4. Refer to the lecture slides on folding phi values to answer this question.. T

Question

4. Refer to the lecture slides on folding phi values to answer this question.. The ? values for the folding of SH3 and C12 are shown pictorially below. A) Write the equation for phi values and use this to explain which colored residues, which when mutated to destabilize the protein, would most slow down the folding SH3 Distal Loo 1.0 0.5 0.0 B) Which parts of the protein are likely to fold last in any folding event? ldentify these by phi value and/or color. Explain your reasoning and any weaknesses in your argument (hint: this was also on a slide from lecture) 1.0 0.5 5. All atom molecular dvnamics simulations differ from Go model simulations in the energy function that is used in the simulation. In each case, the molecule is allowed to sample configurations for which the energy is evaluated 0.0 (A) What are the parameters in the energy function used in a Go model? (B) What are the parameters in the energy function used in an all-atom forcefield? (C)Write the entire force field equation for the AMBER force field and explain what each term does and how? (D) Why do all-atom MD simulations take so much computer time? List at least 2 key reasons.

Explanation / Answer

the energy function for the model the representation can be d one by each atom describing as a single point that may be connected via bonds to other atoms bonds . the force acting on the atom is a sum that caused by these bonds as well as non bonded interaction .

molecular dynamics is a computer method of studying the physical movements of atoms and molecules . the atoms nd molecules are allowed to interact for a fixed period of time .as a more simplified representation of the system is used much larger time is steps are posssible which takes more time therefore the effective length is greater.

molecular dynamics is used to examine the dynamics of atomic level phenomena that cannot be observed directly such as a thin film growth and a ion subplantation and also to examine the the physical properties of the nano technologycal device.

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