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Veronesi_Giulia_Tesi.pdf

Veronesi_Giulia_Tesi.pdf

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Published by soumendra ghorai
theory of exfas........spectroscopy of solid statte chemistry .....nanoscience technlogy
theory of exfas........spectroscopy of solid statte chemistry .....nanoscience technlogy

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Published by: soumendra ghorai on Jul 02, 2013
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08/14/2013

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ADVANCED APPLICATIONS OF X-RAY ABSORPTIONSPECTROSCOPY TO THE STUDY OFPROTEIN METAL SITESGiulia Veronesi
Advisor: Prof. Federico Boscherini Co-advisor: Prof. Giovanni VenturoliA thesis submitted for the degree of Doctor of PhilosophySchool of PhysicsALMA MATER STUDIORUM - UNIVERSITY OF BOLOGNAMarch 2010
 
 Alma Mater Studiorum – Università di Bologna Alma Mater Studiorum – Università di BolognaDOTTORATO DI RICERCA IN
FISICA
Ciclo XXII
Settore scientifico-disciplinare di afferenza:
FIS/03
 Advanced applications of X-ray Absorption Spectroscopy tothe study of protein metal sites.
Presentata da:Giulia Veronesi
Coordinatore Dottorato: Relatore:Prof. Fabio Ortolani Prof. Federico BoscheriniCo-relatore: Prof. Giovanni Venturoli
Esame finale anno 2010
 
Contents
1.1 Phenomenology of X-ray absorption. . . . . . . . . . . . . . . . . 31.2 Approaches to the derivation of the absorption coefficient. . . . . 71.2.1 Choice of the potential. . . . . . . . . . . . . . . . . . . . 101.2.2 The EXAFS function. . . . . . . . . . . . . . . . . . . . . 111.3 Experimental techniques. . . . . . . . . . . . . . . . . . . . . . . 131.3.1 Detection modes. . . . . . . . . . . . . . . . . . . . . . . 141.3.2 Standard XAFS beamline setup. . . . . . . . . . . . . . . 161.4 Current status of BioXAS. . . . . . . . . . . . . . . . . . . . . . 18
2.1 XANES analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . 222.1.1 Database search. . . . . . . . . . . . . . . . . . . . . . . . 232.1.2 XANES spectra data base. . . . . . . . . . . . . . . . . . 242.1.3 Correlation between spectral features and ligation patterns262.2 EXAFS analysis in the Rigid Body Refinement scheme. . . . . . 282.3 Testing the method on model proteins. . . . . . . . . . . . . . . 372.3.1 Materials and Methods. . . . . . . . . . . . . . . . . . . . 382.3.2 Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
in native and genetically modified TH. . . . 493.3.1 Materials and methods. . . . . . . . . . . . . . . . . . . . 493.3.2 Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513.3.3 Discussion. . . . . . . . . . . . . . . . . . . . . . . . . . . 59i

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