Dear Hayder, The most prominent representatives of positively charged proteins are histones able to associate with DNA due to negative charge of phosphate groups in DNA.Chemical modifications of histones (methylation, acetylation, phosphorylation) are involved in regulation of transcription (epigenetic), DNA repair and chromatin condensation. Changes in level of histone modification are applicable in diseases, including cancer, inflammation, neurological disorders.

Dear Hayder,

The key industrial application I am aware of for positively charged proteins is in the food sector. 

Naturally occurring positively charged proteins, such as wheat and potato proteins, can interact with negatively charged polysaccharides to form electrostatic complexes, which are capable of encapsulating bioactives, and acting as Pickering particles for emulsion stabilisation. 

The following is a good study work on electrostatic complexation:

http://www.sciencedirect.com/science/article/pii/S0268005X1500082X

Hope this helps,

Jonathan

Doesn't that sort of depend on the actuall protein?

For example, many antimicrobial peptides are also positively charged, but their function depends on sequence, so you cannot just replace it with anything.