Lab Report 1 - 01.14.07 CHM417 Lab Report # 1 CHOON LIANG...

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01.14.07 CHM417 Lab Report # 1 CHOON LIANG TAN: 007156760 LINDA PHAM: Analyzing Proteins with VMD Introduction: The first session of working with VMD was merely to load three structures of the same compound, first as the ‘cleaned structure’, second as the molecular mechanically optimized structure and lastly as the quantum mechanically optimized structure. This session was to learn how to use the ‘Representations’ options to alter the graphics of each of the three overlaying each other. This experimental exercise was vital in giving us hands on approach on how to modify the graphics for more accurate and efficient assessment. The figure rendered is labeled as Figure 1.1. The second session was more advanced, as it combined our previous knowledge of using specific enzymatic structures available on ‘Pubmed’ 1 and our newly gained knowledge on using VMD. We were asked to search for a certain ‘serine ß-lactamase (SHV-1) which followed certain criteria’s such as, being a wild type, having a resolution of 1.5Ǻ or better, and being as recently published as possible. After loading this protein into VMD, we were asked to alter its graphics for easier representations and to hunt through a list of all the details on this enzyme for the exact amino acid residues that coded for the inhibitor of SHV-1. The images were rendered, as figure 1.2 and this session taught us a great deal on how to search through the complicated files of a single enzyme and how to scan through a list of notes for details on the chemical name of the inhibitor, which amino acid its attached to, how to locate the inhibitor and render it all onto the same display diagram. Methods: For the first session, the VMD program had already been installed thus we were able to move quickly onwards to loading the three structures on the same display panel. To do this, you begin to load the first model (eg. ‘Cleaned structure’), once loaded, you
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Lab Report 1 - 01.14.07 CHM417 Lab Report # 1 CHOON LIANG...

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