Molecular Structure of Biological Materials (BE.442)

Branden, Carl, and John Tooze. Introduction to Protein Structure. 2nd ed. New York, NY: Routledge, 1999. ISBN: 9780815323051.

LEC #: 1 · TOPICS: Important Role of Water Molecule, Hydration of Amino Acids, Protein and other Biological Materials · READINGS: Campbell, I. D. “The March of Structural Biology.” Molecular Cell Biology 3 (May 2002): 377.

Matsumoto, M., et al. “Molecular Dynamics Simulation the Ice Nucleation and Growth Process Leading to Water Freezing.” Nature 416 (March 28, 2002): 409-413.

Ramachandran Plot Pauling, L., and R. B. Corey. “Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains.” PNAS 37, no. 5 (May 15, 1951): 235-240.

———. “The Structure of Synthetic Polypeptides.” PNAS 37, no. 5 (May 15, 1951): 241-250.

———. “The Pleated Sheet, a New Layer Configuration of Polypeptide Chains.” PNAS 37, no. 5 (May 15, 1951): 251-256.

———. “The Structure of Feather Rachis Keratin.” PNAS 37, no. 5 (May 15, 1951): 256-261.

———. “The Structure of Hair, Muscle, and Related Proteins.” PNAS 37, no. 5 (May 15, 1951): 261-271.

———. “The Structure of Fibrous Proteins of the Collagen-Gelatin Group.” PNAS 37, no. 5 (May 15, 1951): 272-281.

———. “The Polypeptide-Chain Configuration in Hemoglobin and Other Globular Proteins.” PNAS 37, no. 5 (May 15, 1951): 282-285.

Sung, C. H., et al. “Crystal Structure of a Junction Between B-DNA and Z-DNA Reveals Two Extruded Bases.” Nature 437 (October 20, 2005): 1183-1186.

Sinden, R. R. “DNA Twists and Flips.” Nature 437 (October 20, 2005): 1097-1098.

Pauling, L., et al. “The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain.” PNAS 37, no. 4 (April 15, 1951): 205-211.

Applying Coiled-coils to Nanomaterials, Molecular Springs, Switches, etc. Crick, F. H. C. “The Packing of α-Helices: Simple Coiled-Coils” Acta Crystallographica 6 (March 14, 1953): 689-697.

O’Shea, Erin K., et al. “X-ray Strucure of the GCN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil.” Science 254, no. 5031 (October 25, 1991): 539-544. (New series)

Beta Sheets in Biological Materials Pauling, L., and R. B. Corey. “Configurations of Polypeptide Chains with Favored Orientations around Single Bonds: Two New Pleated Sheets.” PNAS 37, no. 11 (November 15, 1951): 729-740.

Hecht, M. H. “De novo Design of Beta-sheet Proteins.” PNAS 91 (September 1994): 8729-8730.

Preparation of the Samples for Diffraction Analyses Campbell, I. D. “The March of Structural Biology.” Molecular Cell Biology 3 (May 2002): 377-381.

LEC #: 11 · TOPICS: Silk · READINGS: Tirrell, D. A. “Putting a New Spin on Spider Silk.” Science 271 (January 5, 1996): 39-40.

Hayashi, C. Y., and R. V. Lewis. “Molecular Architecture and Evolution of a Modular Spider Silk Protein Gene.” Science 287 (February 25, 2000): 1477-1479.

Valluzzi, R., et al. “Silk: Molecular Organization and Control of Assembly.” Phil Trans Royal Society London B 357 (February 28, 2002): 165-167.

Hayashi, C. Y., and R. V. Lewis. “Evidence from Flagelliform Silk cDNA for the Structural Basis of Elasticity and Modular Nature of Spider Silks.” J Mol Biol 275 (1998): 773-784.

Jin, H., and D. L. Kaplan “Mechanism of Silk Processing in Insects and Spiders.” Nature 424 (August 28, 2003): 1057-1061.

Lazaris, A., et al. “Spider Silk Fibers Spun from Soluble Recombinant Silk Produced in Mammalian Cells.” Science 295 (January 18, 2002): 472-476.

Vollrath, F., and D. P. Knight. “Liquid Crystalline Spinning of Spider Silk.” Nature 410 (March 29, 2001): 541-548.

Vollrath, F., et al. “The Effect of Spinning Conditions on the Mechanics of a Spider’s Dragline Silk.” Proc R Soc Lond B 268 (2001): 2339-2346.

Shao, Z., and F. Vollrath. “Surprising Strength of Silkworm Silk.” Nature 418 (August 15, 2002): 741.

Reference Books

Kaplan, D., et al., eds. Silk Polymers: Materials Science and Biotechnology . Washington, DC: ACS, 1994. ISBN: 9780841227439. (ACS Sympoisum Series 544)

McGrath, K., and K. Kaplan, eds. Protein-based Materials . Boston, MA: Birkhüaser, 1996. ISBN: 9783764338480.

LEC #: 12 · TOPICS: Biomineralization: Sea Creatures · READINGS: Belcher, A. M., et al. “First Steps in Harnessing Potential of Biomineralization as a Route to New High-Performance Composite Materials.” Acta Mater 46, no. 3 (1998): 733-736.

Morse, D. E. “Silicon Biotechnology: Harnessing Biological Silica Production to Construct New Materials.” Tibtech 17 (June 1999): 230-232.

Aizenberg, J., et al. “Calcitic Microlenses as Part of the Photoreceptor System in Brittlestars.” Nature 412 (August 23, 2001): 819-822.

Kröger, N., et al. “Polycationic Peptides from Diatom Biosilica that Direct Silica Nanosphere Formation.” Science 286 (November 5, 1999): 1129-1132.

Aizenberg, J., et al. “Skeleton of Euplectella sp.: Structural Hierarchy from the Nanoscale to the Macroscale.” Science 309 (July 8, 2005): 275-278.

———. “Biological glass fibers: Correlation between optical and structural properties.” PNAS 101, no. 10 (March 9, 2004): 3358-3363.

LEC #: 13 · TOPICS: Biomineralization: Bones and Teeth · READINGS: Weiner, S., and H. D. Wagner. “The Material Bone: Structure-Mechanical Function Relations.” Annu Rev Mater Sci 28 (1998): 271-298.

Weiner, S., et al. “Lamellar Bone: Structure-Function Relations.” Journal of Structural Biology 126 (1999): 241-255.

———. “Peritubular Dentin Formation: Crystal Organization and the Macromolecular Constituents in Human Teeth.” Journal of Structural Biology 126 (1999): 27-41.

Mann, S., ed. Biomimetic Materials Chemistry . New York, NY: VCH Publishers, 1996. ISBN: 9781560816690.

Simkiss, K., and K. Wilbur. Biomineralization: Cell Biology and Mineral Deposition . Burlington, MA: Academic Press, 1989. ISBN: 9780126438307.

Frankel, R., and R. Blackmore. Iron Biominerals . New York, NY: Springer, 1991. ISBN: 9780306437182.

LEC #: 14 · TOPICS: Bioadhesives · READINGS: Smith, B. L., et al. “Molecularmechanistic Origin of the Toughness of Natural Adhesives, Fibres and Composites.” Nature 399 (June 24, 1999): 761-763.

Coyne, K., et al. “Extensible Collagen in Mussel Byssus: A Natural Block Copolymer.” Science 277 (September 9, 1997): 1830-1832.

Pennisi, E. “Biology Reveals New Ways To Hold on Tight.” Science 296 (April 12, 2002): 250-251.

Deming, T. J. “Mussel Byssus and Biomolecular Materials.” Current Opinion in Chemical Biology 3 (1999): 100-105.

Autumn, K., et al. “Evidence for van der Waals Adhesion in Gecko Setae.” PNAS 99, no. 19 (September 17, 2002): 12252-12256.

Geim, A. K., et al. “Microfabricated Adhesive Mimicking Gecko Foot-hair.” Nature Materials 2 (July 2003): 461-463.

Autumn, K. “Adhesive Force of a Single Gecko Foot-hair.” Nature 405 (June 8, 2000): 681-685.

LEC #: 15 · TOPICS: Lipids as Building Materials · READINGS: Schnur, J. M. “Lipid Tubules: A Paradigm for Molecularly Engineered Structures.” Science 262, no. 5140 (December 10, 1993): 1669-1676. (New series)

Mahadevan, L. “Non-stick Water.” Nature 411 (June 21, 2001): 895-862.

Lvov, Y. M., et al. “Imaging Nanoscale Patterns on Biologically Derived Microstructures.” Langmuir 16 (2000): 5932-5935.

Schnur, J. M., et al. “Diacetylenic Lipid Tubules: Experimental Evidence for a Chiral Molecular Architecture.” Science 264, no. 5161 (May 13, 1994): 945-947. (New series)

Spector, M. S., et al. “Chiral Self-Assembly of Nanotubules and Ribbons from Phospholipid Mixtures” Nano Letters 1, no. 7 (2001): 375-378.

LEC #: 18 · TOPICS: Molecular Structure and Self-assembly of DNA and RNA · READINGS: Watson, J. D., and F. C. H. Crick. “Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid.” Nature, no. 4356 (April 25, 1953): 737-739.

Wang, A. H. J., et al. “Molecular Structure of a Left-Handed Double Helical DNA Fragment at Atomic Resolution.” Nature 282 (December 13, 1979): 680-686.

West, M. W., et al. “De novo Amyloid Proteins from Designed Combinatorial Libraries.” PNAS 96 (September 1999): 11211-11216.

Scheibel, T., et al. “Bidirectional Amyloid Fiber Growth for a Yeast Prion Determinant.” Current Biology 11, no. 5 (March 6, 2001): 366-369.

Nowak, A. P., et al. “Rapidly Recovering Hydrogel Scaffolds from Self-assembling Diblock Copolypeptide Amphiphiles.” Nature 417 (May 23, 2002): 424-428.

Kisiday, J., et al. “Self-assembling Peptide Hydrogel Fosters Chondrocyte Extracellular Matrix Production and Cell Division: Implications for Cartilage Tissue Repair.” PNAS 99, no. 15 (July 23, 2002): 9996-10001.

Wei, Y., et al. “Stably Folded De Novo Proteins from a Designed Combinatorial Library.” Protein Science 12 (2003): 92-102.

LEC #: 20 · TOPICS: DNA Molecular Machines · READINGS: Hamad-Schifferli, K., et al. “Remote Electronic Control of DNA Hybridization through Inductive Coupling to an Attached Metal Nanocrystal Antenna.” Nature 415 (January 10, 2002): 152-155.

Alivisados, A. P., et al. “Organization of ‘Nanocrystal Molecules’ Using DNA.” Nature 382 (August 15, 1996): 609-611.

Braun, E., et al. “DNA-templated Assembly and Electrode Attachment of a Conducting Silver Wire.” Nature 391 (February 19, 1998): 775-778.

Yurke, B., et al. “A DNA-fuelled Molecular Machine Made of DNA.” Nature 406 (August 10, 2000): 605-608.

Mao, C. “A Nanomechanical Device Based on the B-Z Transition of DNA.” Nature 397 (January 14, 1999): 144-146.

Winfree, E., et al. “Design and Self-Assembly of Two-dimensional DNA Crystals.” Nature 394 (August 6, 1998): 539-544.

Whaley, S. R., et al. “Selection of Peptides with Semiconductor Binding Specificity for Directed Nanocrystal Assembly.” Nature 405 (June 8, 2000): 665-668.

Chen, J., and N. C. Seeman. “Synthesis from DNA of a Molecule with the Connectivity of a Cube.” Nature 350 (April 18, 1991): 631-633.

LEC #: 21 · TOPICS: Fluorescent Proteins · READINGS: Yang, F., et al. “The Molecular Structure of Green Fluorescent Protein.” Nature Biotechnology 14 (October 1996): 1246-1251.

Peelle, B., et al. “Intracellular Protein Scaffold-mediated Display of Random Peptide Libraries for Phenotypic Screens in Mammalian Cells.” Chemistry and Biology 8 (2001): 521-534.

Matz, M. V., et al. “Fluorescent Proteins from Nonbioluminescent Anthozoa Species.” Nature Biotechnology 17 (October 1999): 969-973.

Crameri, A., et al. “Improved Green Fluorescent Protein by Molecular Evolution Using DNA Shuffling.” Nature Biotechnology 14 (March 1996): 315-319.

LEC #: 22 · TOPICS: Self-assembling Peptide Systems (Dr. Zhang’s Research) · READINGS: Zhang, S. “Fabrication of Novel Biomaterials through Molecular Self-Assembly.” Nature: Biotechnology 21, no. 10 (October 2003): 1171-1178.

———. “Emerging Biological Materials Through Molecular Self-Assembly.” Biotechnology Advances 20 (2002): 321-339.

Zhang, S., et al. “Spontaneous Assembly of a Self-Complementary Oligopeptide to Form a Stable Macroscopic Membrane.” PNAS 90 (April 1993): 3334-3338.

Santoso, S., et al. “Self-assembly of Surfactant-like Peptides with Variable Glycine Tails to Form Nanotubes and Nanovesicles.” Nano Letters 2, no. 7 (2002): 687-691.

Marini, D. M., et al. “Left-Handed Helical Ribbon Intermediates in the Self-Assembly of a Beta-Sheet Peptide.” Nano Letters 2, no. 4 (2002): 295-299.

Vauthey, S., et al. “Molecular Self-Assembly of Surfactant-Like Peptides to Form Nanotubes and Nanovesicles.” PNAS 99, no. 8 (April 16, 2002): 5355-5360.

Holmes, T. C., et al. “Extensive Neurite Outgrowth and Active Synapse Formation on Self-Assembling Peptide Scaffolds.” PNAS 97, no. 12 (June 6, 2000): 6728-6733.

Aggeli, A., et al. “Responsive Gels Formed by the Spontaneous Self-Assembly of Peptides into Polymeric Beta-sheet Tapes.” Nature 386 (March 20, 1997): 259-262.

Hartgerink, Jeffrey D. “Peptide-amphiphile Nanofibers: A Versatile Scaffold for the Preparation of Self-assembling Materials.” PNAS 99, no. 8 (April 16, 2002): 5133-5138.

Robbins, J. “Second Nature: More and More, Innovative Scientists Are Turning to the Natural World for Inspiration&hellipand Design Solutions.” Smithsonian 33, no. 4 (July 2002): 78-82

Ball, P. “Natural Strategies for the Molecular Engineer.” Nanotechnology 13 (2002): R15-R28.

Abbott, A. “Biology’s New Dimension.” Nature 424, no. 6951 (August 21, 2003): 870-872.

Editorial. “Goodbye, Flat Biology?” Nature 424, no. 6951 (August 21, 2003): 861.

_Reference Books _ Aksay, I., and M. Sarikaya. Biomimetics: Design and Processing of Materials . New York, NY: AIP Press, 1993. ISBN: 9781563961960.

Stryer, L. Biochemistry . 4th ed. New York, NY: W.H. Freeman, 1995. ISBN: 0216720094.

Zubay, G. L. Biochemistry . 3rd ed. Dubuque, IA: William C. Brown Publishers, 1993. ISBN: 9780697142672.

Matthews, C. K., and K. E. Van Holde. Biochemistry . 2nd ed. Menlo Park, CA: Benjamin/Cummings Pub. Co., Inc., 1995. ISBN: 9780805339314.

Creighton, T. E. Proteins: Structures and Molecular Properties . 2nd ed. New York, NY: W.H. Freeman, 1993. ISBN: 9780716723172.

Pauling, L. “The Nature of the Chemical Bond and the Structure of Molecules and Crystals.” An Introduction to Modern Structural Chemistry . 3rd ed. Ithaca, NY: Cornell University Press, 1960.

Dickerson, R. The Structure and Action of Proteins . Reading, MA: Addison-Wesley, 1969. ISBN: 9780805323924.

McGrath, K., and D. Kaplan, eds. Protein-based Materials . Boston, MA: Birkhüaser, 1997. ISBN: 9780817638481.

Ball P. Life’s Matrix: A Biography of Water . Berkeley, CA: University of California Press, 2001. ISBN: 9780520230088.

Aggeli, A., et al. Self-assembling Peptide Systems in Biology, Engineering and Medicine . New York, NY: Springer, 2001. ISBN: 9780792370901.