This page lists readings assigned per class session, followed by a list of suggested reference books.
Required Textbook
Branden, Carl, and John Tooze. Introduction to Protein Structure. 2nd ed. New York, NY: Routledge, 1999. ISBN: 9780815323051.
Assigned Readings
| LEC # | TOPICS | READINGS |
|---|---|---|
| 1 | Important Role of Water Molecule, Hydration of Amino Acids, Protein and other Biological Materials |
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. |
| 2 |
Amino Acids: Their Chemical and Physical Properties
Influence of Ionic Strength, pH, etc. |
|
| 3 |
Primary and Secondary Structures of Proteins
Dihedral Angles, Peptide Bonds, Planar Structure, Relationship and Propensity of Amino Acid Sequence, Secondary Structure 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. |
| 4 |
Alpha-helices, 310 Helix, pi Helix, Beta-helices, etc.
Variation of Helices and their Helical Bundles, Two Strand Coiled-coils, Three or Four Strand Coiled-coils, Supercoils Various Helical Rich Protein Structure Models Alpha-helices in Biological Materials |
Watson, J. D., and F. H. Crick. “Molecular Structure of Nucleic Acids.” Nature 171, no. 4356 (April 25, 1953): 737-8.
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. Letter from J. D. Watson to L. Pauling, March 4, 1963. 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. |
| 5 |
Helical Coiled-coils
Two-, Three-, Four- Stranded Helical Bundles 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) |
| 6 |
Beta Sheets: Antiparallel, Parallel, and Twist
Beta Sheet Rich Proteins 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.
———. “The Pleated Sheet, a New Layer Configuration of Polypeptide Chains.” PNAS 37, no. 5 (May 15, 1951): 251-256. Hecht, M. H. “De novo Design of Beta-sheet Proteins.” PNAS 91 (September 1994): 8729-8730. |
| 7 |
Practical Aspects of Single Crystal X-ray Crystallography, Part 1
X-ray Single Crystal Diffraction, Fiber Diffraction Preparation of the Samples for Diffraction Analyses |
Campbell, I. D. “The March of Structural Biology.” Molecular Cell Biology 3 (May 2002): 377-381. |
| 8 | NMR (Guest Lecturer: Peter Carr, MIT Media Lab) | |
| 9 | Practical Aspects of Single Crystal X-ray Crystallography, Part 2 | |
| 10 | Analytical Approaches and Instrumentation (Guest Lecturer: Sotirus Koutsopoulos, Ph.D) | |
| 11 | Silk |
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. |
| 12 | Biomineralization: Sea Creatures |
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. |
| 13 | Biomineralization: Bones and Teeth |
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. Reference Books 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. |
| 14 | Bioadhesives |
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. |
| 15 | Lipids as Building Materials |
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. |
| 16 | Polysaccharides and Oligosaccharides | |
| 17 | Francis Crick Film | |
| 18 | Molecular Structure and Self-assembly of DNA and RNA |
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. |
| 19 |
Macromolecular Interactions and Protein and Adsorption (Guest Lecturer: Larry Unsworth, Ph.D., National Institute for Nanotechnology)
Crystallography (Guest lecturer: Liselotte Kaiser, MIT Center for Biomedical Engineering) |
|
| 20 | DNA Molecular Machines |
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. |
| 21 | Fluorescent Proteins |
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. |
| 22 | Self-assembling Peptide Systems (Dr. Zhang’s Research) |
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. |
| 23 |
Self-assembling Peptide Systems (Dr. Zhang’s Research) (cont.)
Applying Biomimicry to Nanotechnology (Guest Lecture by Andreas Mershin) |
Benyus, Janine. Biomimicry Web site.
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 |
| 24 | Research in Biomaterials | |
| 25-26 | Student Research Activity Presentations |
Suggested Reference Books
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.
