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Readings

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: Garland Publishing, Inc, 1999. ISBN: 0815323050.

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, 1993. ISBN: 0841227438. (ACS Sympoisum Series 544)

McGrath, K., and K. Kaplan, eds. Protein-based Materials. Boston, MA: Birkhüaser, 1997. ISBN: 3764338482.
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. Biomineralization. New York, NY: VCH Publishers, 1996. ISBN: 1560816694.

Simkiss, K., and K. Wilbur. Biomineralization: Cell Biology and Mineral Deposition. San Diego, CA: Academic Press, 1989. ISBN: 0126438307.

Frankel, R., and R. Blackmore. Iron Biominerals. New York, NY: Plenum Press, 1991. ISBN: 030643718X.
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

Aksay, I., and M. Sarikaya. Biomimetics: Design and Processing of Materials. New York, NY: AIP Press, 1995. ISBN: 1563961962.
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: 0697142671.

Matthews, C. K., and K. E. Van Holde. Biochemistry. 2nd ed. Menlo Park, CA: Benjamin/Cummings Pub. Co., Inc., 1996. ISBN: 0805339310.

Creighton, T. E. Proteins: Structures and Molecular Properties. 2nd ed. New York, NY: W.H. Freeman, 1993. ISBN: 0716723174.

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. New York, NY: Harper & Row, 1969. ISBN: 0805323929.

McGrath, K., and D. Kaplan, eds. Protein-based Materials. Boston, MA: Birkhüaser, 1997. ISBN: 0817638482.

Ball P. Life's Matrix: A Biography of Water. Berkeley, CA: University of California Press, 2001. ISBN: 0520230086

Aggeli, A., et al. Self-assembling Peptide Systems in Biology, Engineering and Medicine. Dordrecht, the Netherlands: Kluwer Academic Publishers, 2001. ISBN: 0792370902.