If I am the designer of a protein, an information messenger, how can I design it?

From Personalgenome.net

What is the good composition of hydrophobic and hydrophilic amino acids for a globular and soluble protein?
2008-11-15
Ho Ghang

Conclusion
I think that compositing a protein with a half (or slightly more half) of hydrophobic residues be reasonable in nature.

A protein and outer medium interaction model
I think the two prerequisites of a stable globular and soluble protein could be interpreted as follows,
1.    Globular protein
The meaning of globularity in nature is the stability. All materials having their specificity with their specific morphology lose their nature when they are degraded or lose the original shape.
2.    Soluble protein
The meaning of protein solubility on the earth using the water as a medium can be interpreted as they can interact with other material via water.

However the solubility contradicts with the globularity in some aspect. Thus a stable and soluble protein has to sustain the equilibrium between these two requests. Really, the collision of two forces--the protein degradation, interaction, or outgoing force and the protein globularity, non-interaction, or a black hole attraction--is the nature of life in the swelling cosmos.

Here I made a protein and outer medium interaction model to represent the forces which could affect the shape of a stable protein (Fig 1). A protein-inner circle-is divided into N force fields (unit skin 1~N donuts) to calculate the unit forces affecting the shape of each donut skin. The forces affecting a skin, "unit skin 1", can be calculated as follows,

 F_UnitSkin1 = ∑(F_UnitSpace1 + F_UnitSpace2 +… + F_UnitSpaceN)                 …… 1)

Where F_UnitSpaceN is a unit space for the calculation of two opposite types of forces.
Now I can find there are four types of forces working in a "UnitSpace". Two forces constraint the proteins to conglomerate. One is repulsion from an outer medium (F_IN1) and the other is gravity from inner compositions (F_IN2). The two other forces which intermediate interaction or degradation are repulsion from inner "UnitSpace" (F_OUT1) and attraction from outer medium (F_OUT2). Thus the powers working on a "UnitSpace N" can be expressed as follows,

F_UnitSpaceN = F_IN1 + F_IN2 + F_OUT1 + F_OUT2                                         …. 2)

The forces between two neighboring "Unit spaces" in a "Unit skin" are not important than those of two neighboring field of "Unit skins" for the stability of protein. Just the force working on two neighboring "Unit Spaces" could affect the morphology diversity of proteins. Thus it could be neglected in the modeling of protein composition.
The sum of forces over all unit fields (Unit skins) can be expressed as "function 3)" and it could be applied for the explanation of protein stability.

F = F_UnitSpace1 + F_UnitSpace2 + … + F_UnitSpaceN                        … 3)

When the "function2)" is applied in function 3, we can write function 3 again as follows,

F = ∑F_IN1 + ∑F_IN2 +∑F_OUT1 + ∑F_OUT2                                      ……… 4)

A functionally working protein should be under an equilibrium status between two categorical forces. Thus function 4 could be re-written for a functional or equilibrium status protein as follows,

(∑F_IN1 + ∑F_IN2 ) - (∑F_OUT1 + ∑F_OUT2 ) ≥ 0                                   ……… 5)

If the value of function 5 is bigger, the level of interaction is lower. Otherwise, if the value is lower to 0, the degradation probability will be higher.

When the composition of hydrophobic and hydrophilic residues is considered with the function 5, I think that compositing a protein with a half (or slightly more half) of hydrophobic residues be reasonable in nature.

However there could be another composition (or model) if the neglected "Unit space force" of outmost skin (or donut) is fully higher dividing the in and out of a protein. Then the diversity of protein composition could be higher. Furthermore, this model use more complicated folding mechanism than above model.
 

Reference
1.    Origins of globular structure in proteins. Nobuhide Doia, b and Hiroshi Yanagawaa, *
Abstract
Since natural proteins are the products of a long evolutionary process, the structural properties of present-day proteins should depend not only on physico-chemical constraints, but also on evolutionary constraints. Here we propose a model for protein evolution, in which membranes play a key role as a scaffold for supporting the gradual evolution from flexible polypeptides to well-folded proteins. We suggest that the folding process of present-day globular proteins is a relic of this putative evolutionary process. To test the hypothesis that membranes once acted as a cradle for the folding of globular proteins, extensive research on membrane proteins and the interactions of globular proteins with membranes will be required.
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-3T8F754-2&_user=79782&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=79782&md5=09b3d8454801d77a2422c1ad9df8797a