Introduction to tertiary structure prediction and model evaluation. a. Provide c

Question

Introduction to tertiary structure prediction and model evaluation. a. Provide concise definitions of primary structure, secondary structure, tertiary structure and quaternary structure. b. Briefly describe what the problem of tertiary structure prediction is. c. Briefly describe what the tertiary structure prediction method known as homology modeling is. d. What are the basic steps involved in homology modeling (list and briefly discuss each step)? e. What does the process of model evaluation refer to? Name two web-accessible methods available for model evaluation f. Provide the names and web address for two automated homology modeling servers.

Explanation / Answer

Ans-(a) primary structure is a chain of amino acids.

Secondary structure is chain of amino acids linked with hydrogen bonds.

Tertiary structure is when there is some linkage between alpha helix and plated sheets.

Quaternary structure is a protein having more than one amino acid chain.

Ans-(b) the main problems are calculation of free energy of proteins and the other problem is finding its minimum.

Ans-(c) in this method the questioned proteins is converted into atomic resolution model which is then compared with a homologue proteins 3D structure.some advance instrument like x ray crystallography is used to resolve the problem.

Ans-(d) it has four steps

Template selection- a template is selected carefully.

Target-Template alignment - in this both are alinged accordingly.

Model construction- in this atomic resolution model of target sequence is prepared.

Model assessment- both are assessed by x ray crystallography.

Ans-(e) it is assessing the potential of prepared model. The two method for assessment are statistical potential or physics based calculation.

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