Atomic force microscopy (AFM) and axisymmetric drop shape analysis-profile (ASDA-P) were used to investigate the mechanism of self-assembly of peptides. The peptides chosen consisted of 16 alternating hydrophobic and hydrophilic amino acids, where the hydrophilic residues possess alternating negative and positive charges. Two types of peptides, AEAEAKAKAEAEAKAK (EAK16-II) and AEAEAEAE-AKAKAKAK (EAK16-IV), were investigated in terms of nanostructure formation through self-assembly. The experimental results, which focused on the effects of the amino acid sequence and pH, show that the nanostructures formed by the peptides are dependent on the amino acid sequence and the pH of the solution. For pH conditions around neutrality, one of the peptides used in this study, EAK16-IV, forms globular assemblies and has lower surface tension at air-water interfaces than another peptide, EAK16-II, which forms fibrillar assemblies at the same pH. When the pH is lowered below 6.5 or raised above 7.5, there is a transition from globular to fibrillar structures for EAK16-IV, but EAK16-II does not show any structural transition. Surface tension measurements using ADSA-P showed different surface activities of peptides at air-water interfaces. EAK16-II does not show a significant difference in surface tension for the pH range between 4 and 9. However, EAK16-IV shows a noticeable decrease in surface tension at pH around neutrality, indicating that the formation of globular assemblies is related to the molecular hydrophobicity.

The construction of “smart” materials able to perform specific functions at the molecular scale through the application of various stimuli is highly attractive but still challenging. The most recent applications indicate that the outstanding flexibility of self-assembled architectures can be employed as a powerful tool for the development of innovative molecular devices, functional surfaces and smart nanomaterials. Structural flexibility of these materials is known to be conferred by weak intermolecular forces involved in self-assembly strategies. However, some fundamental mechanisms responsible for conformational lability remain unexplored. Furthermore, the role played by stronger bonds, such as coordination, ionic and covalent bonding, is sometimes neglected while they can be employed readily to produce mechanically robust but also chemically reversible structures. In this review, recent applications of structural flexibility and molecular motions in self-assembled nanostructures are discussed. Special focus is given to advanced materials exhibiting significant performance changes after an external stimulus is applied, such as light exposure, pH variation, heat treatment or electromagnetic field. The crucial role played by strong intra- and weak intermolecular interactions on structural

I herby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Seeding is an important variable in controlling or directing the assembly of peptides. The presence of impurities, responsible for creating a ‘dip ’ in the surface tension versus peptide concentration profile, is used to determine the critical aggregation concentration (CAC). This phenomenon is investigated to differentiate crude and high purity EAK16-II peptide. The purified peptide did not show this ‘dip ’ and clearly indicated a critical aggregation concentration for EAK16-II at 0.09 mg/mL by surface tension measurements. Conversely, a surface tension ‘dip ’ is clearly observed for the crude EAK16-II peptide. Atomic Force Microscopy imaged the nanostructures of aggregates. The presence of impurities induces fibre formation below the CAC. This study provides information about the seeding effect of peptide assembly at low concentrations as well as the modification of surface activity of assembled peptide particles.

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Copyright © 2015 Vladimir Egorov et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Changes in protein conformation can occur both as part of normal protein functioning and during disease pathogenesis. Themost common conformational diseases are amyloidoses. Sometimes the development of a number of diseases which are not traditionally related to amyloidoses is associated with amyloid-like conformational transitions of proteins. Also, amyloid-like aggregates take part in normal physiological processes such as memorization and cell signaling. Several primary structural features of a protein are involved in conformational transitions. Also the protein proteolytic fragments can cause the conformational transitions in the protein. Short peptides which could be produced during the protein life cycle or which are encoded by short open reading frames can affect the protein conformation and function. 1. Conformational Diseases Conformational diseases are caused by changes in pro-tein tertiary structures and the associated loss of existing functions or the appearing of the new properties such as oligomerization ability. The most common conformational

Understanding of new materials at the molecular level has become increasingly critical for a new generation of nanomaterials for nanotechnology, namely, the design, synthesis and fabrication of nanodevices at the molecular scale. New technology through molecular self-assembly as a fabrication tool will become tremendously important in the coming decades. Basic engineering principles for microfabrication can be learned by understanding the molecular self-assembly phenomena. Self-assembly phenomenon is ubiquitous in nature. The key elements in molecular self-assembly are chemical complementarity and structural compatibility through noncovalent interactions. We have defined the path to understand these principles. Numerous self-assembling systems have been developed ranging from models to the study of protein folding and protein conformational diseases, to molecular electronics, surface engineering, and nanotechnology. Several distinctive types of self-assembling peptide systems have been developed. Type I, ‘‘molecular Lego’ ’ forms a hydrogel scaffold for tissue engineering; Type II, ‘‘molecular switch’ ’ as a molecular actuator; Type III, ‘‘molecular hook’’ and ‘‘molecular velcro’ ’ for surface engineering; Type IV, peptide nanotubes and nanovesicles, or ‘‘molecular capsule’ ’ for protein and gene deliveries and Type V, ‘‘molecular cavity’ ’ for biomineralization. These self-assembling peptide systems are simple, versatile and easy to produce. These self-assembly systems represent a significant advance in the molecular engineering for diverse technological innovations.