Bibliography for BS2520: Protein Structure and Function BETA

Ajit Varki, Cummings, R.D. and Esko, J.D. (2015) Essentials of Glycobiology. Cold Spring Harbor Laboratory Press. Available at: https://www.ncbi.nlm.nih.gov/books/NBK310274/.

Anatrace (no date) ‘Detergents and Their Uses in Membrane Protein Science’. Available at: https://www.anatrace.com/Technical-Documentation/Catalogs/Anatrace-Detergents-Booklet-FINAL.

Bazan, J., Całkosiński, I. and Gamian, A. (2012) ‘Phage Display - a Powerful Technique for Immunotherapy’, Human Vaccines & Immunotherapeutics, 8(12), pp. 1817–1828. Available at: https://doi.org/10.4161/hv.21703.

Berg, J.M. et al. (2015a) Biochemistry. Eighth edition. New York: W.H. Freeman & Company, a Macmillan Education Imprint.

Berg, J.M. et al. (2015b) Biochemistry. Eighth edition. New York: W.H. Freeman & Company, a Macmillan Education Imprint.

Berg, J.M. et al. (2015c) Biochemistry. Eighth edition. New York: W.H. Freeman & Company, a Macmillan Education Imprint.

Berg, J.M. et al. (2015d) Biochemistry. Eighth edition. New York: W.H. Freeman & Company, a Macmillan Education Imprint.

Berg, J.M. et al. (2015e) Biochemistry. Eighth edition. New York: W.H. Freeman & Company, a Macmillan Education Imprint.

Berg, J.M., Tymoczko, J.L. and Stryer, L. (2001) Biochemistry. 5th Edition. New York: W. H. Freeman and Co.

Betts, M.J. and Russell, R.B. (2003) ‘Amino Acid Properties and Consequences of Substitutions’, in Bioinformatics for Geneticists. Chichester, West Sussex, England: Wiley, pp. 289–316.

Binz, H.K., Amstutz, P. and Plückthun, A. (2005) ‘Engineering Novel Binding Proteins From Nonimmunoglobulin Domains’, Nature Biotechnology, 23(10), pp. 1257–1268. Available at: https://doi.org/10.1038/nbt1127.

‘Biological Buffers’ (2008). AppliChem. Available at: https://www.applichem.com/fileadmin/Broschueren/BioBuffer.pdf.

BLAST (no date). Available at: http://www.uniprot.org/blast/.

BLAST: Basic Local Alignment Search Tool (no date a). Available at: http://blast.ncbi.nlm.nih.gov/Blast.cgi.

BLAST: Basic Local Alignment Search Tool (no date b). Available at: http://blast.ncbi.nlm.nih.gov/Blast.cgi.

Bordo, D. and Argos, P. (1991) ‘Suggestions for "Safe” Residue Substitutions in Site-Directed Mutagenesis’, Journal of Molecular Biology, 217(4), pp. 721–729. Available at: https://doi.org/10.1016/0022-2836(91)90528-E.

Buchanan, A. et al. (2012) ‘Improved Drug-Like Properties of Therapeutic Proteins by Directed Evolution’, Protein Engineering Design and Selection, 25(10), pp. 631–638. Available at: https://doi.org/10.1093/protein/gzs054.

Cabrita, L.D., Dobson, C.M. and Christodoulou, J. (2010) ‘Protein Folding on the Ribosome’, Current Opinion in Structural Biology, 20(1), pp. 33–45. Available at: https://doi.org/10.1016/j.sbi.2010.01.005.

Cohen, B.I., Presnell, S.R. and Cohen, F.E. (1993) ‘Origins of Structural Diversity Within Sequentially Identical Hexapeptides’, Protein Science: A Publication Of The Protein Society, 2(12), pp. 2134–2145. Available at: https://doi.org/10.1002/pro.5560021213.

Daugherty, P.S. (2007) ‘Protein Engineering With Bacterial Display’, Current Opinion in Structural Biology, 17(4), pp. 474–480. Available at: https://doi.org/10.1016/j.sbi.2007.07.004.

Dobson, C.M. (2001) ‘The Structural Basis of Protein Folding and Its Links With Human Disease’, Philosophical Transactions of the Royal Society B: Biological Sciences, 356(1406), pp. 133–145. Available at: https://doi.org/10.1098/rstb.2000.0758.

Eddy, S.R. (2004) ‘Where Did The BLOSUM62 Alignment Score Matrix Come From?’, Nature Biotechnology, 22(8), pp. 1035–1036. Available at: https://doi.org/10.1038/nbt0804-1035.

ExPASy BLAST form (no date). Available at: http://web.expasy.org/blast/.

ExPASy: SIB Bioinformatics Resource Portal - Resources (no date). Available at: http://www.expasy.org/resources.

Fersht, A. (1999) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. New York: W. H. Freeman.

Furukawa, H. et al. (2005) ‘Subunit Arrangement and Function in NMDA Receptors’, Nature, 438(7065), pp. 185–192. Available at: https://doi.org/10.1038/nature04089.

Genesilico Metaserver - meta2 (no date). Available at: https://genesilico.pl/meta2/.

Gershenson, A. and Gierasch, L.M. (2011) ‘Protein Folding in the Cell: Challenges and Progress’, Current Opinion in Structural Biology, 21(1), pp. 32–41. Available at: https://doi.org/10.1016/j.sbi.2010.11.001.

GlycomeAtlas V5 (no date). Available at: http://rings.t.soka.ac.jp/GlycomeAtlasV5/index.html.

Griffiths, A.D. (2003) ‘Directed Evolution of an Extremely Fast Phosphotriesterase by in Vitro Compartmentalization’, The EMBO Journal, 22(1), pp. 24–35. Available at: https://doi.org/10.1093/emboj/cdg014.

Hammer, S.C., Knight, A.M. and Arnold, F.H. (2017) ‘Design and Evolution of Enzymes for Non-Natural Chemistry’, Current Opinion in Green and Sustainable Chemistry, 7, pp. 23–30. Available at: https://doi.org/10.1016/j.cogsc.2017.06.002.

Hartl, F.U., Bracher, A. and Hayer-Hartl, M. (2011) ‘Molecular Chaperones in Protein Folding and Proteostasis’, Nature, 475(7356), pp. 324–332. Available at: https://doi.org/10.1038/nature10317.

Heim, R. and Tsien, R.Y. (1996) ‘Engineering Green Fluorescent Protein for Improved Brightness, Longer Wavelengths and Fluorescence Resonance Energy Transfer’, Current Biology, 6(2), pp. 178–182. Available at: https://doi.org/10.1016/S0960-9822(02)00450-5.

Hellinga, H.W. and Marvin, J.S. (1998) ‘Protein Engineering and the Development of Generic Biosensors’, Trends in Biotechnology, 16(4), pp. 183–189. Available at: https://doi.org/10.1016/S0167-7799(98)01174-3.

Home - Protein - NCBI (no date). Available at: http://www.ncbi.nlm.nih.gov/protein.

Home - PubMed - NCBI (no date). Available at: http://www.ncbi.nlm.nih.gov/pubmed.

Hou, J. et al. (2005) ‘From the Cover: Global Mapping of the Protein Structure Space and Application in Structure-Based Inference of Protein Function’, Proceedings of the National Academy of Sciences, 102(10), pp. 3651–3656. Available at: https://doi.org/10.1073/pnas.0409772102.

Hovmöller, S., Zhou, T. and Ohlson, T. (2002a) ‘Conformations of Amino Acids in Proteins’, Acta Crystallographica Section D Biological Crystallography, 58(5), pp. 768–776. Available at: https://doi.org/10.1107/S0907444902003359.

Hovmöller, S., Zhou, T. and Ohlson, T. (2002b) ‘Conformations of Amino Acids in Proteins’, Acta Crystallographica Section D Biological Crystallography, 58(5), pp. 768–776. Available at: https://doi.org/10.1107/S0907444902003359.

Jacobson, R.H. et al. (1999) ‘Structure of a Stabilizing Disulfide Bridge Mutant That Closes the Active-Site Cleft of T4 Lysozyme’, Protein Science, 1(1), pp. 46–57. Available at: https://doi.org/10.1002/pro.5560010106.

Johnson, S. and Scott, J. (2014) Study and Communication Skills for the Biosciences. Second edition. Oxford: Oxford University Press.

Jung, H.-I., Cooper, A. and Perham, R.N. (2002) ‘Identification of Key Amino Acid Residues in the Assembly of Enzymes into the Pyruvate Dehydrogenase Complex of                              :  A Kinetic and Thermodynamic Analysis’, Biochemistry, 41(33), pp. 10446–10453. Available at: https://doi.org/10.1021/bi020147y.

Komar, A.A. (2018) ‘Unraveling Co-Translational Protein Folding: Concepts and Methods’, Methods, 137, pp. 71–81. Available at: https://doi.org/10.1016/j.ymeth.2017.11.007.

Korczyn, A.D. (no date) ‘Chapter 4: Human Prion Diseases’. Available at: https://moodle.royalholloway.ac.uk/mod/resource/view.php?id=211177.

Löfblom, J. (2011) ‘Bacterial Display in Combinatorial Protein Engineering’, Biotechnology Journal, 6(9), pp. 1115–1129. Available at: https://doi.org/10.1002/biot.201100129.

Madden, D.R. (2002) ‘The Structure and Function of Glutamate Receptor Ion Channels’, Nature Reviews Neuroscience, 3(2), pp. 91–101. Available at: https://doi.org/10.1038/nrn725.

Martínez-Maqueda, D. et al. (2013) ‘Extraction/Fractionation Techniques for Proteins and Peptides and Protein Digestion’, in Proteomics in Foods: Principles and Applications. 2013th edn. Springer, pp. 21–50.

Murzin, A.G. et al. (1995) ‘SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures’, Journal of Molecular Biology, 247(4), pp. 536–540. Available at: https://doi.org/10.1016/S0022-2836(05)80134-2.

NCBI Structure Group Home Page (no date). Available at: http://www.ncbi.nlm.nih.gov/Structure/index.shtml.

Nilsson, O.B. et al. (2015) ‘Cotranslational Protein Folding Inside the Ribosome Exit Tunnel’, Cell Reports, 12(10), pp. 1533–1540. Available at: https://doi.org/10.1016/j.celrep.2015.07.065.

Olson, C.A. et al. (2008) ‘mRNA Display Selection of a High-Affinity, Modification-Specific Phospho-IκBα-Binding Fibronectin’, ACS Chemical Biology, 3(8), pp. 480–485. Available at: https://doi.org/10.1021/cb800069c.

Plückthun, A. (2012) ‘Ribosome Display: A Perspective’, in Ribosome Display and Related Technologies. New York: Humana Press, pp. 3–28.

Price, N.C. and Stevens, L. (1999) Fundamentals of Enzymology: The Cell and Molecular Biology of Catalytic Proteins. 3rd ed. Oxford: Oxford University Press.

ProZyme - Advancing Glycosciences-index (no date). Available at: https://prozyme.com/.

RCSB Protein Data Bank - RCSB PDB (no date). Available at: http://www.rcsb.org/pdb/home/home.do.

Ruhaak, L.R. et al. (2018) ‘Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses’, Chemical Reviews, 118(17), pp. 7886–7930. Available at: https://doi.org/10.1021/acs.chemrev.7b00732.

Sigma Aldrich (no date) ‘Detergents Properties and Applications’. Available at: https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Instructions/detergent_selection_table.pdf.

Taylor, M.E. and Drickamer, K. (2011) Introduction to Glycobiology. 3rd ed. Oxford: Oxford University Press.

UniProt (no date). Available at: http://www.uniprot.org/.

Voet, D. and Voet, J. (2011a) ‘Enzymatic Catalysis’, in Biochemistry. 4th ed. Hoboken, N.J.: John Wiley.

Voet, D. and Voet, J. (2011b) ‘Enzymatic Catalysis’, in Biochemistry. 4th ed. Hoboken, N.J.: John Wiley.

Voet, D. and Voet, J. (2011c) ‘Enzymatic Catalysis’, in Biochemistry. 4th ed. Hoboken, N.J.: John Wiley.

Voet, D. and Voet, J. (2011d) ‘Enzymatic Catalysis’, in Biochemistry. 4th ed. Hoboken, N.J.: John Wiley.

Voet, D. and Voet, J. (2011e) ‘Enzymatic Catalysis’, in Biochemistry. 4th ed. Hoboken, N.J.: John Wiley.

Voet, D. and Voet, J.G. (2011) Biochemistry. 4th ed. Hoboken, N.J.: John Wiley.

Voet, D., Voet, J.G. and Pratt, C.W. (2013) Principles of Biochemistry. 4th Edition. Hoboken, N.J.: Wiley.

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Wilson, D.S., Keefe, A.D. and Szostak, J.W. (2001) ‘The Use of mRNA Display to Select High-Affinity Protein-Binding Peptides’, Proceedings of the National Academy of Sciences of the United States of America, 98(7). Available at: https://www.jstor.org/stable/3055315?seq=1#metadata_info_tab_contents.

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Yamakawa, N. et al. (2018) ‘Systems Glycomics of Adult Zebrafish Identifies Organ-Specific Sialylation and Glycosylation Patterns’, Nature Communications, 9(1). Available at: https://doi.org/10.1038/s41467-018-06950-3.

Yang, Y., Franc, V. and Heck, A.J.R. (2017) ‘Glycoproteomics: A Balance between High-Throughput and In-Depth Analysis’, Trends in Biotechnology, 35(7), pp. 598–609. Available at: https://doi.org/10.1016/j.tibtech.2017.04.010.