in the near-THz 400-40 cm(-1) range for defined helical AMP templates in reconstituted phospholipid membranes. In particular, we show that a temperature-dependent spectroscopic analysis, supported by 2D correlative tools, provides direct evidence for the membrane-induced and folding-mediated activity of AMPs. The far-FTIR study offers a direct and information-rich probe of membrane-related antimicrobial interactions.},
  language  = {en}
}
@phdthesis{Gomez2016,
  author    = {Gomez, David},
  title     = {Mechanisms of biochemical reactions within crowded environments},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94593},
  school      = {Universit{\"a}t Potsdam},
  pages     = {vii, 112},
  year      = {2016},
  abstract  = {The cell interior is a highly packed environment in which biological macromolecules evolve and function. This crowded media has effects in many biological processes such as protein-protein binding, gene regulation, and protein folding. Thus, biochemical reactions that take place in such crowded conditions differ from diluted test tube conditions, and a considerable effort has been invested in order to understand such differences. In this work, we combine different computationally tools to disentangle the effects of molecular crowding on biochemical processes. First, we propose a lattice model to study the implications of molecular crowding on enzymatic reactions. We provide a detailed picture of how crowding affects binding and unbinding events and how the separate effects of crowding on binding equilibrium act together. Then, we implement a lattice model to study the effects of molecular crowding on facilitated diffusion. We find that obstacles on the DNA impair facilitated diffusion. However, the extent of this effect depends on how dynamic obstacles are on the DNA. For the scenario in which crowders are only present in the bulk solution, we find that at some conditions presence of crowding agents can enhance specific-DNA binding. Finally, we make use of structure-based techniques to look at the impact of the presence of crowders on the folding a protein. We find that polymeric crowders have stronger effects on protein stability than spherical crowders. The strength of this effect increases as the polymeric crowders become longer. The methods we propose here are general and can also be applied to more complicated systems.},
  language  = {en}
}
@phdthesis{Weikl2007,
  author    = {Weikl, Thomas R.},
  title     = {Transition states and loop-closure principles in protein folding},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-26975},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Proteins are chain molecules built from amino acids. The precise sequence of the 20 different types of amino acids in a protein chain defines into which structure a protein folds, and the three-dimensional structure in turn specifies the biological function of the protein. The reliable folding of proteins is a prerequisite for their robust function. Misfolding can lead to protein aggregates that cause severe diseases, such as Alzheimer's, Parkinson's, or the variant Creutzfeldt-Jakob disease. Small single-domain proteins often fold without experimentally detectable metastable intermediate states. The folding dynamics of these proteins is thought to be governed by a single transition-state barrier between the unfolded and the folded state. The transition state is highly instable and cannot be observed directly. However, mutations in which a single amino acid of the protein is substituted by another one can provide indirect access. The mutations slightly change the transition-state barrier and, thus, the folding and unfolding times of the protein. The central question is how to reconstruct the transition state from the observed changes in folding times. In this habilitation thesis, a novel method to extract structural information on transition states from mutational data is presented. The method is based on (i) the cooperativity of structural elements such as alpha-helices and beta-hairpins, and (ii) on splitting up mutation-induced free-energy changes into components for these elements. By fitting few parameters, the method reveals the degree of structure formation of alpha-helices and beta-hairpins in the transition state. In addition, it is shown in this thesis that the folding routes of small single-domain proteins are dominated by loop-closure dependencies between the structural elements.},
  language  = {en}
}