Thesis. 1976. Ph.D.--Massachusetts Institute of Technology. Dept. of Mechanical Engineering. / Microfiche copy available in Archives and Engineering. / Vita. / Includes bibliographical references. / Ph.D.

Typescript (photocopy). / Digitized by Kansas Correctional Industries

<p>Peptides are a fundamental building-block of living systems and play crucial roles at both functional and structural level. Therefore, they have attracted increased attention as a platform to design and engineer new self-assembled systems that span the nano-to-meso scales. The rules of peptide design and folding enable the construction of suitable building-blocks to develop soft materials for biomaterial applications. Herein we present the use of the alpha-helical secondary structure to create two distinct structural motifs, namely coiled-coils and helical bundles. These peptide components can differ in size and incorporate a host of different functional moieties, the effects of which are described through their hierarchical assembly. </p> <p>First, we describe the self-assembly of coiled coil oligomers (trimer and tetramer) of the GCN4 leucine zipper peptide. The trimeric coiled coil was modified with varying number of aromatic groups (one to three) along each helical backbone, to facilitate higher order assemblies into banded nano- to micron-sized structures, the formation of which could be controlled reversibly as a function of pH. In addition, the electrostatic and aromatic interactions of the peptide material were harnessed for non-covalent binding of small drug molecules, followed by their subsequent pH-triggered release. Furthermore, these nanostructures are compatible with MCF-7 breast cancer cells, making them suitable drug-delivery agents for chemotherapeutics. In the absence of aromatic modifications, the coiled-coil trimer assembles into higher-order nanotubes that can be harnessed for selective encapsulation of high molecular weight biomolecules. With an increase in oligomerization from three to four, along with a single aromatic group modification on each helix, the tetrameric coiled-coil mutant successfully demonstrates a metal-assisted two-tier structural assembly into microbarrels and spheres.</p> <p>Second, we present the higher-order assembly of short tetrameric and pentameric helical bundle proteins, covalently stabilized by a belt of disulfide bridges, with metal-binding ligands at each helix termini. The addition of metals like Zn(II) and Cu(II) promote the assembly of the bundles into a 3D globular matrix, which upon thermal annealing transforms into microspheres. Additionally, these microspheres also demonstrate the metal-assisted inclusion of His-tagged fluorophores. Thus, peptide-based materials can be constructed by self-assembly of alpha-helical building blocks into systems with sophisticated, diverse morphologies and dynamic chemical properties, that can be further modulated to enhance performance for medical applications. </p>

This project focused on the study of self-assembling systems that can be inuenced by an external magnetic field, following the PhD research of Hauke Carstensen. My role was to study the behavior of beads and to optimize the tunable parameters so that the main force driving the dynamics of the system is the magnetic dipolar interaction between beads. To make sure that no other force plays an important role, we checked a number of things, the most problematic of which is flocculation in the colloid, which may happen if some beads get stuck to each other; to prevent them from aggregating we have to make sure that they have a large zeta potential, which will result in an electrically repulsive force between beads and will thus increase the stability of the colloid. We also have to make sure that other forces in the sample do not exceed the magnitude of magnetic forces between particles; examples of such forces can be the drag experienced while moving in the viscous ferrofluid, the gravity force or the random thermal movement of the molecules in the fluid. In order to study these efects, I measured the zeta potential of the magnetic and non-magnetic beads and later I added a surfactant compound (SDS) to our sample in order to increase said potential.

The minimization of blood loss represents a significant clinical need in the arena of surgery, trauma, and emergency response medicine. Fibrinogen is our body's native polymer system activated in response to tissue and vasculature injury, and forms the foundation of the most widely employed surgical sealant and hemostatic agent. Non-covalent knob:hole interactions are central to the assembly of fibrin that leads to network and clot formation. This project exploits these affinity interactions as a strategy to direct fibrin polymerization dynamics and network structure so as to develop a temperature-triggered polymerizing fibrin mixture for surgical applications. Short peptides modeled after fibrin knob sequences have been shown to alter fibrin matrix structure by competing with native fibrin knobs for binding to the available holes on fibrinogen and fibrin. The fusion of such knob peptides to a non-native component should facilitate binding of the fused component to fibrinogen/fibrin, and may permit the concomitant modification of the fibrin matrix. We examined this hypothesis in a three-step approach involving (a) analyzing the ability of tetrapeptide knob sequences to confer fibrin(ogen) affinity on a non-fibrin protein, (b) investigating the effect of knob display architecture on fibrin(ogen) structure, and (c) designing a temperature-responsive knob-displaying construct to modulate fibrin(ogen) affinity at different temperature regimes, thus altering fibrin(ogen) structure.

Recent advances in next generation sequencing have provided unprecedented opportunities for high-throughput genomic research, inexpensively producing millions of genomic sequences in a single run. Analysis of massive volumes of data results in a more accurate picture of the genome complexity and requires adequate bioinformatics support. We explore computational challenges of applying next generation sequencing to particular applications, focusing on the problem of reconstructing viral quasispecies spectrum from pyrosequencing shotgun reads and problem of inferring informative single nucleotide polymorphisms (SNPs), statistically covering genetic variation of a genome region in genome-wide association studies. The genomic diversity of viral quasispecies is a subject of a great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software cannot be used to simultaneously assemble and estimate the abundance of multiple closely related (but non-identical) quasispecies sequences. Here, we introduce a new Viral Spectrum Assembler (ViSpA) for inferring quasispecies spectrum and compare it with the state-of-the-art ShoRAH tool on both synthetic and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. While ShoRAH has an advanced error correction algorithm, ViSpA is better at quasispecies assembling, producing more accurate reconstruction of a viral population. We also foresee ViSpA application to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations. Due to the large data volume in genome-wide association studies, it is desirable to find a small subset of SNPs (tags) that covers the genetic variation of the entire set. We explore the trade-off between the number of tags used per non-tagged SNP and possible overfitting and propose an efficient 2LR-Tagging heuristic.

Self-assembling peptides have emerged as new nanobiomaterials and received considerable attention in the areas of nanoscience and biomedical engineering. In this category are ionic-complementary peptides, which contain a repeating charge distribution and alternating hydrophobic and hydrophilic residues in the amino acid sequence, leading to the unusual combination of amphiphilicity and ionic complementarity. Although their self-assembled nanostructures have been successfully applied as scaffoldings for tissue engineering, novel materials for regenerative medicine and nanocarriers for drug and gene/siRNA delivery, aspects of the assembly process remain unclear. Since many of these applications involve peptide-modified interfaces and surfaces, a better understanding and control of the peptide assembly on a surface are very crucial for future development of peptide-based applications in nano-biotechnology. This thesis contains two major parts: (i) fundamental study of the assembly of a model ionic-complementary peptide EAK16-II on surfaces and (ii) potential applications of such a peptide in surface modification and nanofabrication. In the fundamental study, EAK16-II assembly on negatively charged mica was first investigated via in-situ Atomic Force Microscopy (AFM). It was found that EAK16-II nanofiber growth on mica is surface-assisted and follows a nucleation and growth mechanism involving two steps: (i) adsorption of nanofibers and fiber clusters (from the bulk solution) on the surface to serve as the seeds and (ii) fiber elongation from the active ends of the seeds. Such a process can be controlled by adjusting the solution pH since it modulates the adsorption of the seeds and the growth rates. Unlike what is observed on mica, EAK16-II formed well-ordered nanofiber patterns with preferential orientations at angles of 60° or 120° to each other on hydrophobic highly ordered pyrolytic graphite (HOPG) surfaces, resembling the crystallographic structure of the graphite. Nanofiber formation on HOPG is also surface-assisted and adopts a nucleation and growth mechanism that can be affected by solution pH. The pH-dependent adsorption of peptides to HOPG is attributed to the resulting changes in peptide hydrophobicity. It was also found that EAK16-II assembly can be induced by the mechanical force of a tapping AFM tip. It occurs when the tip cuts the adsorbed EAK16-II nanofibers into segments that then serve as seeds for new nanofiber growth. This finding allows one to locally grow nanofibers at specific regions of the surface. The tip cutting has been combined with the effect that solution pH has on peptide assembly to develop a new AFM lithography method to fabricate local patterned peptide nanostructures on HOPG. To study the use of EAK16-II for surface modification applications, the wettability and stability of the peptide-modified surfaces were characterized. EAK16-II-modified mica becomes slightly hydrophobic as the water contact angle increases from <10° to 20.3 ± 2.9°. However, the hydrophobicity of the HOPG surface is significantly reduced, as reflected in a contact angle change from 71.2 ± 11.1° to 39.4 ± 4.3°. The EAK16-II-modified mica surface is stable in acidic solution, while the modified HOPG surface is stable in both acidic and alkaline solutions. The peptide-modified HOPG shows potential as a biocompatible electrode for (bio)molecular sensing. The ability of EAK16-II to form nanofibers on surfaces has also promoted research on peptide-based metallic nanowire fabrication. Our approach is to provide EAK16-II with metal ion binding ability by adding a GGH motif to the C-terminus. This new peptide EAK16(II)GGH has been found to form one-dimensional nanofibers while binding to Cu2+ ions. The dimensions of the nanofibers were significantly affected by the nature of the anions (SO42-, Cl- and NO3-) in the copper salt solution. This work demonstrates the potential usage of EAK16-II for nanowire fabrication.

Self-assembling peptides have emerged as new nanobiomaterials and received considerable attention in the areas of nanoscience and biomedical engineering. In this category are ionic-complementary peptides, which contain a repeating charge distribution and alternating hydrophobic and hydrophilic residues in the amino acid sequence, leading to the unusual combination of amphiphilicity and ionic complementarity. Although their self-assembled nanostructures have been successfully applied as scaffoldings for tissue engineering, novel materials for regenerative medicine and nanocarriers for drug and gene/siRNA delivery, aspects of the assembly process remain unclear. Since many of these applications involve peptide-modified interfaces and surfaces, a better understanding and control of the peptide assembly on a surface are very crucial for future development of peptide-based applications in nano-biotechnology. This thesis contains two major parts: (i) fundamental study of the assembly of a model ionic-complementary peptide EAK16-II on surfaces and (ii) potential applications of such a peptide in surface modification and nanofabrication. In the fundamental study, EAK16-II assembly on negatively charged mica was first investigated via in-situ Atomic Force Microscopy (AFM). It was found that EAK16-II nanofiber growth on mica is surface-assisted and follows a nucleation and growth mechanism involving two steps: (i) adsorption of nanofibers and fiber clusters (from the bulk solution) on the surface to serve as the seeds and (ii) fiber elongation from the active ends of the seeds. Such a process can be controlled by adjusting the solution pH since it modulates the adsorption of the seeds and the growth rates. Unlike what is observed on mica, EAK16-II formed well-ordered nanofiber patterns with preferential orientations at angles of 60° or 120° to each other on hydrophobic highly ordered pyrolytic graphite (HOPG) surfaces, resembling the crystallographic structure of the graphite. Nanofiber formation on HOPG is also surface-assisted and adopts a nucleation and growth mechanism that can be affected by solution pH. The pH-dependent adsorption of peptides to HOPG is attributed to the resulting changes in peptide hydrophobicity. It was also found that EAK16-II assembly can be induced by the mechanical force of a tapping AFM tip. It occurs when the tip cuts the adsorbed EAK16-II nanofibers into segments that then serve as seeds for new nanofiber growth. This finding allows one to locally grow nanofibers at specific regions of the surface. The tip cutting has been combined with the effect that solution pH has on peptide assembly to develop a new AFM lithography method to fabricate local patterned peptide nanostructures on HOPG. To study the use of EAK16-II for surface modification applications, the wettability and stability of the peptide-modified surfaces were characterized. EAK16-II-modified mica becomes slightly hydrophobic as the water contact angle increases from <10° to 20.3 ± 2.9°. However, the hydrophobicity of the HOPG surface is significantly reduced, as reflected in a contact angle change from 71.2 ± 11.1° to 39.4 ± 4.3°. The EAK16-II-modified mica surface is stable in acidic solution, while the modified HOPG surface is stable in both acidic and alkaline solutions. The peptide-modified HOPG shows potential as a biocompatible electrode for (bio)molecular sensing. The ability of EAK16-II to form nanofibers on surfaces has also promoted research on peptide-based metallic nanowire fabrication. Our approach is to provide EAK16-II with metal ion binding ability by adding a GGH motif to the C-terminus. This new peptide EAK16(II)GGH has been found to form one-dimensional nanofibers while binding to Cu2+ ions. The dimensions of the nanofibers were significantly affected by the nature of the anions (SO42-, Cl- and NO3-) in the copper salt solution. This work demonstrates the potential usage of EAK16-II for nanowire fabrication.

Gerbstoffe stabilisieren die Kollagenmatrix der Haut, in dem sie auf unterschiedlichste Art und Weise chemische Quervernetzungen herstellen. Es bleibt jedoch bis heute weitgehend unbeantwortet, auf welcher hierarchischen Ebene der Kollagenstruktur diese Wechselwirkung stattfindet und wie stringent eine solche Bindung mindestens sein muss, um einer Substanz den Charakter eines Gerbstoffes zu verleihen. Im Rahmen der vorliegenden Arbeit wurde ein Modellsystem entwickelt, das es gestattet, Aussagen darüber zu treffen, auf welcher Strukturebene des Kollagens diese Wechselwirkung stattfindet. Dazu wurde auf ein „bottom-up“ Verfahren zurückgegriffen, bei dem der Gerbstoff nicht auf Haut aufgebracht, sondern die Fibrillen in Anwesenheit von verschiedenen Wirkstoffen neu gebildet werden. Für die Untersuchungen wurden Vertreter aus der Substanzklasse der Polymere ausgewählt. Es kam Polyacrylsäure zum Einsatz, die als Fettungsmittel genutzt wird, und Polymethacrylsäure, welche in der Produktion als Nachgerbstoff verwendet wird. Vertreter ungeladener Polymere waren Ethylen-, Diethylen- und Polyethylenglycol, wobei hier die unterschiedlichen Molekülgrößen im Vergleich von Bedeutung waren. Des Weiteren wurde Glutaraldehyd als Vertreter eines gerbenden kovalenten Vernetzers untersucht. Kollagen Typ I Fibrillen wurden in vitro ausgehend von der Monomerform assembliert, und mit UV/Vis-Spektroskopie wurde verfolgt, ob und gegebenenfalls wie die Polymere die Kinetik der in vitro Fibrillogenese verändern. Dabei wurde beobachtet, dass bis auf Polyethylenglycol alle eingesetzten Substanzen auf unterschiedlichste Art schon auf der kleinsten Kollageneinheit - der Tripelhelix wirken. Diese Daten wurden mittels eines mathematischen Modells ausgewertet, das es ermöglicht, die Fibrillogenese in Teilreaktionen zu gliedern und die geschwindigkeitsbestimmenden Schritte zu evaluieren. So konnte ermittelt werden, dass trotz ähnlich erscheinender Fibrillenbildungskinetiken große Unterschiede zwischen Polyacrylsäure und Polymethacrylsäure bezüglich ihres Hauptwirkortes in den hierarchischen Strukturebenen des Kollagens auftreten. Während der Nachgerbstoff Polymethacrylsäure schon in geringen Konzentrationen in großem Maße in alle Teilprozesse der Fibrillogenese eingreift, zeigt Polyacrylsäure die größten Effekte auf mikrofibrillärer Ebene - einer Fibrillensubstruktur. Dieser Einfluss spiegelt sich in Morphologieänderungen in Form von so genannten gesplitteten Fibrillen wider, welche mittels atomkraftmikroskopischen Untersuchungen beobachtet werden konnten. Zusätzlich scheint Polymethacrylsäure ab einer kritischen Konzentration die Fibrillenbildung über einen alternativen Weg ablaufen zu lassen, was sich in der morphologischen Betrachtung in Form von langen, dünnen Fibrillen äußert, welche nicht mehr in der Lage sind zu höheren Strukturen zu verdrillen. Um zusätzlich die Art der Bindung näher zu charakterisieren, wurde ein weiteres Verfahren entwickelt, welches die Umkehrreaktion der in vitro Fibrillogenese beschreibt. Diese Methode der so genannten Deassemblierung ermöglicht eine Unterscheidung zwischen elektrostatischen Wechselwirkungen und kovalenten Bindungen zwischen Kollagen und Polymer, indem die Fibrille wieder in ihre nativen Monomeruntereinheiten zerlegt und gleichzeitig studiert wird, ob sich die Polymere vom Kollagen durch Ladungseintrag lösen lassen. Polyethylenglycol und seine niedermolekularen Äquivalente lassen sich in saurem Milieu problemlos von Kollagen abwaschen, was für sehr schwache Wechselwirkungen spricht. Kovalente Bindungen, wie etwa zwischen Kollagen und Glutaraldehyd lassen sich mit dieser Methode nicht lösen. Polyacrylsäure und Polymethacrylsäure lassen sich nur zu einem geringen Anteil von Kollagen lösen, was auf unterschiedlich affine Bindungsplätze der Polymere an Kollagen deutet. Beeindruckender Weise ist es für ausschließlich mit Polymethacrylsäure vernetztes Kollagen nicht möglich, dieses wieder in seine Untereinheiten zu zerlegen. Polymethacrylsäure ist demnach in der Lage die Kollagenmatrix auch ohne die Ausbildung kovalenter Bindungen ausreichend zu stabilisieren. Damit können die eingesetzten und entwickelten Verfahren als Screeningmethoden gesehen werden, welche schon vor dem eigentlichen Gerbversuch weit reichende Auskünfte über ein mögliches Gerbverhalten der zu Untersuchung eingesetzten Substanz liefern. Die vorliegenden Ergebnisse erlauben Aussagen über den molekularen Charakter der Kollagen - Polymer Wechselwirkung und stellen somit einen Beitrag zum Verständnis der Gerbung dar.

Multivalent interactions are common in nature, such as influenza virus infecting epithelial cells, clearance of pathogens by antibody-mediated attachment to macrophages, etc. To mimic nature, we utilized a bottom-up approach to develop various multivalent self-assembling systems based on leucine-zipper peptides. We tethered several pairs of leucine-zipper peptides to PAMAM dendrimers to form leucine-zipper dendrimers (LZDs). We conjugated Fos/Jun to the dendrimer to make D0Fos4 and D0Jun4, and studied the interactions between these LZDs and their cognate peptide target, either Jun or Fos. Our experiments showed that the D0Fos4 can non-covalently assemble four copies of Jun, and this approach can be further used for the rapid non-covalently assembling of multimeric ligands. We also pursued the multivalent target of GPCRs with a Fos/Jun assembly, and found the complex can potentially be used as a molecular switch to target GPCRs with controlled ligand activity. In a related project for bio-material design based on self-assembly of LZDs, we synthesized a different pair of LZDs, D-Ez4 and D-Kz4, and established that they can assemble at neutral pH to form helical fibrils which display higher order self-organized structures, providing a new methodology for bio-material design. In another effort for studying multivalent interactions, we conjugated three copies of the F23, mini-protein that binds the HIV-1 capsid protein, to a trimesic acid and obtained a trivalent inhibitor, Tri-F23. Tri-F23 showed enhanced binding in ELISA against gp120, but was not significantly more effective preventing HIV entry. This methodology provides a new strategy for developing multivalent inhibitors for preventing HIV-1 infection at the entry level. In a related area, we are developing imaging agents based on quantum dots that can detect GPCRs on whole cells and at the single molecule level. To this end, a new method was developed for biocompatible amphphilic polymers to coat quantum dots. This amphiphilic polymer facilitates rapid quantum dot conjugation to any ligand with a free thiol or engineered cysteine. Several GPCR targeted peptides have been utilized for imaging receptors on whole cells and as single molecules. These efforts will guide the rational design of multivalent ligands for targeting GPCRs and other cell surface proteins.