Essential Cell Biology, Fourth Edition

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 Essential Cell Biology, Fourth Edition REFERENCES Chapter 1 The Unity and Diversity of Life Andersson SGE (2006) The bacterial world gets smaller. Science 314:259–260. Brenner S, Jacob F & Meselson M (1961) An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature 190:576–
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speed multispectral spinning-­‐disk confocal microscope system for fluorescent speckle microscopy of living cells. Methods 29:29–41. Agard DA, Hiraoka Y, Shaw P & Sedat JW (1989) Fluorescence microscopy in three dimensions. In Methods in Cell Biology, vol 30: Fluorescence Microscopy of Living Cells in Culture, part B (DL Taylor, Y-­‐L Wang eds). San Diego: Academic Press. Centonze VE (2002) Introduction to multiphoton excitation imaging for the biological sciences. Methods Cell Biol 70:129–48. Chalfie M, Tu Y, Euskirchen G et al (1994) Green fluorescent protein as a marker for gene expression. Science 263:802–805. Egner A et al. (2002) Fast 100-­‐nm resolution three-­‐
dimensinoal microscope reveals structural plasticity of mitochondria in live yeast. Proc Natl Acad Sci USA 99(6): 3370-­‐5. Giepmans BN, Adams SR, Ellisman MH & Tsien RY (2006) The fluorescent toolbox for assessing protein location and function. Science 312:217–224. Harlow E & Lane D (1988) Antibodies. A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. Haugland RP (ed) (1996) Handbook of Fluorescent Probes and Research Chemicals, 8th ed. Eugene, OR: Molecular Probes, Inc. (Available online at http://www.probes.com/) Jaiswai JK & Simon SM (2004) Potentials and pitfalls of fluorescent quantum dots for biological imaging. Trends Cell Biol 14:497–504. Jares-­‐Erijman EA & Jovin TM (2003) FRET imaging. Nature Biotech 21:1387–1395. Lippincott-­‐Shwartz J, Altan-­‐Bonnet N & Patterson G (2003) Photobleaching and photoactivation: following protein dynamics in living cells. Nature Cell Biol 5:S7–S14. Michalet X et al. (2003) The power and prospects of fluorescence microscopies and spectroscopies. Annu Rev Biophys Biomol Struct 32:161-­‐82. Minsky M (1988) Memoir on inventing the confocal scanning microscope. Scanning 10:128–138. Miyawaki A, Sawano A & Kogure T (2003) Lighting up cells: labeling proteins with fluorophores. Nature Cell Biol 5:S1–S7. Parton RM & Read ND (1999) Calcium and pH imaging in living cells. In Light Microscopy in Biology. A Practical Approach, 2nd ed. (Lacey AJ ed) Oxford: Oxford University Press. Sako Y & Yanagida T (2003) Single-­‐molecule visualization in cell biology. Nature Rev Mol Cell Biol 4:SS1–SS5. Sekar RB & Periasamy A (2003) Fluorescence resonance energy transfer (FRET) microscopy imaging of live cell protein localizations. J Cell Biol 160:629–633. Shaner NC, Steinbach PA & Tsien RY (2005) A guide to choosing fluorescent proteins. Nature Methods 2:905–909. Sheetz MP (ed) (1997) Laser Tweezers in Cell Biology. Methods Cell Biol 55. Sluder G & Wolf DE (2007) Video Microscopy 3rd ed. Methods Cell Biol 81. Stevens DJ & Allan (2003) Light Microscopy Techniques for Live Cell Imaging. Science 300:82–86. Tsien RY (2003) Imagining imaging’s future. Nature Rev Mol Cell Rev 4:SS16–SS21. van Teeffelen S, Shaevitz JW, Gitai Z (2012) Image analysis in fluorescence microscopy: bacterial dynamics as a case study. Bioessays 34(5): 427-­‐36 Weiss DG, Maile W, Wick RA & Steffen W (1999) Video microscopy. In Light Microscopy in Biology: A Practical Approach, 2nd ed. (AJ Lacey ed) Oxford: Oxford University Press. Essential Cell Biology, Fourth Edition REFERENCES White JG, Amos WB & Fordham M (1987) An evaluation of confocal versus conventional imaging of biological structures by fluorescence light microscopy. J Cell Biol 105:41–48. Zernike F (1955) How I discovered phase contrast. Science 121:345–349. Looking at Cells and Molecules in the Electron Microscope Allen TD & Goldberg MW (1993) High resolution SEM in cell biology. Trends Cell Biol 3:203–208. Baumeister W (2002) Electron tomography: towards visualizing the molecular organization of the cytoplasm. Curr Opin Struct Biol 12:679–684. Böttcher B, Wynne SA & Crowther RA (1997) Determination of the fold of the core protein of hepatits B virus by electron cryomicroscopy. Nature 386:88–91. Dubochet J, Adrian M, Chang J-­‐J et al (1988) Cryoelectron microscopy of vitrified specimens. Q Rev Biophys 21:129–228. Frank J (2003) Electron microscopy of functional ribosome complexes. Biopolymers 68:223–233. Hayat MA (2000) Principles and Techniques of Electron Microscopy, 4th ed. Cambridge: Cambridge University Press. Heuser J (1981) Quick-­‐freeze, deep-­‐etch preparation of samples for 3D electron microscopy. Trends Biochem Sci 6:64–68. Lippincott-­‐Schwartz J & Patterson GH (2003) Development and use of fluorescent protein markers in living cells. Science 300:87–91. McIntosh R, Nicastro D & Mastronarde D (2005) New views of cells in 3D: an introduction to electron tomography. Trends Cell Biol 15:43–51. McDonald KL & Auer M (2006) High pressure freezing, cellular tomography, and structural cell biology. Biotechniques 41:137–139. Pease DC & Porter KR (1981) Electron microscopy and ultramicrotomy. J Cell Biol 91:287s–292s. Unwin PNT & Henderson R (1975) Molecular structure determination by electron microscopy of unstained crystal specimens. J Mol Biol 94:425–440. Chapter 2 The Chemical Components of a Cell Abeles RH, Frey PA & Jencks WP (1992) Biochemistry. Boston: Jones & Bartlett. Atkins PW (1996) Molecules. New York: WH Freeman. Branden C & Tooze J (1999) Introduction to Protein Structure, 2nd ed. New York: Garland Science. Bretscher MS (1985) The molecules of the cell membrane. Sci Am 253:100–109. Burley SK & Petsko GA (1988) Weakly polar interactions in proteins. Adv Protein Chem 39:125–
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1018. Tanford C (1980) The Hydrophobic Effect. Formation of Micelles and Biological Membranes, 2nd ed. New York: John Wiley. White SH (2005) How hydrogen bonds shape membrane protein structure. Adv Protein Chem 72:157-­‐72. Chapter 3 Catalysis and the Use of Energy by Cells Atkins PW (1994) The Second Law: Energy, Chaos and Form. New York: Scientific American Books. Atkins PW & De Paula JD (2006) Physical Chemistry for the Life Sciences. Oxford: Oxford University Press. Baldwin JE & Krebs H (1981) The Evolution of Metabolic Cycles. Nature 291:381–382. Berg HC (1983) Random Walks in Biology. Princeton, NJ: Princeton University Press. Dickerson RE (1969) Molecular Thermodynamics. Menlo Park, CA: Benjamin Cummings. Essential Cell Biology, Fourth Edition REFERENCES Dill KA & Bromberg S (2003) Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology. New York: Garland Science. Dressler D & Potter H (1991) Discovering Enzymes. New York: Scientific American Library. Einstein A (1956) Investigations on the Theory of Brownian Movement. New York: Dover. Fruton JS (1999) Proteins, Enzymes, Genes: The Interplay of Chemistry and Biology. New Haven: Yale University Press. Goodsell DS (1991) Inside a living cell. Trends Biochem Sci 16:203–206. Karplus M & McCammon JA (1986) The dynamics of proteins. Sci Am 254:42–51. Karplus M & Petsko GA (1990) Molecular dynamics simulations in biology. Nature 347:631–639. Kauzmann W (1967) Thermodynamics and Statistics: with Applications to Gases. In Thermal Properties of Matter Vol 2. New York: WA Benjamin, Inc. Kornberg A (1989) For the Love of Enzymes. Cambridge, MA: Harvard University Press. Lavenda BH (1985) Brownian Motion. Sci Am 252:70–
85. Lawlor DW (2001) Photosynthesis, 3rd ed. Oxford: BIOS. Lehninger AL (1971) The Molecular Basis of Biological Energy Transformations, 2nd ed. Menlo Park, CA: Benjamin Cummings. Lipmann F (1941) Metabolic generation and utilization of phosphate bond energy. Adv Enzymol 1:99–162. Lipmann F (1971) Wanderings of a Biochemist. New York: Wiley. Nisbet EE & Sleep NH (2001) The habitat and nature of early life. Nature 409:1083–1091. Racker E (1980) From Pasteur to Mitchell: a hundred years of bioenergetics. Fed Proc 39:210–215. Schrödinger E (1944 & 1958) What is Life?: The Physical Aspect of the Living Cell and Mind and Matter, 1992 combined ed. Cambridge: Cambridge University Press. Shi Y (2013) Common folds and transport mechanisms of secondary active transporters. Ann Rev Biophys 42: 51-­‐72. van Holde KE, Johnson WC & Ho PS (2005) Principles of Physical Biochemistry, 2nd ed. Upper Saddle River, NJ: Prentice Hall. Walsh C (2001) Enabling the chemistry of life. Nature 409:226–231. Westheimer FH (1987) Why nature chose phosphates. Science 235:1173–1178. Youvan DC & Marrs BL (1987) Molecular mechanisms of photosynthesis. Sci Am 256:42–49. Chapter 4 The Shape and Structure of Proteins Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223–230. Bray D (2005) Flexible peptides and cytoplasmic gels. Genome Biol 6:106–109. Burkhard P, Stetefeld J & Strelkov SV (2001) Coiled coils: a highly versatile protein folding motif. Trends Cell Biol 11:82–88. Caspar DLD & Klug A (1962) Physical principles in the construction of regular viruses. Cold Spring Harb Symp Quant Biol 27:1–24. Doolittle RF (1995) The multiplicity of domains in proteins. Annu Rev Biochem 64:287–314. Eisenberg D (2003) The discovery of the alpha-­‐helix and beta-­‐sheet, the principle structural features of proteins. Proc Natl Acad Sci USA 100:11207–11210. Fraenkel-­‐Conrat H & Williams RC (1955) Reconstitution of active tobacco mosaic virus from its inactive protein and nucleic acid components. Proc Natl Acad Sci USA 41:690–698. Goodsell DS & Olson AJ (2000) Structural symmetry and protein function. Annu Rev Biophys Biomol Struct 29:105–153. Harrison SC (1992) Viruses. Curr Opin Struct Biol 2:293–
299. Harrison SC (2004) Whither structural biology? Nature Struct Mol Biol 11:12–15. Hudder A, Nathanson L & Deutscher MP (2003) Organization of mammalian cytoplasm. Mol Cell Biol 23:9318–9326. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921. Meiler J & Baker D (2003) Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci USA 100:12105–12110. Nomura M (1973) Assembly of bacterial ribosomes. Science 179: 864–873. Orengo CA & Thornton JM (2005) Protein families and their evolution— a structural perspective. Annu Rev Biochem 74:867–900. Pauling L & Corey RB (1951) Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proc Natl Acad Sci USA 37:729–740. Pauling L, Corey RB & Branson HR (1951) The structure of proteins: two hydrogen-­‐bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 37:205–211. Essential Cell Biology, Fourth Edition REFERENCES Ponting CP, Schultz J, Copley RR et al. (2000) Evolution of domain families. Adv Protein Chem 54:185–244. Reynolds KA, Mc Laughlin RN, Ranganathan R (2011) Hot spots for allosteric regulation on protein surfaces. Cell 147(7): 1564-­‐75. Trinick J (1992) Understanding the functions of titin and nebulin. FEBS Lett 307:44–48. Vogel C, Bashton M, Kerrison ND et al (2004) Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol 14:208–216. Zhang C & Kim SH (2003) Overview of structural genomics: from structure to function. Curr Opin Chem Biol 7:28–32. Protein Function Alberts B (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92:291–294. Benkovic SJ (1992) Catalytic antibodies. Annu Rev Biochem 61:29–54. Berg OG & von Hippel PH (1985) Diffusion-­‐controlled macromolecular interactions. Annu Rev Biophys Biophys Chem 14:131–160. Bhattacharyya RP, Remenyi A, Yeh BJ & Lim WA (2006) Domains, motifs, and scaffolds: The role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem 75:655–680. Bourne HR (1995) GTPases: a family of molecular switches and clocks. Philos Trans R Soc Lond B 349:283–289. Braden BC & Poljak RJ (1995) Structural features of the reactions between antibodies and protein antigens. FASEB J 9:9–16. Dickerson RE & Geis I (1983) Hemoglobin: Structure, Function, Evolution and Pathology. Menlo Park, CA: Benjamin Cummings. Dressler D & Potter H (1991) Discovering Enzymes. New York: Scientific American Library. Eisenberg D, Marcotte, EM, Xenarios, I & Yeates TO (2000) Protein function in the post-­‐genomic era. Nature 405:823–826. Fersht AR (1999) Structure and Mechanisms in Protein Science: A Guide to Enzyme Catalysis. New York: WH Freeman. Johnson, LN & Lewis RJ (2001) Structural basis for control by phosphorylation. Chem Rev 101:2209–
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46. Analyzing Proteins Branden C & Tooze J (1999) Introduction to Protein Structure, 2nd ed. New York: Garland Science. Fields S & Song O (1989) A novel genetic system to detect protein–protein interactions. Nature 340:245–246. Giepmans BN, Adams SR et al (2006) The fluorescent toolbox for assessing protein location and function. Science 312:217–24. Kendrew JC (1961) The three-­‐dimensional structure of a protein molecule. Sci Am 205:96–111. Knight ZA & Shokat KM (2007) Chemical genetics: Where genetics and pharmacology meet. Cell 128:425–30. Rigaut G, Shevchenko A, Rutz B et al (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol 17:1030–1032. Washburn MP, Wolters D and Yates JR (2001) Large-­‐
scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol 19:242–7. Wuthrich K (1989) Protein structure determination in solution by nuclear magnetic resonance spectroscopy. Science 243:45–50. Chapter 5 The Structure and Function of DNA Avery OT, MacLeod CM & McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types. J Exp Med 79:137–158. Meselson M & Stahl FW (1958) The replication of DNA in E. coli. Proc Natl Acad Sci USA 44:671–682. Watson JD & Crick FHC (1953) Molecular structure of nucleic acids. A structure for deoxyribose nucleic acids. Nature 171:737–738. Chromosomal DNA and Its Packaging in the Chromatin Fiber Jin J, Cai Y, Li B et al (2005) In and out: histone variant exchange in chromatin. Trends Biochem Sci 30:680–
687. Kornberg RD & Lorch Y (1999) Twenty-­‐five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285–294. Li G, Levitus M, Bustamante C & Widom J (2005) Rapid spontaneous accessibility of nucleosomal DNA. Nature Struct Mol Biol 12:46–53. Lorch Y, Maier-­‐Davis B & Kornberg RD (2006) Chromatin remodeling by nucleosome disassembly in vitro. Proc Natl Acad Sci USA 103:3090–3093. Luger K, Mader AW, Richmond RK et al (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–260. Luger K & Richmond TJ (1998) The histone tails of the nucleosome. Curr Opin Genet Dev 8:140–146. Malik H S & Henikoff S (2003) Phylogenomics of the nucleosome Nature Struct Biol 10:882-­‐891. Ried T, Schrock E, Ning Y & Wienberg J (1998) Chromosome painting: a useful art. Hum Mol Genet 7:1619–1626. Robinson PJ & Rhodes R (2006) Structure of the 30 nm chromatin fibre: A key role for the linker histone. Curr Opin Struct Biol 16:1–8. Saha A, Wittmeyer J & Cairns BR (2006) Chromatin remodeling: the industrial revolution of DNA around histones. Nature Rev Mol Cell Biol 7:437–446. Woodcock CL (2006) Chromatin architecture. Curr Opin Struct Biol 16:213–220. Essential Cell Biology, Fourth Edition REFERENCES The Regulation of Chromatin Structure Burgess RJ, Zhang Z (2010) Histones, histone chaperone and nucleosome assembly. Protein Cell 1(7): 607-­‐12. Egger G, Liang, G, Aparicio A & Jones PA (2004) Epigenetics in human disease and prospects for epigenetic therapy. Nature 429:457–463. Henikoff S (1990) Position-­‐effect variegation after 60 years. Trends Genet 6:422–426. Henikoff S & Ahmad K (2005) Assembly of variant histones into chromatiin. Annu Rev Cell Dev Biol 21:133–153. Gaszner M & Felsenfeld G (2006) Insulators: exploiting transcriptional and epigenetic mechanisms. Nature Rev Genet 7:703–713. Hake SB & Allis CD (2006) Histone H3 variants and their potential role in indexing mammalian genomes: the “H3 barcode hypothesis.” Proc Natl Acad Sci USA 103:6428–6435. Jenuwein T (2006) The epigenetic magic of histone lysine methylation. FEBS J 273:3121–3135. Martin C & Zhang Y (2005) The diverse functions of histone lysine methylation. Nature Rev Mol Cell Biol 6:838–849. Mellone B, Erhardt S & Karpen GH (2006) The ABCs of centromeres. Nature Cell Biol 8:427–429. Peterson CL & Laniel MA (2004) Histones and histone modifications. Curr Biol 14:R546–R551. Ruthenburg AJ, Allis CD & Wysocka J (2007) Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell 25:15–30. Shahbazian MD & Grunstein M (2007) Functions of site-­‐specific histone acetylation and deacetylation. Annu Rev Biochem 76:75–100. Zentner GE, Henikoff S (2013) Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol 20(3): 259-­‐66. The Global Structure of Chromosomes Akhtar A & Gasser SM (2007) The nuclear envelope and transcriptional control. Nature Rev Genet 8:507–
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