Introduction
The correlation of developments in use of biological materials with the advancement of human civilization. Introduction to the molecular structure of biological materials. History of biological materials.
Water
The importance of the properties of the water molecule in determining the structure of biological materials. Hydration of proteins (collagens and other ECMs), DNA, sugars and other biological molecules discussed.
Amino Acids
Their chemical and physical properties. Acidic, basic, polar, and nonpolar residues, and special properties of specific amino acids. Influence of ionic strength, pH, etc. on the solubility, charge, and protonation of amino acids.
Helices
Alpha helices, 310 helix, pi helix, coiled-coils, etc. Variation of helices based on dihedral angels and residue composition. Helical bundles, two strand coiled-coils, three or four strand coiled-coils, supercoils will be described. Various helical rich protein structure models will be used to reveal the properties of protein helices. Alpha helices in biological materials, and design of alpha-helical structures.
Peptide and Protein Structure
Characteristics of the peptide bond between amino acids. How the planar nature of the peptide bond and restrictions on the dihedral angles produce specific secondary structures. Explanation of the Ramachandran plot. Primary and secondary structures of proteins. The relationship between the composition of amino acid sequence and the propensity to form specific secondary structures. Prediction of secondary structure from peptide sequence.
Beta-Sheets
Antiparallel beta-sheet, parallel beta-sheets, beta-sheet twist, betahelices, etc. Beta-sheet rich proteins and primary sequence composition of betasheets. Properties of the beta-sheet and higher order beta-sheet rich structures. Beta-sheets in various biological materials.
Tools Used in Study and Analyses of Molecular Structures (I): X-Ray Crystallography
X-ray single crystal diffraction, fiber diffraction, powder diffraction. Outline the process of X-ray crystallography for determination of the crystal structure of biological materials: Preparation of the samples, instrumentation, diffraction analyses, and discussion of the current limitations.
Tools Used in Study and Analyses of Molecular Structures (II): Nuclear Magnetic Resonance (NMR)
High resolution NMR analyses, Solution NMR and solid state NMR.
Tools Used in Study and Analyses of Molecular Structures (III)
Circular Dichroism, Raman, FTIR, AFM, TEM, SEM, light scattering, Description of each technology and type of data generated. Discussion of the applications and limitations of each structure analysis tool.
Collagen
Molecular structure of collagen. Primary sequences of collagen I-XVIII and differences between the various types of collagen. The proline rich helix, glycine rich helix, and importance of these residues and water molecules in forming the higher order structure of collagen fibers. The fiber diffraction pattern of the collagen structure and single crystal collagen fragment structure. The importance of building the molecular model of collagen in the understanding of molecular structures. Molecular structure of other fibrous proteins.
Silk
Molecular structure of spider and silkworm silk. The silk protein primary sequences, and the significance of short peptide sequence repeats. The correlation of beta-sheet content with the strength, flexibility, and elasticity of silks. The genetic encoding of the silk fibroin. Several types of spider silk, i.e. dragline silk and capture silk, and silkworm silk are compared. Current approaches to the production and processing of recombinant or synthetic silks. How each silk worm produces over 2 km long silk fiber.
Keratin
Molecular structure of keratin. The differences between wool, hair, feather, horn, nail, cowhide, fur, scale, skin and other keratin rich materials. The properties of these materials as determined by their primary, secondary, and higher order structure compositions.
Molecular Structure of Biominerals (I)
Seashells, diatoms and corals. The biomineralization process and general paradigms for biology creating inorganic structures. The primary sequences and structures of proteins that build the scaffolds for biomineralization. The types of minerals used and how the crystals are organized in the materials. [ + 3 papers]
Molecular Structure of Biominerals (II)
Bone and tooth. Differences in macrostructures of bones and teeth. Molecular basis for formation of bone and teeth biominerals. How the molecular structure of these biomaterials translates to fracture resistance and strength.
Molecular Structure of Biological Adhesives
How the proteins adhere tightly on surfaces in the presence of water. Examples of organisms that produce adhesives and the diversity in types of adhesives. Chitin and others are described in detail.
Molecular Structure of Fluorescent Proteins
Green fluorescent protein (GFP) from the Aequorea jellyfish as the first example of an autonomously fluorescent protein. Origin of other fluorescent proteins. How is GFP fluorescent? The beta-barrel structure of GFP and significance in creating a fluorescent molecule. Other fluorescent variants are discussed: blue, yellow and red proteins.
Nucleic Acids
DNA and RNA as building blocks for nanomaterials. Physical and chemical properties of the nucleic acids. Double helical structure of DNA and types of DNA helices. Importance of hybridization energy and complementarity in directing assembly of DNA/RNA structures. Tools for synthesis, manipulation, and study of DNA or RNA.
Lipids
Lipids as biomaterials. Molecular structure and properties. Organization and assembly of phospholipid molecules into membranes, micelles, tubules, etc. Synthesis and functionalization of lipids.
Saccharides
Molecular structure of saccharide-based biological materials. Structures of hexose and pentose sugars and glycosidic bonds. Higher order structure of cellulose and related materials, and properties of such materials. Biological materials composed of carbohydrates.
Biomimicry and Design
Molecular design and engineering of biological materials inspired by nature. New scaffolds, new biominerals, new adhesives, new fluorescent materials. Biomimicry as a paradigm for creating molecules with modified or novel functions from biomaterials. The importance of self-assembly, molecular alignment, and cross-linking in the construction of macroscale biological material filaments from nano-scale building blocks.
Self-Assembling Peptide Systems
Rational design of short self-assembling peptide sequences. Physical properties and structural features of assembled structures. Applications of such systems in biomedical engineering, biological engineering research and nanotechnology.
Other Self-Assembling Peptide and Protein Systems
Examples from A. Aggeli, A. Belcher, C. Dobson, R. Ghadiri, M. Hecht, J. Kelly, S. Lindquist, S. Stupp, D. Tirrell
DNA Molecular Machines and Assembly
Radio Frequency Biology (RF biology), DNA nanocrystal organization, DNA wires, etc.
Regenerative Medicine
Perspective of advancement in biological materials used in tissue engineering and the impact to society. The bionic future of tissue engineering.
Biocomputing
Recent advances in using biological materials for information processing and computing. Perspectives on use of biological materials in computing.