[Mayo lecture summary] Part 2 Designing Protein Libraries

In this lecture, Prof. Mayo introduces about DBIS (Diversity Benefit applied to Interacting Sets of amino acids) and related success cases.

• Why Computational Protein Design is needed?

'Diversity of function' which is usually achieved by high level of mutation and 'Preservation of function' which is usually achieved by low level of mutation are anti-correlated with each other.

The solution to this problem is the usage of computational protein design. This is about a structure based method that allows for high mutation rate (diversity of function) with maintenance of stably folded struture (preservation of function).

• Result of Mutation
  

Typically lower mutation rates means higher preservation of functions.

Regarding this, the result of SCMF (self-consistent mean field) was counterintuitive. This lower mutation rate gave the lowest preservation of functions. (SCMF mutated two most mutation tolerant positions.)

Likewise, highest mutation rate gave the greatest preservation of functions.

Therefore, this design calculation is good since it shows where to put the mutations for given library size to select AA that most likely to stabilize the fold.

(Random mutation of course, gave the very low preservation of function as expected.)

• Making Diverse Function while Keeping Originally Desired Function

Although I couldn't understand all of this lecture, the main theme of this slide is this: this design calculation method succeeded making diverse functions while keeping the originally desired function (fluorescence). This success can be shown at the result by DBIS-ORBIT (DBIS-Optimization of Rotamers By Iterative Techniques).

Lower mutation rate (DBIS-ORBIT-4 degenerate codons at 4 positions, SCMF-32 degenerate codons at 2 positions) showed little diverse functions.

(Randomly mutated protein and error prone PCR showed no significant change from wild type of AA - no diverse function)

'Fold before Function' is a concept that computed stability is a good surrogate for function in library design, and Mayo team realized this.

• More Success Case
  

Prof. Mayo team introduced another success case. BFP was enhanced in terms of enhanced quantum yield, reduced pH sensitivity, much improved in photobleaching half-life.

source: http://www.youtube.com/watch?v=G76DINEwT0s&feature=channel