Location and Conformation of the LK alpha 14 Peptide in Water/Ethanol Mixtures

It is widely recognized that solvation is one of the major factors determining structure and functionality of proteins and long peptides, however it is a formidable challenge to address it both experimentally and computationally. For this reason, simple peptides are used to study fundamental aspects of solvation. It is well established that alcohols can change the peptide conformation and tuning of the alcohol content in solution can dramatically affect folding and, as a consequence, the function of the peptide. In this work, we focus on the leucine and lysine based LK alpha 14 peptide designed to adopt an alpha-helical conformation at an apolar-polar interface. We investigate LK alpha 14 peptide's bulk and interfacial behavior in water/ethanol mixtures combining a suite of experimental techniques (namely, circular dichroism and nuclear magnetic resonance spectroscopy for the bulk solution, surface pressure measurements and vibrational sum frequency generation spectroscopy for the air-solution interface) with molecular dynamics simulations. We observe that ethanol highly affects both the peptide location and conformation. At low ethanol content LK alpha 14 lacks a clear secondary structure in bulk and shows a clear preference to reside at the air-solution interface. When the ethanol content in solution increases, the peptide's interfacial affinity is markedly reduced and the peptide approaches a stable alpha-helical conformation in bulk facilitated by the amphiphilic nature of the ethanol molecules

Ligand-independent oligomerization of TACI is controlled by the transmembrane domain and regulates proliferation of activated B cells.

In mature B cells, TACI controls class-switch recombination and differentiation into plasma cells during T cell-independent antibody responses. TACI binds the ligands BAFF and APRIL. Approximately 10% of patients with common variable immunodeficiency (CVID) carry TACI mutations, of which A181E and C172Y are in the transmembrane domain. Residues A181 and C172 are located on distinct sides of the transmembrane helix, which is predicted by molecular modeling to spontaneously assemble into trimers and dimers. In human B cells, these mutations impair ligand-dependent (C172Y) and -independent (A181E) TACI multimerization and signaling, as well as TACI-enhanced proliferation and/or IgA production. Genetic inactivation of TACI in primary human B cells impaired survival of CpG-activated cells in the absence of ligand. These results identify the transmembrane region of TACI as an active interface for TACI multimerization in signal transduction, in particular for ligand-independent signals. These functions are perturbed by CVID-associated mutations

Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA

Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg2+ ions or by interaction with ribosomal proteins. In order to provide a quantitative description of ion-induced folding of the ∼350 nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg2+ concentration between 0–30 mM. The Mg2+ dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg2+ concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg2+ ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+- induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome

The disordered- and ordered-state structures of κ-carrageenan : an X-ray scattering, molecular dynamics, and density-functional theory study : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University, Palmerston North, New Zealand

κ-carrageenan is a biopolymer extracted from marine algae. It exists in aqueous solution, at high temperatures and/or low salt concentrations as a ‘disordered-state’, and at low temperatures and in the presence of certain salts as an ‘ordered-state’. The transition between disordered- and ordered-states involves molecular structural changes, which are essential to its interesting viscoelastic properties that are routinely exploited in a plethora of applications. Despite this, the molecular conformations of the disordered- and ordered-states, as well as the details of the transitional pathway connecting them, remain a source of contention. While decades of research have amassed a vast trove of information on the disorder-order transition, an atomistic understanding of the structure in solution has remained elusive. This study takes advantages of recent advances in computational capabilities in order to simulate κ-carrageenan solutions on length scales of ∼10 nm over μs time scales, and thus develop atomistic models of the disordered- and ordered-states. Both models are used to calculate wide-angle X-ray scattering profiles, and these are subsequently validated by comparison to data obtained at a synchrotron facility. The models will be further explored using density functional theory to calculate their expected optical rotation behaviour, which finds that the formation of double-helices from single chains is able to explain the increase in optical rotation measured experimentally when transitioning from the disordered to ordered-state. Structural analysis of both experimentally-verified models find the disordered-state to have a significant amount of residual helical secondary-structure, whereas the ordered-state is mostly double-helical. Crucially, simulations show that the ordered-state arises spontaneously from the so-called disordered-state at a rate dependant on salt concentration, without prior uni-molecular changes. The findings of this research are the most detailed model of the disorder-order transition to-date, and demonstrate that the existing paradigm of a ‘coil-to-helix’ transition is in need of revision

Modelling, synthesis and model-based motion planning for hyper-redundant, binary actuated manipulators

Die Untersuchung von schwer zu erreichenden Hohlräumen durch schmale Zugänge wird im technischen Umfeld als Boroskopie und in der Medizin als Endoskopie bezeichnet. Wenn neben der reinen Inspektion auch eine Manipulation erfolgen soll, wird ergänzend zu einer guten Anpassbarkeit an gekrümmte Pfade auch eine stabile Arbeitsplattform zur Aufnahme von Manipulationskräften benötigt. Einen Ansatz, die daraus resultierenden Anforderungen an die verwendeten Systeme zu adressieren, stellen schlangenartige Roboter dar. Ihre hyperredundante Struktur aus einzelnen Stellgliedern bietet eine vielseitige Positionierbarkeit. Die Verwendung von binären, kippstabilen Aktoren beschränkt zwar den Arbeitsraum auf wenige diskrete Punkte, bietet aber – in Abhängigkeit vom Antriebsmechanismus – besonders hohe Haltemomente und ermöglicht damit eine gezielte Systemversteifung. Eine Kombination beider Ansätze zur Klasse der binär aktuierten, hyperredundanten Manipulatoren ist in der Lage, diese Anforderungen zu erfüllen, jedoch existiert deutlicher Forschungsbedarf hinsichtlich Methoden zur optimalen Auslegung sowie zur gezielten Verfolgung von Referenzpfaden, sodass Kern der vorliegenden Arbeit die Erforschung der modellbasierten Bewegungsplanung dieser Roboterklasse ist. Voraussetzung für eine hohe Pfadfolgegenauigkeit ist, dass der Manipulator sich grundsätzlich gut an einen vorgegebenen Referenzpfad anschmiegen kann. Der Einschränkungsgrad durch die diskrete Positionierbarkeit des Manipulators ist dabei abhängig von den geometrischen Parametern der einzelnen Segmente. Die Untersuchungen in dieser Arbeit zeigen, dass durch die Analyse kinematischer Leistungsmerkmale, wie Arbeitsraum(-dichte) oder erzielbarer Krümmungsradius, kein allgemeingültiges optimales Design gefunden werden kann. Daher wird eine Maßsynthese unter Berücksichtigung von Randbedingungen entworfen, in der optimale geometrische Parameter eines einzelnen binären Aktors synthetisiert werden. Darauf aufbauend wird eine Pfadverfolgung gemäß dem „Follow-the-Leader“-Prinzip erarbeitet. Grundidee ist, dass das Endeffektorsegment den Referenzpfad exploriert, während alle weiteren Aktoren dem führenden Segment automatisch folgen. Da binäre Aktoren einen nicht-kontinuierlichen Schaltprozess aufweisen, wird ein modellbasierter Ansatz für die Bestimmung optimaler Schaltsequenzen vorgeschlagen, die zu jedem Zeitpunkt eine hohe Pfadtreue garantieren. Die anschließende experimentelle Evaluation erfolgt nach der Modellierung und Identifikation relevanter Parameter für den Prototyp einer elektromagnetischen Kippaktorkette. Grundsätzlich kann die Funktionsfähigkeit der in dieser Arbeit erforschten Methoden zur Bewegungsplanung sowohl in der Simulation als auch experimentell nachgewiesen werden.The investigation of difficult to reach cavities through narrow accesses is called borescopy in the technical environment and endoscopy in medicine. If manipulation is to be performed in addition to pure inspection, a stable working platform is required to withstand manipulation forces in combination with good adaptability to curved paths. One approach to address the resulting requirements for the systems used are snake-like robots. Their hyper-redundant structure of individual actuators allows for versatile positioning. Although the use of binary, tilt-stable actuators limits the working space to a few discrete points, they offer - depending on the drive mechanism - particularly high holding torques and thus enable a targeted system stiffening. A combination of both approaches to the class of binary actuated, hyper-redundant manipulators is able to meet the required requirements, however, there is a clear need for research into methods for optimal design and the targeted pursuit of reference paths, so that the core of the present work consists the investigation of model-based motion planning of this robot class. A prerequisite for a high path following accuracy is that the manipulator is able to adapt well to a given reference path. The degree of limitation due to discrete positionability of the manipulator depends on the geometric parameters of the individual segments. The studies in this thesis show that the analysis of kinematic performance characteristics, such as work space (density) or achievable radius of curvature, does not lead to a generally valid optimal design. Therefore, a dimensional synthesis is developed under consideration of boundary conditions, in which optimal geometric parameters of a single binary actuator are synthesized. Based on this, a path following according to the "Follow-the-Leader"principle is elaborated. The basic idea is that the end effector segment explores the reference path, while all other actuators automatically follow the leading segment. Since binary actuators have a discontinuous switching process, a model-based approach is proposed for determining optimal switching sequences that guarantee high path accuracy at all times. The subsequent experimental evaluation is performed after modelling and identification of relevant parameters for the prototype of an electromagnetic tilting actuator chain. In principle, the functionality of the motion planning methods investigated in this thesis are proven both in simulation and experimentally