Peptide protein binding strategies: Structure, Volume 18, Issue 2, 188-199, 10 February 2010
Peptide-Protein Binding
Highlights
After binding its partners, most peptides do not introduce any conformational changes
The interfaces of peptide-protein have more hydrogen bonds
The peptide hotspots are important for the binding
Peptides prefer to bind in the largest pockets on the protein surface
LifeTein is pleased to offer a free, comprehensive web-based peptide analysis tool. This tool will allow your research team to overcome common difficulties inherent in protein analysis and peptide antigen design.
Proteins and most naturally occurring peptides are composed of amino acids in the L-configuration. However, D-amino acids have been detected in a variety of peptides synthesized in animal cells. Examples include opiate and antimicrobial peptides from frog skin, neuropeptides from snails, hormones from crustaceans, and venom from spiders. These D amino acid peptides are considered to be the most promising alternative for anticancer, anti-inflammatory, antimicrobial, and delivery agents.
About D-Amino Acid Peptides
The design of all-D-peptides has been applied to increase bioactive peptides’ resistance to endogenous enzymes, as well as their bioavailability. Retro-inverso peptides are obtained by replacing the standard L-amino acid residues with the corresponding D-amino acids and reversing the direction of the peptide backbone. Therefore, the original spatial orientation and the chirality of the side chains is unchanged. This results in a non-complementary side chain topochemistry between the analog and the parental L-peptide. The significantly improved biostability of D-peptides usually leads to longer in vivo circulation half-time, making the D-peptide based drug delivery system more attractive and efficient than their L-peptide counterparts.
Success has been achieved immunologically in using retro-inverso peptides toward antigenic mimicry of their parent l-peptides. It was found that the retro-all-d-peptide isomer of p53(15–29), like its parent l-peptide, adopted a right-handed helical conformation in the complex. However, in some cases, the retro-inverso isomers are significantly inferior to their parent l-peptides. The low cellular uptake of D-peptides remain an unmet challenge.
So the best way is to insert some key D amino acids into the peptide sequence. For example, some pharmaceutical important peptide antibiotics such as gramicidins, actinomycins, or bacitracins incorporate D-amino acids into the drug design. The assemblies of D-peptides deserve further exploration and may lead to more surprises.
D amino acid peptide with high stability
See more details from here: http://lifetein.com/Peptide-Synthesis-D-Amino-Acid.html
Reference: http://www.pnas.org/content/102/2/413.full.pdf+html
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Cell-penetrating peptides (CPPs) such as the HIV TAT peptides are able to enter cells by direct translocation and endocytosis. Click here to see details about the CPP: http://lifetein.com/Cell_Penetrating_Peptides.html
About Cell-Penetrating Peptides
Cell Penetrating Peptides
The following table shows a selection of currently known CPPs, their origins, and sequences.
Name
Origin
Sequence
Tat (48-60)
HIV-1 protein
GRKKRRQRRRPPQQ
plsl
Igl-1 homeodomain
RVIRVWFQNKRCKDKK
STR-R8
Stearly-RRRRRRRR-amide
(Stearyl = CH3(CH2)16CO-)
STR-(RxR)4
Stearly-(RxR)4-amide
(X=6-aminohexanoic acid)
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