AUTOMATIZACIÓN DEL ENSAYO Y DE LA TOMA DE DATOS

Lysozyme crystallization was done in 8% NaCl and 0.1M CH3COONa at different conditions as a part of learning process. Co-crystallization of lysozyme was also performed at different concentrations of trehalose. After data processing trehalose was not found to be bound to lysozyme. Further interaction of trehalose with lysozyme can be done for co-crystals obtained at different concentration of trehalose.

91

REFERENCES FOR APPENDICES

APPENDIX A

1. Schulz B, Kromer M, Schulz GE (1996). The structure of bacterial outer membrane proteins. Biochemica et Biophysica Acta 1565: 308-317.

2. Linnea E. Hedin, Kristoffer I., Arne E. (2011). An Introduction to Membrane Proteins. Journal of Proteome Research 10: 3324-3331.

3. Imai K. Gromiha, M., Horton P. (2008). Mitochondrial beta-barrelproteins, an exclusive club? Cell 135: 1158-1159.

4. Andrew G Garrow, Alison A., David R Westhead (2005). TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics 6: 56.

5. Benz R. (1985). Porin from bacterial and mitochondiral outer membranes. Crit. Rev. Biochem. 19:145-190.

6. Nakae, T., Ishii J., Tokunagu M. (1979). Subunit structure of functional porin oligomers that form permeability channels in the outer membrane of Escherichia coli. J. Biol. Chem.254:1457-1461.

7. Koebnik R., Locher KP., Van Gelder P. (2000). Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Molecular Microbiology 37:239-253.

8. Cowan SW, Garavito RM, Jansonius JN, Jenkins JA, Karlsson R, Konig N, Pai EF, Pauptit RA, Rizkallah PJ, Rosenbach JP. (1995) . The structure of OmpF porin in a tetragonal crystal form. Structure 3(10): 1041-1050.

92

9. Inokuchi K, Mutoh N, Matsuyama S, Mizushima S. (1982). Primary structure of the OmpF gene that codes for a major outer membrane protein of Escherichia coli K-12. Nucleic Acids Research 10 (21): 6957-6968.

10.Balasubramaniam D, Arockiasamy A, Kumar PD, Sharma A, Krishnaswamy S. (2012). Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhii. Journal of Structural Biology 178 (3): 233-244.

11.Cowan S.W., Garavito R.M, Jansonius JN, Jenkins JA, Karlsson R, Konig N, Pai EF, Pauptit RA. (1992). Crystal structure explains functional properties of two Escherichia coli porins. Nature 358:727-733.

12.Nikaido H. (2003). Molecular basis of Bacterial Outer Membrane permeability Revisited. Microbiology Molecular Biology Reviews 6(4):593-656.

13.Silverman JA, Benson SA. (1987). Bacteriophage K20 requires both OmpF porin and lipopolysaccharide for receptor function. Journal of Bacteriology 169:4830-4833.

14.Secundino I, Lopez-Macias C, Cervanyes-Barragan LC, Gil-Cruz C, Rios-Sarabia N, Pastelin-Palacois R, Villasis-Keever MA, Becker I, Puente JL, Calva E, Isibasi A. (2005). Salmonella porins induce a sustained, lifelong specific bactericidal antibody memory response. Immunology 117:59-70.

15.Sousa C., Kotrba P., Ruml T., Cebolla A. , Lorenzo, V. D. (1998). Metalloadsorption by Escherichia coli cells displaying yeast and mammalian metallothioneins anchored to the outer membrane protein LamB. Journal of Bacteriology 180(9): 2280–2284.

16.Ranquin AN., Caroline De Vocht., Wolfgang Meier .J., Steyaert, Patrick Van G. (2006). Development of a Novel Triblock Copolymer Therapeutic Nanoreactor, NSTI-Nanotech 2:358-361.

93

17.Young RY, Wang I-N, Roof WD. (2000). Phages will out: strategies of hostcell lysis. Trends Microbiol 8:120–128.

18.Srividhya KV, Krishnaswamy S. (2007). Sub classification and targeted characterization of prophase-encoded tow-component cell lysis cassette. J Biosci. 32:979-990.

19.Bhabha. (2010). Expression and purification of Salmonella typhii Ty21a Outer membrabe Protein F (OmpF) and construction of a chimeric OmpF with endolysin. 1- 69.

20.Mathan. (2010). Expression and purification of Salmonella typhii Ty21a Outer membrabe Protein F (OmpF) and construction of a chimeric OmpC with endolysin. 1- 57.

94

APPENDIX B

1. Danley DE. (2006). Crystallization to obtain protein-ligand complexes for structure aided drug design. Biological Crystallography Acta Crystallographica 62(6): 569-575.

2. Anne M. Hassell, Gang AN, Randy K. Bledsoe, Jane M. Bynum, H. Luke Carter, III, Su-Jun J. Deng, Robert T. Gampe, Tamara E. Grisard, Kevin P. Madauss,Robert T. Nolte, Warren J. Rocque, Liping Wang, Kurt L. Weaver, Shawn P. Williams, G. Bruce Wisely, Robert Xu,and Lisa M. Shewchuk (2007). Crystallization of protein– ligand complexes. Acta Crystallographica 63: 72-79.

3. Gruden M , Davudova TB, Malisauskas M, Zamotin VV, Sewell RD, Voskresenskaya NI, Kostanyan IA, Sherstnev VV, Morozova-Roche LA. Autoimmune responses to amyloid structures of Abeta(25-35) peptide and human lysozyme in the serum of patients with progressive Alzheimer's disease. Dementia and Geriatic Cognitive Disorders 18(2): 165-171.

4. Kazuhiro Ohmia, Lili C. Kudob, Sergey Ryazantseva C, Hui-Zhi Zhaoa ,Stanislav L. Karsten and Elizabeth F. Neufelda (2009). Sanfilippo syndrome type B, a lysosomal storage disease, is also a tauopathy. PNAS 10 : 1-6.

5. Jain N., Roy I. (2009). Effect of trehalose on protein structure, Protein Science 18(1): 24–36.

6. Timasheff, S. N. (1993). The control of protein stability and association by weak interactions with water: how do solvents affect these processes. Annu. Rev. Biophys. Biomol. Struct. 22:67–97.

7. Kaushik J., Bhatt R. (2003). Why Is Trehalose an Exceptional Protein Stabilizer? AN ANALYSIS OF THE THERMAL STABILITY OF PROTEINS IN THE PRESENCE OF THE COMPATIBLE OSMOLYTE TREHALOSE.The Journal of Biological Chemistry 278:26458-26465.

95

8. Komes D, Lovrić T, Ganić KK, Gracin L (2003). Study of trehalose addition on aroma retention in dehydrated strawberry puree. Food Technol Biotechnol 41: 111– 120.

9. Datta S., Biswal BK., Vijayan M. (2001). The effect of stabilizing additives on the structure and hydration of proteins: a study involving tetragonal lysozyme. Acta Crystallographica 57: 1614-1620.

10.Martin FJ. (1990). Specialized drug delivery systems, manufacturing and production technology. New York and Basel: Marcel Dekker Inc.; 267-316.

11.Mohamed M, Labiba E, Nawal K, Said K (2005). Influence of different sugar cryoprotectants on the stability and physiochemical characteristics of freeze-dried 5- Fluorouracil plurilamellar vesicles. DARU Journal of Pharmaceutical Sciences. 13:133-142.

12.Corradini D. et al. (2013). Microscopic mechanism of protein cryopreservation in an aqueous solution with trehalose. Science Report 3: 1218.

13.Kwong PD., Liu Y. (1999). Use of cryoprotectants in combination with immiscible oils for flash cooling macromolecular crystals. Journal of Applied crystallography 32: 102-105.

14.Riboldi-Tunnicliffe A., Hilgenfeld R. (1999). Cryocrystallography with oil - an old idea revived. Journal of Applied Crystallography 32: 1003-1005.