Energy landscape ideas can explain some very common observations about natural p
ID: 3165168 • Letter: E
Question
Energy landscape ideas can explain some very common observations about natural proteins. This question explores why proteins are usually made of many different kinds of amino acids and are not homopolymers or even polymers of just two amino acids types. In fact, experimental studies do show that while some highly symmetric structures can artificially be built out of two kinds of amino acids generally structures require a larger variety of amino acids even to be possible (see Nature Struct. Bio. 4, 805-809 i19971) and Science 262, 1680-1685 [1993]). This can be seen in the world of lattice proteins Below are pictured some configurations of lattice proteins having 1, 2 and 3 types of maximally distinct amino acids. Assign reasonable energies to the types of pair interactions (based on what you learned in class about which types of amino acids have attractive or repulsive forces), and use calculations to explain QUANTITATIVELY the main features of the energy diagrams and why having more kinds of amino acids increases the foldability of sequences. 10 1 10 19 18 17 10.6 16 25 11 16 11 16 17 13 14 Energy Energy Configurational CoordinatesExplanation / Answer
Ans.
To determine the reasonable energies to the type of pair interaction of lattice proteins is studied by the Protein Model – HP (hydrophobic model), with the help of this model description of model can characterized by generalized model proposed by Miyezawa and Jernigam (MJ) to study the interactions between the amino acids hydrophobic interaction is studied by using alphabet {H, P} and H/P denotes hydrophobic/polar energy function favors the HH-contacts. Structures of amino acids are discrete, simple, and originally 2D and modelled (C-?). Construction of binary representation of lattice protein where two qubits per bond are used and bond directions are denoted by “00” (downwards), “01” (rightwards), “10” (leftwards), and “11” (upwards).
In the given figure 1,2,3 the interaction of amino acids using attractive or repulsive forces are:
Figure 1:
Figure 2.
Figure 3:
With the help of (HP) with possible N-amino-acid fold is represented by string of variables
Protein sequences and structure depends on the folds in native structures and the certain amino acid motifs. The fold are dependent on structural grounds and it is studied by simple theoretical models that rapid folding of amino acids are dependent on the interactions between the residues. There are mainly two types of transitions in the sequence of amino - folded state at temperature Tf and glassy misfolded state at temperature Tg. With the help of its ratio these two temperatures can determine rapid folding of amino. Random energy model can determine Tf/Tg monotonically increases the function of R = A/F, A is the difference between the energy of the native structure and ensemble of random conformations, F width of the distribution of energy values at the random structures. Foldability of amino acid can be characterized by the value of R.
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