4.  (10 points)  You are studying the binding of a large two-domain protein to a small molecule inhibitor. Each domain is 60 kDa and they are linked by a 15-amino acid linker. There is a crystal structure of one of domain A showing that it adopts an oblong alpha helical bundle. The second domain (B) does not have a crystal structure, but it is 75% identical to domain A. It has been impossible to obtain a crystal structure of the entire protein with both domains. Finally, there is a controversy of whether the protein is a monomer or dimer in solution. You want to test the hypotheses that: The two domains in the apo (unbound) state are in equilibrium between a V-shaped (closed) and linear (open) conformation. The binding of a small molecule inhibitor causes a large conformational change that favors the closed, V-shape conformation. Although the figure depicts a monomer, it is possible that the apo protein may be in a higher order oligomeric state (e.g., dimer, trimer, etc.). How would you determine the oligomeric state of the protein in the absence and presence of a small molecule ligand? Describe how you would use the scattering techniques you learned about in this class to test ALL THREE parts of your hypothesis. a.    (3 points). How would you test if the two domains are in equilibrium between a V-shaped (closed) and linear (open) conformation? b.    (3 points). How would you test if the binding of a small molecule inhibitor causes a large conformational change that favors the closed, V-shape conformation? c.    (4 points). How would you settle the controversy about the oligomeric state of the protein in the absence and presence of a small molecule ligand?

Designing toward inter-domain interoperability should aim to enable every IoT thing in one domain to communicate with every IoT thing in another domain directly.

The process of a removing a node from a system is called:

Payload data ________ defines formats of requests and responses as they appear in transport.

Equation Sheet for Fuentes Exam.pdf

Using structured metadata in IoT systems enables ________-based searches that identify objects of interest based on specific properties.

________ systems rely on a set of known signatures of events to identify suspicious behaviors.

Main memory and disk space are considered as _____ of physical database design.

A(n) ________ is a hardware-assisted segregated secure environment that provides secure storage of encryption keys and dedicated storage and execution of security code.

5.  (10 points).  In class we talked about the steps required for determining a structure using X-ray diffraction. Answer the questions below about X-ray structure determination. a.    (2 points). Why are crystals used for diffraction experiments rather than a single molecule, which in principle could diffract an X-ray? b.    (2 points). Describe Bragg’s law and why it allows for one to see reflections (i.e., a diffraction pattern). c.    (2 points). Why are Miller indices useful for describing an X-ray diffraction experiment? d.    (2 points). Describe the setup for an X-ray diffraction experiment and how one would collect data. e.    (2 points). What is the “phase problem” in X-ray crystallography and describe one method that allows one to solve the phase problem.